218 Works

Data from: Near-infrared spectroscopy aids ecological restoration by classifying variation of taxonomy and phenology of a native shrub

Brecken Robb, Peter Olsoy, Jessica Mitchell, T. Trevor Caughlin, Donna Delparte, Stephanie Galla, Marcella R. Fremgen-Tarantino, Jordan D. Nobler, Janet Rachlow, Lisa A. Shipley & Jennifer Sorensen Forbey

Compiled Idaho sagebrush chemistry and plant herbivore interaction data

Jennifer Sorensen Forbey, Peter Olsoy, Brecken Robb, Marcella R. Fremgen-Tarantino & Jordan D. Nobler

Data from: A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths

Xuankun Li, Chris Hamilton, Ryan Laurent, Liliana Ballesteros-Mejia, Amanda Markee, Rodolphe Rougerie, Ian Kitching & Akito Kawahara
The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The NewWorld hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of...

The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets

Jon Hess, Jeramiah Smith, Nataliya Timoshevskaya, Cyndi Baker, Christopher Caudill, David Graves, Matthew Keefer, Andrew Kinziger, Mary Moser, Laurie Porter, Greg Silver, Steven Whitlock & Shawn Narum
High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome...

Allele frequency files for population genomic and phenotypic association analyses

Zhongqi Chen
Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. One challenge in studying the genetic architecture of local adaptation is to achieve high marker density to detect candidate genes in natural populations that often have small blocks of linkage disequilibrium. Here, we used low coverage whole-genome resequencing (lcWGR) to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits...

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

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: Divergence in an obligate mutualism is not explained by divergent climatic factors

William Godsoe, Eva Strand, Christopher Irwin Smith, Jeremy B. Yoder, Todd C. Esque & Olle Pellmyr
Adaptation to divergent environments creates and maintains biological diversity, but we know little about the importance of different agents of ecological divergence. Coevolution in obligate mutualisms has been hypothesized to drive divergence, but this contention has rarely been tested against alternative ecological explanations. Here, we use a well-established example of coevolution in an obligate pollination mutualism, Yucca brevifolia and its two pollinating yucca moths, to test the hypothesis that divergence in this system is the...

Data from: Ecological opportunity and sexual selection together predict adaptive radiation

Catherine E. Wagner, Luke J. Harmon & Ole Seehausen
A fundamental challenge to our understanding of biodiversity is to explain why some groups of species undergo adaptive radiations, diversifying extensively into many and varied species, while others do not. Both extrinsic environmental factors (e.g. resource availability, climate) and intrinsic lineage-specific traits (e.g. behavioural or morphological traits, genetic architecture) influence diversification, but few studies have addressed how such factors interact. Radiations of cichlid fish in the African great lakes provide some of the most dramatic...

Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest

Genevieve Metzger, Anahi Espindola, Lisette P. Waits & Jack Sullivan
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future...

Data from: Host-adapted aphid populations differ in their migratory patterns and capacity to colonize crops

Sanford D. Eigenbrode, Thomas S. Davis, Jennifer R. Adams, Lisette P. Waits, David Hawthorne & Damon S. Husebye
Although phytophagous insects can vary genetically in host use and exhibit long-range movements, the combined implications of these phenomena for pest management have received limited attention. To address this, we surveyed the genetic diversity of pea aphid Acyrthosiphon pisum using twelve microsatellite loci and assessed host association patterns and annual movement from a putative source region (Columbia River Basin) to the Palouse region of northern Idaho and western Washington, where the aphid is a pest...

Data from: Environmentally dependent host-pathogen and vector-pathogen interactions in the barley yellow dwarf virus pathosystem

Thomas Seth Davis, Nilsa A. Bosque-Perez, Nathaniel E. Foote, Troy Magney & Sanford D. Eigenbrode
1. Understanding environmentally dependent variation in interspecific interactions is needed for evaluating how agroecosystems respond to abiotic stressors, including climate change. Both biotic and abiotic conditions shape crop responses to stress events, but interactions between environmental conditions and insect borne plant pathogens remain poorly understood. 2. We tested the hypothesis that drought stress, as applied by experimental water deprivation, drives conditional outcomes in host–pathogen and host–vector interactions using a cereal–aphid–virus association and greenhouse experiments. 3....

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: Inbreeding depression in pronghorn (Antilocapra americana) fawns

Stacey J. Dunn, Erin Clancey, Lisette P. Waits & John A. Byers
Although inbreeding depression affects survival, fitness and population viability, the extent of inbreeding depression in wild populations remains unclear. We examined inbreeding depression in the small, isolated National Bison Range (NBR), MT, pronghorn (Antilocapra americana) population following a bottleneck. We have studied the NBR pronghorn extensively since 1981, and we have detailed birth, survival and mate choice data. We genotyped all animals in the population between 1999-2010 at 19 microsatellite loci, assigned paternities to all...

Data from: Integrating fossils with molecular phylogenies improves inference of trait evolution

Graham James Slater, Luke J. Harmon & Michael E. Alfaro
Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this paper we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models...

Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

Stephanie M. DeMay, Penny A. Becker, Chad A. Eidson, Janet L. Rachlow, Timothy R. Johnson & Lisette P. Waits
Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method’s efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base...

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: Shifts in diversification rates linked to biogeographic movement into new areas: an example of a recent radiation in the Andes

Simon Uribe-Convers & David C. Tank
PREMISE OF THE STUDY: Clade-specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia. METHODS:...

Data from: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Stefan Laurent, Susanne P. Pfeifer, Matthew Settles, Samuel S. Hunter, Kayla M. Hardwick, Louise Ormond, Vitor C. Sousa, Jeffrey D. Jensen, Erica Bree Rosenblum & Matthew L. Settles
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus...

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: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn

Susannah P. Woodruff, Timothy R. Johnson & Lisette P. Waits
Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark–recapture analyses. Deposition data were collected at...

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: 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: Chloroplast primers for clade-wide phylogenetic studies of Thalictrum (Ranunculaceae)

Diego Fernando Morales-Briones, Tatiana Arias, Verónica Di Stilio & David C. Tank
Premise Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). Methods and Results We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome‐sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly assembled plastomes and one previously sequenced plastome, we designed and validated 28 primer pairs to target variable portions of the chloroplast genome in...

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