21 Works

Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

Philip Lavretsky, Jeffrey Peters, Kevin Winker, Volker Bahn, Irina Kulikova, Yuri Zhuravlev, Robert Wilson, Christopher Barger, Kirsty Gurney, Kevin McCracken, Jeffrey L. Peters, Chris Barger & Kevin G. McCracken
Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup...

Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

Philip Lavretsky, Jeffrey M. DaCosta, Michael D. Sorenson, Kevin G. McCracken & Jeffrey L. Peters
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a...

Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands

Caitlin Wells, Philip Lavretsky, Michael Sorenson, Jeffrey Peters, Jeffrey DaCosta, Stephen Turnbull, Kimberly Uyehara, Christopher Malachowski, Bruce Dugger, John Eadie & Andrew Engilis
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation...

Impact of the Affordable Care Act on Referral to Care for People Living with HIV in Appalachia

Cameron A. Wade, Timothy N. Crawford, Nicole Leedy & Alice C. Thornton
Introduction: The Affordable Care Act (ACA) enacted on March 23, 2010 significantly impacted access to healthcare for people living with HIV (PLWH). Expansion of care was accomplished in three areas: eliminating exclusions for pre-existing conditions, elimination of lifetime caps on healthcare expenditures, and expansion of Medicaid eligibility. Purpose: This study evaluated the impact of state implementation of the ACA Medicaid expansion on referral to HIV care at a Ryan White federally funded clinic in Kentucky...

Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Jeffrey L. Peters, Trina E. Robert, Kevin Winker, Kevin G. McCracken & Trina E. Roberts
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to...

Data from: A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato)

Jeffrey L. Peters, Kevin G. McCracken, Christin L. Pruett, Sievert Rohwer, Sergei V. Drovetski, Yuri N. Zhuravlev, Irina Kulikova, Daniel D. Gibson & Kevin Winker
Speciation is a process in which genetic drift and selection cause divergence over tSpeciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to...

Data from: Heteropatric speciation in a duck, Anas crecca

Kevin Winker, Kevin G. McCracken, Daniel D. Gibson & Jeffrey L. Peters
Heteropatric differentiation is a mode of speciation with gene flow in which divergence occurs between lineages that are in sympatry and allopatry at different times during cyclic spatial movements. Empirical evidence suggests that heteropatric differentiation may prove to be common among seasonally migratory organisms. We examined genetic differentiation between the sedentary Aleutian Islands population of green-winged teal (Anas crecca nimia) and its close migratory relative, the Eurasian, or Old World (OW), Anas c. crecca population,...

Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

Jeffrey L. Peters, Kevin Winker, Kendra C. Millam, Philip Lavretsky, Irina Kulikova, Robert E. Wilson, Yuri N. Zhuravlev & Kevin G. McCracken
Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages...

Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals

Kirandeep K. Dhami, Leo Joseph, David A. Roshier & Jeffrey L. Peters
Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z-chromosome (females are heterogametic, ZW). We tested for elevated Z-differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal Anas gracilis and the dichromatic chestnut teal A. castanea. Despite prominent morphological differences, these two species...

The mechanism underlying transient weakness in myotonia congenita

Jessica Myers, Mark Rich, Kirsten Denman, Chris DuPont, Ahmed Hawash, Kevin Novak, Andrew Koesters, Manfred Grabner, Anamika Dayal & Andrew Voss
In addition to the hallmark muscle stiffness, patients with recessive myotonia congenita (Becker disease) experience debilitating bouts of transient weakness that remain poorly understood despite years of study. We made intracellular recordings from muscle of both genetic and pharmacologic mouse models of Becker disease to identify the mechanism underlying transient weakness. Our recordings reveal transient depolarizations (plateau potentials) of the membrane potential to -25 to -35 mV in the genetic and pharmacologic models of Becker...

Data from: Adaptive shaping of the behavioural and neuroendocrine phenotype during adolescence

Tobias D. Zimmermann, Sylvia Kaiser, Michael B. Hennessy & Norbert Sachser
Environmental conditions during early life can adaptively shape the phenotype for the prevailing environment. Recently, it has been suggested that adolescence represents an additional temporal window for adaptive developmental plasticity, though supporting evidence is scarce. Previous work has shown that male guinea pigs living in large mixed-sex colonies develop a low-aggressive phenotype as part of a queuing strategy that is adaptive for integrating into large unfamiliar colonies. By contrast, males living in pairs during adolescence...

Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state

J. Thad Scott, Mark J. McCarthy & Hans W. Paerl
The concept of lakes “evolving” phosphorus (P) limitation has persisted in limnology despite limited direct evidence. Here, we developed a simple model to broadly characterize nitrogen (N) surpluses and deficits relative to P in lakes, and compared the magnitude of this imbalance to estimates of N gains and losses through biological N transformations. The model suggested that approximately half of oligotrophic lakes in the US had a stoichiometric N deficit, but almost 90% of the...

Data from: Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Philip Lavretsky, Jeffrey M. DaCosta, Blanca E. Hernández-Baños, , Michael D. Sorenson, Jeffrey L. Peters & Andrew Engilis
Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172...

Data from: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)

Eliana Buenaventura, Michael W. Lloyd, Juan Manuel Perilla López, Vanessa L. González, Arianna Thomas-Cabianca & Torsten Dikow
The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems...

The role of action potential changes in depolarization-induced failure of excitation contraction coupling in mouse skeletal muscle

Mark Rich
Excitation-contraction coupling (ECC) is the process by which electrical excitation of muscle is converted into force generation. Depolarization of skeletal muscle resting potential contributes to failure of ECC in diseases such as periodic paralysis, intensive care unit acquired weakness and possibly fatigue of muscle during vigorous exercise. When extracellular K+ is raised to depolarize the resting potential, failure of ECC occurs suddenly, over a narrow range of resting potentials. Intracellular recordings of action potentials (APs)...

Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck

Philip Lavretsky, , John M. Eadie, Jeffrey L. Peters & A. Engilis
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended...

Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

Jeffrey L. Peters, Kimberly A. Bolender & John M. Pearce
Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from panmixia to deep, reciprocally monophyletic lineages. Yet these studies generally found weak or no nuclear (nu) DNA structure which was often attributed to sex-biased gene flow (i.e., male dispersal and female philopatry), a common behavior within this family. An alternative explanation for this “conflict” is that the smaller effective population size and faster sorting rate of mtDNA relative...

Data from: Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies

Robert E. Wilson, Jeffrey L. Peters & Kevin G. McCracken
Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species’ range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America....

Data from: Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure

David R. Roberts, Volker Bahn, Simone Ciuti, Mark S. Boyce, Jane Elith, Gurutzeta Guillera-Arroita, Severin Hauenstein, José J. Lahoz-Monfort, Boris Schröder, Wilfried Thuiller, David I. Warton, Brendan A. Wintle, Florian Hartig & Carsten F. Dormann
Ecological data often show temporal, spatial, hierarchical (random effects), or phylogenetic structure. Modern statistical approaches are increasingly accounting for such dependencies. However, when performing cross-validation, these structures are regularly ignored, resulting in serious underestimation of predictive error. One cause for the poor performance of uncorrected (random) cross-validation, noted often by modellers, are dependence structures in the data that persist as dependence structures in model residuals, violating the assumption of independence. Even more concerning, because often...

Data from: The global distribution of diet breadth in insect herbivores

Matthew L. Forister, Vojtech Novotny, Anna K. Panorska, Leontine Baje, Yves Basset, Philip T. Butterill, Lukas Cizek, Phyllis D. Coley, Francesca Dem, Ivone R. Diniz, Pavel Drozd, Mark Fox, Andrea E. Glassmire, Rebecca Hazen, Jan Hrcek, Joshua P. Jahner, Ondrej Kaman, Tomasz J. Kozubowski, Thomas Kursar, Owen T. Lewis, John Lill, Robert J. Marquis, Scott E. Miller, Helena C. Morais, Masashi Murakami … & Lee A. Dyer
Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here...

Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Jeffrey L. Peters, Trina E. Robert, Kevin Winker, Kevin G. McCracken & Trina E. Roberts
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to...

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