79 Works

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Sarah Hird, Darien Capunitan, Oscar Johnson & Ryan Terrill
How the microbiome interacts with hosts across evolutionary time is poorly understood. To address this question, datasets comprised of many host species are required to conduct comparative analyses. Here, we have analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses and used phylogenetic...

The hornwort genome and early land plant evolution

Jian Zhang, Xin-Xing Fu, Rui-Qi Li, Xiang Zhao, Yang Liu, Ming-He Li, Arthur Zwaenepoel, Hong Ma, Bernard Goffinet, Yan-Long Guan, Jia-Yu Xue, Yi-Ying Liao, Qing-Feng Wang, Qing-Hua Wang, Jie-Yu Wang, Guo-Qiang Zhang, Zhi-Wen Wang, Yu Jia, Mei-Zhi Wang, Shan-Shan Dong, Jian-Fen Yang, Yuan-Nian Jiao, Ya-Long Guo, Hong-Zhi Kong, An-Ming Lu … & Zhi-Duan Chen
Hornworts, liverworts, and mosses are three early diverging clades of land plants, together composing the bryophytes. Here we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage....

Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback

Daniel Bolnick & Kimberly Ballare
Many generalist species consist of specialized individuals that use different resources. This within-population niche variation can stabilize population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favor ecological diversity (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic...

The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity

Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Hong Wu, Weixue Mu, Tong Wei, Na Li, Tao Wan, Huan Liu, Jie Cui, Ruiliang Zhu, Bernard Goffinet & Yang Liu
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded PPR proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059...

Data from: Mortality and morphology in egg masses of unisexual and Jefferson Salamanders

Noah Charney, Jacob Kubel, Craig Woodard, Blanca Carbajal-González, Samantha Avis, Julia Blyth, Charles Eiseman, John Castorino & John Malone
Unisexual Ambystoma salamander egg masses have often been observed to exhibit very high rates of embryo mortality. The ecological consequences and underlying mechanisms are of great concern to researchers and managers studying these and other members of the species complex, all of which are listed as rare species throughout much of their range. Substantial embryo mortality is commonly used by field ecologists as an indicator that unisexual salamanders are present in a pond; egg masses...

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

Antoine Paccard, Dieta Hanson, Yoel E Stuart, Frank A Von Hippel, Martin Kalbe, Tom Klepaker, Skúli Skúlason, Bjarni K Kristjánsson, Daniel I Bolnick, Andrew P Hendry & Rowan D H Barrett
The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among “replicates” leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on...

Data from: Biased movement drives local cryptic colouration on distinct urban pavements

Pim Edelaar, Adrian Baños-Villalba, David P. Quevedo, Graciela Escudero, Daniel Bolnick & Aída Jordán-Andrade
Explanations of how organisms might adapt to urban environments have mostly focused on divergent natural selection and adaptive plasticity. However, differential habitat choice has been suggested as an alternative. Here we test for habitat choice in enhancing crypsis in ground-perching grasshoppers colonising an urbanised environment, composed of a mosaic of four distinctly coloured substrates (asphalt roads and adjacent pavements). Additionally, we determine its relative importance compared to present-day natural selection and phenotypic plasticity. We found...

Data from: Moth body size increases with elevation along a complete tropical elevational gradient for two hyperdiverse clades

Gunnar Brehm, Dirk Zeuss & Robert K. Colwell
The body size of an animal is probably its most important functional trait. For arthropods, environmental drivers of body size variation are still poorly documented and understood, especially in tropical regions. We use a unique dataset for two species-rich, phylogenetically independent moth taxa (Lepidoptera: Geometridae; Arctiinae), collected along an extensive tropical elevational gradient in Costa Rica, to investigate the correlates and possible causes of body-size variation. We studied 15,047 specimens (794 species) of Geometridae and...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Data from: Phylogenetic uncertainty revisited: implications for ecological analyses

Thiago Fernando Rangel, Robert K. Colwell, Gary R. Graves, Karolina Fučíková, Carsten Rahbek, José Alexandre F. Diniz-Filho & Thiago F. Rangel
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify...

Data from: Spatially heterogeneous impact of climate change on small mammals of montane California

Kevin C. Rowe, Karen M. C. Rowe, Morgan W. Tingley, Michelle S. Koo, James L. Patton, Christopher J. Conroy, John D. Perrine, Steven R. Beissinger, Craig Moritz, S. R. Beissinger, C. J. Conroy, M. S. Koo, J. L. Patton, M. W. Tingley, C. Moritz, J. D. Perrine, K. C. Rowe & K. M. C. Rowe
Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one...

Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)

Elizabeth L. Jockusch, Iñigo Martínez-Solano & Elizabeth K. Timpe
Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one...

Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Yang Liu, Cymon J. Cox, Wei Wang & Bernard Goffinet
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants...

Data from: Sensory drive does not explain reproductive character displacement of male acoustic signals in the Upland Chorus Frog (Pseudacris feriarum)

Emily Claire Moriarty Lemmon, Jessica Ribado, John H. Malone & Emily Moriarty Lemmon
Biotic and abiotic factors have been proposed to explain patterns of reproductive character displacement, but which factor is most important to character displacement of acoustic signals is not clear. Male vocalizations of the frog Pseudacris feriarum are known to undergo reproductive character displacement in areas of sympatry with P. brimleyi and P. nigrita. Despite evidence for reinforcement as an important mechanism, local adaptation via sensory drive might explain this pattern because Pseudacris breed in different...

Data from: Advancing population ecology with integral projection models: a practical guide

Cory Merow, Johan P. Dalgren, C. J. E. Metcalf, Dylan Z. Childs, M. E. K. Evans, E. Jongejans, Sydne Record, Mark Rees, Roberto Salguero-Gómez, Sean McMahon, Margaret E.K. Evans, Johan P. Dahlgren, C. Jessica E. Metcalf, Sean M. McMahon & Eelke Jongejans
Integral Projection Models (IPMs) use information on how an individual's state influences its vital rates - survival, growth and reproduction - to make population projections. IPMs are constructed from regression models predicting vital rates from state variables (e.g., size or age) and covariates (e.g., environment). By combining regressions of vital rates, an IPM provides mechanistic insight into emergent ecological patterns such as population dynamics, species geographic distributions, or life history strategies. Here, we review important...

Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

Erica Lasek-Nesselquist & Johann Peter Gogarten
Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life’s reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya...

Data from: Age‐dependent habitat relationships of a burned forest specialist emphasise the role of pyrodiversity in fire management

Andrew N. Stillman, Rodney B. Siegel, Robert L. Wilkerson, Matthew Johnson & Morgan W. Tingley
1. Variation in fire characteristics, termed pyrodiversity, plays an important role in structuring post-fire communities, but little is known about the importance of pyrodiversity for individual species. The availability of diverse post-fire habitats may be key for fire-associated species if they require different resources at different life history stages. 2. We tested for age-specific habitat relationships in the black-backed woodpecker, a post-fire specialist. We used radio-telemetry to track fledgling and adult woodpeckers in burned forests...

Data from: Social context affects thermoregulation but not activity level during avian immune response

Grace J. Vaziri, Manju M. Johny, Petrutza C. Caragea & James S. Adelman
Determining how an animal’s social context alters its immune responses will help us understand how pathogens impact individual health and spread within groups. Several studies have shown that group-housed animals can suppress components of the acute phase immune response, specifically sickness behaviors like lethargy. However, we do not know whether individuals alter sickness behaviors or other components of the acute phase response, including thermoregulation, in response to the infection status of other group members. We...

Data from: Adaptive phenotypic plasticity for life-history and less fitness-related traits

Cristina Acasuso-Rivero, Courtney J. Murren, Carl D. Schlichting & Ulrich Karl Steiner
Organisms are faced with variable environments and one of the most common solutions to cope with such variability is phenotypic plasticity, a modification of the phenotype to the environment. These modifications are commonly modelled in evolutionary theories as adaptive, influencing ecological and evolutionary processes. If plasticity is adaptive, we would predict that the closer to fitness a trait is, the less plastic it would be. To test this hypothesis, we conducted a meta-analysis of 213...

Data from: Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass

Damon L. Smith, James P. Kerns, Nathan R. Walker, Andrea F. Payne, Brandon Horvath, John C. Inguagiato, John E. Kaminski, Maria Tomaso-Peterson, Paul L. Koch, D. L. Smith, P. L. Koch, J. P. Kerns, N. R. Walker, A. F. Payne, B. Horvath, J. C. Inguagiato, J. E. Kaminski & M. Tomaso-Peterson
Dollar spot is one of the most common diseases of golf course turfgrass and numerous fungicide applications are often required to provide adequate control. Weather-based disease warning systems have been developed to more accurately time fungicide applications; however, they tend to be ineffective and are not currently in widespread use. The primary objective of this research was to develop a new weather-based disease warning system to more accurately advise fungicide applications to control dollar spot...

Data from: Defaunation increases the spatial clustering of lowland Western Amazonian tree communities

Robert Bagchi, Varun Swamy, Jean-Paul Latorre Farfan, John Terborgh, César I. A. Vela, Nigel C. A. Pitman & Washington Galiano Sanchez
1.Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance- and density- dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. 2.We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two...

Data from: Quantifying the importance of geographic replication and representativeness when estimating demographic rates, using a coastal species as a case study

Christopher R. Field, Katharine J. Ruskin, Bri Benvenuti, Alyssa C. Borowske, Jonathan B. Cohen, Laura Garey, Thomas P. Hodgman, Rebecca A. Kern, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Brian J. Olsen, Nancy Pau, Samuel G. Roberts, Emma Shelly, W. Gregory Shriver, Jennifer Walsh, Chris S. Elphick & Rebecca A. Longenecker
Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify...

Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

Hilary A. McManus, Karolina Fučíková, Paul O. Lewis, Louise A. Lewis & Kenneth G. Karol
Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired...

Data from: Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae)

Suman Neupane, Paul O. Lewis, Steven Dessein, Hunter Lee Shanks, Sushil Paudyal, Frederic Lens & Hunter Shanks
Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a few lineages are woody, and are found in a diverse range of habitat types. Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua) are characterized by their distribution in the moist tropical mountains, and have disjunct distribution patterns with respect to their closest relatives. In this study, we explore the cases of derived woodiness in these three lineages and their diversification dynamics in...

Data from: Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

Jonathan P. Velotta, Jill L. Wegrzyn, Samuel Ginzburg, Lin Kang, Sergiusz Czesny, Rachel J. O'Neill, Stephen D. McCormick, Pawel Michalak & Eric T. Schultz
Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations...

Registration Year

  • 2012
  • 2013
  • 2014
  • 2015
  • 2016
  • 2017
  • 2018
  • 2019
  • 2020

Resource Types

  • Dataset
  • Text


  • University of Connecticut
  • Australian National University
  • United States Department of Agriculture
  • The University of Texas at Austin
  • Columbia University
  • Duke University
  • University of Georgia
  • The Institute for Bird Populations
  • University of Cambridge
  • University of Maine
  • McGill University
  • University of Colorado Boulder
  • University of Missouri
  • City University of New York
  • Field Museum of Natural History