Li et al. Genetics Selection Evolution 2010, 42:32 http://www.gsejournal.org/content/42/1/32 observed data set: mutation rates (infinite allele model) μ = 1 × 10-2, 1 × 10-3, and 1 × 10-4; ancestor population size Ne = 500, 5,000, and 50,000; times since an assumed bottleneck event T0 = 50, 500, and 5,000 generations; time since divergence t = 50 and 500; and population size before the split N0 = 50 and 500. In order to detect outlier loci potentially selected for the polled trait within the three Finnish native cattle populations, the DetSel program was run for comparison between the two sub- populations representing the definitely polled (n = 19) and horned (n = 19) animals, respectively. Results Genetic diversity and differentiation A complete list of loci and their variability in the 10 cat- tle populations are shown in Table 1. The overall genetic differentiation across loci was 0.117 (FST = 0.117, 95% CI 0.108 - 0.125). FST values for an indivi- dual locus varied from 0.017 (SD = 0.011) at AGLA17 on BTA1 to 0.180 (SD = 0.057) at BMS2461 on BTA20. Mean population differentiations for loci on BTA1 and BTA20 were 0.126 (FST = 0.126, 95% CI 0.103 - 0.143) and 0.118 (FST = 0.118, 95% CI 0.100 - 0.139), respec- tively. Neither of the values indicated significant differ- ence from the average for loci on other chromosomes (FST = 0.114, 95% CI 0.104 - 0.124). Levels of variation across populations, including allelic richness (AR) and expected heterozygosity (HE), were in similar ranges as for microsatellites on BTA1, BTA20 and other autosomes, with the smallest variations observed at AGLA17 (AR = 1.37, HE = 0.08). The highest HE of 0.79 was observed at BM2113 (BTA2) and the highest AR of 11.36 at TGLA122 (BTA21). Most FIS values were positive and for some loci significantly posi- tive. Of the 13 negative FIS values, seven occurred for loci on BTA20, and two for loci on BTA1. Loci on BTA1 and BTA20 did not show a significant reduction or increase in mean FIS compared with the loci on other autosomes (other bovine autosomes, mean FIS = 0.038; BTA1, mean FIS = 0.053, Mann-Whitney test U = 118, P = 0.409; BTA20, mean FIS = 0.011, Mann-Whitney test U = 273.5, P = 0.227). Given the range of observa- tions of FIS at an individual locus, there were no marked difference among the three classes of loci (BTA1, -0.083 - 0.190; BTA20, -0.074 - 0.113; other BTAs, -0.052 - 0.391). Linkage disequilibrium The strength of pairwise linkage disequilibrium (LD) between markers was estimated and the average D′ value of pairwise syntenic markers was 0.32 across BTA1 and 0.28 across BTA20, both of which are signifi- cantly (P < 0.05) higher than for non-syntenic markers (0.15; only the D′ > 0.3 are shown in Figure 1). Figure 1 Page 6 of 14 also shows matrices of LD significance levels for all pos- sible locus combinations of the loci on BTA1 or BTA20 in their chromosomal order. Of the 120 pairwise com- parisons of the 16 loci on BTA20, a total of 22 (22/120, 18.3%) tests showed P values below 0.05. Likewise, LD between markers on BTA1 provided seven (7/21, 33.3%) significant observations. However, a substantially smaller proportion (34/1124, 3.0%) of significant (P < 0.05) pairs was found between non-syntenic markers. In general, significantly higher levels of LD were observed for synte- nic markers on BTA1 and BTA20 than that for non- syntenic markers. There was no evidence of LD blocks on either of the chromosomes. Evidence for selection across the populations The Ewens-Watterson test enables detection of devia- tions from a neutral-equilibrium model as either a defi- cit or an excess of genetic diversity relative to the number of alleles at a locus (see [50]). When applying the tests for all the microsatellites, we detected 13 loci (AGLA17, DIK5019, SOD1, AGLA29, BMS2361, BM2113, ETH10, ETH225, CSSM66, ETH152, TGLA227, HAUT24, and CSRM60) on 10 different chromosomes exhibiting significant probabilities for the Ewens-Watter- son test based on both homozygosity (PH) and Fisher’s exact test (PE) (see Table 1). Of the 13 loci, one (AGLA17) exhibited a significant (P < 0.05) deficit of heterozygosity and all the other 12 loci exhibited a sig- nificant (P < 0.05) excess in genetic diversity relative to the expected values; these patterns are consistent with directional and balancing selection, respectively. The 12 loci generated average P values significantly (Student’s t test: PH = 0.020, t = -5.65, P < 0.0001; PE = 0.014, t = -5.69, P < 0.0001) below than the expected median value of 0.5. However, average P values of 0.313 for PH (t = -4.63, P > 0.1) and 0.232 for PE (t = -8.69, P > 0.1) were observed in the remaining 38 loci which were not under selection. The observation provided further evi- dence that selection affected genetic diversity at the microsatellites under selection. The results of the analyses with the FDIST2 program are presented in Table 1 and Figure 2a. This summary- statistic method, based on simulated and observed FST values, identified four loci (SOD1, BMS2461, DIK5019 and AGLA17) as outliers showing footprints of selection in the analyses, including all 10 populations, at the 5% significance level. Of the four significant loci, three (SOD1, BMS2461 and DIK4519) with higher FST values indicated a sign of directional selection and one locus (AGLA17) appearing in the lower tail of the FST distri- bution suggested a signature potentially affected by bal- ancing selection (Figure 2a). In the Bayesian FST-test (Figure 2b), which was based on a hierarchical regres- sion model, three loci (HEL5, DIK4591and SOD1) were