2016-2020

2017
Charles G. Willis, Edith Law, Williams. Alex C., Brian F. Franzone, Rebecca Bernados, Lian Bruno, Claire Hopkins, Christian Schorn, Ella Weber, Daniel S. Park, and Charles C. Davis. 4/10/2017. “CrowdCurio: an online crowdsourcing platform to facilitate climate change studies using herbarium specimens.” New Phytologist, 215, Pp. 479–488.Abstract
  • Phenology is a key aspect of plant success. Recent research has demonstrated that herbarium specimens can provide important information on plant phenology. Massive digitization efforts have the potential to greatly expand herbarium-based phenological research, but also pose a serious challenge regarding efficient data collection.
  • Here, we introduce CrowdCurio, a crowdsourcing tool for the collection of phenological data from herbarium specimens. We test its utility by having workers collect phenological data (number of flower buds, open flowers and fruits) from specimens of two common New England (USA) species: Chelidonium majus and Vaccinium angustifolium. We assess the reliability of using nonexpert workers (i.e. Amazon Mechanical Turk) against expert workers. We also use these data to estimate the phenological sensitivity to temperature for both species across multiple phenophases.
  • We found no difference in the data quality of nonexperts and experts. Nonexperts, however, were a more efficient way of collecting more data at lower cost. We also found that phenological sensitivity varied across both species and phenophases.
  • Our study demonstrates the utility of CrowdCurio as a crowdsourcing tool for the collection of phenological data from herbarium specimens. Furthermore, our results highlight the insight gained from collecting large amounts of phenological data to estimate multiple phenophases.
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Laura P. Lagomarsino, Elisabeth J. Forrestel, Nathan Muchhala, and Charles C. Davis. 2/23/2017. “Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade.” Journal of Biogeography, 71, Pp. 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'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.
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Daniel S. Park and Charles C. Davis. 2017. “Implications and alternatives of assigning climate data to geographical centroids.” Journal of Biogeography , Pp. 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.

 

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2016
Liming Cai, Zhenxiang Xi, Kylee PEterson, Katherine Rushworth, Jeremy Beaulieu, and Charles C. Davis. 9/29/2016. “Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae (Malpighiaceae,Elatinaceae) Clade.” PLoS ONE, 11, 9, Pp. 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'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.
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Goia M. Lyra, Carlos F. D. Gurgel, Emanuelle S. Costa, Priscilla B. de Jesus, Mariana C. Oliveira, Eurico C. Oliveira, Charles C. Davis, and Jose M. de Castro Nunes. 9/15/2016. “Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data.” Journal of Phycology , 52, Pp. 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.
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Whenheng Zhang, Elena M. Kramer, and Charles C. Davis. 6/23/2016. “Differential Expression of CYC2 Genes and the Elaboration of Floral Morphologies in Hiptage, an Old-World Genus of Malpighiaceae.” International Journal of Plant Sciences, 177, 7, Pp. 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.

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Brad R. Ruhfel, Claudia P. Bove, C. Thomas Philbrick, and Charles C. Davis. 6/22/2016. “Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade.” American Journal of Botany , 103, 6, Pp. 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.
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Léa Bardon, Cynthia Sothers, Ghillean T. Prance, Pierre-Jean G. Malé, Zhenxiang Xi, Charles C. Davis, Jerome Murienne, García-Villacorta Roosevelt, Eric Coissac, Sébastien Lavergne, and Jérôme Chave. 6/21/2016. “Unraveling the biogeographical history of Chrysobalanceae from plastid genomes.” American Journal of Botany , 103, 6, Pp. 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.
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Laura P. Lagomarsino, Fabian L. Condamine, Alexandre Antonelli, Andreas Mulch, and Charles C. Davis. 6/2016. “The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae).” New Phytologist, 210, 4, Pp. 1430-1442.Abstract

The tropical Andes of South America, the world'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's biodiversity.

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Joel H. Nitta, Jean-Yves Meyer, Ravahere Taputuarai, and Charles C. Davis. 3/8/2016. “Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes.” Ecological Monographs , 87, 2, Pp. 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 ~1000–1200 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.
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