Principal component analyses for n = 48 Nordic dogs with 15 648 single nucleotide polymorphism markers.

<p>Norwegian Buhund (n = 10), Norrbottenspets (n = 12), Norwegian Lundehund (n = 17), and Icelandic Sheepdog (n = 9). The plots show the first three principal component (PC) axes, where PC axis 1, 2 and 3 represents respectively 17.4, 10.6 and 8.3% of the variation.</p

Pairwise F_ST-values for Lundehund and three candidate breeds for genetic rescue.

<p>Pairwise F_ST-values for Lundehund and three candidate breeds for genetic rescue.</p

Runs of homozygosity (ROH) locations in the genome for four dog breeds.

<p>The genomic location of runs of homozygosity (ROH) shared by all individuals within each breed. Light grey bars outline the chromosomes, black lines denote the outlier loci from Bayescan analyses and dark grey marks flanking regions of the genome that were examined for genes under possible selection. Colored lines show the ROHs in each breed. On chromosome 30, Lundehund and Icelandic Sheepdog shared the same haplotype for their overlapping ROH, whereas on chromosome 6 they did not.</p

ADMIXTURE results for n = 48 Nordic dogs with K = 2–6 population clusters.

<p>Analyses with 15 648 single nucleotide polymorphism (SNP) loci for the four breeds Norwegian Lundehund (LUN), Norwegian Buhund (BUH), Icelandic Sheepdog (ICE) and Norrbottenspets (NOR). Comparison of cross-validation errors (Figure A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177429#pone.0177429.s001" target="_blank">S1 File</a>) showed highest support for K = 2, with K = 4 having nearly the same support.</p

Outlier single nuclear polymorphism (SNP) loci detected in BayeScan and summary¹ of key functional genes.

<p>Outlier single nuclear polymorphism (SNP) loci detected in BayeScan and summary<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177429#t003fn001" target="_blank">¹</a> of key functional genes.</p

Pearson correlation coefficient between allele frequencies along the chromosome for four dog breeds.

<p>Norwegian Lundehund (n = 17), Norwegian Buhund (n = 10), Icelandic Sheepdog (n = 9) and Norrbottenspets (n = 12). Plots show the correlation coefficient (dots) with 95% confidence intervals (coloured lines) <i>versus</i> SNP position in sliding windows for a) every 100 SNPs and b) every 20 SNPs. Areas marked in grey below the plots show chromosomal regions of the Lundehund genome lacking genetic diversity. Gaps in the line thus reflect diversity although small gaps are not always visible.</p

Genetic diversity measures for the endangered Norwegian Lundehund and three candidate breeds for genetic rescue.

<p>Genetic diversity measures for the endangered Norwegian Lundehund and three candidate breeds for genetic rescue.</p

Data from: Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: a case study of the Norwegian Lundehund

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog (henceforth Lundehund) underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic structure with 16K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subject to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project