Fig. 4: Ancient genetic diversity in two members of the Ancylostoma-secreted protein family.

A 287 kb region on chromosome I of H. bakeri (I:8.92–9.20 Mb) containing two ASP loci that show evidence of haplotype sharing. a Nucleotide alignments between the alternate H. bakeri haplotype (represented by nxHelBake2 primary), each H. polygyrus haplotype (ngHelPoly1 primary, ngHelPoly1 alternate, ngHelPoly2 primary), and the nxHelBake1 reference haplotype. Alignments are coloured by their nucleotide identity. Repetitive alignments are not shown. The position of the two ASP loci (nxHelBake1.g10196 and nxHelBake1.g10198) are indicated by dotted lines. b Gene contents of each haplotype. The alternate H. bakeri haplotype (represented by nxHelBake2 primary) has two homologues of nxHelBake1.g10195 and nxHelBake1.g10196, consistent with the divergent inverted duplication in (a). Green (H. bakeri) and orange (H. polygyrus) boxes represent genes that have a 1:1 relationship across all haplotypes; grey boxes represent genes that have non 1:1 relationship (nxHelBake1.g10195 and nxHelBake1.g10196). Links between genes represent homologous relationships. Gene trees of (c) nxHelBake1.g10196.t1 and its homologues and (d) nxHelBake1.g10198.t1 and its homologues. Gene trees were inferred using IQ-TREE under the LG + Γ substitution model. Scale is shown in substitutions per site. Outgroup not shown. Source data this figure can be found in the GitHub repository.