Recurrent positive selection of the Drosophila hybrid incompatibility gene Hmr

Abstract

Lethality in hybrids between Drosophila melanogaster and its sibling species Drosophila simulans is caused in part by the interaction of the genes Hybrid male rescue (Hmr) and Lethal hybrid rescue (Lhr). Hmr and Lhr have diverged under positive selection in the hybridizing species. Here we test whether positive selection of Hmr is confined only to D. melanogaster and D. simulans. We find that Hmr has continued to diverge under recurrent positive selection between the sibling species D. simulans and Drosophila mauritiana and along the lineage leading to the melanogaster subgroup species pair Drosophila yakuba and Drosophila santomea. Hmr encodes a member of the Myb/SANT-like domain in ADF1 (MADF) family of transcriptional regulators. We show that although MADF domains from other Drosophila proteins have predicted ionic properties consistent with DNA binding, the MADF domains encoded by different Hmr orthologs have divergent properties consistent with binding to either the DNA or the protein components of chromatin. Our results suggest that Hmr may be functionally diverged in multiple species.

FIG. 1.—

Domain structure and MADF domains of Hmr. (A) The positions of four MADF domains and the putative BEAF, Su(var)3-7 and Stonewall (BESS) domain (Brideau et al. 2006) encoded by Drosophila melanogaster Hmr are shown. (B) Alignment and comparison of MADF, MYB, and SANT domains. The four MADF domains from D. melanogaster HMR and the MADF domain from D. melanogaster (Dm) ADF1 were aligned with the second and third MYB domains from Mus musculus (Mm) c-MYB and the SANT domain from D. melanogaster ISWI. This alignment was generated by extracting the alignment of the MADF domains from supplementary figure S1 (Supplementary Material online) and then manually adjusted to the published alignment of MYB and SANT domains (Bhaskar and Courey 2002; Boyer et al. 2004). Asterisks underneath the alignment indicate the conserved tryptophan residues, and the shaded boxes indicate predicted α-helical regions. The ionic properties of each domain are indicated within parentheses after the domain name as (charge, isoelectric point), respectively. HMR MADF1 and ADF1 MADF have ionic properties similar to the DNA-binding MYB domain, whereas HMR MADF3 is distinct in being more similar to the chromatin-associated SANT domain. For comparison, DIP3, another MADF domain–containing transcription factor that has been experimentally shown to bind DNA (Bhaskar and Courey 2002), has a MADF domain with a charge of +8.25 and an isoelectric point of 10.52, which is again similar to the MYB domain. The NCBI Entrez GeneIDs are Mm c-Myb, 17863; Dm Iswi, 36390; Dm Adf1, 47082; and Dm Dip3, 53579.

FIG. 2.—

A maximum parsimony phylogenetic tree constructed using Hmr population samples from the three D. melanogaster sibling species. Bootstrap values of major branches are shown in the rectangles (100 replicates). The lengths of major branches, which are proportional to the number of nucleotide changes for the gene, are indicated along the branches. Hmr has clearly diverged and shares no common alleles among the three sibling species.

FIG. 3.—

A maximum likelihood phylogenetic tree of Hmr built by the free-ratio model in PAML. The likelihood of this model was significantly better than the one-ratio model (2Δl = 54.224, degrees of freedom = 11, P < 10⁻⁷). The tree length is defined as the number of nucleotide substitutions per codon. The number shown above each lineage is the estimated D_N/D_S value of that lineage.