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Divergent patterns of selection on the DAB and DXB MHC class II loci in **phophorus fishes

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Two MHC class II loci, DAB (a classical class II locus) and DXB (putatively a non-classical class II locus), were sequenced in samples of individuals from two populations of swordtail fish, **phophorus multilineatus and X. pygmaeus. The DAB locus showed higher levels of genetic variation in the B1-encoding region, (putative binding region) than the DXB locus. We used two methods to investigate dN/dS ratios. The results from a maximum likelihood method based on phylogenetic relationships indicated positive selection on the B1 region of DAB (this method could not be used on DXB). Results from a coalescent-based method also showed evidence for positive selection in the B1 region of DAB, but only weak evidence for selection on the DXB. Further analyses indicated that recombination is an important source of variation in the B1 region of DAB, but has a relatively small effect on DXB. Overall, our results were consistent with the hypothesis that the DAB locus is under positive selection driven by antagonistic coevolution, and that the DXB locus plays the role of a non-classical MHC II locus. We also used simulations to investigate the presence of an elevated synonymous substitution rate in the binding region. The simulations revealed that the elevated rate could be caused by an interaction between positive selection and codon bias.

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Acknowledgements

This research was supported by NSF grant #MCB 0110541 to Thomas McConnell. We thank Felix Breden and four anonymous reviewers for comments on the manuscript. This paper is dedicated to the memory of Steven Kazianis.

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Authors and Affiliations

  1. Department of Biology, East Carolina University, Greenville, NC, 27858, USA

    Kyle Summers & Thomas J. McConnell

  2. Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA

    Kelly E. Roney

  3. School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, 5005, Australia

    Jack da Silva

  4. Department of Microbiology and Immunology, School of Medicine, Wake Forest University, Winston-Salem, NC, USA

    Gerald Capraro

  5. NIH/NIEHS, Research Triangle Park, Durham, NC, 27709-2233, USA

    Brandon J. Cuthbertson

  6. Wistar Institute, Philadelphia, PA, 19104, USA

    Steven Kazianis

  7. Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA

    Gil G. Rosenthal

  8. Section of Integrative Biology, University of Texas, Austin, TX, 78712, USA

    Michael J. Ryan

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  1. Kyle Summers
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Correspondence to Kyle Summers.

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Summers, K., Roney, K.E., da Silva, J. et al. Divergent patterns of selection on the DAB and DXB MHC class II loci in **phophorus fishes. Genetica 135, 379–390 (2009). https://doi.org/10.1007/s10709-008-9284-4

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