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HLA variation reveals genetic continuity rather than population group structure in East Asia

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Abstract

Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north–south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the “overlapping model” proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.

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Acknowledgments

This study was supported by the Swiss National Science Foundation (FNS) projects Nos. 31003A_112651, 31003A_127465, and 31003A_144180 to Prof. Alicia Sanchez-Mazas. We also thank Mr. Nuno Miguel Da Silva, Mr. Stephan Weber, and Dr. José Manuel Nunes for their technical help and useful recommendations. We would like to thank the anonymous reviewers.

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Authors and Affiliations

  1. Laboratory of Anthropology, Genetics and Peopling History (AGP lab), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 12 rue Gustave-Revilliod, CH-1211, Geneva, Switzerland

    Da Di & Alicia Sanchez-Mazas

  2. Institude of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), 1 rue Michel-Servet, CH-1211, Geneva, Switzerland

    Alicia Sanchez-Mazas

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  1. Da Di
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  2. Alicia Sanchez-Mazas
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Correspondence to Da Di.

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Di, D., Sanchez-Mazas, A. HLA variation reveals genetic continuity rather than population group structure in East Asia. Immunogenetics 66, 153–160 (2014). https://doi.org/10.1007/s00251-014-0757-6

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