22 Works

Data from: Detection of outlier loci and their utility for fisheries management

Michael A Russello, Stephanie L Kirk, Karen K Frazer & Paul J Askey
Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific (“outlier”) effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide (“neutral”) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated...

Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

Zhao Lai, Nolan C. Kane, Alex Kozik, Kathryn A. Hodgins, Katrina M. Dlugosch, Michael S. Barker, Marta Matvienko, Qian Yu, Kathryn G. Turner, Stephanie A. Pearl, Graeme D.M. Bell, Yi Zou, Chris Grassa, Alessia Guggisberg, Keith L. Adams, James V. Anderson, David P. Horvath, Richard V. Kesseli, John M. Burke, Richard W. Michelmore, Loren H. Rieseberg, Stephanie Anne Pearl & Graeme D. M. Bell
PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic...

Data from: Differential selection between the sexes and selection for sex

Denis Roze & Sarah P. Otto
Anisogamy is known to generate an important cost for sexual reproduction (the famous "twofold cost of sex"). However, male-female differences may have other consequences on the evolution of sex, due to the fact that selective pressures may differ among the sexes. On the one hand, intralocus sexual conflict should favor asexual females, which can fix female-beneficial, male-detrimental alleles. On the other hand, it has been suggested repeatedly that sexual selection among males may help to...

Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

Arnaud Le Rouzic, Kjartan Østbye, Tom O. Klepaker, Thomas F. Hansen, Louis Bernatchez, Dolph Schluter & Leif Asbjørn Vøllestad
Measuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading to the reduction or loss of the bony lateral armor, has indeed occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic...

Data from: Dietary stress does not strengthen selection against single deleterious mutations in Drosophila melanogaster

Howard D. Rundle, Kelsie MacLellan, Lucia Kwan, Michael C. Whitlock, M C Whitlock, K MacLellan, L Kwan & H D Rundle
Stress is generally thought to increase the strength of selection, although empirical results are mixed and general conclusions are difficult because data are limited. Here we compare the fitness effects of nine independent recessive mutations in Drosophila melanogaster in a high- and low-dietary-stress environment, estimating the strength of selection on these mutations arising from both a competitive measure of male reproductive success and productivity (female fecundity and the subsequent survival to adulthood of her offspring)....

Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses

Marc T. J. Johnson, Richard Gareth FitzJohn, Stacey D. Smith, Mark D. Rausher & Sarah P. Otto
The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification...

Data from: Intraguild predation drives evolutionary niche shift in threespine stickleback

Travis Ingram, Richard Svanbäck, Nathan J. B. Kraft, Pavel Kratina, Laura Southcott & Dolph Schluter
Intraguild predation – competition and predation by the same antagonist – is widespread, but its evolutionary consequences are unknown. Intraguild prey may evolve antipredator defenses, superior competitive ability on shared resources, or the ability to use an alternative resource, any of which may alter the structure of the food web. We tested for evolutionary responses by threespine stickleback to a benthic intraguild predator, prickly sculpin. We used a comparative morphometric analysis to show that stickleback...

Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

David B Carlon, Ann F Budd, Catherine Lippé & Rose L Andrew
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of...

Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

Julianno Bergoch Monteiro Sambatti, Jared L. Strasburg, Daniel Ortiz-Barrientos, Eric J. Baack & Loren Henry Rieseberg
In several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions...

Data from: Patterns of colonization and spread in the fungal spruce pathogen Onnia tomentosa

Hugo Germain, Marie-Josée Bergeron, Louis Bernier, Gaston Laflamme & Richard C Hamelin
The basidiomycetous fungus Onnia tomentosa is one of the most widespread root rot pathogens in North America. Although the disease is more severe on spruce and pine trees, this pathogen can infect several coniferous species. In order to study the population structure of O. tomentosa, we harvested 180 basidiocarps in a 45-year-old white spruce plantation in western Quebec in autumn 1997, and extracted DNA directly from individual basidiocarps. Using a combination of spatial coordinates and...

Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles

Scott P. Egan, Patrik Nosil & Daniel J. Funk
This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of...

Data from: Increased growth in sunflower correlates with reduced defenses and altered gene expression in response to biotic and abiotic stress

Maya Mayrose, Nolan C. Kane, Itay Mayrose, Katrina M. Dlugosch & Loren H. Rieseberg
Cultivated plants have been selected by humans for increased yield in a relatively benign environment, where nutrient and water resources are often supplemented, and biotic enemy loads are kept artificially low. Agricultural weeds have adapted to this same benign environment as crops, and often have high growth and reproductive rates, even though they have not been specifically selected for yield. Considering the competing demands for resources in any plant, a key question is whether adaptation...

Data from: Adaptation with gene flow across the landscape in a dune sunflower

Rose L. Andrew, Katherine L. Ostevik, Daniel P. Ebert & Loren H. Rieseberg
Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We...

Data from: Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species

Ryan C. Garrick, Edgar Benavides, Michael Russello, James Gibbs, Nikos Poulakakis, Kirstin Dion, Chaz Hyseni, Brittney Kajdacsi, Lady Márquez, Sarah Bahan, Claudio Ciofi, Washington Tapia, Adalgisa Caccone, Kirstin B. Dion, James P. Gibbs & Michael A. Russello
Genes from recently extinct species can live on in the genomes of extant individuals of mixed ancestry. Recently, Poulakakis et al. detected genetic signatures of the giant Galápagos tortoise once endemic to Floreana Island (Chelonoidis elephantopus) within eleven hybrid individuals of otherwise pure C. becki on Volcano Wolf, Isabela Island. Movement of tortoises among islands by pirate and whaling ships was not uncommon during the 1800’s, representing a likely mechanism by which individuals from Floreana...

Data from: Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift

Sam Yeaman & Sarah P. Otto
There is a long tradition in population genetics of exploring the maintenance of variation under migration-selection balance using deterministic models that assume infinite population size. With finite population size, stochastic dynamics can greatly reduce the potential for the maintenance of polymorphism, but this has yet to be explored in detail. Here, classical two-patch models are extended to predict: i) the probability of a locally beneficial mutation rising in frequency in the patch where it is...

Data from: Recombination and hitchhiking of deleterious alleles

Matthew Hartfield & Sarah P. Otto
When new advantageous alleles arise and spread within a population, deleterious alleles at neighbouring loci can hitchhike alongside them and spread to fixation in areas of low recombination, introducing a fixed mutation load. We use branching processes and diffusion equations to calculate the probability that a deleterious allele hitchhikes and fixes alongside an advantageous mutant. As expected, the probability of fixation of a deleterious hitchhiker rises with the selective advantage of the sweeping allele and...

Data from: A test of hybrid growth disadvantage in wild, free-ranging species pairs of threespine sticklebacks (Gasterosteus aculeatus) and its implications for ecological speciation

Eric B. Taylor, Carling Gerlinsky, Nicole Farrell & Jennifer L. Gow
Ecological speciation is the evolution of reproductive isolation as a direct or indirect consequence of divergent natural selection. Reduced performance of hybrids in nature is thought to be an important process by which natural selection can favour the evolution of assortative mating and drive speciation. Benthic and limnetic sympatric species of threespine stickleback (Gasterosteus aculeatus) are adapted to alternative trophic niches (bottom browsing versus open water planktivory, respectively) and reduced feeding performance of hybrids is...

Data from: Recently-formed polyploid plants diversify at lower rates

Itay Mayrose, Shing H. Zhan, Carl J. Rothfels, Karen Magnuson-Ford, Michael S. Barker, Loren H. Rieseberg & Sarah P. Otto
Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macro-evolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead-end, whereas recent genomic studies suggest that polyploidy has been a key driver of macro-evolutionary success. Here we examine the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit...

Data from: Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont the mountain pine beetle

Clement Kin Ming Tsui, Amanda D. Roe, Yousry A. El-Kassaby, Adrianne V. Rice, Sepideh Massoumi Alamouti, Felix A. H. Sperling, Janice E. K. Cooke, Jörg Bohlmann & Richard C. Hamelin
We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect–fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached...

Data from: Reductions in prolonged swimming capacity following freshwater colonization in multiple threespine stickleback populations.

Anne C. Dalziel, Timothy H. Vines & Patricia M. Schulte
We compared ancestral anadromous-marine and nonmigratory, stream-resident threespine stickleback (Gasterosteus aculeatus) populations to examine the outcome of relaxed selection on prolonged swimming performance. We reared marine and stream-resident fish from two locations in a common environment and found that both stream-resident populations had lower critical swimming speeds (Ucrits) than marine populations. F1 hybrids from the two locations displayed significant differences in dominance, suggesting that the genetic basis for variation in Ucrit differs between locations. To...

Data from: Hybrid origin of Audubon's warbler

Alan Brelsford, Borja Milá & Darren E Irwin
Several animal species have recently been shown to have hybrid origins, but no avian examples have been documented with molecular evidence. We investigate whether the Audubon's warbler, one of four visually distinct species in the yellow-rumped warbler (Dendroica coronata) complex, may have originated through hybridization between two other species in this group, the myrtle warbler and black-fronted warbler. Analysis of nuclear AFLP and sequence markers shows that Audubon's warblers are genetically intermediate, and carry a...

Data from: Data archiving is a good investment

Heather A. Piwowar, Todd J. Vision & Michael C. Whitlock
Funding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.

Registration Year

  • 2011
    22

Resource Types

  • Dataset
    22

Affiliations

  • University of British Columbia
    22
  • Duke University
    2
  • University of Arizona
    2
  • Université Laval
    2
  • Ministry of Environment
    1
  • National Evolutionary Synthesis Center
    1
  • University of Massachusetts Amherst
    1
  • University of Crete
    1
  • University of Queensland
    1
  • University of Georgia
    1