170 Works

Data from: Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

Joshua G. Harrison, Matthew L. Forister, Stephanie R. Mcknight, Erin Nordin & Thomas L. Parchman
Premise of the study: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in...

Data from: Rapid buildup of sympatric species diversity in Alpine whitefish

Carmela J. Doenz, David Bittner, Pascal Vonlanthen, Catherine E. Wagner & Ole Seehausen
Adaptive radiations in postglacial fish offer excellent settings to study the evolutionary mechanisms involved in the rapid buildup of sympatric species diversity from a single lineage. Here, we address this by exploring the genetic and ecological structure of the largest Alpine whitefish radiation known, that of Lakes Brienz and Thun, using microsatellite data of more than 2000 whitefish caught during extensive species‐targeted and habitat‐randomized fishing campaigns. We find six strongly genetically and ecologically differentiated species,...

Data from: Is ungulate migration culturally transmitted? Evidence of social learning from translocated animals

Brett R. Jesmer, Jerod A. Merkle, Jacob R. Goheen, Ellen O. Aikens, Jeffrey L. Beck, Alyson B. Courtemanch, Mark A. Hurley, Douglas E. McWhirter, Hollie M. Miyasaki, Kevin L. Monteith & Matthew J. Kauffman
Ungulate migrations are assumed to stem from learning and cultural transmission of information regarding seasonal distribution of forage, but this hypothesis has not been tested empirically. We compared the migratory propensities of bighorn sheep and moose translocated into novel habitats with those of historical populations that had persisted for hundreds of years. Whereas individuals from historical populations were largely migratory, translocated individuals initially were not. After multiple decades, however, translocated populations gained knowledge about surfing...

Data from: The network motif architecture of dominance hierarchies

Daizaburo Shizuka & David B. McDonald
The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high...

Data from: State-dependent behavior alters endocrine-energy relationship: implications for conservation and management

Brett R. Jesmer, Jacob R. Goheen, Kevin L. Monteith & Matthew J. Kauffman
Glucocorticoids (GC) and triiodothyronine (T3) are two endocrine markers commonly used to quantify resource limitation, yet the relationships between these markers and the energetic state of animals has been studied primarily in small-bodied species in captivity. Free-ranging animals, however, adjust energy intake in accordance with their energy reserves, a behavior known as state-dependent foraging. Further, links between life-history strategies and metabolic allometries cause energy intake and energy reserves to be more strongly coupled in small...

Data from: Founder events, isolation, and inbreeding: Intercontinental genetic structure of the domestic ferret

Kyle D. Gustafson, Michelle G. Hawkins, Tracy L. Drazenovich, Robert Church, Susan A. Brown & Holly B. Ernest
Domestication and breeding for human-desired morphological traits can reduce population genetic diversity via founder events and artificial selection, resulting in inbreeding depression and genetic disorders. The ferret (Mustela putorius furo) was domesticated from European polecats (M. putorius), transported to multiple continents, and has been artificially selected for several traits. The ferret is now a common pet, a laboratory model organism, and feral ferrets can impact native biodiversity. We hypothesized global ferret trade resulted in distinct...

Data from: Circadian rhythms vary over the growing season and correlate with fitness components

Matthew J. Rubin, Marcus T. Brock, Amanda M. Davis, Zachary M. German, Mary Knapp, Stephen M. Welch, Stacey L. Harmer, Julin N. Maloof, Seth J. Davis & Cynthia Weinig
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle...

Data from: Endemic chronic wasting disease causes mule deer population decline in Wyoming

Melia T. DeVivo, David R. Edmunds, Matthew J. Kauffman, Brant A. Schumaker, Justin Binfet, Terry J. Kreeger, Bryan J. Richards, Hermann M. Schätzl & Todd E. Cornish
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting white-tailed deer (Odocoileus virginianus), mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces shirasi) in North America. In southeastern Wyoming average annual CWD prevalence in mule deer exceeds 20% and appears to contribute to regional population declines. We determined the effect of CWD on mule deer demography using age-specific, female-only, CWD transition matrix models to estimate the population growth...

Data from: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability

Miguel Arenas, Claudia C. Weber, David A. Liberles & Ugo Bastolla
The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we present ProtASR,...

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

Meaghan Pimsler, Kennan Oyen, James Herndon, Jason Jackson, James Strange, Michael Dillon & Jeff Lozier
Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’ range to correlate...

Data from: Pliant pathogens: Estimating viral spread when confronted with new vector, host, and environmental conditions

Anita Krause, Eric Seabloom, Elizabeth Borer, Lauren Shoemaker, Andrew Sieben, Ryan Campbell, Alexander Strauss & Allison Shaw
Pathogen spread rates are determined, in part, by the performance of pathogens under altered environmental conditions and their ability to persist while switching among hosts and vectors. To determine the effects of new conditions (host, vector, and nutrient) on pathogen spread rate, we introduced a vector-borne, viral plant pathogen, Barley Yellow Dwarf Virus PAV (BYDV-PAV) into hosts, vectors, and host nutrient supplies that it had not encountered for thousands of viral generations. We quantified pathogen...

Probability of occurrence and phenology of pine wilt disease transmission by insect vectors in the Rocky Mountains

David Atkins, Seth Davis & Jane Stewart
1. Pine wilt disease, caused by pinewood nematode (Bursaphelenchus xylophilus; PWN), is a damaging and globally distributed insect-vectored forest pathogen. Native forest tree mortality associated with PWN is newly reported from the Front Range of Colorado, but there is no regional information on PWN frequency or biology of local insect vectors, limiting management options. 2. A sampling array was established to survey PWN in native pines (Pinus ponderosa) and longhorn beetles (Monochamus clamator & Monochamus...

Data related to: Open-system evolution of a crustal-scale magma column, Klamath Mountains, California

Calvin Barnes, Nolwenn Coint, Melanie Barnes, Ariel Strickland, John Cottle, O. Ramo, Kevin Chamberlain & John Valley
Granitic magmas commonly display evidence for some level of interaction with and/or origins from crustal rocks. There is fundamental debate in the community as to the processes that control the origins of these magmas and the potential for their contamination as they pass through the crust. One approach to addressing these issues involves a combination of detailed field mapping combined with geochemical analysis of bulk-rock samples and their constituent minerals. In particular, resolution of debates...

Informed breeding dispersal following stochastic changes to patch quality in a pond-breeding amphibian

Gabriel Barrile, Annika Walters, Matthew Webster & Anna Chalfoun
1. The unidirectional movement of animals between breeding patches (i.e., breeding dispersal) has profound implications for the ecological and evolutionary dynamics of spatially structured populations. In spatiotemporally variable environments, individuals are expected to adjust their dispersal decisions according to information gathered on the environmental and/or social cues that reflect the fitness prospects in a given breeding patch (i.e., informed dispersal). 2. A paucity of empirical work limits our understanding of the ability of animals to...

Data from: Neural modularity helps organisms evolve to learn new skills without forgetting old

Kai Olav Ellefsen, Jean-Baptiste Mouret & Jeff Clune
A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks...

Data from: The many dimensions of diet breadth: phytochemical, genetic, behavioral, and physiological perspectives on the interaction between a native herbivore and an exotic host

Joshua G. Harrison, Zachariah Gompert, James A. Fordyce, C. Alex Buerkle, Rachel Grinstead, Joshua P. Jahner, Scott Mikel, Christopher C. Nice, Aldrin Santamaria & Matthew L. Forister
From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization...

Data from: Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest

Jeane M. Robertson, Melanie A. Murphy, Christopher A. Pearl, Michael J. Adams, Monica I. Páez-Vacas, Susan M. Haig, David S. Pilliod, Andrew Storfer & W. Chris Funk
Comparative landscape genetics has uncovered high levels of variation in which landscape factors affect connectivity among species and regions. However, the relative importance of species traits vs. environmental variation for predicting landscape patterns of connectivity is unresolved. We provide evidence from a landscape genetics study of two sister taxa of frogs, the Oregon spotted frog (Rana pretiosa) and the Columbia spotted frog (R. luteiventris) in Oregon and Idaho, USA. Rana pretiosa is relatively more dependent...

Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Ryan A. Long, Alois Wambua, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey...

Data from: A single migrant enhances the genetic diversity of an inbred puma population

Kyle C. Gustafson, T. Winston Vickers, Walter M. Boyce, Holly B. Ernest & Kyle D. Gustafson
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east...

Data from: The effect of rhizosphere microbes outweighs host plant genotype in reducing insect herbivory

Charley J. Hubbard, Baohua Li, Robby McMinn, Marcus T. Brock, Lois Maignien, Brent E. Ewers, Daniel Kliebenstein & Cynthia Weinig
Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known...

Data from: Humans permanently occupied the Andean highlands by at least 7 ka

Randall Haas, Ioana C. Stefenescu, Alex Garcia-Putnam, Mark S. Aldenderfer, Mark T. Clementz, Melissa S. Murphy, Carlos Viviano Llave, James T. Watson, Alexander Garcia-Putnam & Ioana C. Stefanescu
High-elevation environments above 2500 metres above sea level (m.a.s.l.) were among the planet's last frontiers of human colonization. Research on the speed and tempo of this colonization process is active and holds implications for understanding rates of genetic, physiological and cultural adaptation in our species. Permanent occupation of high-elevation environments in the Andes Mountains of South America tentatively began with hunter–gatherers around 9 ka according to current archaeological estimates, though the timing is currently debated....

Data from: Functional responses in habitat selection: clarifying hypotheses and interpretations

Joseph D. Holbrook, Lucretia E. Olson, Nicholas J. DeCesare, Mark Hebblewhite, John R. Squires & Robin Steenweg
A fundamental challenge in habitat ecology and management is understanding the mechanisms generating animal distributions. Studies of habitat selection provide a lens into such mechanisms, but are often limited by unrealistic assumptions. For example, most studies assume that habitat selection is constant with respect to the availability of resources, such that habitat use remains proportional to availability. To the contrary, a growing body of work has shown the fallacy of this assumption, indicating that animals...

Data from: Experimental evidence for ecological selection on genome variation in the wild

Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Jeffery L. Feder, Thomas L. Parchman, Alex C. Buerkle, Patrik Nosil & Jeffrey L. Feder
Understanding natural selection's effect on genetic variation is a major goal in biology, but the genome-scale consequences of contemporary selection are not well known. In a release and recapture field experiment we transplanted stick insects to native and novel host plants and directly measured allele frequency changes within a generation at 186 576 genetic loci. We observed substantial, genome-wide allele frequency changes during the experiment, most of which could be attributed to random mortality (genetic...

Data from: The influence sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile)

Rebecca Brown Harris, Matthew D. Carling & Irby J. Lovette
In this study, we explore the long-standing issue of how many loci are needed to infer accurate phylogenetic relationships, and whether loci with particular attributes (i.e., parsimony informativeness, variability, gene tree resolution) outperform others. To do so, we use an empirical dataset consisting of the seven species of chickadees (Aves: Paridae), an analytically tractable, recently diverged group, and well studied ecologically but lacking a nuclear phylogeny. We estimate relationships using 40 nuclear loci and mitochondrial...

Data from: Twenty-four years after the Yellowstone fires: are postfire lodgepole pine stands converging in structure and function?

Monica G. Turner, Timothy G. Whitby, Daniel B. Tinker & William H. Romme
Disturbance and succession have long been of interest in ecology, but how landscape patterns of ecosystem structure and function evolve following large disturbances is poorly understood. After nearly 25 years, lodgepole pine (Pinus contorta var. latifolia) forests that regenerated after the 1988 Yellowstone Fires (Wyoming, USA) offer a prime opportunity to track the fate of disturbance-created heterogeneity in stand structure and function in a wilderness setting. In 2012, we resampled 72 permanent plots to ask...

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