39 Works

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

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....

Data from: The genetic basis of speciation in the Giliopsis lineage of Ipomopsis (Polemoniaceae)

Troy E. Wood, Takuya Nakazato & Loren H. Rieseberg
One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL)...

Data from: Genomic islands of divergence are not affected by geography of speciation in sunflowers.

Sebastien Renaut, Christopher J. Grassa, Sam Yeaman, Zhao Lai, Nolan K. Kane, Brook T. Moyers, John E. Bowers, John M. Burke & Loren H. Rieseberg
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic...

Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex

Federico Roda, Luke Ambrose, Gregory M. Walter, Huanle L. Liu, Andrea Schaul, Andrew Lowe, Pieter B. Pelser, Peter Prentis, Loren H. Rieseberg & Daniel Ortiz-Barrientos
Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection...

Data from: Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops)

Katie E. Lotterhos, Stefan J. Dick & Dana R. Haggarty
Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in...

Data from: Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression

Jane M. Reid, Lukas F. Keller, Amy B. Marr, Pirmin Nietlisbach, Rebecca J. Sardell & Peter Arcese
Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete “apparent” pedigree data...

Data from: Lack of parallel genetic patterns underlying the repeated ecological divergence of beach and stream spawning kokanee salmon

Karen K. Frazer & Michael A. Russello
Recent progress in methods for detecting adaptive population divergence in situ shows promise for elucidating the conditions under which selection acts to generate intraspecific diversity. Rapid ecological diversification is common in fishes, however, the role of phenotypic plasticity and adaptation to local environments is poorly understood. It is now possible to investigate genetic patterns to make inferences regarding phenotypic traits under selection and possible mechanisms underlying ecotype divergence, particularly where similar novel phenotypes have arisen...

Data from: Population genetic structure of the western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae) in British Columbia, Canada

Sheri A. Maxwell, Howard M. A. Thistlewood & Nusha Keyghobadi
1. Population connectivity and movement are key ecological parameters influencing the impact of pests, and are important considerations in control strategies. For many insects, these parameters are difficult to assess directly, although they may be assessed indirectly using population genetic data. 2. We used microsatellite markers to examine population genetic structure of the western cherry fruit fly, the main pest of cherry crops in western North America, in British Columbia, Canada, and make inferences about...

Data from: Phylogeography and population history of Leopardus guigna, the smallest American felid

Constanza Napolitano, Warren E. Johnson, Jim Sanderson, Stephen J. O'Brien, Rus Hoelzel, Rachel Freer, Nigel Dunstone, Kermit Ritland, Carol E. Ritland, Elie Poulin & A. Rus Hoelzel
The guigna (Leopardus guigna) is the smallest and most-restricted New World cat species, inhabiting only around 160,000 km2 of temperate rain forests in southern South America and is currently threatened by habitat loss, fragmentation and human persecution. We investigated phylogeographic patterns of genetic diversity, demographic history and barriers to gene flow with 116 individuals sampled across the species geographic range by analyzing 1,798 base pairs of the mtDNA (496 bp HVSI region, 720 bp NADH-5...

Data from: Evolutionarily stable sex ratios and mutation load

Josh Hough, Simone Immler, Spencer C. H. Barrett & Sarah P. Otto
Frequency-dependent selection should drive dioecious populations toward a 1:1 sex ratio, but biased sex ratios are widespread, especially among plants with sex chromosomes. Here, we develop population genetic models to investigate the relationships between evolutionarily stable sex ratios, haploid selection, and deleterious mutation load. We confirm that when haploid selection acts only on the relative fitness of X and Y-bearing pollen and the sex ratio is controlled by the maternal genotype, seed sex ratios evolve...

Data from: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

Armando Geraldes, Steve P. DiFazio, Gancho T. Slavov, Priya Ranjan, Wellington Muchero, Jan Hannemann, Lee E. Gunter, Ann M. Wymore, Christopher J. Grassa, Nima Farzaneh, Ilga Porth, Athena D. Mckown, Oleksandr Skyba, Eryang Li, Miki Fujita, Jaroslav Klápště, Joel Martin, Wendy Schackwitz, Christa Pennacchio, Daniel Rokhsar, Michael C. Friedmann, Geoffrey O. Wasteneys, Robert D. Guy, Yousry A. El-Kassaby, Shawn D. Mansfield … & Gerald A. Tuskan
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a...

Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus

Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre & Carine Brouat
Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague....

Data from: Differential migratory timing of western populations of Wilson’s Warblers revealed by mitochondrial DNA and stable isotopes

Kristina L. Paxton, Monica Yau, Frank R. Moore & Darren E. Irwin
Molecular markers and stable isotopes have provided important insights into the migratory connectivity of small landbirds. Research integrating these two methods has primarily focused on linking breeding and wintering sites, rather than focusing on timing of migratory movement of different breeding populations. We used mitochondrial DNA and isotopic markers to infer the timing of various breeding populations of migrating Wilson's Warblers (Cardellina pusilla) moving through a migratory stopover site, demonstrating the value of multiple sources...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

Registration Year

  • 2013

Resource Types

  • Dataset


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