23 Works

Data from: Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output

Konstans Wells, Rodrigo K. Hamede, Douglas H. Kerlin, Andrew Storfer, Paul A. Hohenlohe, Menna E. Jones & Hamish I. McCallum
Emerging infectious diseases rarely affect all members of a population equally and determining how individuals’ susceptibility to infection is related to other components of their fitness is critical to understanding disease impacts at a population level and for predicting evolutionary trajectories. We introduce a novel state-space model framework to investigate survival and fecundity of Tasmanian devils (Sarcophilus harrisii) affected by a transmissible cancer, devil facial tumour disease. We show that those devils that become host...

Data from: Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification

Katherine A. Cleary, Lisette P. Waits & Bryan Finegan
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled...

Data from: Fire-regime variability impacts forest carbon dynamics for centuries to millennia

Tara W. Hudiburg, Philip E. Higuera & Jeffrey A. Hicke
Wildfire is a dominant disturbance agent in forest ecosystems, shaping important biogeochemical processes including net carbon (C) balance. Long-term monitoring and chronosequence studies highlight a resilience of biogeochemical properties to large, stand-replacing, high-severity fire events. In contrast, the consequences of repeated fires or temporal variability in a fire regime (e.g., the characteristic timing or severity of fire) are largely unknown, yet theory suggests that such variability could strongly influence forest C trajectories (i.e., future states...

Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease

Ailene MacPherson, Sarah P. Otto & Scott L. Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations. Reanalyzing previously...

Data from: Genetic and population monitoring of two small black bear (Ursus americanus) populations in Alabama, within a regional context.

John P. Draper, Lisette P. Waits, Jennifer R. Adams, Christopher L. Seals & Todd D. Steury
One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United...

Data from: Seasonal variation in behavioral thermoregulation and predator avoidance in a small mammal

Charlotte R. Milling, Janet L. Rachlow, Timothy R. Johnson, Jennifer S. Forbey & Lisa A. Shipley
Understanding behavioral responses of animals to the thermal environment is of increasing importance under changing climate regimes. Thermoregulatory behaviors, such as exploitation of thermal refugia or temporal partitioning of activity, can buffer organisms against hot and cold thermal extremes but may conflict with other life history needs. Our objective was to evaluate strategies for behavioral thermoregulation by a small-bodied endotherm to test hypotheses about tradeoffs between thermal and security needs across seasons. We quantified the...

Data from: Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci

Maribeth Latvis, Sarah J. Jacobs, Sebastian M. E. Mortimer, Melissa Richards, Paul D. Blischak, Sarah Mathews & David C. Tank
Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to...

Data from: Nest predation risk explains variation in avian clutch size

Kristen G. Dillon & Courtney J. Conway
Questions about the ecological drivers of, and mechanistic constraints on, productivity have driven research on life history evolution for decades. Resource availability and offspring mortality are considered among the two most important influences on the number of offspring per reproductive attempt. We used a factorial experimental design to manipulate food abundance and perceived offspring predation risk in a wild avian population (red-faced warblers; Cardellina rubrifrons) to identify the mechanistic cause of variation in avian clutch...

Data from: A general model for estimating macroevolutionary landscapes

Florian C. Boucher, Vincent Démery, Elena Conti, Luke J. Harmon & Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios...

Data from: Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

Megan Ruffley, Megan L. Smith, Anahi Espindola, Bryan C. Carstens, Jack Sullivan & David C. Tank
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches –allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in...

Data from: Demographic model selection using random forests and the site frequency spectrum

Megan L. Smith, Megan Ruffley, Anahí Espindola, David C. Tank, Jack Sullivan & Bryan C. Carstens
Phylogeographic data sets have grown from tens to thousands of loci in recent years, but extant statistical methods do not take full advantage of these large data sets. For example, approximate Bayesian computation (ABC) is a commonly used method for the explicit comparison of alternate demographic histories, but it is limited by the “curse of dimensionality” and issues related to the simulation and summarization of data when applied to next-generation sequencing (NGS) data sets. We...

Data from: Effects of breeder turnover and harvest on group composition and recruitment in a social carnivore

David E. Ausband, Michael S. Mitchell & Lisette P. Waits
1. Breeder turnover can influence population growth in social carnivores through changes to group size, composition, and recruitment. 2. Studies that possess detailed group composition data that can provide insights about the effects of breeder turnover on groups have generally been conducted on species that are not subject to recurrent annual human harvest. We wanted to know how breeder turnover affects group composition and how harvest, in turn, affects breeder turnover in cooperatively breeding gray...

Data from: Unmanned aerial systems measure structural habitat features for wildlife across multiple scales

Peter J. Olsoy, Lisa A. Shipley, Janet L. Rachlow, Jennifer S. Forbey, Nancy F. Glenn, Matthew A. Burgess & Daniel H. Thornton
1.Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine-scale resolutions across broad-scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field-based habitat quality measurements and lower spatial resolution, higher spatial extent satellite-based remote sensing. Our goal in this study was to evaluate the potential for UAS structure from motion...

Data from: Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America

Shawn R. Narum, Pablo Gallardo, Cristian Correa, Amanda Matala, Daniel Hasselman, Ben J.G. Sutherland, Louis Bernatchez & Ben J. G. Sutherland
Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in...

Data from: Potential trajectories of old-growth Neotropical forest functional composition under climate change

Adina Chain-Guadarrama, Pablo Imbach, Sergio Vilchez-Mendoza, Lee A. Vierling & Bryan Finegan
Quantifying relationships between plant functional traits and abiotic gradients is valuable for evaluating potential responses of forest communities to climate change. However, the trajectories of change expected to occur in tropical forest functional characteristics as a function of future climate variation are largely unknown. We modeled community level trait values of Costa Rican rain forests as a function of current and future climate, and quantified potential changes in functional composition. We calculated per-plot community weighted...

Data from: Persistence of antibiotic resistance plasmids in bacterial biofilms

Benjamin J. Ridenhour, Genevieve A. Metzger, Michael France, Karol Gliniewicz, Jack Millstein, Larry J. Forney & Eva M. Top
The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multi-drug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better understand the evolution of plasmid persistence in these environments. Here we compared the evolution of plasmid persistence in the pathogen Acinetobacter baumannii...

Data from: RAD sequencing and genomic simulations resolve hybrid origins within North American Canis

Linda Y. Rutledge, S. Devillard, J. Q. Boone, P. A. Hohenlohe & B. N. White
Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes,...

Data from: Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K. Thomason, Houra Merrikh, Jose M. Ponciano & Eva M. Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms, and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multi-drug resistance plasmid RP4, determined plasmid persistence and cost using a joint...

Data from: Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life

Hannah E. Marx, Cédric Dentant, Julien Renaud, Romain Delunel, David C. Tank & Sébastien Lavergne
Aim: Plants occurring on high-alpine summits are generally expected to persist due to adaptations to extreme selective forces caused by the harshest climates where angiosperm life is known to thrive. We assessed the relative effects of this strong environmental filter and of other historical and stochastic factors driving plant community structure in very high-alpine conditions. Location: European Alps, Écrins National Park, France. Methods: Using species occurrence data collected from floristic surveys on 15 summits (2,791–4,102...

Data from: Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

Travis Jay Hagey, Josef C. Uyeda, Kristen E. Crandell, Jorn A. Cheney, Kellar Autumn & Luke J. Harmon
Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics....

Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

James B. Pease, Joseph W. Brown, Joseph F. Walker, Cody E. Hinchliff & Stephen A. Smith
Premise of the Study—Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As datasets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. Methods— We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in...

Data from: Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep

Raina K. Plowright, Kezia R. Manlove, Thomas E. Besser, David J. Páez, Kimberly R. Andrews, Patrick E. Matthews, Lisette P. Waits, Peter J. Hudson & E. Frances Cassirer
Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected...

Data from: Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots

Rosana Zenil-Ferguson, José M. Ponciano & J. Gordon Burleigh
Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Idaho
  • Washington State University
  • The Ohio State University
  • University of Florida
  • University of Montana
  • Boise State University
  • Idaho Department of Fish and Game
  • Centro Agronomico Tropical De Investigacion Y Ensenanza Catie
  • University of Washington
  • Princeton University