18 Works

Data from: Global biogeography of mating system variation in seed plants

David A. Moeller, Ryan D. Briscoe Runquist, Annika M. Moe, Monica A. Geber, Carol Goodwillie, Pierre-Olivier Cheptou, Christopher G. Eckert, Elizabeth Elle, Mark O. Johnston, Susan Kalisz, Richard H. Ree, Risa D. Sargent, Mario Vallejo-Marin & Alice A. Winn
Latitudinal gradients in biotic interactions have been suggested as causes of global patterns of biodiversity and phenotypic variation. Plant biologists have long speculated that outcrossing mating systems are more common at low than high latitudes owing to a greater predictability of plant–pollinator interactions in the tropics; however, these ideas have not previously been tested. Here, we present the first global biogeographic analysis of plant mating systems based on 624 published studies from 492 taxa. We...

Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations

Angela P. Fuentes-Pardo & Daniel E. Ruzzante
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR)....

Data from: Applications of random forest feature selection for fine-scale genetic population assignment

Emma V.A. Sylvester, Paul Bentzen, Ian R. Bradbury, Marie Clément, Jon Pearce, John Horne, Robert G. Beiko & Emma V. A. Sylvester
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest, and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for...

Data from: Regime shifts shorten food chains for mesopredators with potential sublethal effects

Tessa N. Hempson, Nicholas A.J. Graham, Aaron M. MacNeil, Nathalie Bodin, Shaun K. Wilson & Nicholas A. J. Graham
1. Predator populations are in decline globally. Exploitation, as well as habitat degradation and associated changes in prey availability are key drivers of this process of trophic downgrading. In the short term, longevity and dietary adaptability of large-bodied consumers can mask potential sub-lethal effects of a changing prey base, producing a delayed effect that may be difficult to detect. 2. In coral reef ecosystems, regime shifts from coral- to algae-dominated states caused by coral bleaching...

Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Nicholas W. Jeffery, Claudio DiBacco, Mallory Van Wyngaarden, Lorraine C. Hamilton, Ryan R. E. Stanley, Renée Bernier, Jennifer FitzGerald, K. Matheson, C. H. McKenzie, Praveen Nadukkalam Ravindran, Robert Beiko & Ian R. Bradbury
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we...

Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage

Rebekah A. Oomen, Roxanne M. Gillett & Christopher J. Kyle
Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time-intensive and indirect methods of assessment often underestimate total variation. Here, we explored the suitability of 454 pyrosequencing for characterizing multilocus genes for use in population genetic studies. We compared two sample tagging protocols and two bioinformatic procedures for 454...

Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

Paul R. Berg, Bastiaan Star, Christophe Pampoulie, Ian R. Bradbury, Paul Bentzen, Jeffrey A. Hutchings, Sissel Jentoft & Kjetill S. Jakobsen
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions...

Data from: Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution

Jennifer L. Baker, Katherine A. Dunn, Joseph Mingrone, Bernard A. Wood, Beverly A. Karpinski, Chet C. Sherwood, Derek E. Wildman, Thomas M. Maynard & Joseph P. Bielawski
Genes encoding nuclear receptors (NRs) are attractive as candidates for investigating the evolution of gene regulation because they (1) have a direct effect on gene expression and (2) modulate many cellular processes that underlie development. We employed a three-phase investigation linking NR molecular evolution among primates with direct experimental assessment of NR function. Phase 1 was an analysis of NR domain evolution and the results were used to guide the design of phase 2, a...

Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon

Nicholas W. Jeffery, Ryan R. E. Stanley, Brendan F. Wringe, Javier Guijarro-Sabaniel, Vincent Bourret, Louis Bernatchez, Paul Bentzen, Robert G. Beiko, John Gilbey, Marie Clement & Ian R. Bradbury
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe respectively, with 12 clinal loci in common between continents. Clinal...

Data from: Towards an integrated database on Canadian ocean resources: benefits, current states, and research gaps

Andrés M. Cisneros-Montemayor, William Wai Lung Cheung, Karin Bodtker, Louise Teh, Nadja Steiner, Morgan Bailey, Carie Hoover & Ussif Rashid Sumaila
Oceanic ecosystem services support a range of human benefits, and Canada has extensive research networks producing growing data sets. We present a first effort to compile, link, and harmonize available information to provide new perspectives on the status of Canadian ocean ecosystems and corresponding research. The metadata database currently includes 1094 individual assessments and data sets from government (n = 716), nongovernment (n = 320), and academic sources (n = 58), comprising research on marine...

Data from: Small-scale intraspecific patterns of adaptive immunogenetic polymorphisms and neutral variation in Lake Superior lake trout

Shauna M. Baillie, Riley R. Hemstock, Andrew M. Muir, Charles C. Krueger & Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species’ evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake....

Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

Huai-Chun Wang, Bui Quang Minh, Edward Susko & Andrew J. Roger
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum...

Data from: Widespread increases in iron concentration in European and North American freshwaters

Caroline Björnerås, Gesa A. Weyhenmeyer, Chris D. Evans, Mark O. Gessner, Hans-Peter Grossart, Külli Kangur, Ilga Kokorite, Pirkko Kortelainen, Hjalmar Laudon, Jouni Lehoranta, Noah Lottig, Don T. Monteith, Peter Nõges, Tiina Nõges, Filip Oulehle, Gunnhild Riise, James A. Rusak, Antti Räike, Janis Sire, Shannon Sterling & Emma Kritzberg
Recent reports of increasing iron (Fe) concentrations in freshwaters are of concern, given the fundamental role of Fe in biogeochemical processes. Still, little is known about the frequency and geographical distribution of Fe trends, or about the underlying drivers. We analyzed temporal trends of Fe concentrations across 340 water bodies distributed over 10 countries in northern Europe and North America in order to gain a clearer understanding of where, to what extent, and why Fe...

Data from: Recurrent myocardial infarction: mechanisms of free-floating adaptation and autonomic derangement in networked cardiac neural control

Guy Kember, Jeffrey Ardell, Kalyanam Shivkumar & J. Andrew Armour
The cardiac nervous system continuously controls cardiac function whether or not pathology is present. While myocardial infarction typically has a major and catastrophic impact, population studies have shown that longer-term risk for recurrent myocardial infarction and the related potential for sudden cardiac death depends mainly upon standard atherosclerotic variables and autonomic nervous system maladaptations. Investigative neurocardiology has demonstrated that autonomic control of cardiac function includes local circuit neurons for networked control within the peripheral nervous...

Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Čepička, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto & Andrew J. Roger
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed....

Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic

Nicholas W. Jeffery, Claudio DiBacco, Brendan F. Wringe, Ryan R.E. Stanley, Lorraine C. Hamilton, Praveen N. Ravindran & Ian R. Bradbury
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations...

Data from: Ancient chromosomal rearrangement associated with local adaptation of a post-glacially colonized population of Atlantic Cod in the northwest Atlantic

Marion Sinclair-Waters, Ian R. Bradbury, Corey J. Morris, Sigbjorn Lien, Matthew P. Kent & Paul Bentzen
Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analyzed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a non-migratory population and to define conservation units...

Data from: Predation, metabolic priming and early life-history rearing environment affect the swimming capabilities of growth hormone transgenic rainbow trout

Glenn T. Crossin & Robert H. Devlin
The period of first feeding, when young salmonid fishes emerge from natal stream beds, is one fraught with predation risk. Experiments conducted in semi-natural stream mesocosms have shown that growth hormone transgenic salmonids are at greater risk of predation than their non-transgenic siblings, due partly to the higher metabolic demands associated with transgenesis, which force risky foraging behaviours. This raises questions as to whether there are differences in the swim-performance of transgenic and non-transgenic fishes...

Registration Year

  • 2017
    18

Resource Types

  • Dataset
    18

Affiliations

  • Dalhousie University
    18
  • Fisheries and Oceans Canada
    6
  • Bedford Institute of Oceanography
    3
  • Memorial University of Newfoundland
    3
  • Uppsala University
    2
  • Norwegian University of Life Sciences
    2
  • Centre d'Ecologie Fonctionnelle et Evolutive
    1
  • Centre for Ecology and Hydrology
    1
  • Estonian University of Life Sciences
    1
  • George Washington University
    1