212 Works

Data from: Reliability of macrofossils in woodrat (Neotoma) middens for detecting low-density tree populations

Mark R Lesser & Stephen T. Jackson
Macrofossils from woodrat (Neotoma) middens serve as an important proxy for reconstructing past vegetation in arid and semiarid regions of North America. The presence/absence of plant macrofossils in middens can provide valuable information on temporal and spatial patterns of plant migration and range boundaries. The primary aim of this study was to determine how local plant abundance, distance of plant populations from midden sites, and species population density on the landscape affect the probability of...

Data from: Bayesian estimation of genomic clines

Zachariah Gompert & C. Alex Buerkle
We developed a Bayesian genomic cline model to study the genetic architecture of adaptive divergence and reproductive isolation between hybridizing lineages. This model quantifies locus-specific patterns of introgression with two cline parameters that describe the probability of locus-specific ancestry as a function of genome-wide admixture. "Outlier" loci with extreme patterns of introgression relative to most of the genome can be identified. These loci are potentially associated with adaptive divergence or reproductive isolation. We simulated genetic...

Data from: Genome-wide association genetics of an adaptive trait in lodgepole pine

Thomas L. Parchman, Zachariah Gompert, Craig W. Benkman, Faye D. Schilkey, Joann Mudge & C. Alex Buerkle
Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographic variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is...

Data from: Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species

Zachariah Gompert, Lauren K. Lucas, Chris Clark Nice, James Andrew Fordyce, Matthew L. Forister & C. Alex Buerkle
Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two...

Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

Dorothea Lindtke, Zachariah Gompert, Christian Lexer & C. Alex Buerkle
In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the importance of barriers to gene flow that act early versus late in the life...

Data from: An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

Brittany R. Jenkins, Maren N. Vitousek, Joanna K. Hubbard & Rebecca J. Safran
Glucocorticoid hormones (CORT) are predicted to promote adaptation to variable environments, yet little is known about the potential for CORT secretion patterns to respond to selection in free-living populations. We assessed the heritable variation underlying differences in hormonal phenotypes using a cross-foster experimental design with nestling North American barn swallows (Hirundo rustica erythrogaster). Using a bivariate animal model, we partitioned variance in baseline and stress-induced CORT concentrations into their additive genetic and rearing environment components...

Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

Thomas L. Parchman, Zachariah Gompert, Michael J. Braun, Robb T. Brumfield, D. B. McDonald, J. Albert C. Uy, G. Zhang, Erich D. Jarvis, B. A. Schlinger & C. A. Buerkle
The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus candei and M. vitellinus) using 59 100 SNPs, a whole genome assembly, and Bayesian models. Measures of genetic differentiation (inline image) and introgression (genomic cline center [α] and rate [β]) were highly heterogeneous among loci. We identified thousands of...

Data from: The evolutionary origins of modularity

Jeff Clune, Jean-Baptiste Mouret & Hod Lipson
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional, sparsely connected subunits--but there is no consensus regarding why modularity itself evolved. While most hypotheses assume indirect selection for evolvability, here we demonstrate that the ubiquitous, direct selection pressure to reduce the cost of connections between network nodes causes the emergence of...

Data from: Toward a mechanistic understanding of human-induced rapid environmental change: a case study linking energy development, nest predation, and predators

Matthew G. Hethcoat & Anna D. Chalfoun
1. Demographic consequences of human-induced rapid environmental change (HIREC) have been widely documented for many populations. The mechanisms underlying such patterns, however, are rarely investigated and yet are critical to understand for effective conservation and management. 2. We investigated the mechanisms underlying reduced avian nest survival with intensification of natural gas development, an increasing source of HIREC globally. We tested the hypothesis that energy development increased the local activity of important nest predator species thereby...

Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Jeffrey D. Lozier, Jason M. Jackson, Michael E. Dillon & James P. Strange
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into...

Data from: The evolutionary origins of hierarchy

Henok Mengistu, Joost Huizinga, Jean-Baptiste Mouret & Jeff Clune
Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a...

Data from: Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

Hayley C. Lanier, Rob Massatti, Qixin He, Link E. Olson & L. Lacey Knowles
Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate-sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site-associated DNA...

Data from: The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

Dorothea Lindtke & C. Alex Buerkle
Genetic incompatibilities are an important component of reproductive isolation. Although theoretical studies have addressed their evolution, little is known about their maintenance when challenged by potentially high migration rates in secondary contact. Whereas theory predicts that recombination can erode barriers, many empirical systems have been found to retain species-specific differences despite substantial gene flow. By simulating whole genomes in individuals of hybridizing species, we find that the genetic architecture of two contrasting models of epistatic...

Data from: Mitogenomes and relatedness do not predict frequency of tool-use by sea otters

Kathy Ralls, Nancy Rotzel McInerney, Roderick B. Gagne, Holly B. Ernest, M. Tim Tinker, Jessica Fujii, Jesus Maldonado & Katherine Ralls
Many ecological aspects of tool-use in sea otters are similar to those in Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins share a single mitochondrial haplotype and are more related to each other than to the population as a whole. We asked whether sea otters in California showed similar genetic patterns by sequencing mitogenomes of 43 otters and genotyping 154 otters at 38 microsatellite loci. There were six variable sites in the mitogenome that...

Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals

L. Lacey Knowles, Rob Massatti, Qixin He, Link E. Olson & Hayley C. Lanier
Aim: Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species-specific or shared manner. Location: Alaska and adjacent north-western Canada. Methods: For each taxon we generated 3500–7500 single-nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between...

Data from: Elevated CO2 and water addition enhance nitrogen turnover in grassland plants with implications for temporal stability

Feike A. Dijkstra, Yolima Carrillo, Dana M. Blumenthal, Kevin E. Mueller, Daniel R. LeCain, Jack A. Morgan, Tamara J. Zelikova, David G. Williams, Ronald F. Follett, Elise Pendall & Dan R. LeCain
Temporal variation in soil nitrogen (N) availability affects growth of grassland communities that differ in their use and reuse of N. In a seven-year-long climate change experiment in a semiarid grassland, the temporal stability of plant biomass production varied with plant N turnover (reliance on externally acquired N relative to internally recycled N). Species with high N turnover were less stable in time compared to species with low N turnover. In contrast, N turnover at...

Data from: Functional attributes of ungulate migration: landscape features facilitate movement and access to forage

Kevin L. Monteith, Matthew M. Hayes, Matthew J. Kauffman, Holly E. Copeland & Hall Sawyer
Long-distance migration by terrestrial mammals is a phenomenon critical to the persistence of populations, but such migrations are declining globally because of over-harvest, habitat loss, and movement barriers. Increasingly, there is a need to improve existing routes, mitigate route segments affected by anthropogenic disturbance and in some instances, determine if alternative routes are available. Using a hypothesis-driven approach, we identified landscape features associated with the primary functional attributes, stopovers and movement corridors, of spring migratory...

Data from: Measures of effective population size in sea otters reveal special considerations for wide-ranging species

Roderick B. Gagne, M. Timothy Tinker, Kyle D. Gustafson, Katherine Ralls, Larson Shawn, L. Max Tarjan, Melissa A. Miller & Holly B. Ernest
Conservation genetic techniques and considerations of the evolutionary potential of a species are increasingly being applied to species conservation. For example, effective population size (Ne) estimates are useful for determining the conservation status of species, yet accurate estimates of current Ne remain difficult to obtain. The effective population size can contribute to setting federal delisting criteria, as was done for the southern sea otter (Enhydra lutris nereis). After being hunted to near extinction during the...

Data from: Demographic drivers of a refugee species: large-scale experiments guide strategies for reintroductions of hirola

Abdullahi H. Ali, Matthew J. Kauffman, Rajan Amin, Amos Kibara, Juliet King, David Mallon, Charles Musyoki & Jacob R. Goheen
Effective reintroduction strategies require accurate estimates of vital rates and the factors that influence them. We estimated vital rates of hirola (Beatragus hunteri) populations exposed to varying levels of predation and rangeland quality from 2012 to 2015, and then built population matrices to estimate the finite rate of population change (λ) and demographic sensitivities. Mean survival for all age classes and population growth was highest in the low predation/high-rangeland quality setting (λ = 1.08 ±...

Data from: Divergent parasite infections in sympatric cichlid species in Lake Victoria

Anssi Karvonen, Catherine E. Wagner, Oliver M. Selz & Ole Seehausen
Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species rich communities, and as a driver of post-speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species...

Data from: Multiple mechanisms confer stability to isolated populations of a rare endemic plant

Reilly R. Dibner, Megan L. Peterson, Allison M. Louthan & Daniel F. Doak
The persistence of small populations remains a puzzle for ecology and conservation. Especially interesting is how naturally small, isolated populations are able to persist in the face of multiple environmental forces that create fluctuating conditions and should, theory predicts, lead to high probabilities of extirpation. We used a combination of long term census data and a five-year demographic study of a naturally rare, endemic plant, Yermo xanthocephalus, to evaluate the importance of several possible mechanisms...

Data from: Negative frequency-dependent foraging behaviour in a generalist herbivore (Alces alces) and its stabilizing influence on food-web dynamics

Sarah R. Hoy, John A. Vucetich, Rongsong Liu, Don L. DeAngelis, Rolf O. Peterson, Leah M. Vucetich & John J. Henderson
1.Resource selection is widely appreciated to be context‐dependent and shaped by both biological and abiotic factors. However, few studies have empirically assessed the extent to which selective foraging behaviour is dynamic and varies in response to environmental conditions for free‐ranging animal populations. 2.Here, we assessed the extent that forage selection fluctuated in response to different environmental conditions for a free‐ranging herbivore, moose (Alces alces) in Isle Royale National Park, over a 10‐year period. More precisely,...

Data from: Genetic source-sink dynamics among naturally structured and anthropogenically fragmented puma populations

Kyle D. Gustafson, Roderick B. Gagne, T. Winston Vickers, Seth P.D. Riley, Christopher C. Wilmers, Vernon C. Bleich, Becky M. Pierce, Marc Kenyon, Tracy L. Drazenovich, Jeff A. Sikich, Walter M. Boyce & Holly B. Ernest
Fragmentation of wildlife populations is increasing on a global scale and understanding current population genetic structure, genetic diversity, and genetic connectivity is key to informing wildlife management and conservation. We genotyped 992 pumas (Puma concolor) at 42 previously developed microsatellite loci and identified 10 genetic populations throughout the states of California and Nevada, USA. Although some genetic populations had large effective population sizes, others were small and inbred. Genetic diversity was extremely variable (heterozygosity, uHe...

Recent hybrids recapitulate ancient hybrid outcomes

Zachariah Gompert, Samridhi Chaturvedi, Lauren Lucas, C. Alex Buerkle, James Fordyce, Matthew Forister & Chris Nice
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z...

Data from: Migrating bison engineer the green wave

Chris Geremia, Jerod Merkle, Daniel Eacker, Rick Wallen, P.J. White, Mark Hebblewhite & Matthew Kauffman
Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However,...

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