60 Works

Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

Saemundur Sveinsson & Quentin Cronk
Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes...

Data from: Demographic mechanisms of inbreeding adjustment through extra-pair reproduction

Jane M. Reid, A. Bradley Duthie, Matthew E. Wolak & Peter Arcese
1. One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination. 2. We propose three...

Data from: Identifying the African wintering grounds of hybrid flycatchers using a multi–isotope (δ2H, δ13C, δ15N) assignment approach

Thor Veen, Mårten B. Hjernquist, Steven L. Van Wilgenburg, Keith A. Hobson, Eelke Folmer, Laura Font & Marcel Klaassen
Migratory routes and wintering grounds can have important fitness consequences, which can lead to divergent selection on populations or taxa differing in their migratory itinerary. Collared (Ficedula albicollis) and pied (F. hypoleuca) flycatchers breeding in Europe and wintering in different sub-Saharan regions have distinct migratory routes on the eastern and western sides of the Sahara desert, respectively. In an earlier paper, we showed that hybrids of the two species did not incur reduced winter survival,...

Data from: Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

Ellen Cheng, Karen E. Hodges, José Melo-Ferreira, Paulo C. Alves & L. Scott Mills
With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of...

Data from: A test of the umbrella species approach in restored floodplain ponds.

Margaret A. Branton & John S. Richardson
1.The umbrella species approach, where conservation actions targeted for one or a group of species should benefit the broader community, may provide an effective framework to guide habitat restoration. This requires congruence in the response of umbrella and co-occurring species to environmental stress and recovery, and the identification of potential mechanisms by which co-occurring species benefit from conservation of an umbrella species. 2.Past evaluations of this approach have considered only the presence/absence of umbrella species....

Data from: Basal metabolism in tropical birds: latitude, altitude, and the “pace of life”

Gustavo A. Londoño, Mark A. Chappell, María Del Rosario Castañeda, Jill E. Jankowski & Scott K. Robinson
1. Life history varies across latitudes, with the ‘pace of life’ being ‘slower’ in tropical regions. Because life history is coupled to energy metabolism via allocation tradeoffs and links between performance capacity and energy use, low metabolic intensity is expected in tropical animals. Low metabolism has been reported for lowland tropical birds, but it is unclear if this is due to ‘slow’ life history or to a warm, stable environment. 2. We measured Basal Metabolic...

Data from: Ocean circulation model predicts high genetic structure in a long-lived pelagic developer

Jennifer M. Sunday, Iva Popovic, Wendy J. Palen, Michael G. G. Foreman & Michael W. Hart
Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology, and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species’ dispersive life histories. However, genetic structure is the result of time-integrated processes, and may not capture present-day...

Data from: Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive lifespan

Yolanda E. Morbey, Evelyn L. Jensen & Michael A. Russello
Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal...

Data from: QST FST comparisons with unbalanced half-sib designs

Kimberly J. Gilbert & Michael C. Whitlock
QST, a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between QST and FST, but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this...

Data from: Landscape structure and the genetic effects of a population collapse

Serena A. Caplins, Kimberly J. Gilbert, Claudia Ciotir, Jens Roland, Stephen F. Matter & Nusha Keyghobadi
Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did...

Data from: Jerzego, a new hisponine jumping spider from Borneo (Araneae: Salticidae)

Wayne P. Maddison & Edyta K. Piascik
A new genus and species of hisponine jumping spider from Sarawak, Jerzego corticicola Maddison sp. nov. are described, representing one of the few hisponine jumping spiders known from Asia, and the only whose male is known. Although similar to the primarily-Madagascan genus Hispo in having an elongate and flat body, sequences of 28s and 16sND1 genes indicate that Jerzego is most closely related to Massagris and Tomomingi, a result consistent with morphology. Females of Jerzego...

Data from: Indirect genetic effects underlie oxygen-limited thermal tolerance within a coastal population of chinook salmon

Nicolas J. Muñoz, Katja Anttila, Zhongqi Chen, John W. Heath, Anthony P. Farrell, Bryan D. Neff & N. J. Munoz
With global temperatures projected to surpass the limits of thermal tolerance for many species, evaluating the heritable variation underlying thermal tolerance is critical for understanding the potential for adaptation to climate change. We examined the evolutionary potential of thermal tolerance within a population of chinook salmon (Oncorhynchus tshawytscha) by conducting a full-factorial breeding design and measuring the thermal performance of cardiac function and the critical thermal maximum (CTmax) of offspring from each family. Additive genetic...

Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana

David C. Tack, William R. Pitchers & Keith L. Adams
Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns...

Data from: Immune response genes and pathogen presence predict migration survival in wild salmon smolts

Ken M. Jeffries, Scott G. Hinch, Marika Kirsten Gale, Timothy D. Clark, Andrew G. Lotto, Matthew T. Casselman, Shaorong Li, Erin L. Rechisky, Aswea D. Porter, David W. Welch, Kristina M. Miller & Marika Kirstin Gale
We present the first data to link physiological responses and pathogen presence with subsequent fate during migration of wild salmonid smolts. We tagged and non-lethally sampled gill tissue from sockeye salmon (Oncorhynchus nerka) smolts as they left their nursery lake (Chilko Lake, BC, Canada) to compare gene expression profiles and freshwater pathogen loads with migration success over the first ~1150 km of their migration to the North Pacific Ocean using acoustic telemetry. Fifteen percent of...

Data from: Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins

Milica Mandic, Marina L. Ramon, Andrew Y. Gracey & Jeffrey G. Richards
Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low-oxygen (hypoxia) of the hypoxia tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine if these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O2...

Data from: Multiple plant traits shape the genetic basis of herbivore community assembly

Matthew A. Barbour, Mariano A. Rodriguez-Cabal, Elizabeth T. Wu, Riitta Julkunen-Tiitto, Carol E. Ritland, Allyson E. Miscampbell, Erik S. Jules & Gregory M. Crutsinger
1. Community genetics research has posited a genetic basis to the assembly of ecological communities. For arthropod herbivores in particular, there is strong support that genetic variation in host plants is a key factor shaping their diversity and composition. However, the specific plant phenotypes underlying herbivore responses remain poorly explored for most systems. 2. We address this knowledge gap by examining the influence of both genetic and phenotypic variation in a dominant host-plant species, Salix...

Data from: Social evolution in structured populations

Florence Débarre, Christoph Hauert & Michael Doebeli
Understanding the evolution of social behaviours such as altruism and spite is a long-standing problem that has generated thousands of articles and heated debates. Previous theoretical studies showed that whether altruism and spite evolve may be contingent on seemingly artificial model features, such as which rule is chosen to update the population (e.g., Birth-Death or Death-Birth), and whether the benefits and costs of sociality affect fecundity or survival. Here we unify these features in a...

Data from: How much of the world is woody?

Richard G. FitzJohn, Matt W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell & Matthew W. Pennell
1.The question posed by the title of this paper is a basic one, and it is surprising that the answer is not known. Recently assembled trait datasets provide an opportunity to address this, but scaling these datasets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterised,...

Data from: Adaptive divergence along environmental gradients in a climate-change-sensitive mammal

P. Henry & M. A. Russello
In the face of predicted climate change, a broader understanding of biotic responses to varying environments has become increasingly important within the context of biodiversity conservation. Local adaptation is one potential option, yet remarkably few studies have harnessed genomic tools to evaluate the efficacy of this response within natural populations. Here we show evidence of selection driving divergence of a climate change-sensitive mammal, the American pika (Ochotona princeps), distributed along elevation gradients at its northern...

Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

Jennifer R. Mandel, Rebecca B. Dikow, Vicki A. Funk, Rishi R. Masalia, S. Evan Staton, Alex Kozik, Richard W. Michelmore, Loren H. Rieseberg & John M. Burke
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous...

Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

Hsin-Hung Chou, Nigel F. Delaney, Jeremy A. Draghi & Christopher J. Marx
How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most...

Data from: Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs

Marc A. Sze, Masashi Tsuruta, Shun-Wei Julia Yang, Yeni Oh, S. F. Paul Man, James C. Hogg & Don D. Sin
Introduction: Previous reports have shown that the gastrointestinal (GI) bacterial microbiota can have profound effects on the lungs, which has been described as the “gut-lung axis”. However, whether a “lung-gut” axis exists wherein acute lung inflammation perturbs the gut and blood microbiota is unknown. Methods: Adult C57/Bl6 mice were exposed to one dose of LPS or PBS instillation (n = 3 for each group) directly into lungs. Bacterial microbiota of the bronchoalveolar lavage fluid, blood,...

Data from: The deep phylogeny of jumping spiders (Araneae, Salticidae)

Wayne P. Maddison, Daiqin Li, Melissa Bodner, Junxia Zhang, Xu Xin, Qinqing Liu, Fengxiang Liu & Wayne Maddison
In order to resolve better the deep relationships among salticid spiders, we compiled and analyzed a molecular dataset of 169 salticid taxa (and 7 outgroups) and 8 gene regions. This dataset adds many new taxa to previous analyses, especially among the non-salticoid salticids, as well as two new genes – wingless and myosin heavy chain. Both of these genes, and especially the better sampled wingless, confirm many of the relationships indicated by other genes. The...

Data from: Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

Nate B. Hardy & Sarah P. Otto
Evolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant...

Data from: Too much of a good thing: The unique and repeated paths toward copper adaptation

Aleeza C. Gerstein, Jasmine Ono, Dara S. Lo, Marcus L. Campbell, Anastasia Kuzmin & Sarah P. Otto
Copper is a micronutrient essential for growth due to its role as a co-factor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of British Columbia
  • University of Alberta
  • University of Aberdeen
  • Western University
  • Indiana University Bloomington
  • Fisheries and Oceans Canada
  • VU University Amsterdam
  • State University of New York
  • University of Guelph
  • University of Zurich