Li et al. Genetics Selection Evolution 2010, 42:32 http://www.gsejournal.org/content/42/1/32 comparisons for each of the three different measures of lnRθ (Table 2). Of the pairwise comparisons, a total of 28 and 26 significant (P < 0.05) or very significant (P < 0.01) results were observed at AGLA17 and SOD1, respectively, in the three tests. Both loci (AGLA17 and SOD1) appeared in all three different measures of lnRθ for eight or more comparisons (Table 2), that is, lnRθ (lnRH, lnRV and lnRθ’) values deviating by more than 1.96 standard deviations from the mean. Accordingly, the pairwise comparisons between either of Eastern Finncattle and Western Finncattle and populations of Yakutian, Kholmogory and Ukrainian Grey were signifi- cant for all three estimators. All the comparisons between populations yielded at least two significant results for the three estimators. In total, 54 (75% 54/72) significant comparisons involved AGLA17 or SOD1 in the comparisons between Finnish native populations (Northern Finncattle, Eastern Finncattle and Western Finncattle) vs. the native populations from Russia and Ukraine (Istoben, Ukrainian Grey, Kholmogory and Yakutian Cattle), which suggested that selective sweeps had taken place in the Finnish native populations. Tests for selection within the Finnish native populations The coalescent simulation, which was based on a popula- tion split model [49], was performed with the DetSel pro- gram within the Finnish native populations with very similar demographical backgrounds (Eastern Finncattle, Northern Finncattle and Western Finncattle). Among the six BTA1 microsatellites around the candidate loci, all are polymorphic in the three populations involved in the pairwise-subpopulation comparison. In the pairwise com- parison between definitely polled (n = 19) and horned (n = 19) cattle, loci AGLA17 and SOD1 were significantly outside the 99% confidence interval (Figure 3), while locus DIK4591 fell slightly outside the 95% confidence Pairwise comparison Eastern Finncattle - Istoben Eastern Finncattle - Yakutian Eastern Finncattle - Ukrainian Grey Eastern Finncattle - Kholmogory Western Finncattle - Istoben Western Finncattle - Yakutian Western Finncattle - Ukrainian Grey Western Finncattle - Kholmogory Northern Finncattle - Istoben Northern Finncattle - Yakutian Northern Finncattle - Ukrainian Grey Northern Finncattle - Kholmogory * Significance P < 0.05, ** P < 0.01, n.s., not significant * * ** * ** ** * * * * ** * * ** ** ** * ** * * n.s n.s. * n.s. Page 9 of 14 envelope in the three comparisons, which are thus con- sidered as false positives, i.e., the locus was detected as an outlier because of the 5% type I error. The outlier beha- vior for loci AGLA17 and SOD1 was deemed to be the result of strong local effects of hitchhiking selection. Discussion In this study, besides 28 microsatellites on other cattle autosomes used as a reference set of markers, seven microsatellites on BTA1 and 16 on BTA20 around candi- date loci were screened for the footprints of selection among 10 cattle populations with divergent horn or pro- duction traits. Across different statistical analyses, a highly divergent pattern of genetic differentiation and large differences in levels of variability were revealed at the loci SOD1 and AGLA17 among populations, which was inconsistent with neutral expectations. The results indicated divergent ‘selective sweeps’ at AGLA17 and SOD1, probably caused by selection of the closely-linked candidate loci for the horned/polled trait, e.g. the POLL gene. Evidence of selection of microsatellites surrounding the POLL gene Because revealing outlier loci in genome scans currently depends on statistical tests, one of the main concerns is to highlight truly significant loci while minimizing the detection of false positives [44]. Using a multilocus scan of differentiation based on microsatellite data, we com- pared three different methods that aimed at detecting outliers from simulated neutral expectations: 1) the Ewens-Watterson method [44,45], 2) the FDIST2 method [9], and 3) a BAYESFST method [12]. Outliers were identified for 15 loci using a 5% threshold, which was robust across methods for two loci (SOD1 and AGLA17). The locus SOD1 presented a higher n.s. * * * ** * ** * * n.s. n.s. n.s. n.s. ** * * ** * * * n.s. * n.s. * * ** ** * * * * * n.s. n.s. n.s. n.s. n.s. * * * * ** * ** * n.s. n.s. n.s. Table 2 Estimates of lnRV, lnRH and lnRθ’ for the pairwise comparisons lnRV lnRH lnRθ’ AGLA17 SOD1 AGLA17 SOD1 AGLA17 SOD1