Emily K Meineke, Charles C Davis, and Jonathan T Davies. 11/20/2019. “
Herbivory through the ages: Herbarium specimens for determining effects of plant traits on changing insect damage to plants.” Entomology 11/20/2019.
AbstractSome 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.
Lucas Marinho, Liming Cai, Xiaoshan Duan, Brad R. Ruhfel, Pedro Fiaschi, André M. Amorim, Cássio van den Berg, and Charles C. Davis. 5/1/2019. “
Plastomes resolve generic limits within tribe Clusieae (Clusiaceae) and reveal the new genus Arawakia.” Molecular Phylogenetics and Evolution, 134, Pp. 142-151.
Publisher's VersionAbstractClusieae 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.
PDF Charles C. Davis and Sarah Matthews. 4/24/2019. “
Evolution of Land Plants.” Oxford Bibliographies.
Publisher's Version PDF William D. Pearse, Charles C. Davis, David W. Inouye, RIchard B. Primack, and T. Jonathan Davis. 3/2019. “
[Author Correction] A statistical estimator for determining the limits of contemporary and historic phenology.” Nature Ecology & Evolution, 3, 3, Pp. 499.
Publisher's Version PDF Liming Cai, André M. Amorim, Sugumaran Manickam, Liang Liu, Joshua S. Rest, and Charles C. Davis. 2/28/2019. “
Thrive with Additional Sets of Genome: Widespread Paleopolyploidization Buffers plants Through Eocene Climatic Upheaval.” Oxford University Press 59, Pp. E29-E29.
Emily K Meineke, Jonathan T Davies, Barnabas H Daru, and Charles C Davis. 1/7/2019. “
Biological Collections for understanding biodiversity in the Anthropocene.” Philosophical Transactions of the Royal Society B, 374, 1763, Pp. 20170386.
AbstractGlobal 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 …
PDF Rebecca A Povilus, Jeffery M DaCosta, Christopher Grassa, Prasad RV Satyaki, Morgan Moeglein, Johan Jaenisch, Zhenxiang Xi, Sarah Mathews, Mary Gehring, Charles C Davis, and William E Friedman. 1/1/2019. “
Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses.” bioRxiv.
AbstractFor 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 …
PDF Liming Cai, Zhenziang Xi, André M Amorim, Manickam Sugumaran, Joshua S. Rest, Liang Liu, and Charles C. Davis. 1/1/2019. “
Widespread Ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheval.” New Phytologist, 221, 1, Pp. 565-576.
Publisher's Version PDF William D. Pearse, Charles C. Davis, David W. Inouye, RIchard B. Primack, and T. Jonathan Davies. 2019. “
A statistical estimator for determining the limits of contemporary and historic phenology.” Nature Ecology & Evolution, 3, 3, Pp. 499.