@article {1513111, title = {The colonial legacy of herbaria}, journal = {Nature Human Behavior}, year = {2023}, author = {Daniel S. Park and Xiao Feng and Shinobu Akiyama and Marlina Ardiyani and Neida Avenda{\~n}o and Zoltan Barina and Blandine B{\"a}rtschi and Manuel Belgrano and Julio Betancur and Roxali Bijmoer and Ann Bogaerts and Asunci{\'o}n Cano and Ji{\v r}{\'\i} Danihelka and Arti Garg and David E. Giblin and Rajib Gogoi and Ramagwai J. Sebola and Tomoyuki Katagiri and Jonathan A. Kennedy and Tojibaev Sh. Komil and Byoungyoon Lee and Serena M. L. Lee and Donatella Magri and Rossella Marcucci and Siro Masinde and Denis Melnikov and Patrik Mr{\'a}z and Wieslaw Mulenko and Paul Musili and Geoffrey Mwachala and Burrell E. Nelson and Christine Niezgoda and Carla Novoa Sep{\'u}lveda and Sylvia Orli and Alan Paton and Serge Payette and Kent D. Perkins and Maria Jimena Ponce and Heimo Rainer and L. Rasingam and Himmah Rustiami and Natalia M. Shiyan and Charlotte Sletten Bjor{\r a} and James Solomon and Fred Stauffer and Alex Sumadijaya and M{\'e}lanie Thi{\'e}baut and Barbara M. Thiers and Hiromi Tsubota and Alison Vaughan and Risto Virtanen and Timothy J. S. Whitfeld and Dianxiang Zhang and Fernando O. Zuloaga and Charles C. Davis} } @article {1443287, title = {New directions in tropical phenology}, journal = {Trends in Ecology and Evolution}, volume = {37}, year = {2022}, pages = {683-693}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0169534722001124}, author = {Charles C. Davis and Lyra, Goia M. and Park, Daniel S. and Renata Asprino and Rog{\'e}rio Maruyama and D{\'e}bora Torquato and Benjamin I. Cook and Ellison, Aaron M.} } @article {1443257, title = {PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data}, journal = {Applications in Plant Sciences}, volume = {10}, year = {2022}, author = {Cai, Liming and Hongrui Zhang and Charles C. Davis} } @article {1443251, title = {A pragmatic and prudent consensus on the resurrection of extinct plant species using herbarium specimens}, journal = {Taxon}, volume = {71}, year = {2022}, pages = {168-177}, url = {https://onlinelibrary-wiley-com.ezp-prod1.hul.harvard.edu/doi/full/10.1002/tax.12601}, author = {Giulia Albani Rochetti and Charles C. Davis and Giulia Caneva and Gianluigi Bacchetta and Guiseppe Fabrini and Guiseppe Fenu and Bruno Foggi and Gabriele Galasso and Domenico Gargano and Gianpietro Giusso del Galdo and Mauro Iberite and Sara Magrini and Alfred Mayer and Andrea Mondoni and Chiara Nepi and Simone Orsenigo and Lorenzo Peruzzi and Thomas Abeli} } @article {1443255, title = {Widespread homogenization of plant communities in the Anthropocene}, journal = {Nature Communications}, volume = {12}, year = {2021}, url = {https://www.nature.com/articles/s41467-021-27186-8}, author = {Barnabas H. Daru and Jonathan Davies, T. and Willis, Charles G. and Meineke, Emily K. and Argo Ronk and Martin Zobel and Meelis P{\"a}rtel and Antonelli, Alexandre and Charles C. Davis} } @article {1443253, title = {Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta)}, journal = {Molecular Phylogenetics and Evolution}, volume = {165}, year = {2021}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S105579032100227X}, author = {Goia de M. Lyra and Iha, Cintia and Grassa, Christopher J. and Cai, Liming and Hongrui Zhang and Christopher Lane and Nicolas Blouin and Oliveira, Mariana C. and Jos{\'e} Marcos de Castro Nunes and Charles C. Davis} } @article {1402635, title = {Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils}, journal = {Systematic Biology}, volume = {042}, year = {2021}, url = {https://academic.oup.com/sysbio/article/70/6/1256/6295695}, author = {Yujing Yan and Charles C. Davis and Dimitrov, Dimitar and Zhiheng Wang and Carsten Rahbek and Michael Krabbe Borregaard} } @article {1400705, title = {Striking developmental convergence in angiosperm endoparasites}, journal = {American Journal of Botany }, volume = {108}, year = {2021}, pages = {1-13}, url = {https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.1658}, author = {Luiza Teixeira-Costa and Charles C. Davis and Gregorio Ceccantini} } @article {1395912, title = {Phylogenetic Relationships of Tovomita (Clusiaceae): Carpel Number and Geographic Distribution Speak Louder than Venation Pattern}, journal = {Systematic Botany}, volume = {41}, year = {2021}, pages = {102-108}, url = {https://bioone.org/journals/systematic-botany/volume-46/issue-1/036364421X16128061189549/Phylogenetic-Relationships-of-Tovomita-Clusiaceae--Carpel-Number-and-Geographic/10.1600/036364421X16128061189549.short}, author = {Lucas C. Marinho and Fiaschi, Pedro and Moabe F. Fernandes and Cai, Liming and Duan, Xiaoshan and Amorim, Andr{\'e} M. and Charles C. Davis} } @article {1395259, title = {Phenological sensitivity to temperature mediates herbivory}, journal = {Global Change Biology}, year = {2021}, url = {https://onlinelibrary-wiley-com.ezp-prod1.hul.harvard.edu/doi/abs/10.1111/gcb.15600}, author = {Meineke, Emily K. and Charles C. Davis and Jonathan Davies, T.} } @article {1396376, title = {Back to the future: A refined single-user photostation for massively scaling herbarium digitization}, journal = {Taxon}, volume = {00}, year = {2021}, pages = {1-9}, url = {https://onlinelibrary.wiley.com/doi/10.1002/tax.12459}, author = {Charles C. Davis and Jonathan A. Kennedy and Grassa, Christopher J.} } @article {1390106, title = {Deeply Altered genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)}, journal = {Current Biology}, year = {2021}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982220318972}, author = {Cai, Liming and Brian J Arnold and Zhenxiang Xi and Danielle E Khost and Niki Patel and Claire B Hartmann and Manickam, Sugumaran and Sasirat, Sawitree and Lachezar A Nikolov and Sarah Mathews and Sackton, Timothy B and Davis, Charles C} } @article {1441209, title = {Endoparasitic plants and fungi show evolutionary convergence across phylogentic divisions.}, journal = {The New Phytologist}, volume = {10}, year = {2021}, author = {Thorogood, C.J. and Teixeira-Costa, L. and Ceccantini, G. and Davis, C. C. and Hiscock, S. J.} } @article {1380479, title = {Andersoniodoxa, a replacement name for Andersoniella (Malpighiaceae)}, journal = {Phytotaxa}, volume = {470}, year = {2020}, pages = {121-122}, author = {Charles C. Davis and Lucas C. Marinho and Amorim, Andr{\'e} M.} } @article {1443284, title = {Phenological displacement is uncommon among sympatric angiosperms}, journal = {bioRxiv}, year = {2020}, url = {https://www.biorxiv.org/content/10.1101/2020.08.04.236935v1}, author = {Park, Daniel S. and Ian K. Breckheimer and Ellison, Aaron M. and Lyra, Goia M. and Charles C. Davis} } @article {1360905, title = {A New Method for Counting Reproductive Structures in Digitized Herbarium Specimens Using Mask R-CNN}, journal = {Frontiers in Plant Science}, volume = {11}, year = {2020}, author = {Charles C. Davis and Julien Champ and Park, Daniel S. and Breckheimer, Ian and Lyra, Goia M. and Junxi Xie and Alexis Joly and Dharmesh Tarapore and Ellison, Aaron M. and Pierre Bonnet} } @article {1332961, title = {Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae)}, journal = {Molecular Phylogenetics and Evolution}, volume = {151}, year = {2020}, author = {Haiwen Li and Bing Liu and Charles C. Davis and Yong Yang} } @article {1327590, title = {An invasive species spread by threatened diurnal lemurs impacts rainforest structure in Madagascar}, journal = {Biological Invasions}, year = {2020}, pages = {1-14}, author = {Camille M. M. DeSisto and Park, Daniel S. and Charles C. Davis and Veronarindra Ramananjato and Jadelys L. Tonos and Onja H. Razafindratsima} } @article {1327591, title = {Andersoniella: A new genus of neotropical malpighiaceae}, journal = {Harvard Papers in Botany}, volume = {25}, year = {2020}, pages = {51-56}, author = {Charles C. Davis and Lucas C. Marinho and Amorim, Andr{\'e} M.} } @article {1305020, title = {Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research}, journal = {BioScience}, year = {2020}, abstract = {Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens{\textemdash}preserved plant material curated in natural history collections{\textemdash}but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.}, author = {Katelin D Pearson and Nelson, Gil and Myla F J Aronson and Pierre Bonnet and Laura Brenskelle and Davis, Charles C and Ellen G Denny and Elizabeth R Ellwood and Herv{\'e} Go{\"e}au and J Mason Herberling and Alexis Joly and Titouan Lorieul and Susan J Mazer and Emily K Meineke and Brian J Stucky and Patrick Sweeney and Alexander E White and Pamela S Soltis} } @article {1310224, title = {Machine learning predicts large scale declines in native plant phylogenetic diversity}, journal = {New Phytologist}, year = {2020}, author = {Park, Daniel S. and Willis, Charles G. and Zhenxiang Xi and John T. Kartesz and Charles C. Davis and Steven Worthington} } @webarticle {1296515, title = {As m{\'\i}dias sociais inflamam a destui{\c c}{\~a}o da Amaz{\^o}nia}, year = {2020}, author = {Charles Davis and Goia Lyra and Caio Silva and Mariana Guimar{\~a}es and Jean Wyllys and Aaron Ellison} } @article {1296505, title = {Life in the canopy: community trait assessments reveal substantial functional diversity among fern epiphytes}, journal = {New Phytologist}, year = {2020}, author = {Nitta, Joel H. and James E. Watkins and Charles C. Davis} } @article {1296499, title = {Social media are fueling the Amazon{\textquoteright}s destruction}, journal = {Nature}, volume = {580}, year = {2020}, pages = {321}, url = {https://www.nature.com/articles/d41586-020-01078-1}, author = {Charles Davis and Goia Lyra and Caio Silva and Mariana Guimar{\~a}es and Jean Wyllys and Aaron Ellison} } @article {1296501, title = {Water lily (Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses}, journal = {PNAS}, volume = {117}, year = {2020}, pages = {8649-8656}, abstract = {For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms \~{}140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lily\ Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots and\ Nelumbo). This revealed lineage-specific patterns of gene loss and divergence.\ Nymphaea\ is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of\ REVOLUTA, which influences cambial activity in other angiosperms. We also found the\ Nymphaea\ and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids.\ Nelumbo\ displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness{\textemdash}one of the key biological innovations associated with the earliest phases of angiosperm evolution.}, author = {Povilus, Rebecca A. and Jeffrey M. DaCosta and Grassa, Christopher and Prasad R. V Satyaki and Morgan Moeglein and Johan Jaenisch and Zhenxiang Xi and Sarah Mathews and Mary Gehring and Charles C. Davis and Friedman, William E.} } @article {1230735, title = {Digitization and the future of natural history collections}, journal = {BioScience}, volume = {70}, year = {2020}, pages = {243-251}, abstract = {Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization{\textendash}the conversion of specimen data into accessible digital content{\textendash}has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0){\textendash}whereby specimens are digitized within NHCs{\textendash}to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.}, url = {https://peerj.com/preprints/27859/}, author = {Hedrick, Brandon and Heberling, Mason and Meineke, Emily and Turner, Kathryn and Grassa, Christopher and Park, Daniel and Kennedy, Jonathan and Clarke, Julia A. and Cook, Joseph and Blackburn, David and Edwards, Scott V. and Charles C. Davis} } @article {1291597, title = {Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution}, journal = {Nature Plants}, volume = {2020}, year = {2020}, pages = {1-8}, abstract = {Angiosperms represent one of the most spectacular terrestrial radiations on the planet 1, but their early diversification and phylogenetic relationships remain uncertain 2, 3, 4, 5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species{\textemdash}prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales){\textemdash}and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other\ {\textellipsis}}, author = {Jianquan Liu and Davis, Charles C and Xiyin Wang and Zhenxiang Xi and Zhiji Qin and Qinfeng Wang and Man Liu and Lanxing Shan and Beibei Jiao and Fanbo Meng and Xingxing Shen and Zhang, Lei and Tao Ma and Ying Li and Dafu Ru and Donglei Wang and Leke Lv and Pengchuan Sun and Yongzhi Yang} } @article {1230734, title = {Diverse trajectories of plastome degradation in holoparasitic Cistanche and the whereabouts of the lost plastid genes}, journal = {Journal of Experimental Botany}, volume = {71}, year = {2020}, pages = {877-892}, abstract = {The plastid genomes (plastomes) of non-photosynthetic plants generally undergoes gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequenced and assembled the complete plastomes of three holoparasitic\ Cistanche\ species (C. salsa,\ C. tubulosa\ and\ C. sinensis) and compared them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three\ Cistanche\ clades, showing obvious size differences on entire plastome, long single copy region and non-coding region, and different patterns of the retention/loss of functional genes. With few exception of putatively functional genes, massive plastid fragments which have been lost and transferred into the mitochondrial or nuclear genomes are nonfunctional. In contrast with the equivalents of the\ Orobanche\ species, some plastid-derived genes with diverse genomic locations are found in\ Cistanche. The early and initially diverged clades in different genera such as\ Cistanche\ and\ Aphyllon\ possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.}, url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz456/5602659}, author = {Liu, Xiaoqing and Fu, Weirui and Tang, Yiwei and Zhang, Wenju and Soonog, Zhiping and Li, Linfeng and Yang, Ji and Ma, Hong and Yang, Jianhua and Zhou, Chan and Charles C. Davis and Wang, Yugu} } @article {1291610, title = {Climate Change: How to Pack a Punch at Meetings}, journal = {Nature}, volume = {577}, year = {2020}, pages = {472}, author = {Davis, Charles C and Benjamin Goulet-Scott and Jason Beckfield} } @presentation {1291612, title = {Herbivory through the ages: Herbarium specimens for determining effects of plant traits on changing insect damage to plants}, year = {2019}, abstract = {Some of the most consequential interactions expected to shift with climate change are between insect herbivores and plants, both of which are highly sensitive to temperature. Historically, insect herbivores and their host plants display varying levels of synchrony that could be disrupted or enhanced by climate change. Here, we use herbarium specimens collected over the past 100+ years to explore how phenological sensitivity, bloom/leaf-out season, and plant growth form affect changing insect damage to leaves. Our results suggest that warming may lengthen growing seasons for phenologically sensitive species, exposing them to more damage from resident or novel herbivores early in the growing season.}, author = {Emily K Meineke and Davis, Charles C and T Jonathan Davies} } @article {1228340, title = {Freezing and water availability structure the evolutionary diversity of trees across the Americas}, journal = {bioRxiv}, year = {2019}, pages = {728717}, url = {https://www.biorxiv.org/content/biorxiv/early/2019/08/09/728717.full.pdf}, author = {Segovia, Ricardo A. and Pennington, Toby and Baker, Tim and Coelho de Souza, Fernanda and Neves, Danilo and Charles C. Davis and Armesto, Juan J. and Olivera-Filho, Ary and Dexter, Kyle} } @article {1164045, title = {Plastomes resolve generic limits within tribe Clusieae (Clusiaceae) and reveal the new genus Arawakia}, journal = {Molecular Phylogenetics and Evolution}, volume = {134}, year = {2019}, pages = {142-151}, abstract = {Clusieae is an exclusively Neotropical tribe in the family Clusiaceae\ sensu stricto. Although tribes within Clusiaceae are morphologically and phylogenetically well-delimited, resolution among genera within these tribes remains elusive. The tribe Clusieae includes an estimated \~{}500 species distributed among five genera:\ Chrysochlamys,\ Clusia,\ Dystovomita,\ Tovomita, and\ Tovomitopsis. In this study, we used nearly complete plastid genomes from 30 exemplar Clusieae species representing all genera recognized, plus two outgroups to infer the phylogeny of the tribe using Maximum Likelihood and Bayesian Inference. For comparison, we also inferred a phylogeny from the nuclear Internal Transcribed Spacer (ITS) region using the same methods. Our study corroborates earlier findings that\ Clusia\ is monophyletic while\ Tovomita\ is not. It also provides additional support to the hypothesis that\ Chrysochlamys\ and\ Tovomitopsis\ are not closely related despite gross morphological similarity.\ Tovomita\ is divided into three distantly related clades: (i) core\ Tovomita\ (including the type\ T. guianensis), (ii)\ T. croatii, and (iii) the\ T. weddelliana\ species complex. Members of the\ T. weddelliana\ complex are isolated from the core\ Tovomita, and placed in a well-supported clade that is sister to a clade composed of\ Chrysochlamys\ plus\ Clusia.\ Tovomita croatii\ is nested within\ Chrysochlamys. We propose taxonomic revisions to accommodate our phylogenetic findings, including the description of the new genus\ Arawakia, which includes the 18 species formerly recognized in the\ T. weddelliana\ species complex. Lectotypes are also designated for nine species (i.e.,\ Arawakia angustata,\ A. lanceolata,\ A. lingulata,\ A. longicuneata,\ A. macrocarpa,\ A. oblanceolata,\ A. pithecobia,\ A. rhizophoroides, and\ A. weddelliana), and a taxonomic key for the identification of the six genera of Clusieae recognized is presented.}, url = {https://www.sciencedirect.com/science/article/pii/S1055790318303427}, author = {Marinho, Lucas and Cai, Liming and Duan, Xiaoshan and Brad R. Ruhfel and Fiaschi, Pedro and Amorim, Andr{\'e} M. and van den Berg, C{\'a}ssio and Charles C. Davis} } @article {1164048, title = {Evolution of Land Plants}, journal = {Oxford Bibliographies}, year = {2019}, url = {http://www.oxfordbibliographies.com/view/document/obo-9780199941728/obo-9780199941728-0119.xml?rskey=vrIRzK\&result=1\&q=Evolution+of+Land+Plants$\#$firstMatch}, author = {Charles C. Davis and Matthews, Sarah} } @article {1164047, title = {[Author Correction] A statistical estimator for determining the limits of contemporary and historic phenology}, journal = {Nature Ecology \& Evolution}, volume = {3}, year = {2019}, pages = {499}, url = {https://www.nature.com/articles/s41559-019-0825-2}, author = {Pearse, William D. and Charles C. Davis and Inouye, David W. and Primack, RIchard B. and Davis, T. Jonathan} } @presentation {1164046, title = {Thrive with Additional Sets of Genome: Widespread Paleopolyploidization Buffers plants Through Eocene Climatic Upheaval}, volume = {59}, year = {2019}, pages = {E29-E29}, author = {Cai, Liming and Amorim, Andr{\'e} M. and Manickam, Sugumaran and Liu, Liang and Rest, Joshua S. and Charles C. Davis} } @article {1291617, title = {Biological Collections for understanding biodiversity in the Anthropocene}, journal = {Philosophical Transactions of the Royal Society B}, volume = {374}, year = {2019}, pages = {20170386}, abstract = {Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as\ {\textellipsis}}, author = {Emily K Meineke and T Jonathan Davies and Barnabas H Daru and Davis, Charles C} } @article {1291620, title = {Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses}, journal = {bioRxiv}, year = {2019}, abstract = {For more than 225 million years, all seed plants were woody trees, shrubs, or vines (1,2,3,4). Shortly after the origin of angiosperms ~135 million years ago (MYA) (5), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium (6), the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem (7,8,9), which are produced by apical meristems and retained in nearly all seed plants. Here we sequence and assemble a draft genome of the water lily Nymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compare it to genomes from other cambium-bearing and cambium-less lineages (like monocots and Nelumbo). This reveals lineage-specific patterns of gene loss and divergence. Nymphaea is characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss of REVOLUTA, which influences cambial activity in other angiosperms. We also find the Nymphaea and monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids. Nelumbo displays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent vascular cambium loss reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent trait loss events. Our results shed light on the evolution of herbaceousness,which is one\ {\textellipsis}}, author = {Povilus, Rebecca A. and Jeffery M DaCosta and Grassa, Christopher and Prasad RV Satyaki and Morgan Moeglein and Johan Jaenisch and Zhenxiang Xi and Sarah Mathews and Mary Gehring and Davis, Charles C and Friedman, William E.} } @article {1164044, title = {Widespread Ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheval}, journal = {New Phytologist}, volume = {221}, year = {2019}, pages = {565-576}, url = {https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15357}, author = {Cai, Liming and Xi, Zhenziang and Amorim, Andr{\'e} M and Sugumaran, Manickam and Rest, Joshua S. and Liu, Liang and Charles C. Davis} } @article {1230736, title = {A statistical estimator for determining the limits of contemporary and historic phenology}, journal = {Nature Ecology \& Evolution}, volume = {3}, year = {2019}, pages = {499}, author = {Pearse, William D. and Charles C. Davis and Inouye, David W. and Primack, RIchard B. and Jonathan Davies, T.} } @article {1146477, title = {Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States}, journal = {The Royal Society Publishing}, volume = {374}, year = {2018}, abstract = {

Phenology is a key biological trait that can determine an organism{\textquoteright}s survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web tool\ CrowdCurio\ to crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.

This article is part of the theme issue {\textquoteleft}Biological collections for understanding biodiversity in the Anthropocene{\textquoteright}.

}, url = {http://rstb.royalsocietypublishing.org/content/374/1763/20170394}, author = {Park, Daniel S. and Breckheimer, Ian and Williams, Alex C. and Law, Edith and Ellison, Aaron M. and Charles C. Davis} } @article {1152804, title = {Organellar Genomics: A Useful Tool to Study the Evolutionary Relationships and Molecular Evolution in Gracilarilacae (Rhodophyta)}, journal = {Journal of Phycology}, volume = {54}, year = {2018}, pages = {775-787}, abstract = {Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny,\ Melanthalia intermedia\ is sister to a monophyletic clade including\ Gracilaria\ and\ Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes\ cob\ and\ trnL, and\ trnA and\ trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between\ psdD and\ rrs\ genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial\ leuC/leuD operon was found in chloroplast genomes of\ Gracilaria tenuistipitata,\ G.\ chilensis, and\ M.\ intermedia, and in extrachromosomal plasmid of\ G.\ vermiculophylla. Phylogenetic trees show two different origins of\ leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.}, url = {http://www.phycoweb.net/reprints/Iha_2018_GracilariaceaeCPgenomes_JPY.pdf}, author = {Iha, Cintia and Grassa, Christopher J. and Goia de M. Lyra and Charles C. Davis and Verbruggen, Heroen and Oliveira, Mariana C.} } @article {1138937, title = {Mating system does not predict niche breath}, journal = {Global Ecology and Biogeography}, volume = {27}, year = {2018}, pages = {804-813}, abstract = {Self-pollinating plants ({\textquoteleft}selfers{\textquoteright}) have larger geographical ranges and inhabit higher latitudes than their outcrossing relatives. This finding has led to the hypothesis that selfers also have broader climatic niches ({\textquoteleft}niches{\textquoteright}) because the increased likelihood of successful colonization into new areas and the initial purging of deleterious mutations could offset the inability of selfers to adapt to new environments owing to low heterozygosity. Here, we examine the niches of hundreds of closely related selfing and outcrossing species to determine whether selfers do indeed have larger niche breadths.}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.12740}, author = {Park, Daniel S. and Ellison, Aaron M. and Charles C. Davis} } @article {1138938, title = {Microsorum{\texttimes} tohieaense (Polypodiaceae), a New Hybrid Fern from French Polynesia, with Implications for the Taxonomy of Microsorum}, journal = {Systematic Botany}, volume = {43}, year = {2018}, pages = {397-413}, abstract = {A new hybrid microsoroid fern,\ Microsorum{\texttimes}\ tohieaense(Microsorum commutatum\ {\texttimes}\ Microsorum membranifolium) from Moorea, French Polynesia is described based on morphology and molecular phylogenetic analysis.\ Microsorum\ {\texttimes}\ tohieaense\ can be distinguished from other French Polynesian\ Microsorum\ by the combination of sori that are distributed more or less in a single line between the costae and margins, apical pinna wider than lateral pinnae, and round rhizome scales with entire margins. Genetic evidence is also presented for the first time supporting the hybrid origin of\ Microsorum\ {\texttimes}\ maximum(Microsorum grossum\ {\texttimes}\ Microsorum punctatum), and possibly indicating a hybrid origin for the Hawaiian endemic\ Microsorum spectrum. The implications of hybridization for the taxonomy of microsoroid ferns are discussed, and a key to the microsoroid ferns of the Society Islands is provided.}, url = {https://www.ingentaconnect.com/content/aspt/sb/2018/00000043/00000002/art00001$\#$}, author = {Nitta, Joel H. and Amer, Saad and Charles C. Davis} } @article {1139051, title = {Large-scale digitization of herbarium specimens: Development and usage of an automated, high-throughput conveyor system}, journal = {International Association for Plant Taxonomy}, volume = {67}, year = {2018}, pages = {165-178}, abstract = {The billions of specimens housed in natural science collections provide a tremendous source of under-utilized data that are useful for scientific research, conservation, commerce, and education. Digitization and mobilization of specimen data and images promises to greatly accelerate their utilization. While digitization of natural science collection specimens has been occurring for decades, the vast majority of specimens remain un-digitized. If the digitization task is to be completed in the near future, innovative, high-throughput approaches are needed. To create a dataset for the study of global change in New England, we designed and implemented an industrial-scale, conveyor-based digitization workflow for herbarium specimen sheets. The workflow is a variation of an object-to-image-to-data workflow that prioritizes imaging and the capture of storage container-level data. The workflow utilizes a novel conveyor system developed specifically for the task of imaging flattened herbarium specimens. Using our workflow, we imaged and transcribed specimen-level data for almost 350,000 specimens over a 131-week period; an additional 56 weeks was required for storage container-level data capture. Our project has demonstrated that it is possible to capture both an image of a specimen and a core database record in 35 seconds per herbarium sheet (for intervals between images of 30 minutes or less) plus some additional overhead for container-level data capture. This rate was in line with the pre-project expectations for our approach. Our throughput rates are comparable with some other similar, high-throughput approaches focused on digitizing herbarium sheets and is as much as three times faster than rates achieved with more conventional non-automated approaches used during the project. We report on challenges encountered during development and use of our system and discuss ways in which our workflow could be improved. The conveyor apparatus software, database schema, configuration files, hardware list, and conveyor schematics are available for download on GitHub.}, url = {https://www.ingentaconnect.com/contentone/iapt/tax/2018/00000067/00000001/art00012}, author = {Sweeney, Patrick W. and Starly, Binil and Morris, Paul J. and Xy, Yiming and Jones, Aimee and Radhakrishnan, Sridhar and Grassa, Christopher J. and Charles C. Davis} } @article {1128422, title = {The unrealized potential of herbaria for global change biology}, journal = {Ecological Monographs}, volume = {88}, year = {2018}, pages = {505-525}, abstract = {

Plant and fungal specimens in herbaria are becoming primary resources for investigat-

ing how plant phenology and geographic distributions shift with climate change, greatly expanding

inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a

wealth of additional data, including nutrients, defensive compounds, herbivore damage, disease

lesions, and signatures of physiological processes, that capture ecological and evolutionary responses

to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium

data, global change topics to which they have been applied, and new hypotheses they could inform.

We find that herbarium data have been used extensively to study impacts of climate change and inva-

sive species, but that such data are less commonly used to address other drivers of biodiversity loss,

including habitat conversion, pollution, and overexploitation. In addition, we note that fungal speci-

mens are under-explored relative to vascular plants. To facilitate broader application of plant and fun-

gal specimens in global change research, we consider the limitations of these data and modern

sampling and statistical tools that may be applied to surmount challenges they present. Using a case

study of insect herbivory, we illustrate how novel herbarium data may be employed to test hypotheses

for which few data exist. With the goal of positioning herbaria as hubs for global change research, we

suggest future research directions and curation priorities.

Key words: climate change; extinction; global change; habitat conversion; herbarium; historical data; invasive

species; museum specimens.

}, author = {Meineke, Emily K. and Charles C. Davis and Davies, Jonathan} } @article {1138941, title = {Reconstructing deep-time palaeoclimate legacies in the clusioid Malpighiales unveils their role in the evolution and extinction of the boreotropical flora}, journal = {Global Ecology and Biogeography}, volume = {27}, year = {2018}, pages = {616-628}, abstract = {During its entire history, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration and persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH clade) and the genus\ Hypericum\ as test cases.}, url = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/geb.12724}, author = {Meseguer, Andrea S. and Lobo, Jorge M. and Cornualt, Josselin and Beerling, Davis and Brad R. Ruhfel and Charles C. Davis and Jousellin, Emmanuelle and Sanmartin, Isabel} } @article {1118577, title = {Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants}, journal = {Applications in Plant Sciences}, volume = {6}, year = {2018}, pages = {1-11}, abstract = {

Premise of the Study
Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community.

Methods and Results
To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data-sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension.

Conclusions
Our hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed.

}, url = {http://onlinelibrary.wiley.com/doi/10.1002/aps3.1022/full}, author = {Yost, Jennifer M. and Sweeney, Patrick W. and Gilbert, Ed and Nelson, Gil and Guralnick, Robert and Gallnat, Amanda S. and Ellwood, Elizabeth R. and Rossington, Natalie and Willis, Charles G. and Blum, Stanley D. and Walls, Romona L. and Haston, Elspeth M. and Denslow, Michael W. and Zohner, Constantin M. and Morris, Ashley B. and Stucky, Brian J. and Carter, J. Richard and Baxter, David G. and Bolmgren, Kjell and Denny, Ellen G. and Dean, Ellen and Pearson, Katelin D. and Charles C. Davis and Mishler, Brent D. and Soltis, Pamela S. and Mazer, Susan J.} } @article {1123346, title = {The Brave New World of the Digital Herbarium}, journal = {ReVista}, year = {2018}, pages = {8-11}, url = {https://revista.drclas.harvard.edu/book/brave-new-world-digital}, author = {Charles C. Davis and Ellison, Aaron M.} } @article {1103956, title = {Running head: Herbaria for understanding global change}, journal = {BioRxiv}, year = {2017}, abstract = {Plant and fungal specimens in herbaria are becoming primary resources for investigating how plant phenology and geographic distributions shift with climate change, greatly expanding inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a wealth of additional data-including nutrients, defensive compounds, herbivore damage, disease lesions, and signatures of physiological processes-that capture ecological and evolutionary responses to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium data, global change topics to which they have been applied, and new hypotheses they could inform. We find that herbarium data have been used extensively to study impacts of climate change and invasive species, but that such data are less commonly used to address other drivers of biodiversity loss, including habitat conversion, pollution, and overexploitation. In addition, we note that fungal specimens are under-explored relative to vascular plants. To facilitate broader application of plant and fungal specimens in global change research, we outline the limitations of these data and modern sampling and statistical tools that may be applied to surmount challenges they present. Using a case study of insect herbivory, we illustrate how novel herbarium data may be employed to test hypotheses for which few data exist, despite potentially large biases. With the goal of positioning herbaria as hubs for global change research, we suggest future research directions and curation priorities.}, url = {https://www.biorxiv.org/content/early/2017/11/14/218776}, author = {Meineke, Emily K. and Charles C. Davis and Davies, Jonathan T.} } @article {1081351, title = {A statistical estimator for determining the limits of contemporary and historic phenology}, journal = {Nature, Ecology \& Evolution}, year = {2017}, abstract = {

Climate change affects not just where species are found, but also when species{\textquoteright} key life-history events occur{\textemdash}their phenol-

ogy. Measuring such changes in timing is often hampered by a reliance on biased survey data: surveys identify that an event

has taken place (for example, the flower is in bloom), but not when that event happened (for example, the flower bloomed

yesterday). Here, we show that this problem can be circumvented using statistical estimators, which can provide accurate and

unbiased estimates from sparsely sampled observations. We demonstrate that such methods can resolve an ongoing debate

about the relative timings of the onset and cessation of flowering, and allow us to place modern observations reliably within the

context of the vast wealth of historical data that reside in herbaria, museum collections, and written records. We also analyse

large-scale citizen science data from the United States National Phenology Network and reveal not just earlier but also poten-

tially more variable flowering in recent years. Evidence for greater variability through time is important because increases in

variation are characteristic of systems approaching a state change.

}, author = {Pearse, William D. and Davis, Charles D. and Inouye, David W. and Primack, RIchard B. and Jonathan Davies, T.} } @conference {1103921, title = {Deja Vu: Characterizing Worker Reliability Using Task Consistency}, booktitle = {Association for the Advancement of Artificial IntelligenceI Conference on Human Computation and Crowdsourcing }, year = {2017}, publisher = {The AAAI Press, Palo Alto, California}, organization = {The AAAI Press, Palo Alto, California}, address = {Qu{\'e}bec City, Qu{\'e}bec, Canada}, abstract = {Consistency is a practical metric that evaluates an instrument{\textquoteright}s reliability based on its ability to yield the same output when repeatedly given a particular input. Despite its broad usage, little is understood about the feasibility of using consistency as a measure of worker reliability in crowdwork. In this paper, we explore the viability of measuring a worker{\textquoteright}s reliability by their ability to conform to themselves. We introduce and describe Deja Vu, a mechanism for dynamically generating task queues with consistency probes to measure the consistency of workers who repeat the same task twice. We present a study that utilizes Deja Vu to examine how generic characteristics of the duplicate task {\textemdash} such as placement, difficulty, and transformation {\textemdash} affect a workers task consistency in the context of two unique object detection tasks. Our findings provide insight into the design and use of consistency-based reliability metrics.}, url = {http://acw.io/pubs/hcomp2017-dejavu.pdf}, author = {Williams. Alex C. and Goh, Joslin and Willis, Charlie G. and Ellison, Aaron M. and Brusuelas, James H. and Charles C. Davis and Law, Edith} } @article {1103931, title = {Reconstructing deep-time paleoclimate legacies unveil the demise and turnover of the ancient (boreo) tropical flora}, journal = {bioRxiv}, year = {2017}, abstract = {Aim: Since the Late Cretaceous, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration or persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH), and the genus Hypericum as test cases.}, url = {https://www.biorxiv.org/content/biorxiv/early/2017/10/24/208454.full.pdf}, author = {Sanchez Meseguer, Andrea and Lobo, Jorge and Cornuault, Joselin and Beerling, David and Brad R. Ruhfel and Charles C. Davis and Jousselin, Emmanuelle and Sanmartin, Isabel} } @article {1103986, title = {Reading between the vines: Hosts as islands for extreme holoparasitic plants}, journal = {American Journal of Botany}, volume = {104}, year = {2017}, note = {Commentary}, pages = {1382-1389}, abstract = {

PREMISE OF THE STUDY:\ Partitioning of population genetic variation in plants may be affected by numerous factors including life history and dispersal characteristics. In parasitic plants, interactions with host populations may be an additional factor influencing partitioning. To test for hierarchical population genetic patterns related to obligate endoparasitism, we studied three species of Rafflesiaceae, which grow as extremely reduced endophytes infecting\ Tetrastigma\ vines in Southeast Asia.

METHODS:\ Microsatellite markers were developed and multilocus genotypes were determined for\ Rafflesia cantleyi,\ Rafflesia tuan-mudae, and\ Sapria himalayana\ and each of their\ Tetrastigma\ hosts. Relatedness among parasite individuals was estimated, and AMOVAs were used to determine levels of population genetic subdivision.

KEY RESULTS:\ Microsatellite genotypes for 340 paired parasite and host samples revealed that host vines were infected by numerous Rafflesiaceae individuals that may spread for up to 14 m within stem tissues. Surprisingly, Rafflesiaceae parasites within a given host are significantly more closely related to each other than individuals of the same species in other host individuals. The pattern of hierarchical population genetic subdivision we detected across species is likely due to limited seed dispersal with reinfection of natal host vines.

CONCLUSIONS:\ These findings demonstrate common population genetic patterns between animal and plant parasites, potentially indicating advantages of close relatives infecting hosts. This study also has important conservation implications for Rafflesiaceae since our data suggest that destruction of a single infected host vine could result in large genetic losses.

}, url = {http://www.amjbot.org/content/104/9/1382.full.pdf+html}, author = {Barkman, Todd J. and Kloster, Matthew, R. and Gaddis, Keith D. and Franzone, Brian and Calhoun, Sondra and Manickam, Sugumaran and Vessabutr, Suyanee and Sasirat, Sawitree and Charles C. Davis} } @article {1046281, title = {Widespread sampling biases in herbaria revealed from large-scale digitization}, journal = {BioRxiv}, year = {2017}, abstract = {1. Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. 2. We determined spatial, temporal, trait, phylogenetic, and collector biases in ~5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England (NE). 3. We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via {\textquoteright}founder effects{\textquoteright}. 4. Studies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.}, author = {Daru, Barnabas and Park, Daniel S. and Primack, Richard and Willis, Charles G. and Barrington, David S. and Whitfeld, Timothy J. S. and Seidler, Tristram G. and Sweeny, Patrick W. and Foster, David R. and Ellison, Arron M. and Charles C. Davis} } @article {1046356, title = {Old plants, new tricks: phenological research using herbarium specimens}, journal = {Trends in Ecology \& Evolution }, volume = {32}, year = {2017}, pages = {531-546}, abstract = {The timing of phenological events, such as leaf-out and flowering, strongly influence plant success and their study is vital to understanding how plants will respond to climate change. Phenological research, however, is often limited by the temporal, geographic, or phylogenetic scope of available data. Hundreds of millions of plant specimens in herbaria worldwide offer a potential solution to this problem, especially as digitization efforts drastically improve access to collections. Herbarium specimens represent snapshots of phenological events and have been reliably used to characterize phenological responses to climate. We review the current state of herbarium-based phenological research, identify potential biases and limitations in the collection, digitization, and interpretation of specimen data, and discuss future opportunities for phenological investigations using herbarium specimens.}, author = {Willis, Charles G. and Ellwood, Elizabeth R. and Primack, RIchard B. and Charles C. Davis and Pearson, Katelin D, and Gallinat, Amanda S. and Yost, Jenn M. and Neson, Gil and Mazer, Susan J. and Rossington, Natalie L. and Sparks, Tim H. and Soltis, Pamela S.} } @article {1046261, title = {Selfing species exhibit diminished niche breadth over time}, journal = {BioRxiv}, year = {2017}, abstract = {Self-pollinating plants ({\textquotedblleft}selfers{\textquotedblright}) have larger geographic ranges and inhabit higher latitudes than their outcrossing relatives. This finding has led to the hypothesis that selfers also have broader climatic niches. It is possible that the increased likelihood of successful colonization into new areas and the initial purging of deleterious mutations may offset selfers{\textquoteright} inability to adapt to new environments due to low heterozygosity. Here, for the first time, we examine the climatic niches and mutation accumulation rates of hundreds of closely related selfing and outcrossing species. Contrary to expectations, selfers do not have wider climatic niche breadths than their outcrossing sister taxa despite selfers{\textquoteright} greatly expanded geographic ranges. Selfing sister pairs also exhibit greater niche overlap than outcrossing sisters, implying that climatic niche expansion becomes limited following the transition to selfing. Further, the niche breadth of selfers is predicted to decrease significantly faster than that of closely-related outcrossers. In support of these findings, selfers also display significantly higher mutation accumulation rates than their outcrossing sisters, implying decreased heterozygosity, effective population size, and adaptive potential. These results collectively suggest that while the release from mate limitation among selfing species may result in initial range expansion, range size and niche breadth are decoupled, and the limitations of an increasingly homogeneous genome will constrict selfers{\textquoteright} climatic niches and over time reduce their geographic ranges.}, author = {Park, Daniel S. and Ellison, Aaron M. and Charles C. Davis} } @article {1045816, title = {CrowdCurio: an online crowdsourcing platform to facilitate climate change studies using herbarium specimens}, journal = {New Phytologist}, volume = {215}, year = {2017}, pages = {479{\textendash}488}, abstract = {}, author = {Willis, Charles G. and Law, Edith and Williams. Alex C. and Franzone, Brian F. and Bernados, Rebecca and Bruno, Lian and Hopkins, Claire and Schorn, Christian and Weber, Ella and Park, Daniel S. and Charles C. Davis} } @article {1046296, title = {Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade}, journal = {Journal of Biogeography}, volume = {71}, year = {2017}, pages = {1970-1985}, abstract = {Although specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of \~{}550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in the centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved\ \~{}13 times independently, with \~{}11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade{\textquoteright}s rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades.}, author = {Lagomarsino, Laura P. and Forrestel, Elisabeth J. and Muchhala, Nathan and Charles C. Davis} } @article {1046321, title = {Implications and alternatives of assigning climate data to geographical centroids}, journal = {Journal of Biogeography }, year = {2017}, pages = {1-11}, abstract = {

Aim When precise coordinate data for training species distribution models (SDMs) are lacking, climatic variables are often assigned to centroids of geopolitically defined regions, frequently counties. This is problematic because approximations using centroids may not be representative of the regional climate or the locality from where species actually occur, thus leading to spurious conclusions. We evaluated county centroid climate versus simple alternatives for assigning climate to species observations in the absence of precise occurrence data.

Location United States of America.

Methods We assessed the disparity between the actual climate of all points within a county and metrics estimating county climate using the climate of geographical centroid, mean county climate and median county climate. To further evaluate the performance of these metrics, we generated SDMs of four common species using these estimates and compared the results with observed

species distributions (red trillium, Pacific trillium, tall thistle and annual fleabane). Finally, we projected future ranges for annual fleabane to examine the difference in predicted range change between models.

Results Mean and median climate metrics were significantly better fits for approximating the climate of specimen records than climate of the geographical centroid. Moreover, county mean climate SDMs were the most similar to SDMs using actual coordinate data. In contrast, models applying climate to county centroid significantly overpredicted species range. This had implications for future projections of annual fleabane SDMs: the county centroid model predicted a decrease in suitable habitats for this species while other models predicted an increase.

Main conclusions County centroid climate, although commonly applied, is not suitable for SDMs as a means to approximate species climate when locality data are less precise. When only county level data are available, and more computationally intensive methods of accounting for spatial uncertainty cannot be readily implemented, we suggest considering mean county climate as an alternative.

}, author = {Park, Daniel S. and Charles C. Davis} } @article {1046931, title = {Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae (Malpighiaceae,Elatinaceae) Clade}, journal = {PLoS ONE}, volume = {11}, year = {2016}, pages = {1-21}, abstract = {The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including \~{}35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae,\ Bergia\ and\ Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade{\textquoteright}s largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental\ in situ\ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions.}, author = {Cai, Liming and Zhenxiang Xi and PEterson, Kylee and Rushworth, Katherine and Beaulieu, Jeremy and Charles C. Davis} } @article {1046506, title = {Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data}, journal = {Journal of Phycology }, volume = {52}, year = {2016}, pages = {997-1017}, abstract = {Species in the genus\ Gracilaria\ that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the\ Gracilaria domingensiscomplex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and\ rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to\ rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the\ G.\ domingensis\ complex includes seven distinct species, each of which are not all most closely related:\ G.\ cervicornis; a ressurected\ G.\ ferox;\ G.\ apiculata\ subsp.\ apiculata; a new species,\ Gracilaria baiana\ sp. nov.;\ G.\ intermedia\ subsp.\ intermedia;\ G.\ venezuelensis; and\ G.\ domingensis\ sensu stricto, which includes the later heterotypic synonym,\ G.\ yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae.}, author = {Lyra, Goia M. and Gurgel, Carlos F. D. and Costa, Emanuelle S. and de Jesus, Priscilla B. and Oliveira, Mariana C. and Oliveira, Eurico C. and Charles C. Davis and de Castro Nunes, Jose M.} } @article {1046976, title = {Differential Expression of CYC2 Genes and the Elaboration of Floral Morphologies in Hiptage, an Old-World Genus of Malpighiaceae}, journal = {International Journal of Plant Sciences}, volume = {177}, year = {2016}, pages = {551-558}, abstract = {

Premise of research. The primarily Neotropical Malpighiaceae exhibit an elegant suite of floral morphological characteristics associated with a specialized mutualism with oil bee pollinators, including bilaterally symmetrical flowers and paired oil glands on the calyx. One clade within the family,\ Hiptage\ Gaertn., has migrated to the paleotropics and lost its association with oil bees. Corresponding to this transition, some members of\ Hiptage\ have evolved a highly elaborate zygomorphic corolla with strongly reflexed petals and striking dorsoventral heteranthery. Previously, we demonstrated that expression of\ CYCLOIDEA2-like (CYC2-like) genes is correlated with the evolution of floral symmetry in Malpighiaceae. Here, we examine\ CYC2expression in relation to the evolution of elaborate floral zygomorphy in\ Hiptage benghalensis.

Methodology. CYC2-like genes were cloned from\ H. benghalensis. The spatial pattern of\ CYC2\ expression was examined with quantitative reverse-transcription PCR on the dissected floral organs.

Pivotal results. While most Neotropical Malpighiaceae express two\ CYC2-like genes,\ CYC2A\ and\ CYC2B, we demonstrate that\ H. benghalensis\ has experienced further duplications yielding four copies, which are expressed in all four whorls of the flower. As in Neotropical Malpighiaceae,\ CYC2A\ homologs\ HbCYC2A-1\ and\ HbCYC2A-2\ are expressed broadly in the dorsal region of the flower, but unlike that in other Neotropical species, expression also extends to the dorsal stamens. The\ CYC2B\ copies\ HbCYC2B-1\ and\ HbCYC2B-2\ are intensely expressed in the single dorsal petal (as in Neotropical Malpighiaceae), but their expression is further detected in the other floral whorls, especially in the stamens of the dorsal region.

Conclusions. The relaxation of the conserved expression of\ CYC2-like genes in Neotropical Malpighiaceae and the expansion to broader floral regions, including the dorsal androecium, correlate with the development of dorsoventral heteranthery in\ H. benghalensis. We propose that changes in the pattern of\ CYC2\ expression may have contributed to the elaborated androecium of\ H. benghalensis, which was crucial for its adaptation to a novel pollination strategy.

}, author = {Zhang, Whenheng and Kramer, Elena M. and Charles C. Davis} } @article {855496, title = {Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade}, journal = {American Journal of Botany }, volume = {103}, year = {2016}, month = {22 Jun 2016}, pages = {1-12}, abstract = {PREMISE OF THE STUDY: The clusioid clade (Malpighiales) has an ancient fossil record (~90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation. METHODS: Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny. KEY RESULTS: Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia . In contrast, dispersal occurred on \> 25\% of the branches, indicating the current distribution of the clade likely refl ects extensive recent dispersal during the Cenozoic (\< 65 Ma), most of which occurred after the beginning of the Eocene (~56 Ma). CONCLUSIONS: These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been infl uenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.}, author = {Brad R. Ruhfel and Claudia P. Bove and C. Thomas Philbrick and Charles C. Davis} } @article {854826, title = {Unraveling the biogeographical history of Chrysobalanceae from plastid genomes}, journal = {American Journal of Botany }, volume = {103}, year = {2016}, month = {21 Jun 2016}, pages = {1-14}, abstract = {PREMISE OF THE STUDY: The complex geological and climatic history of the Neotropics has had major implications on the diversifi cation of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75\% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversifi cation in the Neotropical fl ora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear. METHODS: We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of fi ve plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversifi cation rates in the family. KEY RESULTS: The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella . The family has diversifi ed starting around the Eocene-Oligocene transition. An ancestral area reconstruction confi rms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversifi cation. CONCLUSIONS: Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversifi cation of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.}, author = {L{\'e}a Bardon and Cynthia Sothers and Ghillean T. Prance and Pierre-Jean G. Mal{\'e} and Zhenxiang Xi and Charles C. Davis and Murienne, Jerome and Roosevelt, Garc{\'\i}a-Villacorta and Eric Coissac and S{\'e}bastien Lavergne and J{\'e}r{\^o}me Chave} } @article {847016, title = {The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)}, journal = {New Phytologist}, volume = {210}, number = {4}, year = {2016}, note = {

Lagomarsino, Laura PCondamine, Fabien LAntonelli, AlexandreMulch, AndreasDavis, Charles CengEngland2016/03/19 06:00New Phytol. 2016 Jun;210(4):1430-42. doi: 10.1111/nph.13920. Epub 2016 Mar 14.

}, month = {Jun}, pages = {1430-1442}, abstract = {

The tropical Andes of South America, the world{\textquoteright}s richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world{\textquoteright}s biodiversity.

}, keywords = {andes, biodiversity hotspot, climate change, diversification, Lobelioideae, Neotropics, pollination syndromes, rapid radiation}, isbn = {1469-8137 (Electronic)0028-646X (Linking)}, author = {Lagomarsino, Laura P. and Condamine, Fabian L. and Antonelli, Alexandre and Mulch, Andreas and Charles C. Davis} } @article {1046451, title = {Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes}, journal = {Ecological Monographs }, volume = {87}, year = {2016}, pages = {278-296}, abstract = {Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid\ rbcL\ and\ trnH-psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field-collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000\ m. We found that species richness of fern sporophytes conforms to the well-known unimodal (i.e., mid-elevation peak) pattern, reaching a maximum at ~1000{\textendash}1200\ m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.}, author = {Nitta, Joel H. and Meyer, Jean-Yves and Taputuarai, Ravahere and Charles C. Davis} } @article {847176, title = {The Impact of Missing Data on Species Tree Estimation}, journal = {Molecular Biology and Evolution}, volume = {33}, number = {3}, year = {2015}, note = {

Xi, ZhenxiangLiu, LiangDavis, Charles Ceng2015/11/22 06:00Mol Biol Evol. 2016 Mar;33(3):838-60. doi: 10.1093/molbev/msv266. Epub 2015 Nov 20.

}, month = {Mar}, pages = {838-60}, abstract = {

Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amount of missing data, there remains no consensus on their impact to species tree estimation. Here, using several simulated and empirical data sets, we assess the effects of missing data on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and gene rate heterogeneity. We demonstrate that concatenation (RAxML), gene-tree-based coalescent (ASTRAL, MP-EST, and STAR), and supertree (matrix representation with parsimony [MRP]) methods perform reliably, so long as missing data are randomly distributed (by gene and/or by species) and that a sufficiently large number of genes are sampled. When data sets are indecisive sensu Sanderson et al. (2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155) and/or ILS is high, however, high amounts of missing data that are randomly distributed require exhaustive levels of gene sampling, likely exceeding most empirical studies to date. Moreover, missing data become especially problematic when they are nonrandomly distributed. We demonstrate that STAR produces inconsistent results when the amount of nonrandom missing data is high, regardless of the degree of ILS and gene rate heterogeneity. Similarly, concatenation methods using maximum likelihood can be misled by nonrandom missing data in the presence of gene rate heterogeneity, which becomes further exacerbated when combined with high ILS. In contrast, ASTRAL, MP-EST, and MRP are more robust under all of these scenarios. These results underscore the importance of understanding the influence of missing data in the phylogenomics era.

}, keywords = {coalescent methods, concatenation methods, gene rate heterogeneity, incomplete lineage sorting, missing data, species tree estimation}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Zhenxiang Xi and Liu, Liang and Charles C. Davis} } @article {847876, title = {Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased}, journal = {Molecular Phylogenetics and Evolution}, volume = {92}, year = {2015}, pages = {63-71}, abstract = {The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014).}, author = {Zhenxiang Xi and Liu, Liang and Charles C. Davis} } @article {855511, title = {Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics}, journal = {Molecular Phylogenetics and Evolution }, volume = {94}, year = {2015}, month = {27 Oct 2015}, pages = {447-462}, abstract = {

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S\&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as {\textquoteleft}{\textquoteleft}species tree{\textquotedblright} methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S\&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S\&G{\textquoteright}s excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S\&G and an appeal to {\textquoteleft}{\textquoteleft}first principles{\textquotedblright} of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S\&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S\&G{\textquoteright}s claims that MSC models explain little or none (0{\textendash}15\%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics.

}, author = {Edwards, Scott V. and Zhenxiang Xi and Axel Janke and Brant C, Faircloth and John E. McCormack and Travis C. Glenn and Bojian Zhong and Shaoyuan Wu and Emily Moriarty Lemmon and Alan R. Lemmon and Adam D. Leach{\'e} and Liu, Liang and Charles C. Davis} } @article {846931, title = {Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species{\textquoteright} phenological cueing mechanisms}, journal = {American Journal of Botany}, volume = {102}, number = {10}, year = {2015}, note = {

Davis, Charles CWillis, Charles GConnolly, BryanKelly, CourtlandEllison, Aaron MengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2015/10/10 06:00Am J Bot. 2015 Oct;102(10):1599-609. doi: 10.3732/ajb.1500237. Epub 2015 Oct 8.

}, month = {Oct}, pages = {1599-609}, abstract = {

PREMISE OF THE STUDY: Climate change has resulted in major changes in the phenology of some species but not others. Long-term field observational records provide the best assessment of these changes, but geographic and taxonomic biases limit their utility. Plant specimens in herbaria have been hypothesized to provide a wealth of additional data for studying phenological responses to climatic change. However, no study to our knowledge has comprehensively addressed whether herbarium data are accurate measures of phenological response and thus applicable to addressing such questions. METHODS: We compared flowering phenology determined from field observations (years 1852-1858, 1875, 1878-1908, 2003-2006, 2011-2013) and herbarium records (1852-2013) of 20 species from New England, United States. KEY RESULTS: Earliest flowering date estimated from herbarium records faithfully reflected field observations of first flowering date and substantially increased the sampling range across climatic conditions. Additionally, although most species demonstrated a response to interannual temperature variation, long-term temporal changes in phenological response were not detectable. CONCLUSIONS: Our findings support the use of herbarium records for understanding plant phenological responses to changes in temperature, and also importantly establish a new use of herbarium collections: inferring primary phenological cueing mechanisms of individual species (e.g., temperature, winter chilling, photoperiod). These latter data are lacking from most investigations of phenological change, but are vital for understanding differential responses of individual species to ongoing climate change.

}, keywords = {climate change, climate variability, herbarium specimens, museum collections, phenology}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Charles C. Davis and Willis, Charles G. and Connolly, Bryan and Kelly, Courtland and Ellison, Aaron M.} } @newspaperarticle {847866, title = {Opinion: Pope Francis{\textquoteright} environmental encyclical cannot be ignored}, year = {2015}, month = {Sep 2015}, url = {http://www.seattletimes.com/opinion/pope-francis-environmental-encyclical-cannot-be-ignored/}, author = {Charles C. Davis and Ellison, Aaron M.} } @article {847126, title = {Extended flowering intervals of bamboos evolved by discrete multiplication}, journal = {Ecology Letters}, volume = {18}, number = {7}, year = {2015}, note = {

Media coverage by Carl Zimmer in\ National Geographic

}, month = {Jul}, pages = {653-9}, abstract = {

Numerous bamboo species collectively flower and seed at dramatically extended, regular intervals - some as long as 120 years. These collective seed releases, termed {\textquoteright}masts{\textquoteright}, are thought to be a strategy to overwhelm seed predators or to maximise pollination rates. But why are the intervals so long, and how did they evolve? We propose a simple mathematical model that supports their evolution as a two-step process: First, an initial phase in which a mostly annually flowering population synchronises onto a small multi-year interval. Second, a phase of successive small multiplications of the initial synchronisation interval, resulting in the extraordinary intervals seen today. A prediction of the hypothesis is that mast intervals observed today should factorise into small prime numbers. Using a historical data set of bamboo flowering observations, we find strong evidence in favour of this prediction. Our hypothesis provides the first theoretical explanation for the mechanism underlying this remarkable phenomenon.

}, keywords = {*Biological Evolution, *Models, Theoretical, *Periodicity, Bamboos, Bambusa/*physiology, biological clocks, Flowers/*physiology, masting, phenology, Poaceae/physiology, Pollination}, isbn = {1461-0248 (Electronic)1461-023X (Linking)}, author = {Carl Veller and Nowak, Martin A. and Charles C. Davis} } @article {846946, title = {Horizontal gene transfer in parasitic plants}, journal = {Current Opinion in Plant Biology}, volume = {26}, year = {2015}, note = {

Davis, Charles CXi, ZhenxiangengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.ReviewEngland2015/06/09 06:00Curr Opin Plant Biol. 2015 Aug;26:14-9. doi: 10.1016/j.pbi.2015.05.008. Epub 2015 Jun 3.

}, month = {Aug}, pages = {14-19}, abstract = {

Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.

}, isbn = {1879-0356 (Electronic)1369-5266 (Linking)}, author = {Charles C. Davis and Zhenxiang Xi} } @article {847141, title = {Rethinking migration}, journal = {Science}, volume = {348}, number = {6236}, year = {2015}, note = {

Willis, Charles GDavis, Charles CengCommentLetter2015/05/16 06:00Science. 2015 May 15;348(6236):766. doi: 10.1126/science.348.6236.766-a.

}, month = {May 15}, pages = {766}, isbn = {1095-9203 (Electronic)0036-8075 (Linking)}, author = {Willis, Charlie G. and Charles C. Davis} } @article {847026, title = {Estimating phylogenetic trees from genome-scale data}, journal = {Annals of the New York Academy of Sciences}, volume = {1360}, year = {2015}, note = {

Liu, LiangXi, ZhenxiangWu, ShaoyuanDavis, Charles CEdwards, Scott VengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.Review2015/04/16 06:00Ann N Y Acad Sci. 2015 Dec;1360:36-53. doi: 10.1111/nyas.12747. Epub 2015 Apr 14.

}, month = {Dec}, pages = {36-53}, abstract = {

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data.

}, keywords = {*Databases, Genetic/standards, *Models, Genetic, *Phylogeny, Animals, anomaly zone, bias-variance dilemma, Genetic Speciation, Genome/*genetics, Humans, isochore, recombination, Transcriptome, Transcriptome/genetics}, isbn = {1749-6632 (Electronic)0077-8923 (Linking)}, author = {Liu, Liang and Zhenxiang Xi and Shaoyuan Wu and Charles C. Davis and Edwards, Scott V.} } @article {847031, title = {Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences}, journal = {Journal of Phycology}, volume = {51}, number = {2}, year = {2015}, note = {

Lyra, Goia de MCosta, Emmanuelle da Sde Jesus, Priscila Bde Matos, Joao Carlos GCaires, Taiara AOliveira, Mariana COliveira, Eurico CXi, ZhenxiangNunes, Jose Marcos de CDavis, Charles Ceng2016/03/18 06:00J Phycol. 2015 Apr;51(2):356-66. doi: 10.1111/jpy.12281. Epub 2015 Mar 12.

}, month = {Apr}, pages = {356-66}, abstract = {

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well-supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.

}, keywords = {Gracilaria, Gracilariopsis, Hydropuntia, Systematics, Taxonomy}, isbn = {1529-8817 (Electronic)0022-3646 (Linking)}, author = {Lyra, Goia M. and de S. Costa, Emmanuelle and de Jesus, Priscilla and de Matos, Joao Carlos and Caires, Taiara A. and Oliveira, Mariana C. and Oliveira, Eurico C. and Zhenxiang Xi and de C. Nunes, Jose Marcos and Charles C. Davis} } @article {847021, title = {Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting}, journal = {Molecular Biology and Evolution}, volume = {32}, number = {3}, year = {2014}, note = {

Liu, LiangXi, ZhenxiangDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}t2014/11/29 06:00Mol Biol Evol. 2015 Mar;32(3):791-805. doi: 10.1093/molbev/msu331. Epub 2014 Nov 26.

}, month = {Mar}, pages = {791-805}, abstract = {

It is well known that species with elevated substitution rates can give rise to disproportionately long branches in the species tree. This combination of long and short branches can contribute to long-branch artifacts (LBA). Despite efforts to remedy LBA via increased taxon sampling and methodological improvements in gene tree estimation, it remains unclear how long and short branches affect species tree estimation in the presence of incomplete lineage sorting (ILS). Here, we examine the combined influence of long external and short internal branches on concatenation and coalescent methods using both simulated and empirical data. Our results demonstrate that the presence of long and short branches alone does not obviously confound the consistency of concatenation and coalescent methods. However, when long external and short internal branches occur simultaneously with high ILS, concatenation methods can be misled, especially when two of these long branches are sister lineages. In contrast, coalescent methods are more robust under these circumstances. This is particularly relevant because this topological pattern also characterizes numerous ancient rapid radiations across the tree of life. Because short internal branches can increase the potential for ILS and gene tree discordance, our results collectively suggest that coalescent methods are more likely to infer the correct species tree in cases of ancient rapid radiations where long external and short internal branches are in close phylogenetic proximity.

}, keywords = {*Evolution, Molecular, *Genetic Speciation, *Models, Genetic, ancient rapid radiation, Animals, coalescent methods, Computational Biology/*methods, concatenation methods, Databases, Genetic, incomplete lineage sorting, long-branch artifacts, Mammals/genetics, Phylogeny, Sequence Analysis, DNA}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Liu, Liang and Zhenxiang Xi and Charles C. Davis} } @article {847146, title = {The establishment of Central American migratory corridors and the biogeographic origins of seasonally dry tropical forests in Mexico}, journal = {Frontiers in Genetics}, volume = {5}, year = {2014}, note = {

Willis, Charles GFranzone, Brian FXi, ZhenxiangDavis, Charles CengSwitzerland2015/01/08 06:00Front Genet. 2014 Dec 19;5:433. doi: 10.3389/fgene.2014.00433. eCollection 2014.

}, pages = {1-14}, abstract = {

Biogeography and community ecology can mutually illuminate the formation of a regional species pool or biome. Here, we apply phylogenetic methods to a large and diverse plant clade, Malpighiaceae, to characterize the formation of its species pool in Mexico, and its occupancy of the seasonally dry tropical forest (SDTF) biome that occurs there. We find that the ~162 species of Mexican Malpighiaceae represent ~33 dispersals from South America beginning in the Eocene and continuing until the Pliocene (~46.4-3.8 Myr). Furthermore, dispersal rates between South America and Mexico show a significant six-fold increase during the mid-Miocene (~23.9 Myr). We hypothesize that this increase marked the availability of Central America as an important corridor for Neotropical plant migration. We additionally demonstrate that this high rate of dispersal contributed substantially more to the phylogenetic diversity of Malpighiaceae in Mexico than in situ diversification. Finally, we show that most lineages arrived in Mexico pre-adapted with regard to one key SDTF trait, total annual precipitation. In contrast, these lineages adapted to a second key trait, precipitation seasonality, in situ as mountain building in the region gave rise to the abiotic parameters of extant SDTF. The timing of this in situ adaptation to seasonal precipitation suggests that SDTF likely originated its modern characteristics by the late Oligocene, but was geographically more restricted until its expansion in the mid-Miocene. These results highlight the complex interplay of dispersal, adaptation, and in situ diversification in the formation of tropical biomes. Our results additionally demonstrate that these processes are not static, and their relevance can change markedly over evolutionary time. This has important implications for understanding the origin of SDTF in Mexico, but also for understanding the temporal and spatial origin of biomes and regional species pools more broadly.

}, keywords = {adaptive lag time, diversification, land bridge, long-distance dispersal, pre-adaptation, South America, species pool, tropical biogeography}, isbn = {1664-8021 (Electronic)1664-8021 (Linking)}, author = {Willis, Charles G. and Franzone, Brian F. and Zhenxiang Xi and Charles C. Davis} } @article {847181, title = {Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies}, journal = {Systematic Biology}, volume = {63}, number = {6}, year = {2014}, note = {

Xi, ZhenxiangLiu, LiangRest, Joshua SDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2014/08/01 06:00Syst Biol. 2014 Nov;63(6):919-32. doi: 10.1093/sysbio/syu055. Epub 2014 Jul 30.

}, month = {Nov}, pages = {919-932}, abstract = {

The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is sister to all other angiosperms across different nucleotide rate partitions. Our results also show that commonly applied concatenation methods produce strongly supported, but incongruent placements of Amborella: slow-evolving nucleotide sites corroborate results from coalescent analyses, whereas fast-evolving sites place Amborella alone as the first lineage of extant angiosperms. We further explored the performance of coalescent versus concatenation methods using nucleotide sequences simulated on (i) the two alternate placements of Amborella with branch lengths and substitution model parameters estimated from each of the 310 nuclear genes and (ii) three hypothetical species trees that are topologically identical except with respect to the degree of deep coalescence and branch lengths. Our results collectively suggest that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites. This appears to be exacerbated by the combination of long branches in stem group angiosperms, Amborella, and Nymphaeales with the short internal branch separating Amborella and Nymphaeales. In contrast, coalescent methods appear to be more robust to elevated substitution rates.

}, keywords = {*Phylogeny, Amborella trichopoda, Angiosperms/*classification/genetics, Classification/*methods, coalescent methods, Computer Simulation, concatenation methods, elevated substitution rates, Genes, Plant/genetics, long-branch attraction, Nymphaea/*classification/genetics, Nymphaeales, Plastids/genetics}, isbn = {1076-836X (Electronic)1063-5157 (Linking)}, author = {Zhenxiang Xi and Liu, Liang and Rest, Joshua S. and Charles C. Davis} } @article {848086, title = {Reply to Angelo: Climate change and species loss in Thoreau{\textquoteright}s woods (Concord, Massachusetts, USA)}, journal = {Phytoneuron}, volume = {59}, year = {2014}, pages = {1-4}, author = {Willis, Charles G. and Charles C. Davis} } @article {847846, title = {Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors}, journal = {Frontiers in Plant Science}, volume = {4}, year = {2014}, pages = {1-13}, abstract = {Malpighiaceae possess flowers with a unique bilateral symmetry (zygomorphy), which is a hypothesized adaptation associated with specialization on neotropical oil bee pollinators. Gene expression of two representatives of the CYC2 lineage of floral symmetry TCP genes, CYC2A and CYC2B, demarcate the adaxial (dorsal) region of the flower in the characteristic zygomorphic flowers of most Malpighiaceae. Several clades within the family, however, have independently lost their specialized oil bee pollinators and reverted to radial flowers (actinomorphy) like their ancestors. Here, we investigate CYC2 expression associated with four independent reversals to actinomorphy. We demonstrate that these reversals are always associated with alteration of the highly conserved CYC2 expression pattern observed in most New World (NW) Malpighiaceae. In NW Lasiocarpus and Old World (OW) Microsteria, the expression of CYC2-like genes has expanded to include the ventral region of the corolla. Thus, the pattern of gene expression in these species has become radialized, which is comparable to what has been reported in the radial flowered legume clade Cadia. In striking contrast, in NW Psychopterys and OW Sphedamnocarpus, CYC2-like expression is entirely absent or at barely detectable levels. This is more similar to the pattern of CYC2 expression observed in radial flowered Arabidopsis. These results collectively indicate that, regardless of geographic distribution, reversals to similar floral phenotypes in this large tropical angiosperm clade have evolved via different genetic changes from an otherwise highly conserved developmental program.}, author = {Zhang, Whenzing and Steinmann, V.ictorW. and Nikolov, Lachezar and Kramer, Elena M. and Charles C. Davis} } @article {846996, title = {Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway}, journal = {Evolution}, volume = {68}, number = {12}, year = {2014}, note = {

Horn, James WXi, ZhenxiangRiina, RicardaPeirson, Jess AYang, YaDorsey, Brian LBerry, Paul EDavis, Charles CWurdack, Kenneth JengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/10/11 06:00Evolution. 2014 Dec;68(12):3485-504. doi: 10.1111/evo.12534. Epub 2014 Nov 20.

}, month = {Dec}, pages = {3485-504}, abstract = {

The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2 -concentrating mechanisms (CCMs)-crassulacean acid metabolism (CAM) and C4 -evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia ( approximately 2000 species) includes a diversity of CAM-using stem succulents, plus a single species-rich C4 subclade. We used ancestral state reconstructions with a dated molecular phylogeny to reveal that CCMs independently evolved 17-22 times in Euphorbia, principally from the Miocene onwards. Analyses assessing among-lineage variation in r identified eight Euphorbia subclades with significantly increased r, six of which have a close temporal relationship with a lineage-corresponding CCM origin. Our trait-dependent diversification analysis indicated that r of Euphorbia CCM lineages is approximately threefold greater than C3 lineages. Overall, these results suggest that CCM evolution in Euphorbia was likely an adaptive strategy that enabled the occupation of increased arid niche space accompanying Miocene expansion of arid ecosystems. These opportunities evidently facilitated recent, replicated bursts of diversification in Euphorbia.

}, keywords = {*Evolution, Molecular, *Photosynthesis, ancestral state reconstruction, C4 photosynthesis, CAM photosynthesis, climate change, diversification, Euphorbia/classification/*genetics/physiology, Miocene, Phylogeny, species selection, succulent}, isbn = {1558-5646 (Electronic)0014-3820 (Linking)}, author = {Horn, J. W. and Xi, Z. and Riina, R. and Peirson, J. A. and Yang, Y. and Dorsey, B. L. and Berry, P. E. and Davis, C. C. and Wurdack, K. J.} } @article {847051, title = {Floral structure and development in Rafflesiaceae with emphasis on their exceptional gynoecia}, journal = {American Journal of Botany}, volume = {101}, number = {2}, year = {2014}, note = {

Nikolov, Lachezar AStaedler, Yannick MManickam, SugumaranSchonenberger, JurgEndress, Peter KKramer, Elena MDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/02/11 06:00Am J Bot. 2014 Feb;101(2):225-43. doi: 10.3732/ajb.1400009. Epub 2014 Feb 8.

}, month = {Feb}, pages = {225-43}, abstract = {

PREMISE OF THE STUDY: The holoparasitic plant family Rafflesiaceae include the world{\textquoteright}s largest flowers. Despite their iconic status, relatively little is known about the morphology and development of their flowers. A recent study clarified the organization of the outer (sterile) floral organs, surprisingly revealing that their distinctive floral chambers arose via different developmental pathways in the two major genera of the family. Here, we expand that research to investigate the structure and development of the reproductive organs of Rafflesiaceae. METHODS: Serial sectioning, scanning electron microscopy, and x-ray tomography of floral buds were employed to reconstruct the structure and development of all three Rafflesiaceae genera. KEY RESULTS: Unlike most angiosperms, which form their shoot apex from the primary morphological surface, the shoot apex of Rafflesiaceae instead forms secondarily via internal cell separation (schizogeny) along the distal boundary of the host-parasite interface. Similarly, the radially directed ovarial clefts of the gynoecium forms via schizogeny within solid tissue, and no carpels are initiated from the floral apex. CONCLUSIONS: The development of the shoot apex and gynoecium of Rafflesiaceae are highly unusual. Although secondary formation of the morphological surface from the shoot apex has been documented in other plant groups, secondary derivation of the inner gynoecium surface is otherwise unknown. Both features are likely synapomorphies of Rafflesiaceae. The secondary derivation of the shoot apex may protect the developing floral shoot as it emerges from within dense host tissue. The secondary formation of the ovarial clefts may generate the extensive placental area necessary to produce hundreds of thousands of ovules.

}, keywords = {androecium, Angiosperms/anatomy \& histology/*growth \& development, floral anatomy, floral development, Flowers/anatomy \& histology/*growth \& development, gynoecium, Meristem/*growth \& development, Ovule/growth \& development, Rafflesia, Rafflesiaceae, Rhizanthes, Sapria, shoot apex}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Nikolov, L.achezar A. and Staedler, Yost M. and Manickam, Sugumaram and Schonenberger, Jurg and Endress, Peter K. and Kramer, Elena M. and Charles C. Davis} } @article {847056, title = {Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world{\textquoteright}s largest flowers}, journal = {Ann Bot}, volume = {114}, number = {2}, year = {2014}, note = {

Nikolov, Lachezar ATomlinson, P BManickam, SugumaranEndress, Peter KKramer, Elena MDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2014/06/20 06:00Ann Bot. 2014 Aug;114(2):233-42. doi: 10.1093/aob/mcu114. Epub 2014 Jun 18.

}, month = {Aug}, pages = {233-42}, abstract = {

BACKGROUND AND AIMS: Species in the holoparasitic plant family Rafflesiaceae exhibit one of the most highly modified vegetative bodies in flowering plants. Apart from the flower shoot and associated bracts, the parasite is a mycelium-like endophyte living inside their grapevine hosts. This study provides a comprehensive treatment of the endophytic vegetative body for all three genera of Rafflesiaceae (Rafflesia, Rhizanthes and Sapria), and reports on the cytology and development of the endophyte, including its structural connection to the host, shedding light on the poorly understood nature of this symbiosis. METHODS: Serial sectioning and staining with non-specific dyes, periodic-Schiff{\textquoteright}s reagent and aniline blue were employed in order to characterize the structure of the endophyte across a phylogenetically diverse sampling. KEY RESULTS: A previously identified difference in the nuclear size between Rafflesiaceae endophytes and their hosts was used to investigate the morphology and development of the endophytic body. The endophytes generally comprise uniseriate filaments oriented radially within the host root. The emergence of the parasite from the host during floral development is arrested in some cases by an apparent host response, but otherwise vegetative growth does not appear to elicit suppression by the host. CONCLUSIONS: Rafflesiaceae produce greatly reduced and modified vegetative bodies even when compared with the other holoparasitic angiosperms once grouped with Rafflesiaceae, which possess some vegetative differentiation. Based on previous studies of seeds together with these findings, it is concluded that the endophyte probably develops directly from a proembryo, and not from an embryo proper. Similarly, the flowering shoot arises directly from the undifferentiated endophyte. These filaments produce a protocorm in which a shoot apex originates endogenously by formation of a secondary morphological surface. This degree of modification to the vegetative body is exceptional within angiosperms and warrants additional investigation. Furthermore, the study highlights a mechanical isolation mechanism by which the host may defend itself from the parasite.

}, keywords = {Angiosperms/*anatomy \& histology/*microbiology, Comparative morphology, endophyte, Endophytes/cytology/*physiology, Flowers/*anatomy \& histology, gigantism, heterochrony, holoparasitism, host-parasite relationship, Plant Roots/anatomy \& histology/microbiology, Plant Shoots/microbiology, proembryo, Rafflesia, Rafflesiaceae, Rhizanthes, Sapria, Tetrastigma}, isbn = {1095-8290 (Electronic)0305-7364 (Linking)}, author = {Nikolov, L. A. and Tomlinson, P. B. and Manickam, S. and Endress, P. K. and Kramer, E. M. and Davis, C. C.} } @article {847061, title = {Leaf out times of temperate woody plants are related to phylogeny, deciduousness, growth habit and wood anatomy}, journal = {New Phytol}, volume = {203}, number = {4}, year = {2014}, note = {

Panchen, Zoe APrimack, Richard BNordt, BirgitEllwood, Elizabeth RStevens, Albert-DieterRenner, Susanne SWillis, Charles GFahey, RobertWhittemore, AlanDu, YanjunDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2014/06/20 06:00New Phytol. 2014 Sep;203(4):1208-19. doi: 10.1111/nph.12892. Epub 2014 Jun 18.

}, month = {Sep}, pages = {1208-19}, abstract = {

Leaf out phenology affects a wide variety of ecosystem processes and ecological interactions and will take on added significance as leaf out times increasingly shift in response to warming temperatures associated with climate change. There is, however, relatively little information available on the factors affecting species differences in leaf out phenology. An international team of researchers from eight Northern Hemisphere temperate botanical gardens recorded leaf out dates of c. 1600 woody species in 2011 and 2012. Leaf out dates in woody species differed by as much as 3 months at a single site and exhibited strong phylogenetic and anatomical relationships. On average, angiosperms leafed out earlier than gymnosperms, deciduous species earlier than evergreen species, shrubs earlier than trees, diffuse and semi-ring porous species earlier than ring porous species, and species with smaller diameter xylem vessels earlier than species with larger diameter vessels. The order of species leaf out was generally consistent between years and among sites. As species distribution and abundance shift due to climate change, interspecific differences in leaf out phenology may affect ecosystem processes such as carbon, water, and nutrient cycling. Our open access leaf out data provide a critical framework for monitoring and modelling such changes going forward.

}, keywords = {*Ecosystem, *Phylogeny, Angiosperms/anatomy \& histology/physiology, botanical gardens, leaf out, Least-Squares Analysis, Linear Models, phenology, Phylogeny, Plant Leaves/*physiology, shrubs, Species Specificity, Time Factors, trees, Trees/*anatomy \& histology/*growth \& development, vines, Wood/*anatomy \& histology/*growth \& development, woody plants}, isbn = {1469-8137 (Electronic)0028-646X (Linking)}, author = {Panchen, Z. A. and Primack, R. B. and Nordt, B. and Ellwood, E. R. and Stevens, A. D. and Renner, S. S. and Willis, C. G. and Fahey, R. and Whittemore, A. and Du, Y. and Davis, C. C.} } @article {846926, title = {Long-term morphological stasis maintained by a plant-pollinator mutualism}, journal = {Proc Natl Acad Sci U S A}, volume = {111}, number = {16}, year = {2014}, note = {

Davis, Charles CSchaefer, HannoXi, ZhenxiangBaum, David ADonoghue, Michael JHarmon, Luke JengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2014/04/08 06:00Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5914-9. doi: 10.1073/pnas.1403157111. Epub 2014 Apr 4.

}, month = {Apr 22}, pages = {5914-5919}, abstract = {

Many major branches in the Tree of Life are marked by stereotyped body plans that have been maintained over long periods of time. One possible explanation for this stasis is that there are genetic or developmental constraints that restrict the origin of novel body plans. An alternative is that basic body plans are potentially quite labile, but are actively maintained by natural selection. We present evidence that the conserved floral morphology of a species-rich flowering plant clade, Malpighiaceae, has been actively maintained for tens of millions of years via stabilizing selection imposed by their specialist New World oil-bee pollinators. Nine clades that have lost their primary oil-bee pollinators show major evolutionary shifts in specific floral traits associated with oil-bee pollination, demonstrating that developmental constraint is not the primary cause of morphological stasis in Malpighiaceae. Interestingly, Malpighiaceae show a burst in species diversification coinciding with the origin of this plant-pollinator mutualism. One hypothesis to account for radiation despite morphological stasis is that although selection on pollinator efficiency explains the origin of this unique and conserved floral morphology, tight pollinator specificity subsequently permitted greatly enhanced diversification in this system.

}, keywords = {Animals, Bees/*physiology, Biological Evolution, Centridini, comparative methods, diversification rate, flower morphology, Flowers/*anatomy \& histology/*physiology, Malpighiaceae/*anatomy \& histology/*physiology, Molecular Sequence Data, Phylogeny, Pollination/*physiology, Species Specificity, Symbiosis/*physiology}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Davis, C. C. and Schaefer, H. and Xi, Z. and Baum, D. A. and Donoghue, M. J. and Harmon, L. J.} } @article {847011, title = {Phylogeny, classification, and fruit evolution of the species-rich Neotropical bellflowers (Campanulaceae: Lobelioideae)}, journal = {Am J Bot}, volume = {101}, number = {12}, year = {2014}, note = {

Lagomarsino, Laura PAntonelli, AlexandreMuchhala, NathanTimmermann, AllanMathews, SarahDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}t2014/12/07 06:00Am J Bot. 2014 Dec;101(12):2097-112. doi: 10.3732/ajb.1400339. Epub 2014 Dec 3.

}, month = {Dec}, pages = {2097-112}, abstract = {

* PREMISE OF THE STUDY: The species-rich Neotropical genera Centropogon, Burmeistera, and Siphocampylus represent more than half of the approximately 1200 species in the subfamily Lobelioideae (Campanulaceae). They exhibit remarkable morphological variation in floral morphology and habit. Limited taxon sampling and phylogenetic resolution, however, obscures our understanding of relationships between and within these genera and underscores our uncertainty of the systematic value of fruit type as a major diagnostic character.* METHODS: We inferred a phylogeny from five plastid DNA regions (rpl32-trnL, ndhF-rpl32, rps16-trnK, trnG-trnG-trns, rbcL) using maximum-likelihood and Bayesian inference. Ancestral character reconstructions were applied to infer patterns of fruit evolution.* KEY RESULTS: Our results demonstrate that the majority of species in the genera Centropogon, Burmeistera, and Siphocampylus together form a primarily mainland Neotropical clade, collectively termed the "centropogonids." Caribbean Siphocampylus, however, group with other Caribbean lobelioid species. We find high support for the monophyly of Burmeistera and the polyphyly of Centropogon and mainland Siphocampylus. The ancestral fruit type of the centropogonids is a capsule; berries have evolved independently multiple times.* CONCLUSIONS: Our plastid phylogeny greatly improves the phylogenetic resolution within Neotropical Lobelioideae and highlights the need for taxonomic revisions in the subfamily. Inference of ancestral character states identifies a dynamic pattern of fruit evolution within the centropogonids, emphasizing the difficulty of diagnosing broad taxonomic groups on the basis of fruit type. Finally, we identify that the centropogonids, Lysipomia, and Lobelia section Tupa form a Pan-Andean radiation with broad habitat diversity. This clade is a prime candidate for investigations of Neotropical biogeography and morphological evolution.

}, keywords = {*Biological Evolution, *Phylogeny, andes, Bayes Theorem, Burmeistera, Campanulaceae, Campanulaceae/anatomy \& histology/classification/*genetics, Caribbean Region, Centropogon, Classification, DNA, Plant/*analysis, Ecosystem, Evolution, Molecular, fruit evolution, Fruit/*anatomy \& histology, Lobelioideae, Neotropics, phylogenetic systematics, plastid, Plastids, Sequence Analysis, DNA, Siphocampylus, Species Specificity}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Lagomarsino, L. P. and Antonelli, A. and Muchhala, N. and Timmermann, A. and S. Mathews and Davis, C. C.} } @article {848091, title = {Pitcher plants (Sarracenia) provide a 21st-century perspective on infraspecific ranks and interspecific hybrids: a modest proposal for appropriate recognition and usage}, journal = {Sys Bot}, volume = {39}, year = {2014}, pages = {939-949}, abstract = {

Abstract{\textemdash}The taxonomic use of infraspecific ranks (subspecies, variety, subvariety, form, and subform), and the formal recognition of interspecific hybrid taxa, is permitted by the International Code of Nomenclature for algae, fungi, and plants. However, considerable confusion regarding the biological and systematic merits is caused by current practice in the use of infraspecific ranks, which obscures the meaningful variability on which natural selection operates, and by the formal recognition of those interspecific hybrids that lack the potential for inter-lineage gene flow. These issues also may have pragmatic and legal consequences, especially regarding the legal delimitation and management of threatened and endangered species. A detailed comparison of three contemporary floras highlights the degree to which infraspecific and interspecific variation are treated inconsistently. An in-depth analysis of taxonomy of the North American flowering plant genus Sarracenia (Sarraceniaceae) provides an ideal case study illustrating the confusion that can arise from inconsistent and apparently arbitrary designation of infraspecific ranks and hybrid taxa. To alleviate these problems, we propose the abandonment of infraspecific ranks of {\textquotedblleft}variety{\textquotedblright} and {\textquotedblleft}form,{\textquotedblright} and discourage naming of sterile interspecific hybrids except for use in the horticultural or agronomic trade. Our recommendations for taxonomic practice are in accord with the objectives proposed in the Systematics Agenda 2000, Systematics Agenda 2020, and the Global Strategy for Plant Conservation. Keywords{\textemdash}Flora, nomenclature, Sarracenia, species concept, systematics.

}, author = {Ellison, A.M. and Davis, C. C. and Calie, P. J. and R.F.C. Naczi} } @article {846951, title = {Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there}, journal = {BMC Biol}, volume = {12}, year = {2014}, note = {

Davis, Charles CXi, ZhenxiangMathews, SarahengCommentEngland2014/02/19 06:00BMC Biol. 2014 Feb 17;12:11. doi: 10.1186/1741-7007-12-11.

}, pages = {11}, abstract = {

A study in BMC Evolutionary Biology represents the most comprehensive effort to clarify the phylogeny of green plants using sequences from the plastid genome. This study highlights the strengths and limitations of plastome data for resolving the green plant phylogeny, and points toward an exciting future for plant phylogenetics, during which the vast and largely untapped territory of nuclear genomes will be explored.

}, keywords = {*Genome, Plastid, Angiosperms/*genetics, Chlorophyta/*genetics, Plastids/*genetics, Viridiplantae/*genetics}, isbn = {1741-7007 (Electronic)1741-7007 (Linking)}, author = {Davis, C. C. and Xi, Z. and S. Mathews} } @article {847216, title = {Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes}, journal = {Mol Biol Evol}, volume = {31}, number = {1}, year = {2014}, note = {

Zhong, BojianXi, ZhenxiangGoremykin, Vadim VFong, RichardMcLenachan, Patricia ANovis, Philip MDavis, Charles CPenny, DavidengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/10/19 06:00Mol Biol Evol. 2014 Jan;31(1):177-83. doi: 10.1093/molbev/mst200. Epub 2013 Oct 17.

}, month = {Jan}, pages = {177-183}, abstract = {

The phylogenetic branching order of the green algal groups that gave rise to land plants remains uncertain despite its fundamental importance to understanding plant evolution. Previous studies have demonstrated that land plants evolved from streptophyte algae, but different lineages of streptophytes have been suggested to be the sister group of land plants. To better understand the evolutionary history of land plants and to determine the potential effects of "long-branch attraction" in phylogenetic reconstruction, we analyzed a chloroplast genome data set including three new chloroplast genomes from streptophyte algae: Coleochaetae orbicularis (Coleochaetales), Nitella hookeri (Charales), and Spirogyra communis (Zygnematales). We further applied a site pattern sorting method together with site- and time-heterogeneous models to investigate the branching order among streptophytes and land plants. Our chloroplast phylogenomic analyses support previous hypotheses based on nuclear data in placing Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants.

}, keywords = {*Genome, Chloroplast, Biological Evolution, Chlorophyta/classification/*genetics, chloroplast genomes, DNA, Algal/genetics, DNA, Chloroplast/genetics, Embryophyta/classification/*genetics, heterogeneous models, land plants, phylogenomics, Phylogeny, Sequence Analysis, DNA, streptophyte algae}, isbn = {1537-1719 (Electronic)0737-4038 (Linking)}, author = {Zhong, B. and Xi, Z. and Goremykin, V. V. and Fong, R. and McLenachan, P. A. and Novis, P. M. and Davis, C. C. and Penny, D.} } @article {847836, title = {Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes}, journal = {Molecular Biology and Evolution}, volume = {31}, year = {2014}, pages = {177-183}, abstract = {The phylogenetic branching order of the green algal groups that gave rise to land plants remains uncertain despite its fundamental importance to understanding plant evolution. Previous studies have demonstrated that land plants evolved from streptophyte algae, but different lineages of streptophytes have been suggested to be the sister group of land plants. To better understand the evolutionary history of land plants and to determine the potential effects of {\textquotedblleft}long-branch attraction{\textquotedblright} in phylogenetic reconstruction, we analyzed a chloroplast genome data set including three new chloroplast genomes from streptophyte algae: Coleochaetae orbicularis (Coleochaetales), Nitella hookeri (Charales), and Spirogyra communis (Zygnematales). We further applied a site pattern sorting method together with site- and time-heterogeneous models to investigate the branching order among streptophytes and land plants. Our chloroplast phylogenomic analyses support previous hypotheses based on nuclear data in placing Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants.}, author = {Bojian Zhong and Xi, Zhaoxiang and Goremykin, Vadim V. and Fong, Richard and McLenachan, Patricia A. and Novis, Philip M. and Charles C. Davis and Penny, David} } @article {846981, title = {Advances in the floral structural characterization of the major subclades of Malpighiales, one of the largest orders of flowering plants}, journal = {Ann Bot}, volume = {111}, number = {5}, year = {2013}, note = {

Endress, Peter KDavis, Charles CMatthews, Merran LengResearch Support, Non-U.S. Gov{\textquoteright}tReviewEngland2013/03/15 06:00Ann Bot. 2013 May;111(5):969-85. doi: 10.1093/aob/mct056. Epub 2013 Mar 13.

}, month = {May}, pages = {969-85}, abstract = {

BACKGROUND AND AIMS: Malpighiales are one of the largest angiosperm orders and have undergone radical systematic restructuring based on molecular phylogenetic studies. The clade has been recalcitrant to molecular phylogenetic reconstruction, but has become much more resolved at the suprafamilial level. It now contains so many newly identified clades that there is an urgent need for comparative studies to understand their structure, biology and evolution. This is especially true because the order contains a disproportionally large diversity of rain forest species and includes numerous agriculturally important plants. This study is a first broad systematic step in this endeavour. It focuses on a comparative structural overview of the flowers across all recently identified suprafamilial clades of Malpighiales, and points towards areas that desperately need attention. METHODS: The phylogenetic comparative analysis of floral structure for the order is based on our previously published studies on four suprafamilial clades of Malpighiales, including also four related rosid orders (Celastrales, Crossosomatales, Cucurbitales, Oxalidales). In addition, the results are compiled from a survey of over 3000 publications on macrosystematics, floral structure and embryology across all orders of the core eudicots. KEY RESULTS: Most new suprafamilial clades within Malpighiales are well supported by floral structural features. Inner morphological structures of the gynoecium (i.e. stigmatic lobes, inner shape of the locules, placentation, presence of obturators) and ovules (i.e. structure of the nucellus, thickness of the integuments, presence of vascular bundles in the integuments, presence of an endothelium in the inner integument) appear to be especially suitable for characterizing suprafamilial clades within Malpighiales. CONCLUSIONS: Although the current phylogenetic reconstruction of Malpighiales is much improved compared with earlier versions, it is incomplete, and further focused phylogenetic and morphological studies are needed. Once all major subclades of Malpighiales are elucidated, more in-depth studies on promising structural features can be conducted. In addition, once the phylogenetic tree of Malpighiales, including closely related orders, is more fully resolved, character optimization studies will be possible to reconstruct evolution of structural and biological features within the order.

}, keywords = {*Phylogeny, Flowers/*anatomy \& histology/*physiology, Malpighiaceae/*anatomy \& histology, Ovule/anatomy \& histology, Reproduction}, isbn = {1095-8290 (Electronic)0305-7364 (Linking)}, author = {Endress, P. K. and Davis, C. C. and Matthews, M. L.} } @inbook {847821, title = {Combination of Mascagnia and Triopterys (Malpighiaceae)}, booktitle = {Memoirs of the New York Botanical Garden. Harmony and Grit: papers celebrating the Holmgrens{\textquoteright} completion of Intermountain Flora}, year = {2013}, pages = {191-203}, author = {Anderson, William R. and Charles C. Davis} } @article {848186, title = {Combined morphological and molecular phylogeny of the clusioid clade (Malpighiales) and the placement of the ancient rosid macrofossil Paleoclusia}, journal = {Int J Plant Sci}, volume = {174}, year = {2013}, pages = {910-936}, abstract = {

Premise of research. The clusioid clade is a member of the large rosid order Malpighiales and contains \~{}1900 species in five families: Bonnetiaceae, Calophyllaceae, Clusiaceae sensu stricto (s.s.), Hypericaceae, and Podostemaceae. Despite recent efforts to clarify their phylogenetic relationships using molecular data, no such data are available for several critical taxa, including especially Hypericum ellipticifolium (previously recognized in Lianthus), Lebrunia, Neotatea, Thysanostemon, and the second-oldest rosid fossil (\~{}90 Ma), Paleoclusia chevalieri. Here, we (i) assess congruence between phylogenies inferred from morphological and molecular data, (ii) analyze morphological and molecular data simultaneously to place taxa lacking molecular data, and (iii) use ancestral state reconstructions (ASRs) to examine the evolution of traits that have been important for circumscribing clusioid taxa and to explore the placement of Paleoclusia. Methodology. We constructed a morphological data set including 69 characters and 81 clusioid species (or species groups). These data were analyzed individually and in combination with a previously published molecular data set of four genes (plastid matK, ndhF, and rbcL and mitochondrial matR) using parsimony, maximum likelihood (ML), and Bayesian inference. We used ML ASRs to infer the evolution of morphological characters. Pivotal results. Our phylogeny inferred from morphology alone was poorly supported but largely in agreement with molecular data. Moreover, our combined analyses were much better supported and largely confirm taxonomic hypotheses regarding relationships of extant taxa newly included here. The extinct Paleoclusia was placed as a member of stem group Clusiaceae s.s. or within crown group Clusiaceae s.s. as sister to one of its two major subclades. Conclusions. Despite poor overall bootstrap support for the placement of Paleoclusia, ancestral character state reconstructions are generally in agreement with our placements. Our recommendation is that Paleoclusia be treated as either a minimum stem group or a crown group age constraint of Clusiaceae s.s. Keywords: Clusiaceae, combined analysis, Guttiferae, morphology, Paleoclusia, rosids. Online enhancements: appendixes, figures, supplementary table.

}, author = {Ruhfel, B. R. and P. Stevens and Davis, C. C.} } @article {846956, title = {Deep genetic divergence between disjunct Refugia in the Arctic-Alpine King{\textquoteright}s Crown, Rhodiola integrifolia (Crassulaceae)}, journal = {PLoS One}, volume = {8}, number = {11}, year = {2013}, note = {

DeChaine, Eric GForester, Brenna RSchaefer, HannoDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/11/28 06:00PLoS One. 2013 Nov 1;8(11):e79451. doi: 10.1371/journal.pone.0079451. eCollection 2013.

}, pages = {e79451}, abstract = {

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King{\textquoteright}s Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome.

}, keywords = {*Genetic Variation, Arctic Regions, Genome, Plant, North America, Phylogeny, Rhodiola/*genetics, Species Specificity}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {DeChaine, E. G. and Forester, B. R. and Schaefer, H. and Davis, C. C.} } @article {847046, title = {Developmental origins of the world{\textquoteright}s largest flowers, Rafflesiaceae}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, number = {46}, year = {2013}, note = {

Nikolov, Lachezar AEndress, Peter KSugumaran, MSasirat, SawitreeVessabutr, SuyaneeKramer, Elena MDavis, Charles CengComparative StudyResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/10/30 06:00Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18578-83. doi: 10.1073/pnas.1310356110. Epub 2013 Oct 28.

}, month = {Nov 12}, pages = {18578-83}, abstract = {

Rafflesiaceae, which produce the world{\textquoteright}s largest flowers, have captivated the attention of biologists for nearly two centuries. Despite their fame, however, the developmental nature of the floral organs in these giants has remained a mystery. Most members of the family have a large floral chamber defined by a diaphragm. The diaphragm encloses the reproductive organs where pollination by carrion flies occurs. In lieu of a functional genetic system to investigate floral development in these highly specialized holoparasites, we used comparative studies of structure, development, and gene-expression patterns to investigate the homology of their floral organs. Our results surprisingly demonstrate that the otherwise similar floral chambers in two Rafflesiaceae subclades, Rafflesia and Sapria, are constructed very differently. In Rafflesia, the diaphragm is derived from the petal whorl. In contrast, in Sapria it is derived from elaboration of a unique ring structure located between the perianth and the stamen whorl, which, although developed to varying degrees among the genera, appears to be a synapomorphy of the Rafflesiaceae. Thus, the characteristic features that define the floral chamber in these closely related genera are not homologous. These differences refute the prevailing hypothesis that similarities between Sapria and Rafflesia are ancestral in the family. Instead, our data indicate that Rafflesia-like and Sapria-like floral chambers represent two distinct derivations of this morphology. The developmental repatterning we identified in Rafflesia, in particular, may have provided architectural reinforcement, which permitted the explosive growth in floral diameter that has arisen secondarily within this subclade.

}, keywords = {ABC model, Angiosperms/*growth \& development/metabolism, Base Sequence, Cloning, Molecular, comparative gene expression, DNA Primers/genetics, DNA, Complementary/biosynthesis, evo-devo, Flowers/*anatomy \& histology/*growth \& development/metabolism, Gene Expression Profiling, Gene Expression Regulation, Developmental/*physiology, gigantism, Malaysia, Molecular Sequence Data, parasitic plants, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Nikolov, L. A. and Endress, P. K. and Sugumaran, M. and Sasirat, S. and Vessabutr, S. and Kramer, E. M. and Davis, C. C.} } @article {847211, title = {Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors}, journal = {Front Plant Sci}, volume = {4}, year = {2013}, note = {

Zhang, WenhengSteinmann, Victor WNikolov, LachezarKramer, Elena MDavis, Charles CengSwitzerland2013/08/24 06:00Front Plant Sci. 2013 Aug 20;4:302. doi: 10.3389/fpls.2013.00302. eCollection 2013.

}, pages = {302}, abstract = {

Malpighiaceae possess flowers with a unique bilateral symmetry (zygomorphy), which is a hypothesized adaptation associated with specialization on neotropical oil bee pollinators. Gene expression of two representatives of the CYC2 lineage of floral symmetry TCP genes, CYC2A and CYC2B, demarcate the adaxial (dorsal) region of the flower in the characteristic zygomorphic flowers of most Malpighiaceae. Several clades within the family, however, have independently lost their specialized oil bee pollinators and reverted to radial flowers (actinomorphy) like their ancestors. Here, we investigate CYC2 expression associated with four independent reversals to actinomorphy. We demonstrate that these reversals are always associated with alteration of the highly conserved CYC2 expression pattern observed in most New World (NW) Malpighiaceae. In NW Lasiocarpus and Old World (OW) Microsteria, the expression of CYC2-like genes has expanded to include the ventral region of the corolla. Thus, the pattern of gene expression in these species has become radialized, which is comparable to what has been reported in the radial flowered legume clade Cadia. In striking contrast, in NW Psychopterys and OW Sphedamnocarpus, CYC2-like expression is entirely absent or at barely detectable levels. This is more similar to the pattern of CYC2 expression observed in radial flowered Arabidopsis. These results collectively indicate that, regardless of geographic distribution, reversals to similar floral phenotypes in this large tropical angiosperm clade have evolved via different genetic changes from an otherwise highly conserved developmental program.

}, keywords = {CYC2-like genes, Development, floral symmetry, Malpighiaceae, reversals}, isbn = {1664-462X (Electronic)1664-462X (Linking)}, author = {Zhang, W. and Steinmann, V. W. and Nikolov, L. and Kramer, E. M. and Davis, C. C.} } @article {846856, title = {Evolution: pollen or pollinators - which came first?}, journal = {Curr BiolCurr Biol}, volume = {23}, number = {8}, year = {2013}, note = {

Cappellari, Simone CSchaefer, HannoDavis, Charles CengCommentEngland2013/04/27 06:00Curr Biol. 2013 Apr 22;23(8):R316-8. doi: 10.1016/j.cub.2013.02.049.

}, month = {Apr 22}, pages = {R316-8}, abstract = {

A new study provides the first broad timeline of bee diversification. Several ancient bee clades are identified as ghost lineages that have left little fossil evidence of their existence. This timeline suggests that the rise of bees coincided with the largest flowering plant clade, the eudicots.

}, keywords = {*Biological Evolution, *Evolution, Molecular, Angiosperms/*classification, Animals, Bees/*classification/*genetics}, isbn = {1879-0445 (Electronic)0960-9822 (Linking)}, author = {Cappellari, S. C. and Schaefer, H. and Davis, C. C.} } @article {847196, title = {Massive mitochondrial gene transfer in a parasitic flowering plant clade}, journal = {PLoS Genet}, volume = {9}, number = {2}, year = {2013}, note = {

Xi, ZhenxiangWang, YuguoBradley, Robert KSugumaran, MMarx, Christopher JRest, Joshua SDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/03/06 06:00PLoS Genet. 2013;9(2):e1003265. doi: 10.1371/journal.pgen.1003265. Epub 2013 Feb 14.

}, pages = {e1003265}, abstract = {

Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world{\textquoteright}s largest flowers, about 2.1\% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24\%-41\% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.

}, keywords = {*Evolution, Molecular, DNA, Mitochondrial/genetics, Flowers/genetics, Gene Transfer, Horizontal/*genetics, Genome, Mitochondrial, Genome, Plant, Host-Parasite Interactions/*genetics, Phylogeny, Plants/*genetics/parasitology, RNA, Ribosomal/genetics, symbiosis}, isbn = {1553-7404 (Electronic)1553-7390 (Linking)}, author = {Xi, Z. and Wang, Y. and Bradley, R. K. and Sugumaran, M. and Marx, C. J. and Rest, J. S. and Davis, C. C.} } @article {847186, title = {Phylogenomics and coalescent analyses resolve extant seed plant relationships}, journal = {PLoS One}, volume = {8}, number = {11}, year = {2013}, note = {

Xi, ZhenxiangRest, Joshua SDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}t2013/11/28 06:00PLoS One. 2013 Nov 21;8(11):e80870. doi: 10.1371/journal.pone.0080870. eCollection 2013.

}, pages = {e80870}, abstract = {

The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.

}, keywords = {*Genomics, *Phylogeny, Base Sequence, Cell Nucleus/genetics, Genes, Plant, Genome, Plastid/genetics, Gymnosperms/*genetics, Seeds/*genetics, Species Specificity}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Xi, Z. and Rest, J. S. and Davis, C. C.} } @article {846976, title = {Record-breaking early flowering in the eastern United States}, journal = {PLoS One}, volume = {8}, number = {1}, year = {2013}, note = {

Ellwood, Elizabeth RTemple, Stanley APrimack, Richard BBradley, Nina LDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/01/24 06:00PLoS One. 2013;8(1):e53788. doi: 10.1371/journal.pone.0053788. Epub 2013 Jan 16.

}, pages = {e53788}, abstract = {

Flowering times are well-documented indicators of the ecological effects of climate change and are linked to numerous ecosystem processes and trophic interactions. Dozens of studies have shown that flowering times for many spring-flowering plants have become earlier as a result of recent climate change, but it is uncertain if flowering times will continue to advance as temperatures rise. Here, we used long-term flowering records initiated by Henry David Thoreau in 1852 and Aldo Leopold in 1935 to investigate this question. Our analyses demonstrate that record-breaking spring temperatures in 2010 and 2012 in Massachusetts, USA, and 2012 in Wisconsin, USA, resulted in the earliest flowering times in recorded history for dozens of spring-flowering plants of the eastern United States. These dramatic advances in spring flowering were successfully predicted by historical relationships between flowering and spring temperature spanning up to 161 years of ecological change. These results demonstrate that numerous temperate plant species have yet to show obvious signs of physiological constraints on phenological advancement in the face of climate change.

}, keywords = {Climate Change/*statistics \& numerical data, Flowers/*growth \& development, Phylogeny, Plants/classification, Statistics as Topic, United States}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Ellwood, E. R. and Temple, S. A. and Primack, R. B. and Bradley, N. L. and Davis, C. C.} } @article {847161, title = {Temperature-dependent shifts in phenology contribute to the success of exotic species with climate change}, journal = {Am J Bot}, volume = {100}, number = {7}, year = {2013}, note = {

Wolkovich, Elizabeth MDavies, T JonathanSchaefer, HannoCleland, Elsa ECook, Benjamin ITravers, Steven EWillis, Charles GDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2013/06/26 06:00Am J Bot. 2013 Jul;100(7):1407-21.

}, month = {Jul}, pages = {1407-1421}, abstract = {

PREMISE OF THE STUDY: The study of how phenology may contribute to the assembly of plant communities has a long history in ecology. Climate change has brought renewed interest in this area, with many studies examining how phenology may contribute to the success of exotic species. In particular, there is increasing evidence that exotic species occupy unique phenological niches and track climate change more closely than native species. METHODS: Here, we use long-term records of species{\textquoteright} first flowering dates from fi ve northern hemisphere temperate sites (Chinnor, UK and in the United States, Concord, Massachusetts; Fargo, North Dakota; Konza Prairie, Kansas; and Washington,D.C.) to examine whether invaders have distinct phenologies. Using a broad phylogenetic framework, we tested for differences between exotic and native species in mean annual flowering time, phenological changes in response to temperature and precipitation,and longer-term shifts in first flowering dates during recent pronounced climate change ("flowering time shifts"). KEY RESULTS: Across North American sites, exotic species have shifted flowering with climate change while native species, on average, have not. In the three mesic systems, exotic species exhibited higher tracking of interannual variation in temperature,such that flowering advances more with warming, than native species. Across the two grassland systems, however, exotic species differed from native species primarily in responses to precipitation and soil moisture, not temperature. CONCLUSIONS: Our findings provide cross-site support for the role of phenology and climate change in explaining species{\textquoteright} invasions.Further, they support recent evidence that exotic species may be important drivers of extended growing seasons observed with climate change in North America.

}, keywords = {*Climate Change, *Introduced Species, *Plant Physiological Phenomena, *Temperature, demography, Great Britain, Phylogeny, Plants/*classification/*genetics, Species Specificity, Time Factors, United States}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Wolkovich, E. M. and Davies, T. J. and Schaefer, H. and Cleland, E. E. and Cook, B. I. and Travers, S. E. and Willis, C. G. and Davis, C. C.} } @article {847806, title = {Proposal to conserve the name Mascagnia against Triopterys (Malpighiaceae)}, journal = {Taxon}, volume = {61}, year = {2012}, pages = {1124-1125}, author = {Anderson, William R. and Charles C. Davis} } @article {847816, title = {The botanical teaching legacy of Edward G. Voss at the University of Michigan Biological station}, journal = {The Michigan Botanist}, volume = {50-51}, year = {2012}, pages = {32-41}, author = {Charles C. Davis and Gunn, Melanie and C.Erik Hellquist} } @article {847171, title = {Horizontal transfer of expressed genes in a parasitic flowering plant}, journal = {BMC Genomics}, volume = {13}, year = {2012}, note = {

Xi, ZhenxiangBradley, Robert KWurdack, Kenneth JWong, KmSugumaran, MBomblies, KirstenRest, Joshua SDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2012/06/12 06:00BMC Genomics. 2012 Jun 8;13:227.

}, pages = {227}, abstract = {

BACKGROUND: Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur. RESULTS: We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives. CONCLUSIONS: Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.

}, keywords = {Angiosperms/classification/*genetics/parasitology, Codon/genetics, DNA, Plant/genetics, Gene Transfer, Horizontal/*genetics, Host-Parasite Interactions/genetics, Phylogeny, Transcriptome/genetics}, isbn = {1471-2164 (Electronic)1471-2164 (Linking)}, author = {Xi, Z. and Bradley, R. K. and Wurdack, K. J. and Wong, K. and Sugumaran, M. and Bomblies, K. and Rest, J. S. and Davis, C. C.} } @article {847191, title = {Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, number = {43}, year = {2012}, note = {

Xi, ZhenxiangRuhfel, Brad RSchaefer, HannoAmorim, Andre MSugumaran, MWurdack, Kenneth JEndress, Peter KMatthews, Merran LStevens, Peter FMathews, SarahDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/10/10 06:00Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17519-24. doi: 10.1073/pnas.1205818109. Epub 2012 Oct 8.

}, month = {Oct 23}, pages = {17519-24}, abstract = {

The angiosperm order Malpighiales includes ~16,000 species and constitutes up to 40\% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life.

}, keywords = {*Genome, Plant, *Phylogeny, Likelihood Functions, Malpighiaceae/classification/*genetics, Molecular Sequence Data, Species Specificity}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Xi, Z. and Ruhfel, B. R. and Schaefer, H. and Amorim, A. M. and Sugumaran, M. and Wurdack, K. J. and Endress, P. K. and Matthews, M. L. and Stevens, P. F. and S. Mathews and Davis, C. C.} } @article {846971, title = {Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae}, journal = {PLoS One}, volume = {7}, number = {6}, year = {2012}, note = {

Ellison, Aaron MButler, Elena DHicks, Emily JeanNaczi, Robert F CCalie, Patrick JBell, Charles DDavis, Charles CengP20 RR16481/RR/NCRR NIH HHS/Research Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/06/22 06:00PLoS One. 2012;7(6):e39291. doi: 10.1371/journal.pone.0039291. Epub 2012 Jun 13.

}, pages = {e39291}, abstract = {

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family{\textquoteright}s phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44-53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25-44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14-32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2-7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, \<3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade.

}, keywords = {*Geography, *Phylogeny, Sarraceniaceae/*classification}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Ellison, A.M. and Butler, E. D. and Hicks, E. J. and Naczi, R. F. and Calie, P. J. and Bell, C. D. and Davis, C. C.} } @article {847206, title = {Similar genetic mechanisms underlie the parallel evolution of floral phenotypes}, journal = {PLoS One}, volume = {7}, number = {4}, year = {2012}, note = {

Zhang, WenhengKramer, Elena MDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2012/05/05 06:00PLoS One. 2012;7(4):e36033. doi: 10.1371/journal.pone.0036033. Epub 2012 Apr 27.

}, pages = {e36033}, abstract = {

The repeated origin of similar phenotypes is invaluable for studying the underlying genetics of adaptive traits; molecular evidence, however, is lacking for most examples of such similarity. The floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to result from specialization on oil-bee pollinators. We recently demonstrated that CYCLOIDEA2-like genes (CYC2A and CYC2B) are associated with the development of the stereotypical floral zygomorphy that is critical to this plant-pollinator mutualism. Here, we build on this developmental framework to characterize floral symmetry in three clades of Malpighiaceae that have independently lost their oil bee association and experienced parallel shifts in their floral morphology, especially in regard to symmetry. We show that in each case these species exhibit a loss of CYC2B function, and a strikingly similar shift in the expression of CYC2A that is coincident with their shift in floral symmetry. These results indicate that similar floral phenotypes in this large angiosperm clade have evolved via parallel genetic changes from an otherwise highly conserved developmental program.

}, keywords = {*Biological Evolution, Flowers/*anatomy \& histology/*genetics/growth \& development/ultrastructure, Gene Expression Regulation, Plant, Genes, Plant/genetics, Malpighiaceae/*anatomy \& histology/*genetics/ultrastructure, Phenotype, Phylogeny, Plant Proteins/genetics/metabolism, Reverse Transcriptase Polymerase Chain Reaction}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Zhang, W. and Kramer, E. M. and Davis, C. C.} } @article {847111, title = {Angiosperm phylogeny: 17 genes, 640 taxa}, journal = {Am J BotAm J Bot}, volume = {98}, number = {4}, year = {2011}, note = {

Soltis, Douglas ESmith, Stephen ACellinese, NicoWurdack, Kenneth JTank, David CBrockington, Samuel FRefulio-Rodriguez, Nancy FWalker, Jay BMoore, Michael JCarlsward, Barbara SBell, Charles DLatvis, MaribethCrawley, SunnyBlack, ChelseaDiouf, DiagaXi, ZhenxiangRushworth, Catherine AGitzendanner, Matthew ASytsma, Kenneth JQiu, Yin-LongHilu, Khidir WDavis, Charles CSanderson, Michael JBeaman, Reed SOlmstead, Richard GJudd, Walter SDonoghue, Michael JSoltis, Pamela SengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2011/05/27 06:00Am J Bot. 2011 Apr;98(4):704-30. doi: 10.3732/ajb.1000404. Epub 2011 Apr 8.

}, month = {Apr}, pages = {704-30}, abstract = {

PREMISE OF THE STUDY: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS: Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS: Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

}, keywords = {*Evolution, Molecular, *Genes, Plant, *Genome, Plant, *Phylogeny, Angiosperms/classification/*genetics, Cell Nucleus/genetics, Chloroplasts/genetics, DNA, Plant/*analysis, Mitochondria/genetics, Nucleotides/*analysis, Sequence Analysis, DNA}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Soltis, D. E. and Smith, S. A. and Cellinese, N. and Wurdack, K. J. and Tank, D. C. and Brockington, S. F. and Refulio-Rodriguez, N. F. and Walker, J. B. and Moore, M. J. and Carlsward, B. S. and Bell, C. D. and Latvis, M. and Crawley, S. and Black, C. and Diouf, D. and Xi, Z. and Rushworth, C. A. and Gitzendanner, M. A. and Sytsma, K. J. and Qiu, Y. L. and Hilu, K. W. and Davis, C. C. and Sanderson, M. J. and Beaman, R. S. and Olmstead, R. G. and Judd, W. S. and Donoghue, M. J. and Soltis, P. S.} } @article {847801, title = {Phylogenetic analysis of the plastid inverted repeat for 244 species: insights into deeper-level angiosperm relationships from a long, slowly evolving sequence region}, journal = {Int J Plant Sci}, volume = {172}, year = {2011}, pages = {541-558}, author = {Moore, M. J. and N. Hassan and Gitzendanner, M. A. and R.A. Bruenn and M. Croley and A. Vandeventer and Horn, J. W. and A. Dhingra and S.F. Brokington and Latvis, M. and J. Ramdial and Alexandre, R. and A. Piedrahita and Xi, Z. and Davis, C. C. and Soltis, P. S. and Soltis, D. E.} } @article {847081, title = {Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes}, journal = {Am J BotAm J Bot}, volume = {98}, number = {2}, year = {2011}, note = {

Ruhfel, Brad RBittrich, VolkerBove, Claudia PGustafsson, Mats H GPhilbrick, C ThomasRutishauser, RolfXi, ZhenxiangDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2011/05/27 06:00Am J Bot. 2011 Feb;98(2):306-25. doi: 10.3732/ajb.1000354. Epub 2011 Jan 26.

}, month = {Feb}, pages = {306-25}, abstract = {

PREMISE OF THE STUDY: The clusioid clade includes five families (i.e., Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae) represented by 94 genera and approximately 1900 species. Species in this clade form a conspicuous element of tropical forests worldwide and are important in horticulture, timber production, and pharmacology. We conducted a taxon-rich multigene phylogenetic analysis of the clusioids to clarify phylogenetic relationships in this clade. METHODS: We analyzed plastid (matK, ndhF, and rbcL) and mitochondrial (matR) nucleotide sequence data using parsimony, maximum likelihood, and Bayesian inference. Our combined data set included 194 species representing all major clusioid subclades, plus numerous species spanning the taxonomic, morphological, and biogeographic breadth of the clusioid clade. KEY RESULTS: Our results indicate that Tovomita (Clusiaceae s.s.), Harungana and Hypericum (Hypericaceae), and Ledermanniella s.s. and Zeylanidium (Podostemaceae) are not monophyletic. In addition, we place four genera that have not been included in any previous molecular study: Ceratolacis, Diamantina, and Griffithella (Podostemaceae), and Santomasia (Hypericaceae). Finally, our results indicate that Lianthus, Santomasia, Thornea, and Triadenum can be safely merged into Hypericum (Hypericaceae). CONCLUSIONS: We present the first well-resolved, taxon-rich phylogeny of the clusioid clade. Taxon sampling and resolution within the clade are greatly improved compared to previous studies and provide a strong basis for improving the classification of the group. In addition, our phylogeny will form the foundation for our future work investigating the biogeography of tropical angiosperms that exhibit Gondwanan distributions.

}, keywords = {*DNA, Chloroplast, *DNA, Plant, *Evolution, Molecular, *Genome, Mitochondrial, *Genome, Plant, *Phylogeny, Angiosperms/*genetics, Base Sequence, Climate, Ecosystem, Sequence Analysis, DNA, trees}, isbn = {1537-2197 (Electronic)0002-9122 (Linking)}, author = {Ruhfel, B. R. and Bittrich, V. and Bove, C. P. and Gustafsson, M. H. and Philbrick, C. T. and Rutishauser, R. and Xi, Z. and Davis, C. C.} } @article {846921, title = {Plant evolution: pulses of extinction and speciation in gymnosperm diversity}, journal = {Curr BiolCurr Biol}, volume = {21}, number = {24}, year = {2011}, note = {

Davis, Charles CSchaefer, HannoengEngland2011/12/24 06:00Curr Biol. 2011 Dec 20;21(24):R995-8. doi: 10.1016/j.cub.2011.11.020.

}, month = {Dec 20}, pages = {R995-8}, abstract = {

Living gymnosperms represent the survivors of ancient seed plant lineages whose fossil record reaches back 270 million years. Two recent studies find that recent pulses of extinction and speciation have shaped today{\textquoteright}s gymnosperm diversity, contradicting the widespread assumption that gymnosperms have remained largely unchanged for tens of millions of years.

}, keywords = {*Biological Evolution, Angiosperms/genetics/physiology, Biodiversity, climate change, Extinction, Biological, Fossils, Genes, Plant, Genetic Speciation, Gymnosperms/*genetics/physiology, Phylogeny, Time Factors}, isbn = {1879-0445 (Electronic)0960-9822 (Linking)}, author = {Davis, C. C. and Schaefer, H.} } @inbook {848161, title = {A clades-eye view of global climate change}, booktitle = {Evolution Since Darwin: The First 150 Years}, year = {2010}, pages = {623-627}, publisher = {Sinauer}, organization = {Sinauer}, address = {Sunderland, Massachusetts}, author = {Davis, C. C. and E.J. Edwards and Donoghue, M. J.}, editor = {M.A. Bell and Futuyma, D. J. and W.F. Eanes and J.S. Levinton} } @article {846871, title = {A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology}, journal = {Am J Bot}, volume = {97}, number = {12}, year = {2010}, note = {

Davis, Charles CAnderson, William Reng2011/05/28 06:00Am J Bot. 2010 Dec;97(12):2031-48. doi: 10.3732/ajb.1000146.

}, month = {Dec}, pages = {2031-48}, abstract = {

PREMISE OF THE STUDY: The Malpighiaceae include approximately 1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. * METHODS: We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. * KEY RESULTS AND CONCLUSIONS: The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.

}, isbn = {0002-9122 (Print)0002-9122 (Linking)}, author = {Davis, C. C. and Anderson, W. R.} } @article {847156, title = {Favorable climate change response explains non-native species{\textquoteright} success in Thoreau{\textquoteright}s woods}, journal = {PLoS One}, volume = {5}, number = {1}, year = {2010}, note = {

Willis, Charles GRuhfel, Brad RPrimack, Richard BMiller-Rushing, Abraham JLosos, Jonathan BDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2010/02/04 06:00PLoS One. 2010 Jan 26;5(1):e8878. doi: 10.1371/journal.pone.0008878.

}, pages = {e8878}, abstract = {

Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes than native species. Recent evidence indicates that species that respond to climate change by adjusting their phenology (i.e., the timing of seasonal activities, such as flowering) have historically increased in abundance. The extent to which non-native species success is similarly linked to a favorable climate change response, however, remains untested. We analyzed a dataset initiated by the conservationist Henry David Thoreau that documents the long-term phenological response of native and non-native plant species over the last 150 years from Concord, Massachusetts (USA). Our results demonstrate that non-native species, and invasive species in particular, have been far better able to respond to recent climate change by adjusting their flowering time. This demonstrates that climate change has likely played, and may continue to play, an important role in facilitating non-native species naturalization and invasion at the community level.

}, keywords = {*Biodiversity, *Climate, Conservation of Natural Resources, Massachusetts, Plants/*classification}, isbn = {1932-6203 (Electronic)1932-6203 (Linking)}, author = {Willis, C. G. and Ruhfel, B. R. and Primack, R. B. and Miller-Rushing, A. J. and Losos, J. B. and Davis, C. C.} } @article {847201, title = {Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism}, journal = {Proc Natl Acad Sci U S A}, volume = {107}, number = {14}, year = {2010}, note = {

Zhang, WenhengKramer, Elena MDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}t2010/04/07 06:00Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6388-93. doi: 10.1073/pnas.0910155107. Epub 2010 Apr 2.

}, month = {Apr 6}, pages = {6388-93}, abstract = {

The evolution of floral zygomorphy is an important innovation in flowering plants and is thought to arise principally from specialization on various insect pollinators. Floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to be caused by selection by its oil-bee pollinators. We sought to characterize the genetic basis of floral zygomorphy in Malpighiaceae by investigating CYCLOIDEA2-like (CYC2-like) genes, which are required for establishing symmetry in diverse core eudicots. We identified two copies of CYC2-like genes in Malpighiaceae, which resulted from a gene duplication in the common ancestor of the family. A likely role for these loci in the development of floral zygomorphy in Malpighiaceae is demonstrated by the conserved pattern of dorsal gene expression in two distantly related neotropical species, Byrsonima crassifolia and Janusia guaranitica. Further evidence for this function is observed in a Malpighiaceae species that has moved to the paleotropics and experienced coincident shifts in pollinators, floral symmetry, and CYC2-like gene expression. The dorsal expression pat-tern observed in Malpighiaceae contrasts dramatically with their actinomorphic-flowered relatives, Centroplacaceae (Bhesa paniculata) and Elatinaceae (Bergia texana). In particular, B. texana exhibits a previously undescribed pattern of uniform CYC2 expression, suggesting that CYC2 expression among the actinomorphic ancestors of zygomorphic lineages may be much more complex than previously thought. We consider three evolutionary models that may have given rise to this patterning, including the hypothesis that floral zygomorphy in Malpighiaceae arose earlier than standard morphology-based character reconstructions suggest.

}, keywords = {*Pollination, *Symbiosis, DNA-Binding Proteins, Flowers/*anatomy \& histology/*genetics/physiology, Gene Duplication, Gene Expression Regulation, Plant, Molecular Sequence Data, Phylogeny, Plant Proteins/genetics, Transcription Factors}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Zhang, W. and Kramer, E. M. and Davis, C. C.} } @article {846936, title = {The importance of phylogeny to the study of phenological response to global climate change}, journal = {Philos Trans R Soc Lond B Biol Sci}, volume = {365}, number = {1555}, year = {2010}, note = {

Davis, Charles CWillis, Charles GPrimack, Richard BMiller-Rushing, Abraham JengComparative StudyResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2010/09/08 06:00Philos Trans R Soc Lond B Biol Sci. 2010 Oct 12;365(1555):3201-13. doi: 10.1098/rstb.2010.0130.

}, month = {Oct 12}, pages = {3201-13}, abstract = {

Climate change has resulted in major changes in the phenology--i.e. the timing of seasonal activities, such as flowering and bird migration--of some species but not others. These differential responses have been shown to result in ecological mismatches that can have negative fitness consequences. However, the ways in which climate change has shaped changes in biodiversity within and across communities are not well understood. Here, we build on our previous results that established a link between plant species{\textquoteright} phenological response to climate change and a phylogenetic bias in species{\textquoteright} decline in the eastern United States. We extend a similar approach to plant and bird communities in the United States and the UK that further demonstrates that climate change has differentially impacted species based on their phylogenetic relatedness and shared phenological responses. In plants, phenological responses to climate change are often shared among closely related species (i.e. clades), even between geographically disjunct communities. And in some cases, this has resulted in a phylogenetically biased pattern of non-native species success. In birds, the pattern of decline is phylogenetically biased but is not solely explained by phenological response, which suggests that other traits may better explain this pattern. These results illustrate the ways in which phylogenetic thinking can aid in making generalizations of practical importance and enhance efforts to predict species{\textquoteright} responses to future climate change.

}, keywords = {*Climate Change, *Ecosystem, *Phylogeny, *Plant Development, Animals, Birds/*growth \& development, Flowers/*physiology, Great Britain, Massachusetts, Multivariate Analysis, Regression Analysis}, isbn = {1471-2970 (Electronic)0962-8436 (Linking)}, author = {Davis, C. C. and Willis, C. G. and Primack, R. B. and Miller-Rushing, A. J.} } @article {847166, title = {Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life}, journal = {Am J Bot}, volume = {96}, number = {8}, year = {2009}, note = {

Wurdack, Kenneth JDavis, Charles Ceng2009/08/01 00:00Am J Bot. 2009 Aug;96(8):1551-70. doi: 10.3732/ajb.0800207.

}, month = {Aug}, pages = {1551-70}, abstract = {

The eudicot order Malpighiales contains approximately 16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world{\textquoteright}s largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.

}, isbn = {0002-9122 (Print)0002-9122 (Linking)}, author = {Wurdack, K. J. and Davis, C. C.} } @article {847796, title = {Reply to McDonald et al.: Climate change, not deer hebivory, has shaped species decline in Concord, Massachusetts}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, pages = {E29}, author = {Willis, C. G. and Ruhfel, B. and Primack, R. B. and Miller-Rushing, A. J. and Davis, C. C.} } @article {847136, title = {Rosid radiation and the rapid rise of angiosperm-dominated forests}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, number = {10}, year = {2009}, note = {

Wang, HengchangMoore, Michael JSoltis, Pamela SBell, Charles DBrockington, Samuel FAlexandre, RoolseDavis, Charles CLatvis, MaribethManchester, Steven RSoltis, Douglas EengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2009/02/19 09:00Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3853-8. doi: 10.1073/pnas.0813376106. Epub 2009 Feb 17.

}, month = {Mar 10}, pages = {3853-8}, abstract = {

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; \>18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; \>25,000 bp) datasets for \>100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100\%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of \<15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.

}, keywords = {*Biological Evolution, Angiosperms/*classification/*genetics, Likelihood Functions, Molecular Sequence Data, Phylogeny, Time Factors, Trees/*classification/*genetics}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Wang, H. and Moore, M. J. and Soltis, P. S. and Bell, C. D. and Brockington, S. F. and Alexandre, R. and Davis, C. C. and Latvis, M. and Manchester, S. R. and Soltis, D. E.} } @article {846906, title = {The evolution of floral gigantism}, journal = {Curr Opin Plant Biol}, volume = {11}, number = {1}, year = {2008}, note = {

Davis, Charles CEndress, Peter KBaum, David AengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.ReviewEngland2008/01/22 09:00Curr Opin Plant Biol. 2008 Feb;11(1):49-57. doi: 10.1016/j.pbi.2007.11.003. Epub 2008 Jan 22.

}, month = {Feb}, pages = {49-57}, abstract = {

Flowers exhibit tremendous variation in size (\>1000-fold), ranging from less than a millimeter to nearly a meter in diameter. Numerous studies have established the importance of increased floral size in species that exhibit relatively normal-sized flowers, but few studies have examined the evolution of floral size increase in species with extremely large flowers or flower-like inflorescences (collectively termed blossoms). Our review of these record-breakers indicates that blossom gigantism has evolved multiple times, and suggests that the evolutionary forces operating in these species may differ from their ordinary-sized counterparts. Surprisingly, rather than being associated with large-bodied pollinators, gigantism appears to be most common in species with small-bodied beetle or carrion-fly pollinators. Such large blossoms may be adapted to these pollinators because they help to temporarily trap animals, better facilitate thermal regulation, and allow for the mimicry of large animal carcasses. Future phylogenetic tests of these hypotheses should be conducted to determine if the transition to such pollination systems correlates with significant changes in the mode and tempo of blossom size evolution.

}, keywords = {*Biological Evolution, Animals, Flowers/genetics/*growth \& development/physiology, Pollination/physiology, Selection, Genetic}, isbn = {1369-5266 (Print)1369-5266 (Linking)}, author = {Davis, C. C. and Endress, P. K. and Baum, D. A.} } @article {846866, title = {Floral evolution: dramatic size change was recent and rapid in the world{\textquoteright}s largest flowers}, journal = {Curr Biol}, volume = {18}, number = {23}, year = {2008}, note = {

Davis, Charles CengEngland2008/12/17 09:00Curr Biol. 2008 Dec 9;18(23):R1102-4. doi: 10.1016/j.cub.2008.10.011.

}, month = {Dec 9}, pages = {R1102-4}, abstract = {

Recent studies clarifying the closest relatives of the world{\textquoteright}s largest flowers, Rafflesiaceae, whose floral diameters range from approximately 11 to approximately 100 cm, indicated that they evolved from tiny-flowered ancestors in a burst of floral gigantism. New data now suggest that floral size evolution within Rafflesiaceae may be more dynamic than expected, with both recent and rapid changes in flower size.

}, keywords = {*Biological Evolution, Adaptation, Biological, Angiosperms/genetics/*physiology, Flowers/genetics/*physiology, Phylogeny, Time Factors}, isbn = {1879-0445 (Electronic)0960-9822 (Linking)}, author = {Davis, C. C.} } @article {847151, title = {Phylogenetic patterns of species loss in Thoreau{\textquoteright}s woods are driven by climate change}, journal = {Proc Natl Acad Sci U S A}, volume = {105}, number = {44}, year = {2008}, note = {

Willis, Charles GRuhfel, BradPrimack, Richard BMiller-Rushing, Abraham JDavis, Charles CengResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2008/10/29 09:00Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17029-33. doi: 10.1073/pnas.0806446105. Epub 2008 Oct 27.

}, month = {Nov 4}, pages = {17029-33}, abstract = {

Climate change has led to major changes in the phenology (the timing of seasonal activities, such as flowering) of some species but not others. The extent to which flowering-time response to temperature is shared among closely related species might have important consequences for community-wide patterns of species loss under rapid climate change. Henry David Thoreau initiated a dataset of the Concord, Massachusetts, flora that spans approximately 150 years and provides information on changes in species abundance and flowering time. When these data are analyzed in a phylogenetic context, they indicate that change in abundance is strongly correlated with flowering-time response. Species that do not respond to temperature have decreased greatly in abundance, and include among others anemones and buttercups [Ranunculaceae pro parte (p.p.)], asters and campanulas (Asterales), bluets (Rubiaceae p.p.), bladderworts (Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), mints (Lamiaceae p.p.), orchids (Orchidaceae), roses (Rosaceae p.p.), saxifrages (Saxifragales), and violets (Malpighiales). Because flowering-time response traits are shared among closely related species, our findings suggest that climate change has affected and will likely continue to shape the phylogenetically biased pattern of species loss in Thoreau{\textquoteright}s woods.

}, keywords = {*Extinction, Biological, *Phylogeny, Biodiversity, Climate, Ecosystem, Environmental Monitoring, Flowers/growth \& development/*physiology, Greenhouse Effect, Massachusetts, Rubiaceae/physiology, Seasons, Species Specificity}, isbn = {1091-6490 (Electronic)0027-8424 (Linking)}, author = {Willis, C. G. and Ruhfel, B. and Primack, R. B. and Miller-Rushing, A. J. and Davis, C. C.} } @article {847786, title = {Phylogenetic placement of Rheopteris and the polyphyly of Momogramma (Pteridaceae s.l.): evidencre from rbcl sequence data}, journal = {Sys Bot}, volume = {11}, year = {2008}, pages = {49-57}, author = {Ruhfel, B. and S. Lindsay and Davis, C. C.} } @article {847776, title = {Floral gigantism in Rafflesiaceae}, journal = {Science}, volume = {315}, year = {2007}, pages = {1812}, author = {Davis, C. C. and Latvis, M. and Nickrent, D. L. and Wurdack, K. J. and Baum, D. A.} } @article {847781, title = {Generic adjustments in neotropical Malpighiaceae}, journal = {Contributions from the University of Michigan Herbarium}, volume = {25}, year = {2007}, pages = {137-166}, author = {Anderson, W. R. and Davis, C. C.} } @article {847771, title = {Monophyly and relationships of the enigmatic family Peridiscaceae}, journal = {Taxon}, volume = {56}, year = {2007}, pages = {65-73}, author = {Soltis, D. E. and J.W. Clayton and Davis, C. C. and Gitzendanner, M. A. and M. Cheek and V. Savolainen and Amorim, A. M. and Soltis, P. S.} } @article {847071, title = {The deepest divergences in land plants inferred from phylogenomic evidence}, journal = {Proc Natl Acad Sci U S A}, volume = {103}, number = {42}, year = {2006}, note = {

Qiu, Yin-LongLi, LiboWang, BinChen, ZhiduanKnoop, VolkerGroth-Malonek, MilenaDombrovska, OlenaLee, JunghoKent, LivijaRest, JoshuaEstabrook, George FHendry, Tory ATaylor, David WTesta, Christopher MAmbros, MathewCrandall-Stotler, BarbaraDuff, R JoelStech, MichaelFrey, WolfgangQuandt, DietmarDavis, Charles CengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2006/10/13 09:00Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15511-6. Epub 2006 Oct 9.

}, month = {Oct 17}, pages = {15511-6}, abstract = {

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.

}, keywords = {*Genome, Plant, *Phylogeny, *Plants/classification/genetics, Likelihood Functions, Molecular Sequence Data, Multigene Family}, isbn = {0027-8424 (Print)0027-8424 (Linking)}, author = {Qiu, Y. L. and Li, L. and Wang, B. and Chen, Z. and Knoop, V. and Groth-Malonek, M. and Dombrovska, O. and Lee, J. and Kent, L. and Rest, J. and Estabrook, G. F. and Hendry, T. A. and Taylor, D. W. and Testa, C. M. and Ambros, M. and Crandall-Stotler, B. and Duff, R. J. and Stech, M. and Frey, W. and Quandt, D. and Davis, C. C.} } @article {847661, title = {Expansion of Diplopterys at the expense of Banisteriopsis (Malpighiaceae)}, journal = {Harvard Papers in Botany}, volume = {11}, year = {2006}, pages = {1-16}, author = {Anderson, W. R. and Davis, C. C.} } @article {847626, title = {The Mascagnia cordifolia group (Malpighiaceae)}, journal = {Contributions from the University of Michigan Herbarium}, volume = {24}, year = {2005}, pages = {33-44}, author = {Anderson, W. R. and Davis, C. C.} } @article {847641, title = {Explosive radiation of Malpighiales supports a mid-Cretaceous origin of modern tropical rain forests}, journal = {Am Nat}, volume = {165}, year = {2005}, pages = {E36-E65}, author = {Davis, C. C. and C.O. Webb and Wurdack, K. J. and C.A. Jaramillo and Donoghue, M. J.} } @article {846881, title = {Gene transfer from a parasitic flowering plant to a fern}, journal = {Proc Biol Sci}, volume = {272}, number = {1578}, year = {2005}, note = {

Davis, Charles CAnderson, William RWurdack, Kenneth JengComparative StudyResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.England2005/09/30 09:00Proc Biol Sci. 2005 Nov 7;272(1578):2237-42.

}, month = {Nov 7}, pages = {2237-42}, abstract = {

The rattlesnake fern (Botrychium virginianum (L.) Sw.) is obligately mycotrophic and widely distributed across the northern hemisphere. Three mitochondrial gene regions place this species with other ferns in Ophioglossaceae, while two regions place it as a member of the largely parasitic angiosperm order Santalales (sandalwoods and mistletoes). These discordant phylogenetic placements suggest that part of the genome in B. virginianum was acquired by horizontal gene transfer (HGT), perhaps from root-parasitic Loranthaceae. These transgenes are restricted to B. virginianum and occur across the range of the species. Molecular and life-history traits indicate that the transfer preceded the global expansion of B. virginianum, and that the latter may have happened very rapidly. This is the first report of HGT from an angiosperm to a fern, through either direct parasitism or the mediation of interconnecting fungal symbionts.

}, keywords = {*Phylogeny, Angiosperms/*genetics, Ferns/*genetics, Gene Transfer, Horizontal/*genetics, Geography, Likelihood Functions, Loranthaceae/genetics, Models, Genetic}, isbn = {0962-8452 (Print)0962-8452 (Linking)}, author = {Davis, C. C. and Anderson, W. R. and Wurdack, K. J.} } @article {847086, title = {Molecular phylogenetics of Phyllanthaceae: evidence from plastid MATK and nuclear PHYC sequences}, journal = {Am J Bot}, volume = {92}, number = {1}, year = {2005}, note = {

Samuel, RosabelleKathriarachchi, HashendraHoffmann, PetraBarfuss, Michael H JWurdack, Kenneth JDavis, Charles CChase, Mark Weng2005/01/01 00:00Am J Bot. 2005 Jan;92(1):132-41. doi: 10.3732/ajb.92.1.132.

}, month = {Jan}, pages = {132-41}, abstract = {

Plastid matK and a fragment of the low-copy nuclear gene PHYC were sequenced for 30 genera of Phyllanthaceae to evaluate tribal and generic delimitation. Resolution and bootstrap percentages obtained with matK are higher than that of PHYC, but both regions show nearly identical phylogenetic patterns. Phylogenetic relationships inferred from the independent and combined data are congruent and differ from previous, morphology-based classifications but are highly concordant with those of the plastid gene rbcL previously published. Phyllanthaceae is monophyletic and gives rise to two well-resolved clades (T and F) that could be recognized as subfamilies. DNA sequence data for Keayodendron and Zimmermanniopsis are presented for the first time. Keayodendron is misplaced in tribe Phyllantheae and belongs to the Bridelia alliance. Zimmermanniopsis is sister to Zimmermannia. Phyllanthus and Cleistanthus are paraphyletic. Savia and Phyllanthus subgenus Kirganelia are not monophyletic.

}, isbn = {0002-9122 (Print)0002-9122 (Linking)}, author = {Samuel, R. and Kathriarachchi, H. and Hoffmann, P. and Barfuss, M. H. and Wurdack, K. J. and Davis, C. C. and Chase, M. W.} } @article {847651, title = {Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes}, journal = {Int J Plant Sci}, volume = {166}, year = {2005}, pages = {815-842}, author = {Qiu, Y.-L. and Dombrovska, O. and Lee, J. and Li, L. and B.A. Whitlock and F. Bernasconi-Quadroni and Rest, J. S. and Davis, C. C. and T. Borsch and Hilu, K. W. and Renner, S. S. and Soltis, D. E. and Soltis, P. S. and M.J. Zanis and J.J. Cannone and R.R. Gutell and M. Powell and V. Savolainen and L.W. Chatrou and Chase, M. W.} } @article {847631, title = {Transfer of Mascagnia leticiana to Malpighia (Malpighiaceae)}, journal = {Contributions from the University of Michigan Herbarium}, volume = {24}, year = {2005}, pages = {45-49}, author = {Anderson, W. R. and Davis, C. C.} } @article {847621, title = {Elatinaceae are sister to Malpighiaceae; Peridiscaceae belong to Saxifragales}, journal = {Am J Bot}, volume = {91}, year = {2004}, pages = {262-273}, author = {Davis, C. C. and Chase, M. W.} } @article {847616, title = {High latitude Tertiary migrations of an exclusively tropical clade: evidence from Malpighiaceae.}, journal = {Int. J Plant Sci}, volume = {165}, year = {2004}, pages = {S107-S121}, author = {Davis, C. C. and Fritsch, P. W. and Bell, C. D. and S. Mathews} } @article {846941, title = {Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales}, journal = {Science}, volume = {305}, number = {5684}, year = {2004}, note = {

Davis, Charles C., Wurdack, Kenneth Jeng, Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2004/07/17 05:00 Science. 2004 Jul 30;305(5684):676-8. Epub 2004 Jul 15.

}, month = {Jul 30}, pages = {676-8}, abstract = {

Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochondrial (matR) and nuclear loci (18S ribosomal DNA and PHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrial nad1B-C, however, groups them within Vitaceae, near their obligate host Tetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.

}, keywords = {*Gene Transfer, Horizontal, Angiosperms/*classification/*genetics, Cell Nucleus/genetics, DNA, Mitochondrial/genetics, Flowers, Genes, Plant, Mitochondria/genetics, Mitochondrial Proteins/genetics, Phylogeny, Plant Proteins/genetics, Vitaceae/*classification/*genetics/parasitology}, isbn = {1095-9203 (Electronic)0036-8075 (Linking)}, author = {Davis, C. C. and Wurdack, K. J.} } @article {846896, title = {Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae}, journal = {Proc Natl Acad Sci U S A}, volume = {99}, number = {10}, year = {2002}, note = {

Davis, Charles C, Bell, Charles D Mathews, Sarah Donoghue, Michael Jeng Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2002/05/02 10:00Proc Natl Acad Sci U S A. 2002 May 14;99(10):6833-7. Epub 2002 Apr 30.

}, month = {May 14}, pages = {6833-7}, abstract = {

Explanations for biogeographic disjunctions involving South America and Africa typically invoke vicariance of western Gondwanan biotas or long distance dispersal. These hypotheses are problematical because many groups originated and diversified well after the last known connection between Africa and South America (approximately 105 million years ago), and it is unlikely that "sweepstakes" dispersal accounts for many of these disjunctions. Phylogenetic analyses of the angiosperm clade Malpighiaceae, combined with fossil evidence and molecular divergence-time estimates, suggest an alternative hypothesis to account for such distributions. We propose that Malpighiaceae originated in northern South America, and that members of several clades repeatedly migrated into North America and subsequently moved via North Atlantic land connections into the Old World during episodes starting in the Eocene, when climates supported tropical forests. This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions.

}, keywords = {*Arabidopsis Proteins, *Evolution, Molecular, *Plant Proteins, Base Sequence, DNA, Plant, Malpighiaceae/classification/*genetics, Molecular Sequence Data, NADH Dehydrogenase/*genetics, North America, Phylogeny, Phytochrome/*genetics, South America}, isbn = {0027-8424 (Print)0027-8424 (Linking)}, author = {Davis, C. C. and Bell, C. D. and S. Mathews and Donoghue, M. J.} } @article {846861, title = {Madagasikaria (Malpighiaceae): a new genus from Madagascar with implications for floral evolution in Malpighiaceae}, journal = {Am J Bot}, volume = {89}, number = {4}, year = {2002}, note = {

Davis, Charles Ceng2002/04/01 00:00Am J Bot. 2002 Apr;89(4):699-706. doi: 10.3732/ajb.89.4.699.

}, month = {Apr}, pages = {699-706}, abstract = {

Madagasikaria andersonii is described here as a new genus and species of Malpighiaceae from Madagascar. The phylogenetic placement of Madagasikaria was estimated by using combined data from ndhF and trnL-F chloroplast sequences and phytochrome (PHYC) and ITS nuclear sequences. It forms a strongly supported clade with the Malagasy endemic genera Rhynchophora and Microsteira. Despite nearly identical floral morphology among species in this clade (here called the madagasikarioid clade), these genera are easily distinguishable on the basis of their fruits. The schizocarpic fruits of Madagasikaria have distinctive mericarps. Each mericarp has a lateral wing, which completely encircles the nut, and a peculiar dorsal wing, which folds over on itself. The morphology of this fruit suggests that the homology of the unusual wing in Rhynchophora is lateral in nature and represents a reduced wing similar to the lateral wing in Madagasikaria. Taxa in the madagasikarioid clade all appear to be morphologically androdioecious and functionally dioecious, producing both staminate and "bisexual" (i.e., functionally carpellate) individuals. This condition appears to be exceedingly rare in flowering plants and has important implications for floral evolution within Malpighiaceae. Neotropical Malpighiaceae are pollinated by specialized oil-collecting anthophorine bees of the tribe Centridini and exhibit highly conserved floral morphology despite tremendous diversity in fruit morphology and habit. These oil-collecting bees are absent from the paleotropics, where most members of the Malpighiaceae lack both the oil glands and the typical floral orientation crucial to pollination by neotropical oil-collecting bees. The madagasikarioids represent one shift from the neotropical pollination syndrome among Old World Malpighiaceae.

}, isbn = {0002-9122 (Print)0002-9122 (Linking)}, author = {Davis, C. C.} } @article {847611, title = {Phylogeny and biogeography of Cercis (Fabaceae): evidence from nuclear ribosomal ITS and chloroplast ndhF sequence data}, journal = {Sys. Bot.}, volume = {27}, year = {2002}, pages = {289-302}, author = {Davis, C. C. and PA Fritsch and J. Li and Donoghue, M. J.} } @article {846891, title = {Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography}, journal = {Evolution}, volume = {56}, number = {12}, year = {2002}, note = {

Davis, Charles CBell, Charles DFritsch, Peter WMathews, SarahengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.2003/02/14 04:00Evolution. 2002 Dec;56(12):2395-405.

}, month = {Dec}, pages = {2395-405}, abstract = {

A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF, and trnL-F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal-vicariance analysis and divergence-time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high-latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Aeridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.

}, keywords = {*Environment, *Phylogeny, Africa, Animals, Asia, Biological Evolution, Fossils, Genes, Plant, Madagascar, Malpighiaceae/*classification/*genetics, New Caledonia, Time Factors}, isbn = {0014-3820 (Print)0014-3820 (Linking)}, author = {Davis, C. C. and Bell, C. D. and Fritsch, P. W. and S. Mathews} } @article {847586, title = {Monograph of Lophopterys (Malpighiaceae)}, journal = {Contributions from the University of Michigan Herbarium}, volume = {23}, year = {2001}, pages = {83-105}, author = {Anderson, W. R. and Davis, C. C.} } @article {847606, title = {Phylogenetic relationships of Torreya (Taxaceae) inferred from sequences of nuclear ribosomal DNA ITS region}, journal = {Harvard Papers in Botany}, volume = {6}, year = {2001}, pages = {275-281}, author = {J. Li and Davis, C. C. and Donoghue, M. J. and S. Kelley and P. Del Tredici} } @article {847591, title = {Phylogeny and biogeography of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA}, journal = {Harvard Papers in Botany}, volume = {6}, year = {2001}, pages = {267-274}, author = {J. Li and Davis, C. C. and P. Del Tredici and Donoghue, M. J.} } @article {846876, title = {Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences}, journal = {Am J Bot}, volume = {88}, number = {10}, year = {2001}, note = {

Davis, C C, Anderson, WR Donoghue, M Jeng2001/10/01 00:00Am J Bot. 2001 Oct;88(10):1830-46.

}, month = {Oct}, pages = {1830-46}, abstract = {

The Malpighiaceae are a family of approximately 1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3{\textquoteright} region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu{\textquoteright}s tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu{\textquoteright}s tribe Gaudichaudieae and Anderson{\textquoteright}s tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.

}, isbn = {0002-9122 (Print)0002-9122 (Linking)}, author = {Davis, C. C. and Anderson, W. R. and Donoghue, M. J.} }