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Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

Dejian Yuan, Xiaoyun Lei, Yuanyuan Gui, Mingrui Wang, Ye Zhang, Zuobin Zhu, Dapeng Wang, Jun Yu, Shi Huang
doi: https://doi.org/10.1101/101410
Dejian Yuan
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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Xiaoyun Lei
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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Yuanyuan Gui
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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Mingrui Wang
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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Ye Zhang
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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Zuobin Zhu
2Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
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Dapeng Wang
3CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, P.R. China
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Jun Yu
3CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, P.R. China
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Shi Huang
1State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, P.R. China
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  • For correspondence: huangshi@sklmg.edu.cn
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Abstract

The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.

Footnotes

  • Dejian Yuan, yuandejian{at}163.com, Xiaoyun Lei, leixiaoyun{at}sklmg.edu.cn, Yuanyuan Gui, guiyuanyuan{at}sklmg.edu.cn, Mingrui Wang, wangmingrui{at}sklmg.edu.cn, Ye Zhang, zhangye{at}sklmg.edu.cn, Zuobin Zhu, zhuzuobin2010{at}163.com, Dapeng Wang, wangdp123{at}gmail.com, Jun Yu, junyu{at}big.ac.cn

  • Added new Figure 1 to show that sharing of genetic variations among racial groups is due to parallel mutations rather than common ancestry and admixture. Added coauthors who contributed new data. Previous Figure 4 has been revised and is now Figure 5. Update reference list and added new reference to support the notion that observed variants in slow evolving genes are more neutral and more suitable for phylogenetic inferences.

  • Abbreviations

    AMH
    anatomically modern humans
    MGD
    maximum genetic diversity
    SNP
    single nucleotide polymorphisms
    AUA
    Aboriginal Australian
    PGD
    pairwise genetic distance
    PCA
    principal component analysis
    Myr
    million years
    AFR
    African
    ASN
    East Asian
    EUR
    European
    SAS
    South Asian
    ESN
    Esen in Nigeria
    GBR
    British in England and Scotland
    CHS
    Southern Han Chinese
    CHB
    Han Chinese in Beijing
    JPT
    Japanese in Tokyo
    BEB
    Bengali from Bangladesh
    YRI
    Yoruba in Ibadan, Nigeria
    CEU
    Utah Residents with Northern and Western European Ancestry
    LWK
    Luhya in Webuye, Kenya
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    Posted June 09, 2019.
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    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA
    Dejian Yuan, Xiaoyun Lei, Yuanyuan Gui, Mingrui Wang, Ye Zhang, Zuobin Zhu, Dapeng Wang, Jun Yu, Shi Huang
    bioRxiv 101410; doi: https://doi.org/10.1101/101410
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    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA
    Dejian Yuan, Xiaoyun Lei, Yuanyuan Gui, Mingrui Wang, Ye Zhang, Zuobin Zhu, Dapeng Wang, Jun Yu, Shi Huang
    bioRxiv 101410; doi: https://doi.org/10.1101/101410

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