Fig. 5.
(a) Patterns of genetic differentiation on scaffold4484_cov51 where two paralogous Collagen alpha-6 (VI) chain (COL6A6) genes are located. First panel shows the degree of genetic differentiation between species based on the weighted mean of FST and the positions of representative genes. The values of FST were calculated for each 10-kb window. The three lower panels show absolute values for the integrated haplotype score (iHS) for each species. Extreme values of iHS, which are suggestive of selection, are indicated by the filled data points. Highly differentiated regions (HDRs) based on the FST values are shaded in gray. (b) Allele frequency of SNPs in the genomic region of two COL6A6 genes. Vertical axis shows allele frequencies and horizontal axis shows the relative position of each SNP in the HDRs. Note that the allele frequencies of Haplochromis sauvagei do not exceed 0.5 because the SNPs were identified against the major alleles of H. sauvagei. Vertical bars of a deep shade represent the SNPs in exon regions, and those of a light shade indicate the SNPs in intron regions. Open vertical bars indicate the SNPs in the surrounding regions of two COL6A6 genes. In the lowest plot, the triangles show the position of SNPs on the scaffold. In particular, SNPs exhibiting large differences in allele frequencies (≥0.6) between H. chilotes and Lithochromis rufus are highlighted in orange. (c) Species tree of East African Great Lakes cichlids based on Brawand et al. (2014). (d) Maximum likelihood estimated phylogenetic tree with 100 bootstrap replicates of COL6A6_a using nine cichlid species: Oreochromis niloticus, one Lake Tanganyika cichlid (Neolamprologus brichardi), a riverine species near Lake Tanganyika (H. burtoni), two Lake Malawi cichlids (Astatotilapia calliptera and Maylandia zebra) and four Lake Victoria cichlids (blue, H. chilotes, H. sauvagei, L. rufus, and Pundamilia nyererei). (e) Maximum likelihood estimated phylogenetic tree with 100 bootstrap replicates of COL6A6_b using eight of the cichlid species included in (d) (i.e., without P. nyererei). Note that some species in (d) and (e) were not included in the species tree because their genome sequences were fragmented due to assembly problems.