19 Works

Data from: Individual variation in cone photoreceptor density in house sparrows: implications for between-individual differences in visual resolution and chromatic contrast

Amanda L. Ensminger & Esteban Fernández-Juricic
Between-individual variation has been documented in a wide variety of taxa, especially for behavioral characteristics; however, intra-population variation in sensory systems has not received similar attention in wild animals. We measured a key trait of the visual system, the density of retinal cone photoreceptors, in a wild population of house sparrows (Passer domesticus). We tested whether individuals differed from each other in cone densities given within-individual variation across the retina and across eyes. We further...

Data from: Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq

Nicholas J. Marra, Andrea Romero & J. Andrew DeWoody
One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in Heteromyid rodents. We sequenced kidney tissue...

Data from: A novel system for bi-ocular eye-tracking in vertebrates with laterally placed eyes

Luke P. Tyrrell, Shannon R. Butler, Jessica L. Yorzinski & Esteban Fernández-Juricic
1. Animals use vision to gather information about their environment and then use that information to make behavioural decisions that affect fitness. They will often move their heads or eyes to inspect areas of interest with their centres of acute vision, such as foveae, to gather high resolution information about potential mates, predation risks, or other aspects of the environment. Few studies to date have been able to accurately determine where laterally eyed animals direct...

Data from: A tapetal ablation transgene induces stable male-sterility and slows field growth in Populus

Estefania Elorriaga, Richard Meilan, Cathleen Ma, Jeffrey S. Skinner, Elizabeth Etherington, Amy Brunner & Steven H. Strauss
The field performance of genetic containment technologies–considered important for certain uses of transgenic trees in forestry–is poorly known. We tested the efficiency of a barnase gene driven by the TA29 tapetum-dominant promoter for influencing growth rate and inducing male sterility in a field trial of transgenic hybrid poplar (Populus tremula × Populus tremuloides). When the growth of 18 transgenic insertion events with the sterility transgene were compared to non-transgenic controls after two growing seasons, they...

Data from: Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss

Matthew C. Hale, Frank P. Thrower, Ewann A. Berntson, Michael R. Miller & Krista M. Nichols
Next generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. Using the two approaches in parallel is an especially attractive approach in non-models organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a non-model fish species, rainbow...

Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)

Jacqueline M. Doyle, Gregor Siegmund, Joseph D. Ruhl, Soo Hyung Eo, Matthew C. Hale, Nicholas J. Marra, Peter M. Waser & J. Andrew DeWoody
Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence...

Data from: Natural enemy ecology: comparing the effects of predation risk, infection risk and disease on host behavior

Daniel L. Preston, Clara E. Boland, Jason T. Hoverman & Pieter T. J. Johnson
1. Growing interest in unifying the field of natural enemy ecology has revealed similarities between predation and parasitism. In parallel with predation, parasite infection – and even the threat of infection – can alter host traits and indirectly affect community interactions. Nonetheless, few studies have considered multiple mechanisms of natural enemy-induced behavioural alteration in parallel (e.g. effects before and after enemy contact) or the factors that drive variation in behavioural responses. 2. We first evaluated...

Data from: Harmonic calls and indifferent females: no preference for human consonance in an anuran

Karin L. Akre, Ximena Bernal, A. Stanley Rand & Michael J. Ryan
The human music faculty might have evolved from rudimentary components that occur in non-human animals. The evolutionary history of these rudimentary perceptual features is not well understood and rarely extends beyond a consideration of vertebrates that possess a cochlea. One such antecedent is a preferential response to what humans perceive as consonant harmonic sounds, which are common in many animal vocal repertoires. We tested the phonotactic response of female túngara frogs (Physalaemus pustulosus) to variations...

Data from: Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success

Timothy J. Pusack, Mark R. Christie, Darren W. Johnson, Christopher D. Stallings & Mark A. Hixon
Many marine organisms can be transported hundreds of kilometers during their pelagic larval stage, yet little is known about spatial and temporal patterns of larval dispersal. Although traditional population-genetic tools can be applied to infer movement of larvae on an evolutionary time scale, large effective population sizes and high rates of gene-flow present serious challenges to documenting dispersal patterns over shorter, ecologically-relevant, time scales. Here, we address these challenges by combining direct parentage analysis and...

Data from: Speed kills: ineffective avian escape responses to oncoming vehicles

Travis L. DeVault, Bradley F. Blackwell, Thomas W. Seamans, Steven L. Lima, Esteban Fernández-Juricic & E. Fernandez-Juricic
Animal–vehicle collisions cause high levels of vertebrate mortality worldwide, and what goes wrong when animals fail to escape and ultimately collide with vehicles is not well understood. We investigated alert and escape behaviours of captive brown-headed cowbirds (Molothrus ater) in response to virtual vehicle approaches of different sizes and at speeds ranging from 60 to 360 km h−1. Alert and flight initiation distances remained similar across vehicle speeds, and accordingly, alert and flight initiation times...

Data from: Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss)

Matthew C. Hale, John A. Colletti, Scott A. Gahr, Julie Scardina, Frank P. Thrower, Matthew Harmon, Megan Carter, Ruth B. Phillips, Gary H. Thorgaard, Caird E. Rexroad & Krista M. Nichols
Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a Quantitative Trait Locus (QTL) for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression,...

Data from: The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations

Janna R. Willoughby, Nadia B. Fernandez, Maureen C. Lamb, Jamie A. Ivy, Robert C. Lacy & J. Andrew DeWoody
The goal of captive breeding programs is often to maintain genetic diversity until reintroductions can occur. However, due in part to changes that occur in captive populations, approximately one-third of reintroductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analyzed six populations of white-footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK), and selection for docility (DOC). We...

Data from: A proteomic strategy for global analysis of plant protein complexes

Uma K. Aryal, Yi Xiong, Zachary McBride, Daisuke Kihara, Jun Xie, Mark C. Hall & Daniel B. Szymanski
Global analyses of protein complex assembly, composition, and location are needed to fully understand how cells coordinate diverse metabolic, mechanical, and developmental activities. The most common methods for proteome-wide analysis of protein complexes rely on affinity purification-mass spectrometry or yeast two-hybrid approaches. These methods are time consuming and are not suitable for many plant species that are refractory to transformation or genome-wide cloning of open reading frames. Here, we describe the proof of concept for...

Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Nicholas J. Marra & J. Andrew DeWoody
Background: When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis...

Data from: The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos)

Jacqueline M. Doyle, Todd E. Katzner, Peter H. Bloom, Yanzhu Ji, Bhagya K. Wijayawardena & J. Andrew DeWoody
Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data...

Data from: Mechanistic insights into landscape genetic structure of two tropical amphibians using field-derived resistance surfaces

A. Justin Nowakowski, J. Andrew DeWoody, Matthew E. Fagan, Janna R. Willoughby & Maureen A. Donnelly
Conversion of forests to agriculture often fragments distributions of forest species and can disrupt gene flow. We examined effects of prevalent land uses on genetic connectivity of two amphibian species in northeastern Costa Rica. We incorporated data from field surveys and experiments to develop resistance surfaces that represent local mechanisms hypothesized to modify dispersal success of amphibians, such as habitat-specific predation and desiccation risk. Because time lags can exist between forest conversion and genetic responses,...

Data from: Below-ground causes and consequences of woodland shrub invasions: a novel paired-point framework reveals new insights

, Liam Heneghan, Dev Rijal, David H. Wise & Basil V. Iannone
1. Confirming the impacts of invasive plants is essential for prioritizing management efforts, but is challenging, especially if impacts occur below ground and over long periods as hypothesized for woodland shrub invasions. 2. For this reason, we developed a novel “paired-point” framework capable of detecting the below-ground impacts of slow-growing invasive plants from short-term datasets in an investigation into the below-ground consequences of European buckthorn Rhamnus cathartica L. (hereafter buckthorn) invasions into Chicago-area woodlands. We...

Data from: Song structure, not high-frequency song content, determines high-frequency auditory sensitivity in nine species of New World sparrows (Passeriformes: Emberizidae)

Alejandro Velez, Megan D. Gall, Jianing Fu & Jeffrey R. Lucas
1. The evolution of vocal signals can be constrained by a host of factors including habitat effects on sound propagation, morphology of sound-producing structures, and phylogenetic relationships among species. Here, we asked whether auditory sensitivity over a broad range of frequencies correlates with the spectral content of conspecific vocalizations, or whether it is constrained by the overall structure of vocalizations, habitat effects on sound propagation, or relatedness among species. 2. We studied nine New World...

Data from: Life-stage differences in spatial genetic structure in an irruptive forest insect: implications for dispersal and spatial synchrony

Patrick M. A. James, Barry Cooke, Bryan Brunet, Lisa Lumley, Felix Sperling, Marie-Josée Fortin, Vanessa S. Quinn, Brian R. Sturtevant, Bryan M. T. Brunet, Lisa M. Lumley & Felix A. H. Sperling
Dispersal determines the flux of individuals, energy, and information and is therefore a key determinant of ecological and evolutionary dynamics. Yet, it remains difficult to quantify its importance relative to other factors. This is particularly true in cyclic populations in which demography, drift, and dispersal contribute to spatio-temporal variability in genetic structure. Improved understanding of how dispersal influences spatial genetic structure is needed to disentangle the multiple processes that give rise to spatial synchrony in...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Purdue University
  • Oregon State University
  • University of Kansas
  • Indiana State University
  • Duke University
  • West Virginia University
  • University of Alberta
  • University of Montreal
  • Goddard Space Flight Center
  • Northern Research Station