Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity
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The major histocompatibility complex (MHC) is integral to the vertebrate adaptive immune system. Characterizing diversity at functional MHC genes is invaluable for elucidating patterns of adaptive variation in wild populations, and is particularly interesting in species of conservation concern, which may suffer from reduced genetic diversity and compromised disease resilience. Here, we use next generation sequencing to investigate MHC class II B (MHCIIB) diversity in two sister taxa of New Zealand birds: South Island saddleback (SIS), Philesturnus carunculatus, and North Island saddleback (NIS), Philesturnus rufusater. These two species represent a passerine family outside the more extensively studied Passerida infraorder, and both have experienced historic bottlenecks. We examined exon 2 sequence data from populations that represent the majority of genetic diversity remaining in each species. A high level of locus co-amplification was detected, with from 1 to 4 and 3 to 12 putative alleles per individual for South and North Island birds, respectively. We found strong evidence for historic balancing selection in peptide-binding regions of putative alleles, and we identified a cluster combining non-classical loci and pseudogene sequences from both species, although no sequences were shared between the species. Fewer total alleles and fewer alleles per bird in SIS may be a consequence of their more severe bottleneck history; however, overall nucleotide diversity was similar between the species. Our characterization of MHCIIB diversity in two closely related species of New Zealand saddlebacks provides an important step in understanding the mechanisms shaping MHC diversity in wild, bottlenecked populations.
KeywordsIon Torrent Population decline Philesturnus Class Aves Order Passeriformes Songbird
We wish to thank Sabrina Taylor, Craig Millar, and Kevin Parker for providing blood samples from contemporary specimens. Canterbury Museum, American Museum of Natural History, and Naturhistorisches Museum Wien graciously supplied toepad samples from historic specimens (Accessions AV.309, 669746, NMW52.593, and NMW51.174). We are very grateful to Martyn Kennedy for input regarding phylogenetic analysis. Three anonymous reviewers provided constructive comments that greatly improved the manuscript. This research was funded by Landcare Research (contract no. C09X0503), University of Otago, and Allan Wilson Centre for Molecular Ecology and Evolution. J. Sutton is supported by scholarships from Natural Sciences and Engineering Research Council of Canada (NSERC) and New Zealand Ministry of Education (NZIDRS).
- Abbas AK, Lichtman AH (2001) Basic immunology: functions and disorders of the immune system. WB Saunders Company, PhiladelphiaGoogle Scholar
- Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2012) Geneious v5.6.5 created by Biomatters. Available from http://www.geneious.com
- Hale K (2008) Disease outbreak amongst South Island saddlebacks (Philesturnus carunculatus carunculatus) on Long Island. DOC Research & Development Series 289. Department of Conservation, Wellington, New ZealandGoogle Scholar
- Heather B, Robertson H (1996) The field guide to the birds of New Zealand. Viking, AucklandGoogle Scholar
- Kalbe M, Eizaguirre C, Dankert I, Reusch TBH, Sommerfeld RD, Wegner KM, Milinski M (2009) Lifetime reproductive success is maximized with optimal major histocompatibility complex diversity. Proc Natl Acad Sci USA 276:925Google Scholar
- Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352PubMedCrossRefGoogle Scholar