Genetic subdivision and candidate genes under selection in North American grey wolves.
Previous genetic studies of the highly mobile grey wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat colour and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42 036 single-nucleotide polymorphisms (SNPs) in 111 North American grey wolves. Using these SNP data and individual-level measurements of 12 environmental variables, we identified six ecotypes: West Forest, Boreal Forest, Arctic, High Arctic, British Columbia and Atlantic Forest. Next, we explored signals of selection across these wolf ecotypes through the use of three complementary methods to detect selection: FST /haplotype homozygosity bivariate percentilae, bayescan, and environmentally correlated directional selection with bayenv. Across all methods, we found consistent signals of selection on genes related to morphology, coat coloration, metabolism, as predicted, as well as vision and hearing. In several high-ranking candidate genes, including LEPR, TYR and SLC14A2, we found variation in allele frequencies that follow environmental changes in temperature and precipitation, a result that is consistent with local adaptation rather than genetic drift. Our findings show that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan. These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
Rena M
RM
Schweizer
Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA.
Bridgett M
BM
vonHoldt
Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
Ryan
R
Harrigan
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9.
James C
JC
Knowles
Faculties of Environmental Design and Veterinary Medicine (Joint Appointment), EVDS, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4.
Marco
M
Musiani
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9.
David
D
Coltman
Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.
John
J
Novembre
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
Robert K
RK
Wayne
D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D001499:Bayes Theorem; D017753:Ecosystem; D060146:Ecotype; D019143:Evolution, Molecular; D051456:Gene Flow; D005787:Gene Frequency; D040961:Genetic Drift; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D009656:North America; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D019596:Wolves / Q000235:genetics*
Canis lupus; SNP array; adaptation; ecological genetics; genomics; mammals; population genetics