Li et al. Genetics Selection Evolution 2010, 42:32 http://www.gsejournal.org/content/42/1/32 Page 8 of 14 Figure 2 Results of (A) the FDIST2 and (B) BAYESFST tests. The solid lines indicate the critical cutoff for the P-value at the 0.05 level. HAUT24, CSRM60, BMS2461, HEL5 and DIK4591) can be regarded as candidates affected by selection, but were revealed only in one of the three tests. Interestingly, according to ENSEMBL cow genome http://www. ensembl.org/Bos_taurus/Info/Index the significant locus AGLA17 under balancing selection was about 1.78 cM upstream from the candidate locus for POLL, whereas locus SOD1 under directing selection was located about 3.87 cM downstream from the candidate locus. It should be noted that the FST-based tests of selection are prone to false positives because of sensitivity to demographic history [51], heterozygosity among loci in mutation rate [52] and locus-specific phenomena not related to selec- tion [48]. Nevertheless, we expect the set of loci identi- fied by FST-based tests to be enriched for the true positives in further tests. Tests for selection for pairwise populations Since each of the five tests used above relies on some- what different assumptions, loci that are repeatedly found to be outside the range expected for neutrality are extremely good candidates for markers under selec- tion. Moreover, LD is known to be extremely high for the six BTA1 microsatellites near the candidate gene affecting the presence or absence of horns in Bos taurus, thus the region under selection is likely to be quite wide. Despite the possible presence of a few false posi- tives, the full set of seven loci (SOD1, BMS2461, DIK5019, HEL5, DIK4591, TGLA227 and AGLA17) was used for further analyses. The lnRθ methods (lnRH, lnRV and lnRθ’) use heterozygosity or variance differ- ence, rather than population divergence, to test for selection. Significant results for the lnRθ tests for selec- tive sweeps involve the two loci (AGLA17 and SOD1) detected by the Ewens-Watterson test and the FST-based tests for pairwise combinations (n = 12) of three native Finnish cattle populations and four old native popula- tions from Russia and Ukraine (Table 2). Significant results for selective sweeps at loci AGLA17 and SOD1 were obtained for 12 pairwise population