Li et al. Genetics Selection Evolution 2010, 42:32 http://www.gsejournal.org/content/42/1/32 Page 10 of 14 Figure 3 Pairwise comparison of Finnish native cattle populations performed with DetSel. The test was at the 95% confidence envelope: plot of F2 against F1 estimates for the subpopulation pair polled vs. horned. differentiation (FST value) than expected, suggesting that it could have been affected by the action of diversifying selection among homogeneous gene pools and popula- tions. In contrast, the locus AGLA17 presented a lower genetic differentiation than expected, which could repre- sent signatures of homogenizing selection among popu- lations and/or balancing selection within populations. All three methods identified loci SOD1 and AGLA17 as good candidates for selection on the polled trait. How- ever, several significant loci were detected only by one or two of the tests and thus could not be accepted as reliable outliers with the remaining tests. The results obtained by the three methods are not totally consistent, probably because of the difference in statistical power using multiple measures of variability, each of which measures different parameters and relies on different assumptions, e.g. heterozygosity and variance in allele size [48], as detailed in e.g. [53-55]. Besides the global analyses, detection of outlier loci was also done using pairwise analyses. This helped to reveal loci with a major overall effect as well as loci responding with different strengths to artificial selection on the individual populations. Among the population chosen for the pairwise analyses, the lnRθ (lnRV, lnRH and lnRθ’) tests yielded a high number of significant (P < 0.05) results at SOD1 and AGLG17 according to the three estimators of lnRθ (Table 2). This finding con- forms well to the previous results of selective sweeps associated with hitchhiking selection with one or more genes with locally beneficial mutations. Although there is difference in the statistical power to detect selection, as discussed in [6,48,56], the three estimators of lnRθ provide additional robust evaluation of potential selec- tive sweeps for the pairwise population comparisons. Neutrality tests for microsatellites focus mainly on unlinked loci and are based on either population differ- entiation (FST) or reduced variability (lnRθ). Our pro- posed tests consider lnRθ of several linked loci for the inference of selection. While the single-locus lnRθ-test is largely independent of the demographical past, the additional power of linked loci is balanced by the cost of an increasing dependence of the demographic past due to the fact that LD is extremely sensitive to the demographic history. Thus, pairwise analyses between sub-populations may decrease the demographic effects in accounting for the selection. As indicated in Figure 3, the great majority of loci always fall in the confidence region of the conditional pairwise-subpopulation