High-throughput sequencing reveals inbreeding depression in a natural population

Joseph I. Hoffman; Fraser Simpson; Patrice DavidJolianne M. RijksThijs KuikenMichael A. S. ThorneRobert C. LacyKanchon K. Dasmahapatra

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High-throughput sequencing reveals inbreeding depression in a natural population

机译：High-throughput sequencing reveals inbreeding depression in a natural population

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Proxy measures of genome-wide heterozygosity based on approximately 10microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged.

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《Proceedings of the National Academy of Sciences of the United States of America》 |2014年第10期|3775-3780|共6页
作者
Joseph I. Hoffman; Fraser Simpson; Patrice DavidJolianne M. RijksThijs KuikenMichael A. S. ThorneRobert C. LacyKanchon K. Dasmahapatra;
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作者单位

Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany;

Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom;

Centre d'Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, 34293 Montpellier, FranceDutch Wildlife Health Centre, Pathology Division, Department of Pathobiology, Faculty of Veterinary Medicine, University of Utrecht, Yalelaan 1, 3584 CL, Utrecht, The NetherlandsDepartment of Viroscience, Erasmus University Medical Centre, 3000 CA, Rotterdam, The NetherlandsBritish Antarctic Survey, Natural Environment Research Council, Cambridge CB3 OET, United KingdomDepartment of Conservation Science, Chicago Zoological Society, Brookfield, IL 60513Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom;

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收录信息美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
原文格式 PDF
正文语种英语
中图分类自然科学总论;
关键词
inbreeding; genetic variability; heterozygosity fitness correlation; single nucleotide polymorphism; RAD sequencing;

High-throughput sequencing reveals inbreeding depression in a natural population

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