168 Works

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 We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for...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: Fast and cost-effective genetic mapping in apple using next-generation sequencing

Kyle M. Gardner, Thomas F. Cooke, Patrick J. Brown, Scott Cann, Fabrizio Costa, Carlos D. Bustamante, Riccardo Velasco, Michela Troggio, Sean Myles, P. Brown & C. Bustamante
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called...

Data from: Relative risks of inbreeding and outbreeding depression in the wild in endangered salmon

Aimee Lee S Houde, Dylan J Fraser, Patrick O'Reilly & Jeffrey A Hutchings
Conservation biologists routinely face the dilemma of keeping small, fragmented populations isolated, wherein inbreeding depression may ensue, or mixing such populations, which may exacerbate population declines via outbreeding depression. The joint evaluation of inbreeding and outbreeding risks in the wild cannot be readily conducted in endangered species, so a suggested 'safe' strategy is to mix ecologically and genetically similar populations. To evaluate this strategy, we carried out a reciprocal transplant experiment involving three neighbouring populations...

Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude

Daniel J. Hasselman, Daniel Ricard & Paul Bentzen
Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using...

Data from: Edge influence on vegetation at natural and anthropogenic edges of boreal forests in Canada and Fennoscandia

Karen A. Harper, S. Ellen Macdonald, Michael S. Mayerhofer, Shekhar R. Biswas, Per-Anders Esseen, Kristoffer Hylander, Katherine J. Stewart, Azim U. Mallik, Pierre Drapeau, Bengt-Gunnar Jonsson, Daniel Lesieur, Jari Kouki & Yves Bergeron
1. Although anthropogenic edges are an important consequence of timber harvesting, edges due to natural disturbances or landscape heterogeneity are also common. Forest edges have been well-studied in temperate and tropical forests, but less so in less productive, disturbance-adapted boreal forests. 2. We synthesized data on forest vegetation at edges of boreal forests and compared edge influence among edge types (fire, cut, lake/wetland; old vs. young), forest types (broadleaf vs. coniferous) and geographic regions. Our...

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: 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...

Human-induced habitat fragmentation effects on connectivity, diversity and population persistence of an endemic fish, Percilia irwini, in the Biobío river basin (Chile)

Francisca Valenzuela-Aguayo, Gregory McCracken, Aliro Manosalva, Evelyn Habit & Daniel Ruzzante
An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including the disruptions of migratory processes and gene flow among populations. In Chile, the Biobío river basin exhibits a high...

Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs

Tony Kess, J. Brian Dempson, Sarah J. Lehnert, Kara Layton, Anthony Einfeldt, Paul Bentzen, Sarah Salisbury, Amber Messmer, Steven Duffy, Daniel Ruzzante, Cameron Nugent, Moira Ferguson, Jong Leong, Ben Koop, Michael O'Connell, Ian Bradbury, Kara K. S. Layton, Sarah J. Salisbury, Amber M. Messmer, Daniel E. Ruzzante, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Michael F. O’Connell … & Ian R. Bradbury
Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in these environments are rarely known. Post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Here, we compare genomic and morphometric divergence...

Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)

Sarah J. Salisbury, Gregory R. McCracken, Robert Perry, Donald Keefe, Kara K. S. Layton, Tony Kess, Cameron M. Nugent, Jong S. Leong, Ian R. Bradbury, Ben F. Koop, Moira M. Ferguson & Daniel E. Ruzzante
The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation...

Data from: Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

Loay Jabre, Andrew E. Allen, J. Scott P. McCain, John P. McCrow, Nancy Tenenbaum, Jenna L. Spackeen, Rachel E. Sipler, Beverley R. Green, Deborah A. Bronk, David A. Hutchins & Erin M. Bertrand
The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at -0.5 °C, 3 °C, and 6 °C....

Atlantic salmon survival at sea: temporal changes that lack regional synchrony

Maria Tirronen, Jeffrey A. Hutchings, Sebastián A. Pardo & Anna Kuparinen
Spatial and temporal synchrony in abundance or survival trends can be indicative of whether populations are affected by common environmental drivers. In Atlantic salmon (Salmo salar L.), return rates to natal rivers have generally been assumed to be affected primarily by shared oceanic conditions, leading to spatially synchronous trends in mortality. Here, we investigate the existence of parallel trends in salmon sea survival, using data on migrating smolts and returning adults from seven Canadian populations...

Niche conservation in copepods between ocean basins

Niall McGinty, Andrew Barton, David Johns, Zoe Finkel & Andrew Irwin
This dataset provides the necessary data to test for niche conservatism as demonstrated in the article "Niche conservatism in copepods between ocean basins; 10.1111/ecog.05690". Our study examined niche conservatism (i.e. a species' niche remains stable in space and time) between populations of the same species of marine copepod in different ocean basins. We used two approaches to test for niche conservatism which can be defined as a Princpial Component Analysis (PCA) and Environmental Niche Model...

The survey data of patients, prescribers, and pharmacists' feedback on ePrescription systems security and privacy

Bader Aldughayfiq & Srinivas Sampalli
Objective: To evaluate the attitudes of the parties (i.e. patients, prescribers, and pharmacists) involved in the ePrescription systems toward the new features and measure the potential benefits of introducing the use of blockchain and machine learning (ML) to strengthen the in-place methods for safely prescribing and dispensing medication. Methods: The survey contains questions about the features introduced in the proposed approach of using blockcahin and ML in the ePrescription system to evaluate the security, privacy,...

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

Halvor Knutsen, Diana Catarino, Lauren Rogers, Marte Sodeland, Morten Mattingsdal, Marlene Jahnke, Jeffrey Hutchings, Ida Mellerud, Sigurd Espeland, Kerstin Johanneson, Olivia Roth, Michael Hansen, Sissel Jentoft, Carl Andre & Per Erik Jorde
Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to...

Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom

J. Scott P. McCain, Andrew E. Allen & Erin M. Bertrand
Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a...

Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

Dayana Salas-Leiva, Eelco Tromer, Bruce Curtis, Jon Jerlström-Hultqvist, Martin Kolisko, Zhenzhen Yi, Joan Salas-Leiva, Lucie Gallot-Lavallée, Shelby Williams, Geert Kops, John Archibald, Alastair Simpson & Andrew Roger
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out...

Climate change exacerbates nutrient disparities from seafood

William Cheung, Eva Maire, Muhammed Oyinlola, James Robinson, Nicholas Graham, Aaron MacNeil & Christina Hicks
Seafood is an important source of bioavailable micronutrients supporting human health, yet it is unclear how climate change will influence its availability. Here, combining observational databases and predictive models, we assess nutrient availability from fisheries and mariculture in the past, and project their future under climate change. Since the 1990s, availability of iron, calcium, omega-3 and protein from seafood has declined, with increasing contributions of invertebrates and mariculture failing to compensate for these loses. Nutrient...

Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

Daniel J. Hasselman, Emily E. Argo, Meghan C. McBride, Paul Bentzen, Thomas F. Schultz, Anna A. Perez-Umphrey & Eric P. Palkovacs
Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry has received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites we examined hybridization between...

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: Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish

Iván Vera-Escalona, Evelyn Habit & Daniel E. Ruzzante
The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions, and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on, and competing with native species, including the fish Galaxias platei. Here we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term...

Data from: Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating

Alice A Winn, Elizabeth Elle, Susan Kalisz, Pierre-Olivier Cheptou, Christopher G Eckert, Carol Goodwillie, Mark O. Johnston, David A Moeller, Richard H Ree, Risa D Sargent & Mario Vallejo-Marín
Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Greater average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary...

Data from: Heme pathway evolution in kinetoplastid protists

Ugo Pierre Cenci, Daniel Moog, Bruce A. Curtis, Goro Tanifuji, Laura Eme, Julius Lukeš & John M. Archibald
Background: Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway—a core metabolic pathway in a wide range of organisms—is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far...

Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs

Mallory Van Wyngaarden, Paul V.R. Snelgrove, Claudio DiBacco, Lorraine C. Hamilton, Naiara Rodríguez-Ezpeleta, Nicholas W. Jeffery, Ryan R. Stanley, Ian R. Bradbury, Ryan R. E. Stanley & Paul V. R. Snelgrove
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled range-wide at 12 locations from Newfoundland to the Mid-Atlantic Bight we identified and genotyped 7163 Single Nucleotide Polymorphisms; 112 (1.6%)...

Data from: QTL analysis of soft scald in two apple populations

Kendra A. McClure, Kyle M. Gardner, Peter M. A. Toivonen, Cheryl R. Hampson, Jun Song, Charles F. Forney, John DeLong, Istvan Rajcan & Sean Myles
The apple (Malus×domestica Borkh.) is one of the world’s most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches...

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
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  • 2014
  • 2013

Resource Types

  • Dataset


  • Dalhousie University
  • Fisheries and Oceans Canada
  • Memorial University of Newfoundland
  • University of Guelph
  • Bedford Institute of Oceanography
  • Simon Fraser University
  • Aarhus University
  • University of British Columbia
  • East Carolina University
  • Norwegian University of Life Sciences