73 Works

Data from: Genetic evidence for ecological divergence in kokanee salmon

Matthew A. Lemay & Michael A. Russello
The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of non-model organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines), however outside of the spawning season...

Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

Armando Geraldes, Charles A. Hefer, Arnaud Capron, Natalia Kolosova, Felix Martinez-Nuñez, Raju Y. Soolanayakanahally, Brian Stanton, Robert D. Guy, Shawn D. Mansfield, Carl J. Douglas & Quentin C. B. Cronk
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of...

Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Kira E. Delmore, Sariel Hübner, Nolan C. Kane, Richard Schuster, Rose L. Andrew, Francisco Câmara, Roderic Guigo & Darren E. Irwin
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for...

Data from: Evolution of haploid selection in predominantly diploid organisms

Sarah P. Otto, Michael F. Scott & Simone Immler
Diploid organisms manipulate the extent to which their haploid gametes experience selection. Animals typically produce sperm with a diploid complement of most proteins and RNA, limiting selection on the haploid genotype. Plants, however, exhibit extensive expression in pollen, with actively transcribed haploid genomes. Here we analyze models that track the evolution of genes that modify the strength of haploid selection to predict when evolution intensifies and when it dampens the “selective arena” within which male...

Data from: Adaptive plasticity and niche expansion in an invasive thistle

Kathryn G. Turner, Hélène Fréville & Loren H. Rieseberg
Phenotypic differentiation in size and fecundity between native and invasive populations of a species has been suggested as a causal driver of invasion in plants. Local adaptation to novel environmental conditions through a micro-evolutionary response to natural selection may lead to phenotypic differentiation and fitness advantages in the invaded range. Local adaptation may occur along a stress tolerance trade-off, favoring individuals that, in benign conditions, shift resource allocation from stress tolerance to increased vigor and...

Data from: Additive genetic variance and effects of inbreeding, sex and age on heterophil to lymphocyte ratio in song sparrows

Sylvain Losdat, Peter Arcese, Laura Sampson, Nacho Villar & Jane M. Reid
1. Physiological traits can influence individual fitness and evolutionary changes in stress-related physiological traits have been hypothesized to mediate the evolution of life-history traits and trade-offs. The hypothesis that such physiological variation could drive ongoing life-history evolution requires non-zero additive genetic variance in individual stress-related physiological traits. However, the magnitude of genetic and environmental components of phenotypic variation in stress-related physiological traits has not been estimated in fully developed vertebrates under natural environmental conditions. 2....

Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

Sebastien Renaut & Loren H. Rieseberg
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has...

Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

Simon Roux, Steven J. Hallam, Tanja Woyke & Matthew B. Sullivan
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown'...

Data from: Fitness costs in spatially structured environments

Florence Débarre
The clustering of individuals that results from limited dispersal is a double-edged sword: while it allows for local interactions to be mostly among related individuals, it also results in increased local competition. Here I show that, because they mitigate local competition, fitness costs such as reduced fecundity or reduced survival are less costly in spatially structured environments than in non spatial settings. I first present a simple demographic example to illustrate how spatial structure weakens...

Data from: Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

Seth M. Rudman, Mariano A. Rodriguez-Cabal, Adrian Stier, Takuya Sato, Julian Heavyside, Rana W. El-Sabaawi & Gregory M. Crutsinger
Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an...

Data from: aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

Julie M Allen, Daisie I. Huang, Quentin C Cronk & Kevin P Johnson
Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of...

Data from: Predator kairomones change food web structure and function, regardless of cues from consumed prey

Nicholas A. C. Marino, Diane S. Srivastava & Vinicius F. Farjalla
Predation risk in aquatic systems is often assessed by prey through chemical cues, either those released by prey or by the predator itself. Many studies on predation risk focus on simple pairwise interactions, with only a few studies examining community-level and ecosystem responses to predation risk in species-rich food webs. Further, of these few community-level studies, most assume that prey primarily assess predation risk through chemical cues from consumed prey, even heterospecific prey, rather than...

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer & Sarah Mathews
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is...

Data from: The conservation value of high elevation habitats to North American migrant birds

W. Alice Boyle & Kathy Martin
The basic patterns of faunal community composition and habitat associations of high elevation mountainous regions are poorly-known. This is true for the avifauna of western North America where our knowledge of high elevation use is primarily restricted to breeding assemblages. Here we report on systematic avian surveys of high elevation habitats over four years in British Columbia conducted during the post-breeding and fall migration periods (Aug–Oct). We detected a remarkable diversity of birds (95 species...

Data from: Historical dynamics of ecosystem services bundles

Delphine Renard, Jeanine M. Rhemtulla & Elena M. Bennett
Managing multiple ecosystem services (ES), including addressing trade-offs between services and preventing ecological surprises, is among the most pressing areas for sustainability research. These challenges require ES research to go beyond the currently common approach of snapshot studies limited to one or two services at a single point in time. We used a spatiotemporal approach to examine changes in nine ES and their relationships from 1971 to 2006 across 131 municipalities in a mixed-use landscape...

Data from: A simple approach for maximizing the overlap of phylogenetic and comparative data

Matthew W. Pennell, Richard G. FitzJohn & William K. Cornwell
Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data. A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that...

Data from: Resources alter the structure and increase stochasticity in bromeliad microfauna communities

Jana S. Petermann, Pavel Kratina, Nicolas A. C. Marino, A. Andrew M. MacDonald, Diane S. Srivastava & Nicholas A. C. Marino
Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down...

Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests

Kevin J. Beiler, Suzanne W. Simard & Daniel M. Durall
1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional...

Data from: Time to get moving: assisted gene flow of forest trees

Sally N. Aitken & Jordan B. Bemmels
Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a ‘local is best’ seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of...

Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen

Simren Brar, Clement K. M. Tsui, Braham Dhillon, Marie-Josée Bergeron, David L. Joly, P. J. Zambino, Yousry A. El-Kassaby & Richard C. Hamelin
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola....

Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day

Adriana Suarez-Gonzalez, Jolene T. Sutton, Andrew J. Trant, Elena Zamlynny & Sara V. Good
Premise of study: Molecular population genetics is a powerful tool to infer how species responded to past environmental change. In the northern hemisphere, interest is increasing in how species responded to changes in ice coverage and temperature during the last glaciation maximum (LGM, between 18000–21000 yr ago) with a common assumption that glacial refugia were located at the southern edge of a species range. Methods: We reconstructed the glacial and postglacial phylogeography of Sabatia kennedyana,...

Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection

Pim Edelaar, Severine Roques, Elizabeth A. Hobson, Anders Gonçalves Da Silva, Michael L. Avery, Michael A. Russello, Juan Carlos Senar, Timothy F. Wright, Martina Carrete & Jose Luis Tella
While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained...

Data from: Flowering time of butterfly nectar food plants is more sensitive to temperature than the timing of butterfly adult flight

Heather M. Kharouba & Mark Vellend
1. Variation among species in their phenological responses to temperature change suggests that shifts in the relative timing of key life cycle events between interacting species are likely to occur under climate warming. However, it remains difficult to predict the prevalence and magnitude of these shifts given that there have been few comparisons of phenological sensitivities to temperature across interacting species. 2. Here, we used a broad-scale approach utilizing collection records to compare the temperature...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages

Jean-Sébastien Moore, Robert Bajno, James D. Reist & Eric B. Taylor
Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of British Columbia
  • University of Alberta
  • Duke University
  • University of Aberdeen
  • University of California, Berkeley
  • The Bronx Defenders
  • Centre for Australian National Biodiversity Research
  • University of Cologne
  • Oregon State University
  • University of Minnesota