14 Works

Data from: Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

Xinshuai Qi, André S. Chanderbali, Gane Ka-Shu Wong, Douglas E. Soltis & Pamela S. Soltis
Background: GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze...

Data from: \"White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery\" in Genomic Resources Notes accepted 1 June 2013-31 July 2013

Rene Malenfant, Corey Davis, Stephen Moore & David Coltman
White-tailed deer (Odocoileus virginianus) are among the most abundant and widespread large mammals in the Americas, comprising up to 38 subspecies ranging from Northern Canada to Peru. Although believed to have high genetic diversity, surprisingly few genomic resources are currently available, despite the species’ ecological and economic importance. White-tailed deer and other cervids throughout central North America are currently being afflicted by chronic wasting disease (CWD), one of the degenerative prion diseases collectively known as...

Data from: Genes underlying altruism

Graham J. Thompson, Peter L. Hurd & Bernard J. Crespi
William D. Hamilton postulated the existence of 'genes underlying altruism', under the rubric of inclusive fitness theory, a half-century ago. Such genes are now poised for discovery. In this article we develop a set of intuitive criteria for the recognition and analysis of genes for altruism, and describe the first candidates for altruism genes from social insects and humans. We also provide evidence from a human population for genetically-based tradeoffs, underlain by oxytocin-system polymorphisms, between...

Data from: \"Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery\" in Genomic Resources Notes accepted 1 August 2013-30 September 2013

René M. Malenfant, David L. Coltman, Evan S. Richardson, Nicholas J. Lunn, Corey S. Davis, David W. Coltman & Nick J. Lunn
Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential...

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Gaddy Bergmann, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Karri Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos … & Pierre Taberlet
Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many...

Data from: \"RAD Sequencing for SNP Discovery in Two Populations of Bighorn Sheep (Ovis canadensis)\" in Genomic Resources Notes accepted 1 April 2013 - 31 May 2013

Joshua M. Miller, John T. Hogg & David W. Coltman
In this work we present the development of a large set of single nucleotide polymorphisms (SNPs) discovered in two populations of bighorn sheep (Ovis canadensis). To do so we used restriction-site associated DNA (RAD) sequencing of four individuals from each population. Through alignment of reads to the domestic sheep (Ovis aries) genome we discovered >83,000 SNPs, of which >38,000 are suitable for assays such as an Illumina SNP chip. These loci will allow for fine-mapping...

Data from: Estimating genome-wide heterozygosity: effects of demographic history and marker type

Joshua M. Miller, René M. Malenfant, Patrice David, Corey S. Davis, Jocelyn Poissant, John T. Hogg, Marco Festa-Bianchet & David W. Coltman
Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms...

Data from: Density triggers maternal hormones that increase adaptive offspring growth in a wild mammal

Ben Dantzer, Amy E. M. Newman, Rudy Boonstra, Rupert Palme, Stan Boutin, Murray M. Humphries & Andrew G. McAdam
Spruce cone and squirrel density dataData used to investigate how previous year spruce cones and food-supplementation affected red squirrel density. All data collected in Kluane, Yukon, Canada.Spruce cone and density data.csvTable S2 Results - neonate mass and growth rateData used for results shown in Table 2. Only neonate mass and offspring growth data. All data collected in Kluane, Yukon, Canada.Table S2 - neonate mass and growth rate.csvTable S2-S3 ResultsData for results shown in Table S2...

Data from: High resolution mapping of community structure in three glass sponge reefs (Porifera, Hexactinellida).

Jackson W. F. Chu, Sally P. Leys, JWF Chu & SP Leys
ABSTRACT: Glass sponge reefs (Porifera, Hexactinellida) are unique to the Pacific coast of Canada. To date, the locations and extents of reefs have only been assessed by multibeam echosounders, a method that does not resolve where live, dead and buried sponges are within a reef. We performed fine-scale (25 and 12.5 m grids) photographic surveys using remote operated vehicles and carried out GIS and semivariogram analysis to produce high resolution maps of the spatial distribution...

Data from: Does learning or instinct shape habitat selection?

Scott E. Nielsen, Aaron B. A. Shafer, Mark S. Boyce & G. B. Stenhouse
Habitat selection is an important behavioural process widely studied for its population-level effects. Models of habitat selection are, however, often fit without a mechanistic consideration. Here, we investigated whether patterns in habitat selection result from instinct or learning for a population of grizzly bears (Ursus arctos) in Alberta, Canada. We found that habitat selection and relatedness were positively correlated in female bears during the fall season, with a trend in the spring, but not during...

Data from: \"Blood transcriptome sequencing of Common Crossbills (Loxia curvirostra) experimentally infected by the avian malaria parasite Plasmodium relictum (lineage SGS1)\" in Genomic Resources Notes accepted 1 June 2013-31 July 2013

Olof Hellgren, Staffan Bensch, Tomas Johansson, Gediminas Valkiunas, Vaidas Palinauskas, David W. Coltman, Corey S. Davis, René M. Malenfant & Stephen S. Moore
In order to understand the epidemiology of this avian malaria infections both geographically and across host species there is a need of more polymorphic markers and knowledge about genes expressed during the infection of the host. However, technical difficulties have hindered the development of such molecular markers. The main difficulty is the fact that the host (birds) has nucleated erythrocytes and there is a 52-fold difference in the genome size between the host and the...

Data from: Linking genotype, ecotype, and phenotype in an intensively managed large carnivore

Aaron B. A. Shafer, Scott E. Nielsen, Joseph M. Northrup & Gordon B. Stenhouse
Numerous factors influence fitness of free-ranging animals, yet often these are uncharacterized. We integrated GPS habitat use data and genetic profiling to determine their influence on fitness proxies (mass, length, and body condition) in a threatened population of grizzly bears (Ursus arctos) in Alberta, Canada. We detected distinct genetic and habitat use (ecotype) clusters, with individual cluster assignments, or genotype/ecotype, being correlated (Pearson r = 0.34, P < 0.01). Related individuals showed evidence of similar...

Data from: Predicting local and non-local effects of resources on animal space use using a mechanistic step-selection model

Jonathan R. Potts, Guillaume Bastille-Rousseau, Dennis L. Murray, James A. Schaefer & Mark A. Lewis
1. Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis, where animal space use is derived from available habitat quality, and mechanistic movement models, where detailed movement processes of an animal are used to predict its emergent utilisation distribution. Such models bias the animal's movement towards patches...

Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility

Teresita M. Porter, G. Brian Golding, Christine King, Duane Froese, Grant Zazula & Hendrik N. Poinar
DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Alberta
  • Lund University
  • Nature Research Centre
  • University of Adelaide
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • Zhejiang University
  • University of Sussex
  • Atomic Energy and Alternative Energies Commission
  • University of Wollongong
  • Université de Sherbrooke