18 Works

Data from: Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species

Claire Kremen & Leithen K. M'Gonigle
1. Agriculture now constitutes 40–50% of terrestrial land use globally. By enhancing habitat suitability and connectivity, restoration within agricultural landscapes could have a major influence on biodiversity conservation. However, habitat management within intensive agricultural landscapes may primarily boost abundances of common, highly mobile generalists, rather than vulnerable or endangered species. We studied pollinator community response to small-scale habitat restoration in the intensively farmed Central Valley of California to determine whether restoration could also promote more...

Data from: Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood

David Houle & Karin Meyer
We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance–covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of...

Data from: Evolution of reduced postcopulatory molecular interactions in Drosophila populations lacking sperm competition

Brian Hollis, David Houle & Tadeusz J. Kawecki
In many species with internal fertilization, molecules transferred in the male ejaculate trigger and interact with physiological changes in females. It is controversial to what extent these interactions between the sexes act synergistically to mediate the female switch to a reproductive state or instead reflect sexual antagonism evolved as a byproduct of sexual selection on males. To address this question, we eliminated sexual selection by enforcing monogamy in populations of Drosophila melanogaster for 65 generations...

Data from: Population genomics of the euryhaline teleost Poecilia latipinna

J. C. B. Nunez, T. P. Seale, M. A. Fraser, T. L. Burton, T. N. Fortson, D. Hoover, J. Travis, M. F. Oleksiak & Douglas L. Crawford
Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and...

Data from: Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Sara Ruane, Christopher J. Raxworthy, Alan R. Lemmon, Emily Moriarty Lemmon & Frank T. Burbrink
Background: Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS....

Data from: A quantitative framework for investigating risk of deadly collisions between marine wildlife and boats

Julien Martin, Quentin Sabatier, Timothy A. Gowan, Christophe Giraud, Eliezer Gurarie, Charles Scott Calleson, Joel G. Ortega-Ortiz, Charles J. Deutsch, Athena Rycyk & Stacie M. Koslovsky
Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife. We apply encounter rate theory to demonstrate how marine mammal-boat encounter rate can be used to predict the expected number of deaths associated with management scenarios. We illustrate our approach with management scenarios for two endangered species: the Florida...

Data from: Shape variation in the least killifish: ecological associations of phenotypic variation and the effects of a common garden

Joseph Alex Landy & Joseph Travis
Studies of the adaptive significance of variation among conspecific populations often focus on a single ecological factor. However, habitats rarely differ in only a single ecological factor, creating a challenge for identifying the relative importance of the various ecological factors that might be maintaining local adaptation. Here we investigate the ecological factors associated with male body shape variation among nine populations of the poeciliid fish, Heterandria formosa, from three distinct habitats and combine those results...

Data from: Phenotypic integration in the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus)

Mark J. Margres, Kenneth P. Wray, Margaret Seavy, James J. McGivern, Dragana Sanader & Darin R. Rokyta
Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits...

Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Yi Zhang, Yongfang Lu, Marnoch Yindee, Kuan-Yi Li, Hsiao-Yun Kuo, Yu-Ten Ju, Shaohui Ye, , Qiang Li, Yachun Wang, Vu Chi Cuong, Lan Doan Pham, Bounthong Bouahom, Bingzhuang Yang, Xianwei Liang, Zhihua Cai, Dianne Vankan, Wallaya Manatchaiworakul, Nonglid Kowlim, Somphot Duangchantrasiri, Worawidh Wajjwalku, Ben Colenbrander, Yuan Zhang, Peter Beerli, Johannes A. Lenstra … & J. Stuart F. Barker
The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY,...

Data from: Local pain dynamics during constant exhaustive exercise

Agnė Slapšinskaitė, Selen Razon, Natàlia Balagué, Robert Hristovski, Gershon Tenenbaum & Natàlia Balagué Serre
The purpose of this study was to delineate the topological dynamics of pain and discomfort during constant exercise performed until volitional exhaustion. Eleven physical education students were tested while cycling and running at a “hard” intensity level (e.g., corresponding to Borg’s RPE (6–20) = 15). During the tests, participants reported their discomfort and pain on a body map every 15s. “Time on task” for each participant was divided into five equal non-overlapping temporal windows within...

Data from: Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster

Geir H. Bolstad, Jason A. Cassara, Eladio Márquez, Thomas F. Hansen, Kim Van Der Linde, David Houle & Christophe Pélabon
Precise exponential scaling with size is a fundamental aspect of phenotypic variation. These allometric power laws are often invariant across taxa and have long been hypothesized to reflect developmental constraints. Here we test this hypothesis by investigating the evolutionary potential of an allometric scaling relationship in drosophilid wing shape that is nearly invariant across 111 species separated by at least 50 million years of evolution. In only 26 generations of artificial selection in a population...

Data from: The Centennial Trends Greater Horn of Africa precipitation dataset

Chris C. Funk, Sharon E. Nicholson, Martin Landsfeld, Douglas Klotter, Pete Peterson & Laura Harrison
East Africa is a drought prone, food and water insecure region with a highly variable climate. This complexity makes rainfall estimation challenging, and this challenge is compounded by low rain gauge densities and inhomogeneous monitoring networks. The dearth of observations is particularly problematic over the past decade, since the number of records in globally accessible archives has fallen precipitously. This lack of data coincides with an increasing scientific and humanitarian need to place recent seasonal...

Data from: Geographic variation in the Pine Barrens Treefrog (Hyla andersonii): concordance of genetic, morphometric, and acoustic signal data

Alexa R. Warwick, Joseph Travis & Emily Moriarty Lemmon
Delimiting species is important to every subfield in biology. Templeton's cohesion species concept uses genetic and ecological exchangeability to identify sets of populations that ought to be considered as the same species, and the lack of exchangeability helps determine which populations can be grouped as evolutionarily significant units (ESU) in conservation science. However, previous work assessing genetic and ecological interchangeability among populations has been limited in scope. Here, we provide a method for assessing exchangeability...

Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex

Lisa N. Barrow, Alyssa T. Bigelow, Christopher A. Phillips & Emily Moriarty Lemmon
Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois...

Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

Pedro L. V. Peloso, Darrel R. Frost, Stephen J. Richards, Miguel T. Rodrigues, Stephen Donnellan, Masafumi Matsui, Cristopher J. Raxworthy, S. D. Biju, Emily Moriarty Lemmon, Ward C. Wheeler, Alan R. Lemmon, Pedro L.V. Peloso & S.D. Biju
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for...

Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel

David Houle & Eladio J. Marquez
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the...

Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

Ron I. Eytan, Benjamin R. Evans, Alex Dornburg, Alan R. Lemmon, Emily Moriarty Lemmon, Peter C. Wainwright & Thomas J. Near
Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes...

Data from: Consumer trait variation influences tri-trophic interactions in salt marsh communities

Anne Randall Hughes, Torrance C. Hanley, Nohelia P. Orozco & Robyn A. Zerebecki
The importance of intraspecific variation has emerged as a key question in community ecology, helping to bridge the gap between ecology and evolution. Although much of this work has focused on plant species, recent syntheses have highlighted the prevalence and potential importance of morphological, behavioral, and life history variation within animals for ecological and evolutionary processes. Many small-bodied consumers live on the plant that they consume, often resulting in host plant-associated trait variation within and...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Florida State University
  • University of New England
  • American Museum of Natural History
  • University of Adelaide
  • National Institute of Animal Sciences
  • Ball State University
  • University of California System
  • University of Queensland
  • University of Lausanne
  • University of California, Berkeley