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Link to original content: http://pubmed.ncbi.nlm.nih.gov/24346500
Genome-wide signatures of population bottlenecks and diversifying selection in European wolves - PubMed Skip to main page content
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. 2014 Apr;112(4):428-42.
doi: 10.1038/hdy.2013.122. Epub 2013 Dec 18.

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

M Pilot  1 , C Greco  2 , B M vonHoldt  3 , B Jędrzejewska  4 , E Randi  5 , W Jędrzejewski  4 , V E Sidorovich  6 , E A Ostrander  7 , R K Wayne  3
Affiliations

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

M Pilot et al. Heredity (Edinb). 2014 Apr.

Abstract

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.

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Figures

Figure 1
Figure 1
(a) Map of sample distribution. The black circles represent sampling locations, which are exact, except for the Iberian Peninsula, where the exact sample locations were unknown. A sampling location may be shared by several individuals. The range of the grey wolf is marked in pale red on the main map and in red on the small map showing the worldwide distribution of this species based on the most recent data available from IUCN. Due to the recent expansion of wolf populations, some samples occur outside of the established range. (b) Subdivision into local populations in Eastern Europe based on the geographical proximity of the samples and data on their genetic differentiation from Pilot et al., (2006). Local populations with sample size of at least five individuals were used in the LD decay and ROH analyses.
Figure 2
Figure 2
Results of (a) ADMIXTURE and (b) STRUCTURE clustering analysis of European wolf populations in comparison with other wolf populations and the coyotes, for K=6 and K=7. The analysis was performed for the LD-pruned 34K SNP set. Within Eastern Europe, the samples are sorted according to their geographical locations, from the Kirov region in Russia on the left to the Balkans and Carpathians on the right.
Figure 3
Figure 3
Principal component analysis illustrating the extent of genetic diversification at the genome-wide 34K SNP set (a–c), and at loci putatively under diversifying selection in European wolves (d, e) among the following populations: (a) and (d) European, Asian and North American grey wolves, and coyotes; (b) and (e) European grey wolves; and (c) Eastern European grey wolves.
Figure 4
Figure 4
Evolutionary relationships among X chromosome haplotypes of females inferred using the neighbour-joining method. The distances were computed using the p-distance measure. Bootstrap support is shown if higher than 50% of 1000 replicates.
Figure 5
Figure 5
(a) Extent of linkage disequilibrium in European wolf populations. Average genotypic association coefficient r2 is presented as a function of inter-SNP distance for each local wolf population. (b) Frequency distribution of runs of homozygosity in European wolf populations. (c) Temporal changes of NE in European wolves, with North American wolves presented for a comparison.
Figure 6
Figure 6
Signatures of selection in the Iberian, Italian and Eastern European wolf populations inferred using the program BAYESCAN. The vertical axis indicates mean FST values between each of the three populations, and the horizontal axis indicates the logarithm of posterior odds (log(PO)). The vertical line indicates the log(PO) value corresponding to the false discovery rate threshold of 0.05. Loci on the right of this line are putatively under selection.
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References

    1. Allendorf FW, Hohenlohe PA, Luikart G. Genomics and the future of conservation genetics. Nat Rev Genet. 2010;11:697–709. - PubMed
    1. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–1664. - PMC - PubMed
    1. Altobello G.1921[Fauna of Abruzzo and Molise] Mammiferi 438–45.[In Italian].
    1. Alvarez RH, Kantarjian HM, Cortes JE. Biology of platelet-derived growth factor and its involvement in disease. Mayo Clin Proc. 2006;81:1241–1257. - PubMed
    1. Axelsson E, Ratnakuma A, Arendt ML, Maqbool K, Webster MT, Perloski M, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495:360–364. - PubMed

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