39 Works

Data from: Complementary and alternative asthma treatments and their association with asthma control: a population-based study

Wenjia Chen, J. Mark FitzGerald, Roxanne Rousseau, Larry D. Lynd, Wan C. Tan & Mohsen Sadatsafavi
Objectives: Many patients with asthma spend time and resources consuming complementary and alternative medicines (CAMs). This study explores whether CAM utilization is associated with asthma control and the intake of asthma controller medications. Design: Population-based, prospective cross-sectional study Setting: general population residing in two census areas in the province of British Columbia, Canada. Recruitment was based on random-digit dialing of both landlines and cell phones. Participants: 486 patients with self-reported physician-diagnosis of asthma (mean age...

Data from: Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an Artichoke

Dan G. Bock, Nolan C. Kane, Daniel P. Ebert & Loren H. Rieseberg
The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today. Despite the cultural and economic importance...

Data from: Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

Sebastien Renaut, Gregory L. Owens & Loren H. Rieseberg
The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterized. Here, through the use of transcriptome sequencing, we examined genomic divergence for three pairs of sister species of sunflowers. Two of the pairs...

Data from: Comparative analysis reveals that polyploidy does not decelerate diversification in fish

Shing H. Zhan, Lior Glick, Costas S. Tsigenopoulos, Sally P. Otto & Itay Mayrose
While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and...

Data from: Variation in body shape across species and populations in a radiation of Diaptomid copepods

Stephen Hausch, Jonathan B. Shurin & Blake Matthews
Inter and intra-population variation in morphological traits, such as body size and shape, provides important insights into the ecological importance of individual natural populations. The radiation of Diaptomid species (~400 species) has apparently produced little morphological differentiation other than those in secondary sexual characteristics, suggesting sexual, rather than ecological, selection has driven speciation. This evolutionary history suggests that species, and conspecific populations, would be ecologically redundant but recent work found contrasting ecosystem effects among both...

Data from: Decomposing variation in male reproductive success: age-specific variances and covariances through extra-pair and within-pair reproduction

Christophe Lebigre, Peter Arcese & Jane M. Reid
1. Age-specific variances and covariances in reproductive success shape the total variance in lifetime reproductive success (LRS), age-specific opportunities for selection, and population demographic variance and effective size. Age-specific (co)variances in reproductive success achieved through different reproductive routes must therefore be quantified to predict population, phenotypic and evolutionary dynamics in age-structured populations. 2. While numerous studies have quantified age-specific variation in mean reproductive success, age-specific variances and covariances in reproductive success, and the contributions of...

Data from: Migration, mitochondria, and the yellow-rumped warbler

David P. L. Toews, Milica Mandic, Jeffrey G. Richards & Darren E. Irwin
Discordance between mitochondrial and nuclear DNA has been noted in many systems. Asymmetric introgression of mitochondria is a common cause of such discordances, although in most cases the drivers of introgression are unknown. In the yellow-rumped warbler, evidence suggests that mtDNA from the eastern, myrtle warbler, has introgressed across much of the range of the western form, the Audubon's warbler. Within the southwestern United States myrtle mtDNA comes into contact with another clade that occurs...

Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias

Austen C. Thomas, Simon N. Jarman, Katherine H. Haman, Andrew W. Trites & Bruce E. Deagle
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical...

Data from: Pain and pessimism: dairy calves exhibit negative judgement bias following hot-iron disbudding

Heather W. Neave, Rolnei R. Daros, João H. C. Costa, Marina A. G. Von Keyserlingk & Daniel M. Weary
Pain is defined as an unpleasant sensory and emotional experience associated with actual or potential tissue damage, but emotional states are difficult to directly assess in animals. Researchers have assessed pain using behavioural and physiological measures, but these approaches are limited to understanding the arousal rather than valence of the emotional experience. Cognitive bias tasks show that depressed humans judge ambiguous events negatively and this technique has been applied to assess emotional states in animals....

Data from: Multiple origins of sex chromosome fusions correlated with chiasma localization in Habronattus jumping spiders (Araneae: Salticidae)

Wayne P. Maddison & Geneviève Leduc-Robert
Entelegyne spiders rarely show fusions yielding neo-Y chromosomes, which M. J. D. White attributed to a constraint in spiders, namely their proximal chiasma localization acting to upset meiotic segregation in males with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have X1X20 sex chromosomes in males, 10 have X1X2Y, 15 have X1X2X3Y, 2 have X0, and one has both X1X20 and X1X2X3Y. Chromosome numbers and behavior suggest neo-Ys formed by an autosome-X...

Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

François Olivier Hébert, Sébastien Renaut & Louis Bernatchez
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole...

Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Kathryn A. Hodgins, Zhao Lai, Luiz O. Oliveira, David W. Still, Moira Scascitelli, Michael S. Barker, Nolan C. Kane, Hannes Dempewolf, Alex Kozik, Richard V. Kesseli, John M. Burke, Richard W. Michelmore & Loren H. Rieseberg
Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium...

Data from: Sociality influences cultural complexity

Michael Muthukrishna, Ben W. Shulman, Vlad Vasilescu & Joseph Henrich
Archaeological and ethnohistorical evidence suggests a link between a population's size and structure, and the diversity or sophistication of its toolkits or technologies. Addressing these patterns, several evolutionary models predict that both the size and social interconnectedness of populations can contribute to the complexity of its cultural repertoire. Some models also predict that a sudden loss of sociality or of population will result in subsequent losses of useful skills/technologies. Here, we test these predictions with...

Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

Bruce E. Deagle, Austen C. Thomas, Amanda K. Shaffer, Andrew W. Trites & Simon N. Jarman
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a...

Data from: Divergence is focused on few genomic regions early in speciation: incipient speciation of sunflower ecotypes

Rose L. Andrew & Loren H. Rieseberg
Early in speciation, when populations are undergoing the transition from local adaptation to incipient species, is when a number of transient, but potentially important, processes appear to be most easily detected. These include signatures of selective sweeps that can point to asymmetry in selection between habitats, divergence hitchhiking and associations of adaptive genes with environments. In a genomic comparison of ecotypes of the prairie sunflower, Helianthus petiolaris, occurring at Great Sand Dunes National Park (Colorado),...

Data from: Weak habitat isolation in a threespine stickleback (Gasterosteus spp.) species pair

Laura Southcott, Laura Nagel, Todd Hatfield & Dolph Schluter
Reproductive isolation is central to the study of speciation. Multiple isolating barriers may prevent species from hybridizing, although their individual strength and the interactions between them are rarely measured. We quantified habitat isolation in a recently diverged threespine stickleback species pair (Gasterosteus aculeatus complex) and controlled for any such interactions. Using enclosures in an outdoor pond, we confirm that males of the two species strongly prefer different nesting habitats: limnetic males build nests in open...

Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

Florence Débarre, Ophélie Ronce & Sylvain Gandon
How do mutation and gene flow influence population persistence, niche expansion, and local adaptation in spatially heterogeneous environments? In this article, we analyse a demographic and evolutionary model of adaptation to an environment containing two habitats in equal frequencies, and we bridge the gap between different theoretical frameworks. Qualitatively, our model yields four qualitative types of outcomes: (i) global extinction of the population (ii) adaptation to one habitat only, but also adaptation to both habitats...

Data from: Temporal variation favors the evolution of generalists in experimental populations of Drosophila melanogaster

Catriona Condon, Brandon S. Cooper, Sam Yeaman, & Michael J. Angilletta
In variable environments, selection should favor generalists that maintain fitness across a range of conditions. However, costs of adaptation may generate fitness trade-offs and lead to some compromise between specialization and generalization that maximizes fitness. Here, we evaluate the evolution of specialization and generalization in 20 populations of Drosophila melanogaster experimentally evolved in constant and variable thermal environments for 3 years. We developed genotypes from each population at two temperatures after which we measured fecundity...

Data from: The magnitude of local adaptation under genotype-dependent dispersal

Daniel I. Bolnick & Sarah P. Otto
Dispersal moves individuals from patches where their immediate ancestors were successful to sites where their genotypes are untested. As a result, dispersal generally reduces fitness, a phenomenon known as “migration load.” The strength of migration load depends on the pattern of dispersal and can be dramatically lessened or reversed when individuals move preferentially toward patches conferring higher fitness. Evolutionary ecologists have long modeled nonrandom dispersal, focusing primarily on its effects on population density over space,...

Data from: Lineage-specific mapping of quantitative trait loci

Charles Chen & Kermit Ritland
We present an approach for quantitative trait locus (QTL) mapping, termed "lineage-specific QTL mapping", for inferring allelic changes of QTL evolution along branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. While comparisons of QTL maps among species can identify homology of QTLs by apparent...

Data from: The availability of research data declines rapidly with article age

Timothy H. Vines, Arianne Y. K. Albert, Rose L. Andrew, Florence Débarre, Dan G. Bock, Michelle T. Franklin, Kimberly J. Gilbert, Jean-Sébastien Moore, Sébastien Renaut & Diana J. Rennison
Policies ensuring that research data are available on public archives are increasingly being implemented at the government, funding agency, and journal level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term, and indeed many studies have found that authors are often unable or unwilling to share their data. However, there are no systematic estimates of how the availability of research data changes with time...

Data from: Replicate divergence between and within sounds in a marine fish: the copper rockfish (Sebastes caurinus)

Eric B. Taylor, Jonathan B. Shurin & Stefan Dick
The evolution of population structure in marine organisms and its relevance to conservation has recently received increasing attention. We tested the degree of genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of five replicate sounds on the west coast of Vancouver Island, British Columbia using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031), but consistently higher between paired coast and...

Data from: \"Transcriptome resources for three hybrid sunflower species (Helianthus anomalus, H. deserticola, H paradoxus)\" in Genomic Resources Notes accepted 1 February 2013–31 March 2013

Loren H. Rieseberg, Sébastien Renaut, Heather C. Rowe & Matthew G. King
This article documents the public availability of three transcriptome sequences. These genomic resources were developed for the following species: Helianthus anomalus, Helianthus deserticola and Helianthus paradoxus.

Data from: Calculating the ecological impacts of animal-borne instruments on aquatic organisms

T. Todd Jones, Kyle S. Van Houtan, Brian L. Bostrom, Peter Ostafichuk, Jon Mikkelsen, Emre Tezcan, Michael Carey, Brittany Imlach & Jeffrey A. Seminoff
1. Animal-borne instruments provide researchers with valuable data to address important questions on wildlife ecology and conservation. However, these devices have known impacts on animal behaviour and energetics. Tags deployed on migrating animals may reduce reproductive output through increased energy demands or cause phenological mismatches of foraging and nesting events. For marine organisms, the only tagging guidelines that exist are based on lift and thrust impacts on birds – concepts that do not translate well...

Data from: Molecular phylogeny of an ancient rodent family (Aplodontiidae)

Antoinette J. Piaggio, Brett A. Coghlan, Allyson E. Miscampbell, Wendy M. Arjo, Douglas B. Ransome & Carol E. Ritland
The family Aplodontiidae contains a single, monotypic extant genus, Aplodontia (mountain beaver), which was 1st described by Rafinesque in 1817. Phylogenetic studies have shown that it is the sister lineage to squirrels. Aplodontia rufa is endemic to the Pacific Northwest and ranges from central California to British Columbia. Currently, 7 described subspecies are recognized based on morphological taxonomic studies. In this study, mitochondrial and nuclear genes were sequenced to infer molecular phylogenies of A. rufa....

Registration Year

  • 2013
    39

Resource Types

  • Dataset
    39

Affiliations

  • University of British Columbia
    39
  • Indiana University Bloomington
    6
  • University of Idaho
    4
  • University of Georgia
    3
  • University of Aberdeen
    2
  • University of Minnesota
    2
  • University of Tennessee at Knoxville
    2
  • University of Colorado Boulder
    2
  • Queen's University
    2
  • University of Missouri–St. Louis
    2