40 Works

Data from: Temporal population genetic instability in range edge Western Toads, Anaxyrus boreas

Iris A. Holmes
In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2...

Data from: Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards

Daniel L. Rabosky, Stephen C. Donnellan, Michael Grundler & Irby J. Lovette
The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+ scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait...

Data from: Modeling the effects of anthropogenic exploitation and climate change on an endemic stag beetle, Lucanus miwai, of Taiwan

Jen-Pan Huang
Loss of biodiversity is a worldwide phenomenon and conservation of endemic species is becoming a pressing issue. However, species differ in life history characteristics, causing the best strategy for conservation to vary among species. Lucanus miwai is an endemic stag beetle of Taiwan, but the natural history and the conservation status of L. miwai have not been fully studied. Lucanus miwai adults live in forest-edge grassland habitats and are experiencing threats from anthropogenic exploitation. Additionally,...

Data from: \"De novo transcriptome assembly and polymorphism detection in ecological important widely distributed Neotropical toads from the Rhinella marina species complex (Anura: Bufonidade)\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Coralie Nourisson, Miguel Carneiro, Marcelo Vallinoto & Fernando Sequeira
The toads Rhinella marina and R. schneideri are large terrestrial true toads widely distributed in the Neotropical region, which can hybridize in areas of transition between Amazon rain forest and Cerrado biomes. The former is in particular an important ecological species, and a very successful invader. Here, we report de novo transcriptome of R. marina and R. schneideri and polymorphism SNPs identified between the two species. The transcriptome sequencing was performed on an Illumina platform...

Data from: Temporal trends of predation resistance in Paleozoic crinoid arm branching morphologies

Tomasz K. Baumiller & V. J. Syverson
The rise of durophagous predators during the Paleozoic represents an ecological constraint imposed on sessile marine fauna. In crinoids, it has been suggested that increasing predation pressure drove the spread of adaptations against predation. Damage to a crinoid's arms from nonlethal predation varies as a function of arm branching pattern. Here, using a metric for resilience to predation (“expected arm loss,” EAL), we test the hypothesis that the increase in predation led to more predation-resistant...

Data from: Harnessing ant defence at fruits reduces bruchid seed predation in a symbiotic ant-plant mutualism

Elizabeth G. Pringle
In horizontally transmitted mutualisms, mutualists disperse separately and reassemble in each generation with partners genetically unrelated to those in the previous generation. Because of this, there should be no selection on either partner to enhance the other's reproductive output directly. In symbiotic ant–plant mutualisms, myrmecophytic plants host defensive ant colonies, and ants defend the plants from herbivores. Plants and ants disperse separately, and, although ant defence can indirectly increase plant reproduction by reducing folivory, it...

Data from: Cross-scale interactions and the distribution-abundance relationship

Earl E. Werner, Christopher Davis, David K. Skelly, Rick A. Relyea, Michael F. Benard, Shannon J. McCauley & Christopher J. Davis
Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was positively related to number of ponds occupied by species; employing the fraction of...

Data from: Some limitations of public sequence data for phylogenetic inference (in plants)

Cody E. Hinchliff & Stephen Andrew Smith
The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data–mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera—an estimated 80% of extant plant diversity—to illustrate the potential...

Data from: Evolution of antipredator behavior in an island lizard species, Podarcis erhardii (Reptilia: Lacertidae): the sum of all fears?

Kinsey M. Brock, Peter A. Bednekoff, Panayiotis Pafilis & Johannes Foufopoulos
Organisms generally have many defenses against predation yet may lack effective defenses if from populations without predators. Evolutionary theory predicts that ‘costly’ antipredator behaviors will be selected against when predation risk diminishes. We examined antipredator behaviors in Aegean wall lizards, Podarcis erhardii, across an archipelago of land-bridge islands that vary in predator diversity and period of isolation. We examined two defenses, flight initiation distance and tail autotomy. Flight initiation distance generally decreased with declining predator...

Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Benjamin Roche, John M. Drake, Justin Brown, David E. Stallknecht, Trevor Bedford & Pejman Rohani
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker...

Data from: Do polycultures promote win-wins or tradeoffs in agricultural ecosystem services? A meta-analysis

Aaron L. Iverson, Linda E. Marín, Katherine K. Ennis, David J. Gonthier, Benjamin T. Connor-Barrie, Jane L. Remfert, Bradley J. Cardinale & Ivette Perfecto
1. Agriculture comprises the largest global land use, makes it a leading cause of habitat loss. It is therefore critical to identify how to best construct agricultural systems that can simultaneously provide food and other ecosystem services. This challenge requires that we determine how to maximize win-win relationships and minimize trade-offs between services. 2. Through meta-analysis, we tested whether within-field crop diversification (polyculture) can lead to win-win relationships between two ecosystem services: yield of a...

Data from: The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio

Na Wei, Jordan B. Bemmels & Christopher W. Dick
The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule real-time DNA sequencing (Pacific Biosciences, or PacBio) remain viable alternatives. We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS). We then...

Data from: Constructing predictive models of human running

Horst-Moritz Maus, Shai Revzen, John Guckenheimer, Christian Ludwig, Johann Reger & Andre Seyfarth
Running is an essential mode of human locomotion, during which ballistic aerial phases alternate with phases when a single foot contacts the ground. The spring-loaded inverted pendulum (SLIP) provides a starting point for modelling running, and generates ground reaction forces that resemble those of the centre of mass (CoM) of a human runner. Here, we show that while SLIP reproduces within-step kinematics of the CoM in three dimensions, it fails to reproduce stability and predict...

Data from: Understanding the role of physician attire on patient perceptions: a systematic review of the literature— targeting attire to improve likelihood of rapport (TAILOR) investigators

Christopher Michael Petrilli, Megan Mack, Jennifer Janowitz Petrilli, Andy Hickner, Sanjay Saint & Vineet Chopra
Objectives: Despite a growing body of literature, uncertainty regarding the influence of physician dress on patients’ perceptions exists. Therefore, we performed a systematic review to examine the influence of physician attire on patient perceptions including trust, satisfaction and confidence. Setting, participants, interventions and outcomes: We searched MEDLINE, Embase, Biosis Previews and Conference Papers Index. Studies that: (1) involved participants ≥18 years of age; (2) evaluated physician attire; and (3) reported patient perceptions related to attire...

Data from: \"De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Wolfgang Arthofer, Francesco Cicconardi, Nicola Palmieri, Viola Nolte, Christian Schlötterer, Birgit C. Schlick-Steiner, Florian M. Steiner, Marcelo Vallinoto, David A. Weese, B. L. Banbury, R. B. Harris, David S. Kang, Cheolho Sim, Thomas F. Duda, A. D. Leaché, Miguel Carneiro, Coralie Nourisson & Fernando Sequeira
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo...

Data from: Host species composition influences infection severity among amphibians in the absence of spillover transmission

Barbara A. Han, Jacob L. Kerby, Catherine L. Searle, Andrew Storfer, Andy R. Blaustein & Andrew R. Blaustein
Wildlife epidemiological outcomes can depend strongly on the composition of an ecological community, particularly when multiple host species are affected by the same pathogen. However, the relationship between host species richness and disease risk can vary with community context and with the degree of spillover transmission that occurs among co-occurring host species. We examined the degree to which host species composition influences infection by Batrachochytrium dendrobatidis (Bd), a widespread fungal pathogen associated with amphibian population...

Data from: The costs and benefits of tolerance to competition in Ipomoea purpurea, the common morning glory

Lindsay Chaney & Regina S. Baucom
Tolerance to competition has been hypothesized to reduce the negative impact of plant-plant competition on fitness. Although competitive interactions are a strong selective force, an analysis of net selection on tolerance to competition is absent in the literature. Using fifty-five full/half-sibling families from 18 maternal lines in the crop weed Ipomoea purpurea we measured fitness and putative tolerance traits when grown with and without competition in an agricultural field. We tested for the presence of...

Data from: Effects of feral cats on the evolution of anti-predator behaviours in island reptiles: insights from an ancient introduction

Binbin Li, Anat Belasen, Panayiotis Pafilis, Peter Bednekoff & Johannes Foufopoulos
Exotic predators have been the driving force behind the extinction of many island endemic species. We examined impacts of feral cats (Felis catus) on the abundance and anti-predator behaviors of Aegean wall lizards (Podarcis erhardii) in the Cyclades (Greece), where cats were introduced thousands of years ago. We compared populations with high and low cat density on Naxos and populations on surrounding islets with no cats. Results show that cats have strong negative effects on...

Data from: Trans-generational parasite protection associated with paternal diet

Eleanore D. Sternberg, Jacobus C. De Roode & Mark D. Hunter
Multiple generations of hosts are often exposed to the same pathogens, favoring the evolution of trans-generational defenses. Because females have more opportunities to transfer protective molecules to offspring, many studies have focused on maternally derived protection. However, males of many species can transfer compounds along with sperm, including chemicals that could provide protection. Here, we assess maternally and paternally derived protection in a monarch butterfly-protozoan parasite system where parasite resistance is heavily influenced by secondary...

Data from: Biodiversity conservation in agriculture requires a multi-scale approach

David J. Gonthier, Katherine K. Ennis, Serge Farinas, Hsun-Yi Hsieh, Aaron L. Iverson, Péter Batáry, Jörgen Rudolphi, Teja Tscharntke, Bradley J. Cardinale, Ivette Perfecto, H.-Y. Hsieh & P. Batary
Biodiversity loss—one of the most prominent forms of modern environmental change—has been heavily driven by terrestrial habitat loss and, in particular, the spread and intensification of agriculture. Expanding agricultural land-use has led to the search for strong conservation strategies, with some suggesting that biodiversity conservation in agriculture is best maximized by reducing local management intensity, such as fertilizer and pesticide application. Others highlight the importance of landscape-level approaches that incorporate natural or semi-natural areas in...

Data from: Microhabitat differences impact phylogeographic concordance of co-distributed species: genomic evidence in montane sedges (Carex L.) from the Rocky Mountains

Rob Massatti & L. Lacey Knowles
By selecting co-distributed, closely related montane sedges from the Rocky Mountains that are similar in virtually all respects but one – their microhabitat affinities – we test predictions about how patterns of genetic variation are expected to differ between Carex nova, an inhabitant of wetlands, and Carex chalciolepis, an inhabitant of drier meadows, slopes, and ridges. Although contemporary populations of the taxa are similarly isolated, the distribution of glacial moraines suggests thattheirpast population connectedness would...

Data from: \"Identification and assessment of single nucleotide polymorphisms (SNPs) between Culex complex mosquitoes.\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

David S. Kang & Cheolho Sim
Culex pipiens complex mosquitoes are important vectors for many human pathogens including West Nile encephalitis, Rift Valley fever and Lymphatic filariasis. In this study we characterized a set of SNP markers between two biotypes of the Culex pipiens complex, Culex pipiens form molestus and Culex pipiens form pipiens, for use in a high-resolution genetic mapping and population genetics. DNA pooled from 10 specimens of each biotype were sequenced and analyzed for variation in 28 genes....

Data from: Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline

Daniel Zinder, Trevor Bedford, Edward B. Baskerville, Robert J. Woods, Manojit Roy & Mercedes Pascual
Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics has not yet been established. In this study, we incorporate time-varying migration rates in a Bayesian MCMC framework. We focus on migration within China and between China and North-America as case studies, then expand the analysis to global communities. Results: Incorporating seasonally varying migration rates...

Data from: \"Transcriptomic resources for three populations of Conus miliaris (Mollusca: Conidae) from Easter Island, American Samoa and Guam\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

David A. Weese & Thomas F. Duda
Species interactions represent fundamental ecological processes that can have significant impacts on the evolutionary trajectories of species. However, the contribution of predator-prey interactions to genetic and phenotypic divergence within and between species remains largely unknown. In this context, predatory marine snails of the genus Conus exhibit considerable variation in venom composition, a phenomenon that may be due to the evolution of conotoxins in response to predator-prey interactions. It has been hypothesized that geographic differences in...

Data from: Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns

Evan P. Economo, Pavel Klimov, Eli M. Sarnat, Benoit Guénard, Michael D. Weiser, Beatrice Lecroq, L. Lacey Knowles & B. Guenard
Adaptive radiations are of particular interest owing to what they reveal about the ecological and evolutionary regulation of biodiversity. This applies to localized island radiations such as Darwin's finches, and also to rapid radiations occurring on a global scale. Here we analyse the macroevolution and macroecology of Pheidole, a famously hyperdiverse and ecologically dominant ant genus. We generate and analyse four novel datasets: (i) a robust global phylogeny including 285 Pheidole species, (ii) a global...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • University of Porto
  • Baylor University
  • Fred Hutchinson Cancer Research Center
  • University of Washington
  • Duke University
  • University of Georgia
  • Smithsonian Institution
  • Eastern Michigan University
  • Yale University