298 Works

Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains

Jaanus Suurväli, Andrew R. Whiteley, Yichen Zheng, Karim Gharbi, Maria Leptin & Thomas Wiehe
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of ‘personalized medicine’. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic...

Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy–Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis)

Kerry Gendreau, Michael Hague, Chris Feldman, , & Joel McGlothlin
The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T....

Data from: Developing a Stopover-CORT hypothesis: corticosterone predicts body composition and refueling rate in Gray Catbirds during migratory stopover

Joely DeSimone, Mariamar Gutierrez Ramirez, Cory Elowe, Michael Griego, Creagh Breuner & Alexander Gerson
Migratory flight is energetically challenging, requiring alternating phases of fuel catabolism and fuel accumulation, accompanied by dramatic changes in body composition and behavior. Baseline corticosterone (CORT; the primary glucocorticoid in birds) is thought to underlie transitions between fuel catabolism during flight, fuel deposition during stopover, and the initiation of migratory flight. However, studies of CORT on stopover physiology and behavior remain disparate efforts, lacking the cohesion of a general hypothesis. Here we develop a Stopover-CORT...

Data from: Riparian habitat restoration increases the availability and occupancy of Yellow-breasted Chat territories but brood parasitism is the primary influence on reproductive performance

Timothy Robert Forrester, David J. Green, René McKibbin, A. Michael Bezener & Christine A. Bishop
Implementation and evaluation of conservation efforts requires an understanding of the habitat selection and reproductive success of endangered populations. As populations recover, established territory holders may force new arrivals into lower-quality habitat, which can reduce reproductive success, especially in disturbed landscapes where suitable habitat is scarce. The endangered Western Yellow-breasted Chat (Icteria virens auricollis) population in the fragmented riparian zone of the Okanagan Valley, British Columbia, Canada, has rapidly increased in response to habitat restoration....

Phylogenomic resolution of sea spider diversification through integration of multiple data classes

Jesus Ballesteros, Emily Setton, Carlos Santibáñez-López, Claudia Arango, Georg Brenneis, Saskia Brix, Kevin Corbett, Esperanza Cano-Sánchez, Merai Dandouch, Geoffrey Dilly, Marc Eleaume, Guilherme Gainett, Cyril Gallut, Sean McAtee, Lauren McIntyre, Randy Moran, Pablo López-González, Gerhard Scholtz, Clay Williamson, Arthur Woods, Jakob Zehms, Ward Wheeler & Prashant Sharma
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and three nuclear...

Data from: Arctic and boreal paleofire records reveal drivers of fire activity and departures from Holocene variability

Tyler Hoecker, Philip Higuera, Ryan Kelly & Feng Sheng Hu
Boreal forest and tundra biomes are key components of the Earth system because the mobilization of large carbon stocks and changes in energy balance could act as positive feedbacks to ongoing climate change. In Alaska, wildfire is a primary driver of ecosystem structure and function, and a key mechanism coupling high-latitude ecosystems to global climate. Paleoecological records reveal sensitivity of fire regimes to climatic and vegetation change over centennial-millennial time scales, highlighting increased burning concurrent...

Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

Nathalie LeBlanc, Benjamin Gahagan, Samuel Andrews, Trevor Avery, Gregory Puncher, Benjamin Reading, Colin Buhariwalla, R Allen Curry, Andrew Whitely & Scott Pavey
Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations...

Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants

Aubrie James, Timothy Burnette, Jasmine Mack, David James, Vince Eckhart & Monica Geber
1. Spatial partitioning is a classic hypothesis to explain plant species coexistence, but evidence linking local environmental variation to spatial sorting, demography, and species’ traits is sparse. If co-occurring species’ performance is optimized differently along environmental gradients because of trait variation, then spatial variation might facilitate coexistence. 2. We used a system of four naturally co-occurring species of Clarkia (Onagraceae) to ask if distribution patchiness corresponds to variation in two environmental variables that contribute to...

Data from: Snow-mediated plasticity does not prevent camouflage mismatch

Alexander Kumar, Marketa Zimova, James Sparks & L Scott Mills
Global reduction in snow cover duration is one of the most consistent and widespread climate change outcomes. Declining snow duration has severe negative consequences for diverse taxa including seasonally color molting species, which rely on snow for camouflage. However, phenotypic plasticity may facilitate adaptation to reduced snow duration. Plastic responses could occur in the color molt phenology or through behavior that minimizes coat color mismatch or its consequences. We quantified molt phenology of 200 wild...

Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate

Eric Michel, Bronson Strickland, Stephen Demarais, Jerrold Belant, Todd Kautz, Jared Duquette, Dean Beyer, Michael Chamberlain, Karl Miller, Rebecca Shuman, John Kilgo, Duane Diefenbach, Bret Wallingford, Justin Vreeland, Steve Ditchkoff, Christopher DePerno, Christopher Moorman, Michael Chitwood & Marcus Lashley
1. Degree of reproductive synchronization in prey is hypothesized as a predator defense strategy reducing prey risk via predator satiation or predator avoidance. Species with precocial young, especially those exposed to specialist predators, should be highly synchronous to satiate predators (predator satiation hypothesis), while prey with nonprecocial (i.e., altricial) young, especially those exposed to generalist predators, should become relatively asynchronous to avoid predator detection (predator avoidance hypothesis). The white-tailed deer (Odocoileus virginianus) in North America...

Bedrock weathering controls on terrestrial carbon-nitrogen-climate interactions

Pawlok Dass, Benjamin Houlton, Yingping Wang, David Warlind & Scott Morford
Anthropogenic nitrogen deposition is widely considered to increase CO2 sequestration by land plant communities on a global scale. Here, we suggest that bedrock nitrogen weathering contributes significantly more to nitrogen-carbon interactions than anthropogenic nitrogen deposition. This working hypothesis is based on the application of empirical results into a global biogeochemical simulation model from the mid-1800s to the end of the 21st century. We demonstrate that rock nitrogen inputs have contributed roughly 2 to 11 times...

Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers

Lila Fishman, Findley Finseth & Thomas Nelson
Under the selfish centromere model, costs associated with female meiotic drive by centromeres select on interacting kinetochore proteins to restore Mendelian inheritance. We directly test this model in yellow monkeyflowers (Mimulus guttatus), which are polymorphic for a costly driving centromere (D). We show that the D haplotype is structurally and genetically distinct and swept to a high stable frequency within the past 1500 years. Quantitative genetic analyses reveal that variation in the strength of drive...

Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

William Conner, Emily Delaney, Michael Bronski, Paul Ginsberg, Timothy Wheeler, Kelly Richardson, Brooke Peckenpaugh, Kevin Kim, Masayoshi Watada, Ary Hoffmann, Michael Eisen, Artyom Kopp, Brandon Cooper & Michael Turelli
The Drosophila montium species group is a clade of 94 named species closely related to the model D. melanogaster species group. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times...

Data from: Hybridization alters growth and migratory life history expression of native trout

Jeffrey T. Strait, Lisa A. Eby, Ryan P. Kovach, Clint C. Muhlfeld, Matthew C. Boyer, Stephen J. Amish, Seth Smith, Winsor H. Lowe & Gordon Luikart
Human-mediated hybridization threatens many native species, but the effects of introgressive hybridization on life history expression are rarely quantified, especially in vertebrates. We quantified the effects of non-native rainbow trout admixture on important life history traits including growth and partial migration behavior in three populations of westslope cutthroat trout over five years. Rainbow trout admixture was associated with increased summer growth rates in all populations, and decreased spring growth rates in two populations with cooler...

Data from: Invasive hybridization has variable effects on survival among salmonid populations

Jeffrey Strait, Ryan Kovach, Lisa Eby, Clint Muhlfeld, Matthew Boyer, Stephen Amish, Paul Lukacs, Winsor Lowe & Gordon Luikart
Human-mediated hybridization threatens global biodiversity, but the fitness consequences of hybridization are poorly understood, especially in vertebrates. We used capture-recapture data from 5,249 individuals in three hybridizing populations of invasive rainbow trout (Oncorhynchus mykiss) and native cutthroat trout (O. clarkii) to quantify the effects of rainbow trout genetic admixture and environmental conditions on survival. Seasonal variation in environmental conditions interacted with individual admixture to influence seasonal survival. Overall, annual survival declined with admixture at the...

Winter damage is more important than summer temperature for maintaining the krummholz growth form above alpine treeline

Colin T. Maher, Cara R. Nelson & Andrew J. Larson
1. Understanding the processes that control alpine treelines, the elevational limits of tree growth forms, has been a central question in ecology and is growing in importance with concern over climate change. Cool summer air temperatures are currently thought to be the ultimate limiter of upright tree growth at alpine treelines globally. However, winter damage has long been recognized as a shaping force near alpine treelines. Low-growing krummholz growth forms provide an opportunity to test...

How climate impacts the composition of wolf killed-elk in northern Yellowstone National Park

Christopher Wilmers, Matthew Metz, Daniel Stahler, Michel Kohl, Chris Geremia & Douglas Smith
1. While the functional response of predators is commonly measured, recent work has revealed that the age and sex composition of prey killed is often a better predictor of prey population dynamics because the reproductive value of adult females is usually higher than that of males or juveniles. 2. Climate is often an important mediating factor in determining the composition of predator kills, but we currently lack a mechanistic understanding of how the multiple facets...

Behavior and diet data collected from i) GPS video camera collars and ii) fecal samples collected from individuals from the Fortymile Caribou Herd

Libby Ehlers, Gabrielle Coulombe, Jim Herriges, Torsten Bentzen, Mike Suitor, Kyle Joly & Mark Hebblewhite
Summer diets are crucial for large herbivores in the subarctic and are affected by weather, harassment from insects and a variety of environmental changes linked to climate. Yet understanding foraging behavior and diet of large herbivores is challenging in the subarctic because of their remote ranges. We used GPS video-camera collars to observe behaviors and summer diets of the migratory Fortymile Caribou Herd (Rangifer tarandus granti) across Alaska, USA and the Yukon, Canada. First, we...

Shrub Consumption and Immediate Changes in Shrub Community and Spatial Patterns by Reintroduced Fire in Yosemite National Park, California, USA; Supplemental Information

James Lutz, T. J. Furniss, S. J. Germain, K. M. L. Becker, Erika Blomdahl, S. A. Jeronimo, C. Alina Cansler, J. A. Freund, M. E. Swanson & A. J. Larson
Fire behavior in the Yosemite Forest Dynamics Plot during the Rim Fire as captured by the USFS Fire Behavior Assessment Team and reported in Ewell, C., D.F. Smith, M. Hilden, S. Greene, D. Coultrap, K. Robinson, N. Vaillant, A. Reiner, T. Norman. 2015. 2013 Rim Fire Stanislaus National Forest and Yosemite National Park Fire Behavior Assessment Team Summary Report. Each video was started based on a thermocouple trigger when the fire reached it.

Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

Kerry Gendreau, Joel McGlothlin, Angela Hornsby & Michael Hague
Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. Taricha newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance...

Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)

Lila Fishman, Kory Kolis, Colette Berg & Thomas Nelson
Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for...

Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Are trait combinations facilitated, independent, or constrained?

Vincent Eckhart & Timothy Burnette
Premise: Whether drought-adaptation mechanisms tend to evolve together, evolve independently, and/or evolve constrained by genetic architecture is incompletely resolved, particularly for water relations traits besides gas exchange. We addressed this issue in two subspecies of Clarkia xantiana (Onagraceae), California winter annuals that separated approximately 65,000 years ago and are adapted, partly by differences in flowering time, to native ranges differing in precipitation. Methods: In these subspecies and in recombinant inbred lines (RILs) from a cross...

Data from: Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

Lindy Mullen, H. Woods, Michael Schwartz, Adam Sepulveda & Winsor Lowe
The network architecture of streams and rivers constrains evolutionary, demographic, and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (1) examining hierarchical...

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