Neutral and functional genetic differentiation estimates between <i>Pseudotropheus fainzilberi</i> and <i>P. emmiltos</i> samples.

Neutral Fst values were calculated from intron 1, exon 2 synonymous alleles (exon 2 dS) and the 65 exon 2 amino acid sites evolving under a mixture of purifying and nearly neutral evolution (dN/dS≤1 sites). Functional Fst estimate was obtained from the 19 amino acid exon 2 putative ABS (dN/dS>1 sites). Association indices (AI) were obtained for intron 1 and for exon 2 phylogenies from neighbor-joining trees using Kimura 2-parameters distances and a Salmo salar outgroup sequence (gi:57335063) in the HYPHY package. AI values reflect the level of phylogenetic compartmentalization and correspond to the mean ratio of the sum over all nodes of the association values d = (1-f)/2n−1 from 100 bootstrapped tree of the test sequences on species-reassigned control. Lower values reflect higher divergence of samples. 1(Hudson et al. 1992); 2 (Wang et al. 2001); †significantly different from zero (p<0.01) from 200 permutations; ††significantly different from zero (p = 0.015) from 200 permutations; ‡significantly different from zero (P<0.01) from 100 bootstrap tree replicates; * dS calculated using the modified Nei and Gojobori method with transition/transversion = 1.26 estimated from the data; ** Experimental exchangeability distance (EX) for amino acid [81] estimated by maximum likelihood.