21 Works

Data from: Reproduction as a bottleneck to treeline advance across the circumarctic forest tundra ecotone

Carissa D. Brown, Geneviève Dufour-Tremblay, Ryan G. Jameson, Steven D. Mamet, Andrew J. Trant, Xanthe J. Walker, Stéphane Boudraeu, Karen A. Harper, Greg H.R. Henry, Luise Hermanutz, Annika Hofgaard, Ludmila Isaeva, G. Peter Kershaw, Jill F. Johnstone & Gregory H. R. Henry
The fundamental niche of many species is shifting with climate change, especially in sub-arctic ecosystems with pronounced recent warming. Ongoing warming in sub-arctic regions should lessen environmental constraints on tree growth and reproduction, leading to increased success of trees colonising tundra. Nevertheless, variable responses of treeline ecotones have been documented in association with warming temperatures. One explanation for time lags between increasingly favourable environmental conditions and treeline ecotone movement is reproductive limitations caused by low...

Data from: Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America

Emma V.A. Sylvester, Robert G. Beiko, Paul Bentzen, Ian Paterson, John B. Horne, Beth Watson, Sarah Lehnert, Steven Duffy, Marie Clément, Martha J. Robertson, Ian R. Bradbury & Emma V. A. Sylvester
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations...

Data from: Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes.

Aaron A. Heiss, Martin Kolisko, Fleming Ekelund, Matthew W. Brown, Andrew J. Roger, Alastair G.B. Simpson & Alastair G. B. Simpson
Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes, and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, small heterotrophic flagellates that resemble Excavata by morphology, but group with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a...

Data from: Estimating the relative fitness of escaped farmed salmon offspring in the wild and modeling the consequences of invasion for wild populations

Emma V.A. Sylvester, Brendan F. Wringe, Steven J. Duffy, Lorraine C. Hamilton, Ian A. Fleming, Marco Castellani, Paul Bentzen, Ian R. Bradbury & Emma V. A. Sylvester
Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in lab and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here we follow a single large escape event of farmed Atlantic salmon...

Data from: Genome-wide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America

Nicholas W. Jeffery, Ian R. Bradbury, Ryan R.E. Stanley, Brendan F. Wringe, Mallory Van Wyngaarden, J. Ben Lowen, Cynthia H. McKenzie, Kyle Matheson, Philip S. Sargent, Claudio DiBacco & Ryan R. E. Stanley
Genetic-environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation-by-distance. Here we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of the invasive European green crab (Carcinus maenas) in eastern North America. Green crab populations in eastern North America are associated with two independent invasions, previously shown to consist of distinct northern and...

Data from: A range-wide domino effect and resetting of the annual cycle in a migratory songbird

Elizabeth A. Gow, Lauren Burke, David W. Winkler, Samantha M. Knight, Robert G. Clark, Marc Bélisle, Lisha L. Berzins, Tricia Blake, Eli S. Bridge, Russell D. Dawson, Peter O. Dunn, Dany Garant, Geoff Holroyd, Andrew G. Horn, David J.T. Hussell, Olga Lansdorp, Andrew J. Laughlin, Marty L. Leonard, Fanie Pelletier, Dave Shutler, Lynn Siefferman, Caz M. Taylor, Helen Trefry, Carol M. Vleck, David Vleck … & D. Ryan Norris
Latitudinal differences in timing of breeding are well documented but how such differences carry over to influence timing of events in the annual cycle of migratory birds is not well understood. We examined geographic variation in timing of events throughout the year using light-level geolocator tracking data from 133 migratory tree swallows (Tachycineta bicolor) originating from 12 North American breeding populations. A swallow’s breeding latitude influenced timing of breeding, which then carried over to affect...

Data from: Combined measurements of prey availability explain habitat selection in foraging seabirds

James J. Waggitt, Pierre W. Cazenave, Leigh M. Howarth, Peter G.H. Evans, Jeroen Van Der Kooij & Jan G. Hiddink
Understanding links between habitat characteristics and foraging efficiency help to predict how environmental change could influence populations of top-predators. This study examines whether measurements of prey (clupeids) availability varied over stratification gradients, and determined if any of those measurements coincided with aggregations of foraging seabirds (common guillemot Uria aalge, Manx shearwater Puffinus puffinus) in the Celtic Sea, UK. The probability of encountering foraging seabirds was highest around fronts between mixed and stratified water. Prey were...

Data from: Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing

Bjarne Larsen, Kyle Gardner, Carsten Pedersen, Marian Ørgaard, Zoë Migicovsky, Sean Myles & Torben Bo Toldam-Andersen
In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single...

Data from: Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

Mallory Van Wyngaarden, Paul V. R. Snelgrove, Claudio DiBacco, Lorraine C. Hamilton, Naiara Rodriguez-Ezpeleta, Luyao Zhan, Robert Beiko, Ian R. Bradbury & Robert G. Beiko
Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and...

Data from: Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

Katherine A. Dunn, Toby Kenney, Hong Gu & Joseph P. Bielawski
Background: An excess of nonsynonymous substitutions, over neutrality, is considered evidence of positive Darwinian selection. Inference for proteins often relies on estimation of the nonsynonymous to synonymous ratio (ω=dN/dS) within a codon model. However, to ease computational difficulties, ω is typically estimated assuming an idealized substitution process where (i) all nonsynonymous substitutions have the same rate (regardless of impact on organism fitness) and (ii) instantaneous double and triple (DT) nucleotide mutations have zero probability (despite...

Data from: Modifying maternal sleep position in the third trimester of pregnancy with positional therapy: a randomized pilot trial

Allan J. Kember, Heather M. Scott, Louise M. O'Brien, Ali Borazjani, Michael B. Butler, Jesse H. Wells, Andre Isaac, Kaishin Chu, Jerry Coleman & Debra L. Morrison
OBJECTIVE: To evaluate whether the percentage of time spent supine during sleep in the third trimester of pregnancy could be reduced using a positional therapy device (PrenaBelt) compared with a sham device. DESIGN: A double-blind, randomized, sham-controlled, crossover pilot trial. SETTING: Conducted between March 2016 and January 2017, at a single, tertiary-level center in Canada. PARTICIPANTS: Twenty-three participants entered the study. Twenty participants completed the study. Participants were low-risk, singleton, third-trimester pregnant women aged 18...

Data from: Evaluation of the novel avocado/soybean unsaponifiable Arthrocen to alter joint pain and inflammation in a rat model of osteoarthritis

Ramin Goudarzi, Allison Reid & Jason J. McDougall
Background: Avocado/soybean unsaponifiables such as Arthrocen have been reported to reduce cartilage catabolism and chondrocytic synthesis of inflammatory mediators associated with osteoarthritis (OA). While there is some clinical evidence that avocado/soybean unsaponifiables can reduce OA pain, no preclinical studies have corroborated this observation. The present study determined whether addition of an avocado/soybean unsaponifiable (Arthrocen) to the drinking water of OA rats reduced direct and referred joint pain. Methods: OA was induced in male Wistar rats...

Data from: Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

Courtney W. Stairs, Laura Eme, Sergio Muñoz-Gómez, Alejandro Cohen, Graham Dellaire, Jennifer N. Shepherd, James P. Fawcett & Andrew J. Roger
Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rqua, a gene encoding an RQ biosynthetic enzyme. Rqua is very...

Data from: Hemimastigophora is a novel supra-kingdom-level lineage of Eukaryotes

Gordon Lax, Yana Eglit, Laura Eme, Erin M. Bertrand, Andrew J. Roger & Alastair G.B. Simpson
Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics1,2,3,4. The ‘phylum’ Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture5,6,7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here...

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson & Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci,...

Data from: Kin selection and allocare in sperm whales

Christine M. Konrad, Timothy R. Frasier, Hal Whitehead & Shane Gero
Cooperative care and defense of young are hypothesized to be foundational to the societies of several species, including the sperm whale (Physeter macrocephalus). However, the extent of allocare among sperm whales and the mechanisms driving it have not been well-characterized. Sperm whale social units are matrilineally-based, making kin selection a likely key driver of allocare, but the relationship between kinship and calf care is essentially unknown. We investigate calf care in the context of kinship,...

Data from: Spatio-temporal dynamics of density-dependent dispersal during a population colonisation

Sebastiano De Bona, Matthieu Bruneaux, Alex E.G. Lee, David N. Reznick, Paul Bentzen & Andrés López-Sepulcre
Predicting population colonisations requires understanding how spatio-temporal changes in density affect dispersal. Density can inform on fitness prospects, acting as a cue for either habitat quality, or competition over resources. However, when escaping competition, high local density should only increase emigration if lower-density patches are available elsewhere. Few empirical studies on dispersal have considered the effects of density at the local and landscape scale simultaneously. To explore this, we analyze 5 years of individual-based data...

Data from: A single Tim translocase in the mitosomes of Giardia intestinalis illustrates convergence of protein import machines in anaerobic eukaryotes

Eva Pyrihova, Alžběta Motyčková, Luboš Voleman, Natalia Wandyszewska, Radovan Fišer, Gabriela Seydlová, Andrew J. Roger, Martin Kolisko, Pavel Dolezal & Andrew Roger
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anaerobiosis. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondrial and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist,...

Data from: Kinship influences sperm whale social organization within, but generally not among, social units

Christine M. Konrad, Shane Gero, Timothy Frasier & Hal Whitehead
Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346bp mtDNA control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour. Social units were clearly matrilineally-based, evidenced by greater relatedness within social units...

Data from: Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish

Nancy E. Roney, Rebekah A. Oomen, Halvor Knutsen, Esben M. Olsen & Jeffrey A. Hutchings
Successful resource-management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4000 offspring, we document fine-scaled temporal differences in individual reproductive success for two spatially adjacent (<10km) populations of a broadcast-spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from...

Data from: Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Robert Fairweather, Ian R. Bradbury, Sarah J. Heylar, Mark De Bruyn, Nina O. Therkildsen, Paul Bentzen, Jakob Hemmer-Hansen & Gary R. Carvalho
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP)...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Dalhousie University
  • Memorial University of Newfoundland
  • Fisheries and Oceans Canada
  • Bedford Institute of Oceanography
  • Bangor University
  • Aarhus University
  • University of Copenhagen
  • Acadia University
  • Université de Sherbrooke
  • University of Saskatchewan