The study of local adaptation is a main focus of evolutionary biology since it may contribute to explain the current species diversity. The genomic scan procedures permit for the first time to study the connection between specific DNA patterns and processes as natural selection, genetic drift, recombination, mutation and gene flow. Accordingly, the information on genomes from non-model organisms increases and the interest on detecting the signal of natural selection in the DNA sequences of different populations also raises. The main goal of the present work is to explore a sequence-based method for detecting natural selection in divergent populations connected by migration. In doing so, we rely on a recently published statistic based upon th e definition of haplotype allelic classes (HAC). The original measure was modified to be more sensitive to intermediate frequencies in non-model species. A linkage-disequilibrium-based method was also assayed and individual-based simulations were performed to test the methods. The results suggest that the HAC-based methods and, specifically, the new proposed method are quite powerful for detecting the footprint of moderate divergent selection. They are also robust to reasonable model misspecification. One obvious advantage of the new algorithm is that it does not require knowledge of the allelic state.

Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.