239 Works

Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

Martin P. Schilling, Paul G. Wolf, Aaron M. Duffy, Hardeep S. Rai, Carol A. Rowe, Bryce A. Richardson & Karen E. Mock
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in...

Data from: Stick insect genomes reveal natural selection's role in parallel speciation

Victor Soria-Carrasco, Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Thomas L. Parchman, J. Spencer Johnston, C. Alex Buerkle, Jeffrey L. Feder, Jens Bast, Tanja Schwander, Scott P. Egan, Bernard J. Crespi & Patrik Nosil
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess...

Data from: Developmental and evolutionary history affect survival in stressful environments

Gareth R. Hopkins, , Susannah S. French & Edmund D. Brodie
The world is increasingly impacted by a variety of stressors that have the potential to differentially influence life history stages of organisms. Organisms have evolved to cope with some stressors, while with others they have little capacity. It is thus important to understand the effects of both developmental and evolutionary history on survival in stressful environments. We present evidence of the effects of both developmental and evolutionary history on survival of a freshwater vertebrate, the...

Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems

Trisha B. Atwood, Edd Hammill, Pavel Kratina, Hamish S. Greig, Jonathan B. Shurin & John S. Richardson
Evidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO2 uptake by...

Data from: Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators

Michael T. J. Hague, Leleña A. Avila, Charles T. Hanifin, W. Andrew Snedden, Amber N. Stokes, , , Michael T.J. Hague & Edmund D. Brodie
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa)...

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?

Chris C. Nice, James A. Fordyce, Katherine L. Bell, Matthew L. Forister, Zachariah Gompert & Phil J. DeVries
Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understory, however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understory and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly...

Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

Brittany J. Teller, James H. Marden & Katriona Shea
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact...

Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?

Nate B. Hardy, Daniel A. Peterson & Carol D. Von Dohlen
For decades, biologists have debated why many parasites have obligate multi-host life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, i.e., change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (non-aphidines) – groups that differ in...

Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Torrey W. Rodgers, Charles C. Y. Xu, Jacalyn Giacalone, Karen M. Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W. Yu, Panu Somervuo, W. Owen McMillan & Patrick A. Jansen
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For...

Data from: Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance

Joel McGlothlin, Megan Kobiela, Chris R. Feldman, Todd A. Castoe, Shana L. Geffeney, Charles T. Hanifin, Gabriela Toledo, Freek J. Vonk, Michael K. Richardson, , Michael Pfrender &
Novel adaptations must originate and function within an already established genome [ 1 ]. As a result, the ability of a species to adapt to new environmental challenges is predicted to be highly contingent on the evolutionary history of its lineage [ 2–6 ]. Despite a growing appreciation of the importance of historical contingency in the adaptive evolution of single proteins [ 7–11 ], we know surprisingly little about its role in shaping complex adaptations...

Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

Zachariah Gompert & Karen E. Mock
Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here we propose and evaluate a statistical approach for distinguishing low-level ploidy variants (e.g., diploids, triploids and tetraploids) based on genotyping-by-sequencing data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands...

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: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities

Michael Cortez & Guenchik Grosklos
Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling...

Climate effects on nesting phenology in Nebraska turtles

John Iverson, Ashley Hedrick, Daniel Greene, Erin Lewis, Andrew Hood & John Iverson
A frequent response of organisms to climate change is altering the timing of reproduction. In particular, advancement of reproductive timing has been a common response to warming temperatures in temperate regions. Over the past three decades in Nebraska, USA, the timing of nesting of the Common Snapping Turtle (Chelydra serpentina) was negatively correlated with mean December maximum temperatures of the preceding year and mean May minimum and maximum temperatures in the nesting year, and positively...

Nocturnal bees feed on diurnal leftovers and pay the price of day–night lifestyle transition

Hema Somanathan, Shivani Krishna, Elsa Mini Jos, Vishwas Gowda, Almut Kelber & Renee Borges
Bees exemplify flights under bright sunlight. A few species across bee families have evolved nocturnality, displaying remarkable adaptations to overcome limitations of their daylight-suited apposition eyes. Phase inversion to nocturnality in a minority of bees that co-exist with diurnal bees provide a unique opportunity to study ecological benefits that mediate total temporal niche shifts. While floral traits and sensory modalities associated with the evolution of classical nocturnal pollination syndromes, e.g. by bats and moths, are...

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Data from: The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks

Kay Lucek, Zach Gompert & Patrik Nosil
Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host-plant associated ecotype formation in Timema cristinae stick insects. Using mate-pair...

Data from: Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America

Karen E. Mock, Jayne C. Brim Box, Jer Pin Chong, Joseph Furnish & Jeanette K. Howard
We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds....

Data from: The evolution of novel host use is unlikely to be constrained by tradeoffs or a lack of genetic variation

Zachariah Gompert, Joshua P. Jahner, Cynthia F. Scholl, Joseph S. Wilson, Lauren K. Lucas, Victor Soria-Carrasco, James A. Fordyce, Chris C. Nice, C. Alex Buerkle & Matthew L. Forister
The genetic and ecological factors that shape the evolution of animal diets remain poorly understood. For herbivorous insects, the expectation has been that trade-offs exist, such that adaptation to one host plant reduces performance on other potential hosts. We investigated the genetic architecture of alternative host use by rearing individual Lycaeides melissa butterflies from two wild populations in a crossed design on two hosts (one native and one introduced) and analysing the genetic basis of...

Data from: Effects of roads and land use on frog distributions across spatial scales and regions in the eastern and central United States

David M. Marsh, Bradley J. Cosentino, Kara S. Jones, Joseph J. Apodaca, Karen H. Beard, Jane M. Bell, Christine Bozarth, Derrick Carper, Julie F. Charbonnier, Andreia Dantas, Elizabeth Forys, Miran Foster, Jaquelyn General, Kristen S. Genet, Macie Hanneken, Kyle R. Hess, Shane A. Hill, Faisal Iqbal, Nancy E. Karraker, Eran S. Kilpatrick, Tom A. Langen, James Langford, Kathryn Lauer, Alison J. McCarthy, Joseph Neale … & Mohammad Tasleem
Aim: Understanding the scales over which land use affects animal populations is critical for conservation planning, and it can provide information about the mechanisms that underlie correlations between species distributions and land use. We used a citizen-science database of anuran surveys to examine the relationship between road density, land use, and the distribution of frogs and toads across spatial scales and regions of the United States. Location: Eastern and Central United States Methods: We compiled...

Data from: Recreational harvest and incident-response management reduce human-carnivore conflicts in an anthropogenic landscape

Jarod D. Raithel, Melissa J. Reynolds-Hogland, David N. Koons, Patrick C. Carr & Lise M. Aubry
Conserving viable large carnivore populations requires managing their interactions with humans in increasingly anthropogenic landscapes. Faced with declining budgets and escalating wildlife conflicts, agencies in North America continue to grapple with uncertainty surrounding the efficacy of socially divisive management actions such as harvest to reduce conflict. We used multistate capture–reencounter methods to estimate cause-specific mortality for a large sample (>3500) of American black bears Ursus americanus in north-western New Jersey, USA over a 33-year period....

Data from: The scaling of population persistence with carrying capacity does not asymptote in populations of a fish experiencing extreme climate variability

Richard S.A. White, Brendan A. Wintle, Peter A. McHugh, Douglas J. Booker, Angus R. McIntosh & Richard S. A. White
Despite growing concerns regarding increasing frequency of extreme climate events and declining population sizes, the influence of environmental stochasticity on the relationship between population carrying capacity and time-to-extinction has received little empirical attention. While time-to-extinction increases exponentially with carrying capacity in constant environments, theoretical models suggest increasing environmental stochasticity causes asymptotic scaling, thus making minimum viable carrying capacity vastly uncertain in variable environments. Using empirical estimates of environmental stochasticity in fish metapopulations, we showed that...

Data from: Associations between blooming plants and their bee visitors in a riparian ecosystem in eastern Oregon

Samantha M. Roof, Sandra J. DeBano, Mary M. Rowland, Skyler Burrows & Sandra DeBano
Native bees are declining world-wide, but conserving or restoring their habitat requires a better understanding of bee-flower associations. High quality bee habitat includes flowers that provide pollen and nectar preferred by bees. However, little data exist about which plants are commonly used by bees in the Pacific Northwest, or whether bees prefer certain plant characteristics over others. We examined bee and plant communities in an Oregon riparian ecosystem. Our purpose was to describe bee-plant associations,...

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  • Utah State University
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