26 Works

Data from: Substantial differences in bias between single-digest and double-digest RAD-seq libraries: a case study

Sarah P. Flanagan & Adam G. Jones
The trade‐offs of using single‐digest vs. double‐digest restriction site‐associated DNA sequencing (RAD‐seq) protocols have been widely discussed. However, no direct empirical comparisons of the two methods have been conducted. Here, we sampled a single population of Gulf pipefish (Syngnathus scovelli) and genotyped 444 individuals using RAD‐seq. Sixty individuals were subjected to single‐digest RAD‐seq (sdRAD‐seq), and the remaining 384 individuals were genotyped using a double‐digest RAD‐seq (ddRAD‐seq) protocol. We analysed the resulting Illumina sequencing data and...

Data from: Thermal exposure of adult Chinook salmon and steelhead: diverse behavioral strategies in a large and warming river system

Matthew L. Keefer, Tami S. Clabough, Michael A. Jepson, Eric L. Johnson, Christopher A. Peery & Christopher C. Caudill
Rising river temperatures in western North America have increased the energetic costs of migration and the risk of premature mortality in many Pacific salmon (Oncorhynchus spp.) populations. Predicting and managing risks for these populations requires data on acute and cumulative thermal exposure, the spatio-temporal distribution of adverse conditions, and the potentially mitigating effects of cool-water refuges. In this study, we paired radiotelemetry with archival temperature loggers to construct continuous, spatially-explicit thermal histories for 212 adult...

Data from: Estimating correlated rates of trait evolution with uncertainty

Daniel S. Caetano & Luke J. Harmon
Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped...

Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Paul D. Blischak, Maribeth Latvis, Diego F. Morales-Briones, Jens C. Johnson, Verónica S. Di Stilio, Andrea D. Wolfe & David C. Tank
Premise of the Study: Targeted enrichment strategies for phylogenomic inference are a time‐ and cost‐efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired‐end Illumina data from double‐barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling...

Data from: Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana

Sean M. Murphy, Jennifer R. Adams, John J. Cox & Lisette P. Waits
Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, USA, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as functionally extinct in the wild, red wolf mitochondrial or nuclear DNA ancestry persists in ~55% of contemporary wild canids sampled in southwestern Louisiana. Surprisingly, one...

Data from: Quantitative trait loci for cold tolerance in chickpea

Clarice J. Coyne, Deus Mugabe, Julia Piaskowski, Ping Zheng, Yu Ma, Erik Landry, Rebecca McGee, Dorrie Main, George Vandemark, Hongbin Zhang & Shahal Abbo
Fall-sown chickpea (Cicer arietinum L.) yields are often double those of spring-sown chickpea in regions with Mediterranean climates that have mild winters. However, winter kill can limit the productivity of fall-sown chickpea. Developing cold-tolerant chickpea would allow the expansion of the current geographic range where chickpea is grown and also improve productivity. The objective of this study was to identify the quantitative trait loci (QTL) associated with cold tolerance in chickpea. An interspecific recombinant inbred...

Data from: Alaskan brown bears (Ursus arctos) aggregate and display fidelity to foraging neighborhoods while preying on Pacific salmon along small streams

Aaron J. Wirsing, Thomas P. Quinn, Curry J. Cunningham, Jennifer R. Adams, Apryle D. Craig & Lisette P. Waits
The interaction between brown bears (Ursus arctos) and Pacific salmon (Oncorhynchus spp.) is important to the population dynamics of both species and a celebrated example of consumer-mediated nutrient transport. Yet, much of the site-specific information we have about the bears in this relationship comes from observations at a few highly visible but unrepresentative locations and a small number of radio-telemetry studies. Consequently, our understanding of brown bear abundance and behavior at more cryptic locations where...

Data from: Spatiotemporal heterogeneity in prey abundance and vulnerability shapes the foraging tactics of an omnivore

Nathaniel D. Rayl, Guillaume Bastille-Rousseau, John F. Organ, Matthew A. Mumma, Shane P. Mahoney, Colleen E. Soulliere, Keith P. Lewis, Robert D. Otto, Dennis L. Murray, Lisette P. Waits & Todd K. Fuller
1. Prey abundance and prey vulnerability vary across space and time, but we know little about how they mediate predator-prey interactions and predator foraging tactics. To evaluate the interplay between prey abundance, prey vulnerability, and predator space use, we examined patterns of black bear (Ursus americanus) predation of caribou (Rangifer tarandus) neonates in Newfoundland, Canada using data from 317 collared individuals (9 bears, 34 adult female caribou, 274 caribou calves). 2. During the caribou calving...

Data from: Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Diego F. Morales-Briones, Aaron Liston & David C. Tank
Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources...

Data from: Soil is the main predictor of secondary rain forest estimated aboveground biomass across a neotropical landscape

Ricardo J. Santiago-García, Bryan Finegan & Nilsa A. Bosque-Pérez.
We studied the relative effects of landscape configuration, environmental variables, forest age and spatial variables on estimated aboveground biomass (AGB) in Costa Rican secondary rain forests patches. We measured trees > 5 cm dbh in 24, 0.25 ha plots and estimated AGB for trees 5-24.9 cm dbh and for trees > 25 cm dbh using two allometric equations based on multispecies models using tree dbh and wood specific gravity. AGB averaged 87.3 Mg/ha for the...

Data from: Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Robert C. Lonsinger, Jennifer R. Adams & Lisette P. Waits
Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long-term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (Ne). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We...

Data from: Incongruence in molecular species delimitation schemes: what to do when adding more data is difficult.

Sarah J. Jacobs, Casey Kristofferson, Simon Uribe-Convers, Maribeth Latvis & David C. Tank
Using multiple, independent approaches in molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential byproduct of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence. We advocate that incongruence within a line of evidence should be...

Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Mark Eric Benbow, Philip S. Barton, Michael D. Ulyshen, James C. Beasley, Travis L. DeVault, Michael S. Strickland, Jeffery K. Tomberlin, Heather R. Jordan & Jennifer L. Pechal
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has...

Data from: Accounting for disturbance history in models: using remote sensing to constrain carbon and nitrogen pool spin‐up

Erin J. Hanan, Christina Tague, Janet Choate, Mingliang Liu, Crystal Kolden & Jennifer Adam
Disturbances such as wildfire, insect outbreaks, and forest clearing, play an important role in regulating carbon, nitrogen, and hydrologic fluxes in terrestrial watersheds. Evaluating how watersheds respond to disturbance requires understanding mechanisms that interact over multiple spatial and temporal scales. Simulation modeling is a powerful tool for bridging these scales; however, model projections are limited by uncertainties in the initial state of plant carbon and nitrogen stores. Watershed models typically use one of two methods...

Data from: Microclimatic buffering in forests of the future: the role of local water balance

Kimberley Davis, Solomon Z. Dobrowski, Zachary A. Holden, Philip E. Higuera, John T. Abatzoglou & Kimberley T. Davis
Forest canopies buffer climate extremes and promote microclimates that may function as refugia for understory species under changing climate. However, the biophysical conditions that promote and maintain microclimatic buffering and its stability through time are largely unresolved. We posited that forest microclimatic buffering is sensitive to local water balance and canopy cover, and we measured this effect during the growing season across a climate gradient in forests of the northwestern United States (US). We found...

Data from: Opening the file drawer: Unexpected insights from a chytrid infection experiment

Allison Q. Byrne, Thomas J. Poorten, Jamie Voyles, Craig K.R. Willis, Erica Bree Rosenblum & Craig K. R. Willis
Infection experiments are critical for understanding wildlife disease dynamics. Although infection experiments are typically designed to reduce complexity, disease outcomes still result from complex interactions between host, pathogen, and environmental factors. Cryptic variation across factors can lead to decreased repeatability of infection experiments within and between research groups and hinder research progress. Furthermore, studies with unexpected results are often relegated to the “file drawer” and potential insights gained from these experimental outcomes are lost. Here,...

Data from: Functional capacity of kangaroo rat hindlimbs: adaptations for locomotor performance

Jeffery W. Rankin, Kelsey M. Doney & Craig P. McGowan
Many cursorial and large hopping species are extremely efficient locomotors with various morphological adaptations believed to reduce mechanical demand and improve movement efficiency, including elongated distal limb segments. However, despite having elongated limbs, small hoppers such as desert kangaroo rats (Dipodomys deserti) are less efficient locomotors than their larger counterparts, which may be in part due to avoiding predators through explosive jumping movements. Despite potentially conflicting mechanical demands between the two movements, kangaroo rats are...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations

Elizabeth Heppenheimer, Kristin E. Brzeski, Joseph W. Hinton, Brent R. Patterson, Linda Y. Rutledge, Alexandra L. DeCandia, Tyler Wheeldon, Steven R. Fain, Paul A. Hohenlohe, Roland Kays, Bradley N. White, Michael J. Chamberlain & Bridgett M. VonHoldt
Range expansion is a widespread biological process, with well described theoretical expectations for the genomic outcomes accompanying the colonization of novel ranges. However, comparatively few empirical studies address the genome-wide consequences associated with the range expansion process, particularly in recent or on-going expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been...

Data from: Golden orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism

Matjaz Kuntner, Chris Hamilton, Ren-Chung Cheng, Matjaz Gregoric, Nik Lupse, Tjasa Lokovsek, Emily Moriarty Lemmon, Alan R. Lemmon, Ingi Agnarsson, Jonathan A. Coddington, Jason Bond, Chris A Hamilton & Jason E Bond
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope’s Rule (phyletic size increase), Rensch’s Rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length ≥ 2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be...

Data from: Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

Zhongqi Chen, Anthony P. Farrell, Amanda Matala, Nicholas Hoffman & Shawn R. Narum
Temperature is a master environmental factor that limits the geographical distribution of species, especially in ectotherms. To address challenges in biodiversity conservation under ongoing climate change, it is essential to characterize relevant functional limitations and adaptive genomic content at population and species levels. Here, we present evidence for adaptive divergence in cardiac function and genomic regions in redband trout (Oncorhynchus mykiss gairdneri) populations from desert and montane streams. Cardiac phenotypes of individual fish were measured...

Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing

Julian R. Dupuis, Forest T. Bremer, Angela Kauwe, Michael San Jose, Luc Leblanc, Daniel Rubinoff & Scott M. Geib
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive...

Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

Charlotte R. Milling, Janet L. Rachlow, Peter J. Olsoy, Mark A. Chappell, Timothy R. Johnson, Jennifer S. Forbey, Lisa A. Shipley & Daniel H. Thornton
1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a...

Data from: Rethinking phylogenetic comparative methods

Josef C. Uyeda, Rosana Zenil-Ferguson & Matthew W. Pennell
As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about...

Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

Michael San Jose, Camiel Doorenweerd, Luc Leblanc, Norman Barr, Scott Geib & Daniel Rubinoff
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Idaho
  • United States Department of Agriculture
  • The Ohio State University
  • Texas A&M University
  • University of Massachusetts Amherst
  • University of Washington
  • University of Georgia
  • University of Vermont
  • South Dakota State University
  • University of Minnesota