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A Comparison of Intraspecific Patterns of DNA Sequence Variation in Mitochondrial DNA, α-Enolase, and MHC Class II B Loci in Auklets (Charadriiformes: Alcidae)

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Abstract

Patterns of DNA sequence variation can be used to learn about mechanisms of organismal evolution, but only if mechanisms of sequence evolution are well understood. Although theories of molecular evolution are well developed, few empirical studies have addressed patterns and mechanisms of sequence evolution in nuclear genes within species. In the present study, we compared DNA sequences among three loci with different evolutionary constraints to determine the influences of effective population size, balancing selection, and linkage on intraspecific patterns of sequence variation. Specifically, we assessed the degree and nature of polymorphism in a 307-base pair (bp) fragment of the mitochondrial cytochrome b gene, intron VIII of the gene for α-enolase (a presumably neutral nuclear gene), and an ~600-bp fragment of an MHC class II B gene, including 155 bp of the hypervariable peptide binding region (a nuclear locus thought to be under balancing selection) for least and crested auklets (Aethia pusilla and A. cristatella; Charadriiformes: Alcidae). Transspecies polymorphism was found in both α-enolase and the MHC but not cytochrome b and, given estimates of effective population size, probably represents retained ancestral variation. Biases in nucleotide composition suggested that mutational bias, tRNA availability, and the secondary structure of mRNA and/or DNA may influence base usage. Several lines of evidence indicated that balancing selection may be acting on the MHC II B exon 2. However, no evidence of balancing selection was observed in the intron and exon sequences immediately downstream of MHC II B exon 2.

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Acknowledgements

Tissue samples for this study were kindly donated by Y. Artukhin, G.V. Byrd, S. Ebbert, I.L. Jones, J.F. Piatt, L. Scharf, D. Siegel-Causey, S. Stephensen, J. Williams, and their respective field crews. G.V. Byrd, L. Climo, L. Scharf, A. Sowls, J. Wachtel, J. Williams, and the crew of R/V Tiglax were instrumental to the success of fieldwork for this project. D. Michaud, B.C. Congdon, and other members of the Friesen lab provided valuable laboratory assistance and discussion. A.J. Baker, P.T. Boag, S.V. Edwards, D. Forsdyke, D. Garrigan, J. Gasper, M. Nordburg, P. Pamilo, and three anonymous reviewers provided helpful comments on previous drafts of the paper. We thank D. Garrigan and S. Edwards for access to their manuscript while in press. Financial and/or logistic support for this study was provided by the Northern Sciences Training Program, the U.S. Fish & Wildlife Service, Alaska Maritime National Wildlife Refuge (Bering Sea and Aleutian Islands units), and the Natural Sciences and Engineering Research Council (NSERC) of Canada (operating grant held by V.L.F. and postgraduate scholarships to H.E.W.).

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  1. Department of Biology, Queen’s University, Kingston, Ontario K7L 3N6, Canada

    Hollie E. Walsh & Vicki L. Friesen

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  1. Hollie E. Walsh
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Correspondence to Vicki L. Friesen.

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Walsh, H.E., Friesen, V.L. A Comparison of Intraspecific Patterns of DNA Sequence Variation in Mitochondrial DNA, α-Enolase, and MHC Class II B Loci in Auklets (Charadriiformes: Alcidae) . J Mol Evol 57, 681–693 (2003). https://doi.org/10.1007/s00239-003-2518-2

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