An-Najah Staff

The development of methods aiming at detecting molecular signatures of selection is one of the major concerns of modern population genetics. Broadly, such methods can be classified into four groups: methods focusing on (i) the interspecific comparison of gene substitution pat- terns, (ii) the frequency spectrum and models of selective sweeps, (iii) linkage disequilibrium (LD) and haplotype structure, and (iv) patterns of genetic differentiation among populations (for a review see Nielsen (2005)).
One approach of detecting loci under selection (outliers) with population genetic data is based on the genetic differentiation between loci only influenced by neutral processes (genetic drift, mutation, migration) and loci influenced by selection. Lewontin and Krakauer’s test - LK test - for the heterogeneity of the inbreeding coefficient ( F ) across loci was the first to be developed with regard to this concept (Lewontin and Krakauer, 1973). The neutral model was a star-like evolution of populations with the same pattern of evolution. This has led to some criticisms in the literature, as well as improvements such as more sophisticated neutral models (Excoffier et al., 2009), conditional distribution on heterozygosity (Beaumont and Nichols, 1996), Bayesian models with McMC estimation (Beaumont and Balding, 2004; Foll and Gaggiotti, 2008).
The key point is a good specification of the neutral model under which the null hypothesis will be based. It should be as close as possible to the real evolutionary history of the set of populations under study. In livestock, the divergence time between breeds in intraspecific studies is small, the history has a complex tree-like pattern, with negligible migrations between breeds. We propose here to take account of this kind of complex demographic history specific to livestock in a new test inspired from the original LK approach. Its application is very fast, making it a method of choice for massive SNP data.