Populations belong to a single genetic lineage. It can be observed

Populations belong to a single genetic lineage. It can be observed, however, that the Gallega breed shows a certain level of genetic divergence when compared to the remaining six breeds (Fig. 1b). Moreover, our data do not show a common clustering of the the Latxa and Churra sheep (Figs 1 and 2), suggesting that they do not have a common origin. tive sweeps in dairy and MS023 site non-dairy sheep breeds with a similar genetic background (all of them were Spanish) in order to minimize the confounding effects of ascertainment bias17. Canaria de Pelo was excluded from selection analyses because of its high genetic divergence with regard to the remaining Spanish breeds (Fig. 1). With BayeScan, we detected 39 genomic regions distributed in 15 chromosomes that displayed significant evidences of being under selection (Table 1, Fig. 3a). The sign of was always positive indicating that, in all cases, we had detected the effects of directional selection. Comparison of our results with those reported in a set of dairy and non-dairy ovine breeds with diverse origins8 showed some matches on Oar2, Oar3, Oar6 and Oar15 (Table 1). We also compared our data with results generated in a worldwide sample of breeds differing at many phenotypes7. Interestingly, we found positional coincidences amongst putative selective sweeps detected on Oar2, Oar3, Oar6, Oar10, Oar14 and Oar19 (Table 1). Co-localizations between selective sweeps identified in different studies should not be taken as irrefutable proof of their existence, because they may emerge just by order A-836339 chance (though the probability of the occurrence of such random co-localizations might be low). In the current work, performance of a circular permutation test (see Methods) demonstrated that the number of positional coincidences detected by us exceeds what would be expected by chance (bootstrapped P-value < 0.05). The hapFLK analysis (Table 2, Fig. 3b) yielded fewer positive results than analyses based on BayeScan (Table 1) or FLK (Supplementary Table S1). Consistent with this, in a previous genome scan focused on layer chicken populations18, the numbers of SNPs under selection detected with Bayescan (212,765 SNPs) and FLK (155,712 SNPs) were 7-fold and 5-fold larger than those detected with hapFLK (28,557 SNPs). The cause of these discrepancies might be that hapFLK is less sensitive than BayeScan to distortions caused by demography (e.g. bottlenecks, differences in effective population sizes amongst breeds, etc) and hierarchical population structure2,7. Moreover, hapFLK is also expected to be more stringent than FLK because it implements a multipoint linkage disequilibrium model19 that takes into account the haplotype structure of the sample. Indeed, our hapFLK analysis only yielded one significant selective sweep at Oar6 (4.3?9.9 Mb) after correction for multiple testing. AScientific RepoRts | 6:27296 | DOI: 10.1038/srepDetection of selective sweeps with BayeScan and hapFLK. Our study was designed to identify selec-www.nature.com/scientificreports/Position (Mb) 256.60 72.00 27.80 183.60 247.00 25.00 141.50 52.40 6.70 52.90 78.60 189.30 18.40 153.50 201.40 93.80 39.40 27.00 43.70 27.00 2.10 14.30 82.50 23.50 72.70 37.90 2.00 74.30 72.00 22.90 9.10 20.60 30.60 20.70 51.30 31.60 13.10 7.70 22.ChrSNP s28145.1 OAR1_77069506.1 s61441.1 OAR2_194667510.1 s38806.1 OAR2_25448426.1 OAR2_150515619.1 s58048.1 s17630.1 OAR2_56768579.1 OAR2_83850165.1 OAR3_203907310.1 s29466.-value 1.32 1.28 1.24 1.49 1.73 1.44 1.36 1.39 1.31 1.29.Populations belong to a single genetic lineage. It can be observed, however, that the Gallega breed shows a certain level of genetic divergence when compared to the remaining six breeds (Fig. 1b). Moreover, our data do not show a common clustering of the the Latxa and Churra sheep (Figs 1 and 2), suggesting that they do not have a common origin. tive sweeps in dairy and non-dairy sheep breeds with a similar genetic background (all of them were Spanish) in order to minimize the confounding effects of ascertainment bias17. Canaria de Pelo was excluded from selection analyses because of its high genetic divergence with regard to the remaining Spanish breeds (Fig. 1). With BayeScan, we detected 39 genomic regions distributed in 15 chromosomes that displayed significant evidences of being under selection (Table 1, Fig. 3a). The sign of was always positive indicating that, in all cases, we had detected the effects of directional selection. Comparison of our results with those reported in a set of dairy and non-dairy ovine breeds with diverse origins8 showed some matches on Oar2, Oar3, Oar6 and Oar15 (Table 1). We also compared our data with results generated in a worldwide sample of breeds differing at many phenotypes7. Interestingly, we found positional coincidences amongst putative selective sweeps detected on Oar2, Oar3, Oar6, Oar10, Oar14 and Oar19 (Table 1). Co-localizations between selective sweeps identified in different studies should not be taken as irrefutable proof of their existence, because they may emerge just by chance (though the probability of the occurrence of such random co-localizations might be low). In the current work, performance of a circular permutation test (see Methods) demonstrated that the number of positional coincidences detected by us exceeds what would be expected by chance (bootstrapped P-value < 0.05). The hapFLK analysis (Table 2, Fig. 3b) yielded fewer positive results than analyses based on BayeScan (Table 1) or FLK (Supplementary Table S1). Consistent with this, in a previous genome scan focused on layer chicken populations18, the numbers of SNPs under selection detected with Bayescan (212,765 SNPs) and FLK (155,712 SNPs) were 7-fold and 5-fold larger than those detected with hapFLK (28,557 SNPs). The cause of these discrepancies might be that hapFLK is less sensitive than BayeScan to distortions caused by demography (e.g. bottlenecks, differences in effective population sizes amongst breeds, etc) and hierarchical population structure2,7. Moreover, hapFLK is also expected to be more stringent than FLK because it implements a multipoint linkage disequilibrium model19 that takes into account the haplotype structure of the sample. Indeed, our hapFLK analysis only yielded one significant selective sweep at Oar6 (4.3?9.9 Mb) after correction for multiple testing. AScientific RepoRts | 6:27296 | DOI: 10.1038/srepDetection of selective sweeps with BayeScan and hapFLK. Our study was designed to identify selec-www.nature.com/scientificreports/Position (Mb) 256.60 72.00 27.80 183.60 247.00 25.00 141.50 52.40 6.70 52.90 78.60 189.30 18.40 153.50 201.40 93.80 39.40 27.00 43.70 27.00 2.10 14.30 82.50 23.50 72.70 37.90 2.00 74.30 72.00 22.90 9.10 20.60 30.60 20.70 51.30 31.60 13.10 7.70 22.ChrSNP s28145.1 OAR1_77069506.1 s61441.1 OAR2_194667510.1 s38806.1 OAR2_25448426.1 OAR2_150515619.1 s58048.1 s17630.1 OAR2_56768579.1 OAR2_83850165.1 OAR3_203907310.1 s29466.-value 1.32 1.28 1.24 1.49 1.73 1.44 1.36 1.39 1.31 1.29.

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