18 Works

Data from: AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

Michael G. Sovic, Anthony C. Fries & H. Lisle Gibbs
An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to...

Data from: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae)

Ryan A. Folk, Jennifer R. Mandel & John V. Freudenstein
Premise of the study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based...

Data from: Irrational time allocation in decision-making

Bastiaan Oud, Ian M. Krajbich, Kevin Miller, Jin Cheong, Matthew Botvinick, Ernst Fehr, Jin Hyun Cheong & Ian Krajbich
Time is an extremely valuable resource but little is known about the efficiency of time allocation in decision making. Empirical evidence suggests that in many ecologically relevant situations, decision difficulty and the relative reward from making a correct choice, compared to an incorrect one, are inversely linked, implying that it is optimal to use relatively less time for difficult choice problems. This applies, in particular, to value-based choices, in which the relative reward from choosing...

Data from: Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations

Michael E. Fraker, Eric J. Anderson, Reed M. Brodnik, Lucia Carreon-Martinez, Kristen M. DeVanna, Brian J. Fryer, Daniel D. Heath, Julie M. Reichert & Stuart A. Ludsin
We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking). To illustrate and test our approach, we focus on western Lake Erie’s yellow perch (Perca flavescens) population during 2006–2007,...

Geological samples available for research from the PRR

Data from: Benefits of turbid river plume habitat for Lake Erie yellow perch (Perca flavescens) recruitment determined by juvenile to larval genotype assignment

Lucia B. Carreon-Martinez, Ryan P. Walter, Timothy B. Johnson, Stuart A. Ludsin & Daniel D. Heath
Nutrient-rich, turbid river plumes that are common to large lakes and coastal marine ecosystems have been hypothesized to benefit survival of fish during early life stages by increasing food availability and (or) reducing vulnerability to visual predators. However, evidence that river plumes truly benefit the recruitment process remains meager for both freshwater and marine fishes. Here, we use genotype assignment between juvenile and larval yellow perch (Perca flavescens) from western Lake Erie to estimate and...

Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

Michael Gruenstaeudl, Noah M. Reid, Gregory L. Wheeler & Bryan C. Carstens
Bayesian inference operates under the assumption that the empirical data are a good statistical fit to the analytical model, but this assumption can be challenging to evaluate. Here, we introduce a novel r package that utilizes posterior predictive simulation to evaluate the fit of the multispecies coalescent model used to estimate species trees. We conduct a simulation study to evaluate the consistency of different summary statistics in comparing posterior and posterior predictive distributions, the use...

Data from: Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Paul D. Blischak, Laura S. Kubatko & Andrea D. Wolfe
Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty–ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population...

Data from: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system

Jordan D. Satler, Amanda J. Zellmer & Bryan C. Carstens
Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here...

Data from: Early phylogeny of crinoids within the pelmatozoan clade

William I. Ausich, Thomas W. Kammer, Elizabeth C. Rhenberg & David F. Wright
Phylogenetic relationships among early crinoids are evaluated by maximizing parsimonious-informative characters that are unordered and unweighted. Primarily Tremadocian–Darriwilian (Early–Middle Ordovician) taxa are analysed. Stratigraphic congruence metrics support the best phylogenetic hypothesis derived using parsimony methods. This study confirms the traditionally recognized lineages of Palaeozoic crinoids and provides new information on the branching order of evolving lineages. Camerates are basal crinoids with progressively more tipward groups (from an Ordovician perspective) being protocrinoids, cladids (paraphyletic), hybocrinids and...

Data from: Reproductive sharing in relation to group and colony-level attributes in a cooperative breeding fish

Jennifer K. Hellmann, Isaac Y. Ligocki, Constance M. O'Connor, Adam R. Reddon, Kelly A. Garvy, Susan E. Marsh-Rollo, H. Lisle Gibbs, Sigal Balshine & Ian M. Hamilton
The degree to which group members share reproduction is dictated by both within-group (e.g. group size and composition) and between-group (e.g. density and position of neighbours) characteristics. While many studies have investigated reproductive patterns within social groups, few have simultaneously explored how within-group and between-group social structure influence these patterns. Here, we investigated how group size and composition, along with territory density and location within the colony, influenced parentage in 36 wild groups of a...

Data from: Size matters: individual variation in ectotherm growth and asymptotic size

Richard B. King, Kristin M. Stanford, Peter C. Jones & Kent Bekker
Body size, and, by extension, growth has impacts on physiology, survival, attainment of sexual maturity, fecundity, generation time, and population dynamics, especially in ectotherm animals that often exhibit extensive growth following attainment of sexual maturity. Frequently, growth is analyzed at the population level, providing useful population mean growth parameters but ignoring individual variation that is also of ecological and evolutionary significance. Our long-term study of Lake Erie Watersnakes, Nerodia sipedon insularum, provides data sufficient for...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: The metabolic cost of changing walking speeds is significant, implies lower optimal speeds for shorter distances, and increases daily energy estimates

Nidhi Seethapathi & Manoj Srinivasan
Humans do not generally walk at constant speed, except perhaps on a treadmill. Normal walking involves starting, stopping and changing speeds, in addition to roughly steady locomotion. Here, we measure the metabolic energy cost of walking when changing speed. Subjects (healthy adults) walked with oscillating speeds on a constant-speed treadmill, alternating between walking slower and faster than the treadmill belt, moving back and forth in the laboratory frame. The metabolic rate for oscillating-speed walking was...

Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification

Brandon T. Sinn, Lawrence M. Kelly & John V. Freudenstein
Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We...

Data from: Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression

Matthew A. Kost, Helen M. Alexander, D. Jason Emry & Kristin L. Mercer
Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early...

Data from: Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci

Ryan A. Folk & John V. Freudenstein
Premise of the study: The use of multiple genetic regions from the nuclear genome, including low-copy markers, has long been recognized as essential to robust phylogenetic construction, addressing gene tree incongruence, and allowing increased resolution to test current taxonomy and resolve basic hypotheses about character evolution, biogeography, and other organismal traits of interest to biologists. Heuchera, the largest genus of Saxifragaceae endemic to North America, has presented an unusually difficult case for systematists with limited...

Data from: The evolution of phylogeographic datasets

Ryan C. Garrick, Isabel A. S. Bonatelli, Chaz Hyseni, Ariadna Morales, Tara A. Pelletier, Manolo F. Perez, Edwin Rice, Jordan D. Satler, Rebecca E. Symula, Maria Tereza C. Thomé & Bryan C. Carstens
Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next-generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here,...

Registration Year

  • 2015

Resource Types

  • Dataset


  • The Ohio State University
  • University of Windsor
  • University of Kansas
  • Federal Institute of São Paulo
  • The Bronx Defenders
  • Sao Paulo State University
  • University of Hohenheim
  • Ghent University
  • Princeton University
  • Duke University