454 screening of individual MHC variation in an endemic island passerine

Gonzalez Quevedo, Catalina, Phillips, Karl, Spurgin, Lewis and Richardson, David (2015) 454 screening of individual MHC variation in an endemic island passerine. Immunogenetics, 67 (3). pp. 149-162. ISSN 0093-7711

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Abstract

Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot’s pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot’s pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot’s pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot’s pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC.

Item Type: Article
Additional Information: This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The online version of this article (doi:10.​1007/​s00251-014-0822-1) contains supplementary material, which is available to authorized users.
Uncontrolled Keywords: 454,major histocompatability complex,berthelot's pipit,allele amplification efficiency,tawny pipit ,anthus berthelotii,anthus campestris
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Pure Connector
Date Deposited: 31 Jul 2015 13:38
Last Modified: 22 Apr 2020 00:22
URI: https://ueaeprints.uea.ac.uk/id/eprint/54005
DOI: 10.1007/s00251-014-0822-1

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