186 Works

Data from: Herbivory enhances the diversity of primary producers in pond ecosystems

Mathew A. Leibold, Spencer R. Hall, Val H. Smith & David A. Lytle
Diversity of primary producer is often surprisingly high, despite few limiting factors such as nutrients and light to facilitate species coexistence. In theory, the presence of herbivores could increase the diversity of primary producers, resolving this “paradox of the plankton”. Little experimental evidence supports this natural enemies hypothesis, but previous tests suffer from several deficiencies. Previous experiments often did not allow for multigeneration effects; utilized low diversity assemblages of herbivores; and limited opportunities for new...

Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

Ylva Lekberg, James D. Bever, Rebecca A. Bunn, Ray M. Callaway, Miranda M. Hart, Stephanie N. Kivlin, John Klironomos, Beau G. Larkin, John L. Maron, Kurt O. Reinhart, Michael Remke, Wim H. Van Der Putten & Ragan M. Callaway
Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition versus plant soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil)...

Data from: Fitness of crop-wild hybrid sunflowers under competitive conditions: implications for crop-to-wild introgression

Kristin L. Mercer, D. Jason Emry, Allison A. Snow, Matthew A. Kost, Brian A. Pace & Helen M. Alexander
Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment...

Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

Rafe M. Brown, Cameron D. Siler, Stephen J. Richards, Arvin C. Diesmos & David C. Cannatella
We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each...

Data from: Lineage space and the propensity of bacterial cells to undergo growth transitions

Arnab Bandyopadhyay, Huijing Wang & J. Christian J. Ray
The molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity. Such regulatory mechanisms form networks that contain thresholds between phenotypes. Populations of cells can be poised near the threshold so that a subset of the population probabilistically undergoes the phenotypic transition. We sought to characterize the diversity of bacterial populations around a growth-modulating threshold via analysis of the...

Data from: Novel traits, flower symmetry, and transcriptional autoregulation: new hypotheses from bioinformatic and experimental data

Aniket Sengupta & Lena C. Hileman
A common feature in developmental networks is the autoregulation of transcription factors which, in turn, positively or negatively regulate additional genes critical for developmental patterning. When a transcription factor regulates its own expression by binding to cis-regulatory sites in its gene, the regulation is direct transcriptional autoregulation (DTA). Indirect transcriptional autoregulation (ITA) involves regulation by proteins expressed downstream of the target transcription factor. We review evidence for a hypothesized role of DTA in the evolution...

Data from: Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

Erin E. Saupe, Corinne E. Myers, A. Townsend Peterson, Jorge Soberón, Joy Singarayer, Paul Valdes & Huijie Qiao
Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth...

Data from: Dispersal to or from an African biodiversity hotspot?

David C Blackburn & John Measey
Biodiversity hotspots are centers of endemism and thus contain many range-restricted species. In addition, within these hotspots are often widespread species that might have originated within a hotspot before dispersing to neighboring or distant regions. We test this hypothesis through a phylogeographic analysis of a miniature leaf litter frog, Arthroleptis xenodactyloides, that has a large distribution throughout the Eastern Arc, a biodiversity hotspot, and other regions in East Africa. Maximum likelihood and Bayesian estimates of...

Data from: A new squeaker frog (Arthroleptidae: Arthroleptis) from the Cameroon Volcanic Line with redescriptions of Arthroleptis adolfifriederici Nieden, 1911 \"1910\" and A. variabilis Matschie, 1893

David C. Blackburn, Legrand N Gonwouo, Raffael Ernst & Mark-Oliver Rödel
We describe a new species of squeaker frog (Arthroleptis) from Mt. Manengouba in southwestern Cameroon. The new species is distinguished from other Cameroonian Arthroleptis by moderately larger body size; a darkened throat and posterior thigh, both with many white spots; and, in females, a fourth finger longer than the first and second fingers. This species corresponds to a Cameroonian taxon previously identified as Arthroleptis adolfifriederici but which has been long recognized as distinct. Multivariate morphometric...

Data from: Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

Robert G. Moyle, Michael J. Andersen, Carl H. Oliveros, Frank Steinheimer & Sushma Reddy
The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a dataset of six genes and almost 300 individuals to assess the evolutionary history of the family. Although...

Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron David Siler, Mark T. Holder & Rafe M. Brown
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the...

Data from: Brazilian marsupial frogs are diphyletic (Anura: Hemiphractidae: Gastrotheca)

David C. Blackburn & William E. Duellman
Molecular phylogenetic analyses based on expanded taxonomic and geographic sampling support the monophyly of the marsupial frog genera (family Hemiphractidae), resolve six geographically circumscribed lineages within Gastrotheca, and, for the first time, reveal that two divergent lineages of Gastrotheca inhabit the Atlantic Coastal Forests of Brazil. Within Gastrotheca, the earliest diverging clade is confined to northeastern Brazil, whereas the three subsequent diverging lineages are restricted to northern Venezuela (G. walkeri), southeastern Brazil, and northwestern South...

Data from: The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

Galina Kislukhin, Elizabeth G. King, Kelli N. Walters, Stuart J. Macdonald & Anthony D. Long
The severity of the toxic side effects of chemotherapy varies among patients, and much of this variation is likely genetically based. Here, we use the model system Drosophila melanogaster to genetically dissect the toxicity of methotrexate (MTX), a drug used primarily to treat childhood acute lymphoblastic leukemia and rheumatoid arthritis. We use the Drosophila Synthetic Population Resource, a panel of recombinant inbred lines derived from a multiparent advanced intercross, and quantify MTX toxicity as a...

Data from: Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus

Julius P. Mojica, Young Wha Lee, John H. Willis & John K. Kelly
Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation-selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency-dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated...

Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

Welton J. Luke, Cameron D. Siler, Charles W. Linkem, Arvin C. Diesmos, Mae L. Diesmos, Emerson Sy, Rafe M. Brown & Luke J. Welton
We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian...

Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Loretta C. Johnson, Matthew Galliart, Sofia Sabates, Hannah Tetreault, Angel DeLaCruz, Johnny Bryant, Jacob Alsdurf, Mary Knapp, Nora Bello, Sara Baer, Brian Maricle, David Gibson, Jesse Poland, Paul St. Amand, Natalie Unruh, Olivia Parrish & Loretta Johnson
Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year-1. We aimed to answer: (1)...

Data from: Effects of the soil microbiome on the demography of two annual prairie plants

Helen Alexander, Hannah Reynolds, Rebekah Wagner, Guangzhou Wang, Haley Burrill & James Bever
Both mutualistic and pathogenic soil microbes are known to play important roles in shaping the fitness of plants, likely affecting plants at different life cycle stages. In order to investigate the differential effects of native soil mutualists and pathogens on plant fitness, we compared survival and reproduction of two annual tallgrass prairie plant species (Chamaecrista fasciculata and Coreopsis tinctoria) in a field study using 3 soil inocula treatments containing different compositions of microbes. The soil...

Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies

Nicholai M. Hensley, Emily A. Ellis, Gretchen A. Gerrish, Elizabeth Torres, John P. Frawley, Todd H. Oakley & Trevor J. Rivers
Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this since amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype...

Data from: The plant microbiome and native plant restoration: the example of native mycorrhizal fungi

Liz Koziol, Peggy A. Schultz, Geoffrey L. House, Jonathan T. Bauer, Elizabeth L. Middleton & James D. Bever
Ecological restoration efforts can increase the diversity and function of degraded areas. However, current restoration practices cannot typically re-establish the full diversity and species composition of remnant plant communities. We present evidence that restoration quality can be improved by reintroducing key organisms from the native plant microbiome. In particular, root symbionts called arbuscular mycorrhizal fungi are critical in shaping grassland communities, but are sensitive to anthropogenic disturbance, which may pose a problem for grassland restoration....

Data from: The hatching mechanism of 130-million-year-old insects: an association of neonates, egg shells and egg bursters in Lebanese amber

Ricardo Pérez-De La Fuente, Michael S. Engel, Dany Azar & Enrique Peñalver
Hatching is a pivotal moment in the life of most animals. Diverse chemical, behavioural and mechanical methods have evolved in metazoans to break the egg membranes. Among them, many arthropod and vertebrate embryos hatch using ephemeral, frequently convergent structures known as egg bursters. However, the evolutionary processes by which hatching mechanisms and related embryonic structures became established in deep time are poorly understood due to a nearly complete absence from the fossil record. Herein we...

On Greek Row: Diversity, Socially Responsible Leadership and Fraternity and Sorority Membership

Eugene T. Parker & Ernest Pascarella

Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird

Ethan Gyllenhaal, Xena Mapel, Tejashree Modak, Lucas DeCicco, Alivereti Naikatini, Ruth Utzurrum, Joshua Seamon, Jean-Claude Thibault, Alice Cibois, Michael Sorenson, Robert Moyle, Lisa Barrow & Michael Andersen
Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region’s numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within...

Data from: A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles

Jamie R Oaks
True crocodiles (Crocodylus) are the most broadly distributed, ecologically diverse, and species-rich crocodylian genus, comprising about half of extant crocodylian diversity and exhibiting a circumtropical distribution. Crocodylus traditionally has been viewed as an ancient group of morphologically conserved species that originated in Africa prior to continental breakup. In this study, these long-held notions about the temporal and geographic origin of Crocodylus are tested using DNA sequence data of 10 loci from 76 individuals representing all...

Data from: Molecular phylogenetics of desmognathine salamanders (Caudata: Plethodontidae): a reevaluation of evolution in ecology, life history, and morphology

Tom A. Titus & Allan Larson
Phylogenetic relationships were reconstructed for salamanders of the plethodontid subfamily Desmognathinae to examine evolution of morphology, ecology, and life history. Mitochondrial DNA sequences encoding 12S and 16S ribosomal RNA and the valine transfer RNA provided 259 phylogenetically informative sites from approximately 1,200 nucleotide positions for 21 specimens representing 15 species and subspecies. These data were analyzed in conjunction with 13 morphological and reproductive characters to generate phylogenetic hypotheses. The directly developing terrestrial desmognathines Phaeognathus hubrichti...

Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays

John E McCormack, Joseph Heled, Kathleen S Delaney, A Townsend Peterson & L Lacey Knowles
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma...

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