MHC adaptive divergence between closely related and sympatric African cichlids

Abstract

Background: The haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa.

Methodology/principal findings: Divergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS) amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites.

Conclusions/significance: We propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.

Figure 1. Sampling Locations.

Individuals of a) Pseudotropheus fainzilberi and b) P. emmiltos were collected at Mpanga Rocks, Luwino Reef, and Chirwa Island off the North Western shore of Lake Malawi. The two species are sympatric at Mpanga Rocks and Luwino Reef. Photograhs show males in full nuptial dress and are courtesy of Ad Konings.

Figure 2. Three-Dimensional Model of the β₁ Domain of Cichlid MHC Class II.

The tertiary structure prediction was based on Psemmil_m58_c exon 2 sequence (Accession number: EF540049) of 41% homology with mouse MHC sequence gi|13399459 in the Protein Data Bank (http://www.pdb.org/pdb/home/home.do) using the 3D-jigsaw server v.2.0 (http://www.bmm.icnet.uk/~3djigsaw/). The graphical representation was created using the program Pymol v.0.99. Amino acid residues under significant positive selection in Pseudotropheus fainzilberi and P. emmiltos and corresponding to peptide binding sites in humans are highlighted in orange. Residues shown in red were under significant positive selection in P. fainzilberi and P. emmiltos but do not correspond with peptide binding sites in humans. Residues in yellow are human peptide binding sites that were not found to evolve under positive selection in cichlids. The 84 amplified exon 2 codons are numbered 1-84 on the graph. Those correspond to codons 6-89 of the mature protein.

Figure 3. Comparison of Secondary Structure of Mouse and Cichlid MHC Class II Exon 2.

Structure predictions were obtained from the PSIPRED server (http://bioinf.cs.ucl.ac.uk/psipred/psiform.html) for a) mouse sequence gi:13399459 and b) cichlid sequence Psemmil_m58_c (Accession number: EF540049). Mammalian and fish secondary structures are similar except for an additional short alpha-helix at position 46–49 predicted for the mouse sequence, and an additional short strand at position 74 predicted for the cichlid sequence.

Figure 4. Comparison of Genetic Divergence Between Heterospecific Sympatric Populations and Conspecific Allopatric Populations.

Fst values (HudSon et al. 1992) from pairwise comparisons of conspecific allopatric populations (Mpanga Rocks (Mpg), Luwino Reef (Lwo), and Chirwa Island (Chw)) and between heterospecific sympatric populations of P. fainzilberi (fainz.), and P. emmiltos (emm.). Neutral Fst estimates were obtained from intron 1 p-distances, modified Nei and Gojobori synonymous distances at exon 2, and from amino acid EX distance at exon 2 sites outside the putative ABS region (dN/dS≤1) and functional Fst were obtained from EX distance at putative exon 2 ABS (dN/dS>1). Negative Fst estimates were forced to zero. Evidence of significant genetic divergence between pairs of allopatric populations was found only for neutral Fst estimates between P. emmiltos populations from Luwino Reef and Mpanga Rocks. Evidence of significant genetic divergence between pairs of P. fainzilberi and P. emmiltos sympatric populations was found only at putative ABS at Mpanga Rocks. ^*Significantly different from zero (p<0.05; 200 permutations)