收稿日期: 2020-07-27
修回日期: 2020-10-10
网络出版日期: 2020-11-06
基金资助
国家自然科学基金(91731303);国家自然科学基金(41925009);国家自然科学基金(41672021);国家自然科学基金(41630102)
Ancient DNA capture techniques and genetic study progress of early southern China populations
Received date: 2020-07-27
Revised date: 2020-10-10
Online published: 2020-11-06
古DNA捕获技术目前已获得极大的发展,能够从骨骼和环境沉积物等多种材料中获取到目的DNA片段,而且对于保存环境较差的低纬度地区,同样能够获取有效的内源DNA片段,极大地丰富了古DNA研究的材料来源。本文围绕这一新技术开展总结和讨论,主要分为两个方面：1）总结并介绍该技术应用前景;2）应用这一技术打开了中国南方早期人群研究的新局面,梳理该新技术的应用对史前中国南方人群古基因组研究所获得的新认识,并对中国南方早期人群古基因组深入分析;另外,利用古DNA捕获技术成功获取云南3446~3180 BP的大阴洞遗址4例高质量线粒体基因组信息,并开展了人群遗传历史的研究。
王恬怡 , 赵东月 , 张明 , 乔诗雨 , 杨帆 , 万杨 , 杨若薇 , 曹鹏 , 刘峰 , 付巧妹 . 古DNA捕获新技术与中国南方早期人群遗传研究新格局[J]. 人类学学报, 2020 , 39(04) : 680 -694 . DOI: 10.16359/j.cnki.cn11-1963/q.2020.0059
Substantial development of the ancient DNA capture techniques allows for obtaining DNA from a wide range of materials, including bone and environmental sediments. Moreover, effective endogenous DNA fragments are also obtainable from low-latitude regions with poor preservation conditions, greatly enriching the material sources for ancient DNA research. This paper summarizes and discusses this new technology in two main aspects: 1) it summarizes and presents the potential application of this technology; and 2) it reviews the knowledge gained from the application of this new technology to the study of ancient genomes. Specifically, this paper focuses on the study of ancient genomes from southern China and covers three points. First, we reveal the new insights gained from the study of ancient genomes. Second, we provide an in-depth analysis of the differences among ancient genomes of early populations in southern China. Third, we discuss the use of ancient DNA capture technology in successfully obtaining high quality mitochondrial genomic information from four individuals (3446-3180 cal BP) of Dayin Cave site in Yunnan Province.
Key words： Ancient DNA; Capture technique; Southern China; Ancient Genome; Dayin Cave
| [1] | Yang MA, Fan X, Sun B, et al. Ancient DNA indicates human population shifts and admixture in northern and southern China[J]. Science, 2020,369(6501):282-288 |
| [2] | Bai F, Zhang X, Ji X, et al. Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes[J]. Journal of Human Genetics, 2020: 1-4 |
| [3] | Ko AMS, Chen CY, Fu QM, et al. Early Austronesians: into and out of Taiwan[J]. American Journal of Human Genetics, 2014,94(3):426-436 |
| [4] | Zhang X, Li C, Zhou Y, et al. A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand[J]. iScience, 2020,23(4):101032 |
| [5] | Wang CC, Yeh HY, Popov AN, et al. The Genomic Formation of Human Populations in East Asia[J]. bioRxiv, 2020 |
| [6] | Yang MA, Gao X, Theunert C, et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia[J]. Current Biology, 2017, 27(20): 3202-3208.e9 |
| [7] | Ko AMS, Zhang Y, Yang MA, et al. Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage[J]. Current Biology, 2018,28(12):R693-R694 |
| [8] | Slon V, Hopfe C, Weiss CL, et al. Neandertal and Denisovan DNA from Pleistocene sediments[J]. Science, 2017,356(6338):605-608 |
| [9] | Burbano HA, Green RE, Maricic T, et al. Analysis of human accelerated DNA regions using archaic hominin genomes[J]. PloS one, 2012,7(3):e32877 |
| [10] | Burbano HA, Hodges E, Green RE, et al. Targeted investigation of the Neandertal genome by array-based sequence capture[J]. Science, 2010,328(5979):723-725 |
| [11] | ávila-Arcos MC, Cappellini E, Romero-Navarro JA, et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA[J]. Scientific reports, 2011,1(1):1-5 |
| [12] | Maricic T, Whitten M, P??bo S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products[J]. PloS one, 2010,5(11):e14004 |
| [13] | Sheng GL, Basler N, Ji XP, et al. Paleogenome reveals genetic contribution of extinct giant panda to extant populations[J]. Current Biology, 2019, 29(10): 1695-1700. e6 |
| [14] | Fu QM, Meyer M, Gao X, et al. DNA analysis of an early modern human from Tianyuan Cave, China[J]. Proceedings of the National Academy of Sciences, 2013,110(6):2223-2227 |
| [15] | Gnirke A, Melnikov A, Maguire J, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing[J]. Nature biotechnology, 2009,27(2):182-189 |
| [16] | Fu QM, Hajdinjak M, Moldovan O T, et al. An early modern human from Romania with a recent Neanderthal ancestor[J]. Nature, 2015,524(7564):216-219 |
| [17] | Fu QM, Li H, Moorjani P, et al. Genome sequence of a 45,000-year-old modern human from western Siberia[J]. Nature, 2014,514(7523):445-449 |
| [18] | Fu QM, Posth C, Hajdinjak M, et al. The genetic history of ice age Europe[J]. Nature, 2016,534(7606):200-205 |
| [19] | Kistler L, Ware R, Smith O, et al. A new model for ancient DNA decay based on paleogenomic meta-analysis[J]. Nucleic Acids Research, 2017,45(11):6310-6320 |
| [20] | Meyer M, Arsuaga JL, de Filippo C, et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins[J]. Nature, 2016,531(7595):504-507 |
| [21] | Gansauge MT, Meyer M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA[J]. Nature protocols, 2013,8(4):737-748 |
| [22] | Glocke I, Meyer M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth[J]. Genome research, 2017,27(7):1230-1237 |
| [23] | Meyer M, Kircher M, Gansauge MT, et al. A high-coverage genome sequence from an archaic Denisovan individual[J]. Science, 2012,338(6104):222-226 |
| [24] | Lipson M, Skoglund P, Spriggs M, et al. Population turnover in Remote Oceania shortly after initial settlement[J]. Current Biology, 2018, 28(7): 1157-1165.e7 |
| [25] | McColl H, Racimo F, Vinner L, et al. The prehistoric peopling of Southeast Asia[J]. Science, 2018,361(6397):88-92 |
| [26] | Zhang M, Sun G, Ren L, et al. Ancient DNA evidence from China reveals the expansion of Pacific dogs[J]. Molecular Biology and Evolution, 2020,37(5):1462-1469 |
| [27] | de Barros Damgaard P, Marchi N, Rasmussen S, et al. 137 ancient human genomes from across the Eurasian steppes[J]. Nature, 2018,557(7705):369-374 |
| [28] | de Barros Damgaard P, Martiniano R, Kamm J, et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia[J]. Science, 2018,360(6396) |
| [29] | Ning C, Wang CC, Gao S, et al. Ancient genomes reveal Yamnaya-related ancestry and a potential source of indo-European speakers in iron age Tianshan[J]. Current Biology, 2019, 29(15): 2526-2532.e4 |
| [30] | Sikora M, Pitulko VV, Sousa VC, et al. The population history of northeastern Siberia since the Pleistocene[J]. Nature, 2019,570(7760):182-188 |
| [31] | Siska V, Jones ER, Jeon S, et al. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago[J]. Science Advances, 2017,3(2):e1601877 |
| [32] | Wong EHM, Khrunin A, Nichols L, et al. Reconstructing genetic history of Siberian and Northeastern European populations[J]. Genome research, 2017,27(1):1-14 |
| [33] | Pei S, Gao X, Wang H, et al. The Shuidonggou site complex: new excavations and implications for the earliest Late Paleolithic in North China[J]. Journal of Archaeological Science, 2012,39(12):3610-3626 |
| [34] | Wu X, Liu W, Wang Z. A human parietal fossil found at the Shuidonggou site, Ningxia, China[J]. Anthropological Science, 2004,112(1):83-89 |
| [35] | Yang S X, Deng C L, Zhu R X, et al. The Paleolithic in the Nihewan Basin, China: Evolutionary history of an Early to Late Pleistocene record in Eastern Asia[J]. Evolutionary Anthropology: Issues, News, and Reviews, 2020,29(3):125-142 |
| [36] | 高星. 更新世东亚人群连续演化的考古证据及相关问题论述[J]. 人类学学报, 2014,33(3):237-253 |
| [37] | Cai P, Huang Q, Zhang X, et al. Adsorption of DNA on clay minerals and various colloidal particles from an Alfisol[J]. Soil Biology and Biochemistry, 2006,38(3):471-476 |
| [38] | Ogram A, Sayler GS, Gustin D, et al. DNA adsorption to soils and sediments[J]. Environmental science & technology, 1988,22(8):982-984 |
| [39] | Willerslev E, Hansen A J, Binladen J, et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments[J]. Science, 2003,300(5620):791-795 |
| [40] | Nichols RV, Curd E, Heintzman PD, et al. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA[J]. Methods in molecular biology (Clifton, NJ), 2019,1963:149-161 |
| [41] | Pedersen MW, Ruter A, Schweger C, et al. Postglacial viability and colonization in North America’s ice-free corridor[J]. Nature, 2016,537(7618):45-49 |
| [42] | Matsumura H, Hung H, Higham C, et al. Craniometrics reveal “two layers” of prehistoric human dispersal in eastern Eurasia[J]. Scientific reports, 2019,9(1):1-12 |
| [43] | Westaway KE, Louys J, Awe RD, et al. An early modern human presence in Sumatra 73,000-63,000 years ago[J]. Nature, 2017,548(7667):322-325 |
| [44] | Demeter F, Shackelford L, Westaway K, et al. Early modern humans from Tam Pà Ling, Laos: Fossil review and perspectives[J]. Current Anthropology, 2017,58(S17):S527-S538 |
| [45] | Matsumura H, Oxenham M. Population dispersal from East Asia into Southeast Asia: Evidence from cranial and dental Morphology[A]. In: Bioarchaeology of East Asia: Movement, Contact, Health[M]. University Press of Florida, 2013: 179-209 |
| [46] | Lipson M, Cheronet O, Mallick S, et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory[J]. Science, 2018,361(6397):92-95 |
| [47] | 焦天龙. 东南沿海的史前文化与南岛语族的扩散[J]. 中原文物, 2002 (2):13-16 |
| [48] | Blust RA. The proto-Austronesian pronouns and Austronesian subgrouping[J]. Working Papers in Linguistics, University of Hawaii, Honolulu, 1977,9:1-15 |
| [49] | Melton T, Peterson R, Redd AJ, et al. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis[J]. American journal of human genetics, 1995,57(2):403-414 |
| [50] | Raghavan M, Skoglund P, Graf KE, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans[J]. Nature, 2014,505(7481):87-91 |
| [51] | Diamond JM. Express train to Polynesia[J]. Nature, 1988,336(6197):307-308 |
| [52] | Jiao T. The Neolithic Archaeology of Southeast China[J]. A Companion to Chinese Archaeology, 2013: 597-611 |
| [53] | 张光直. 中国东南海岸考古与南岛语族起源问题[J]. 南方民族考古, 1987,1 |
| [54] | Chang K. Prehistoric and early historic culture horizons and traditions in South China[J]. Current Anthropology, 1964,5(5):359-375 |
| [55] | Chang K, Goodenough W H. Archaeology of southeastern coastal China and its bearing on the Austronesian homeland[J]. Transactions of the American philosophical society, 1996,86(5):36-56 |
| [56] | Bellwood P. Austronesian prehistory in Southeast Asia: homeland, expansion and transformation[M]. Canberra: ANU E Press, 1995 |
| [57] | 刘益昌. 台湾史前史专论 [M]. 台北: 联经出版事业股份有限公司, 2016 |
| [58] | 赵志军. 中国农业起源概述[J]. 遗产与保护研究, 2019 (1):1 |
| [59] | Crawford GW, Chen X, Luan F, et al. People and plant interaction at the Houli Culture Yuezhuang site in Shandong Province, China[J]. The Holocene, 2016,26(10):1594-1604 |
| [60] | Deng Z, Hung H, Fan X, et al. The ancient dispersal of millets in southern China: New archaeological evidence[J]. The Holocene, 2018,28(1):34-43 |
| [61] | Jeong C, Ozga AT, Witonsky DB, et al. Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc[J]. Proceedings of the National Academy of Sciences, 2016,113(27):7485-7490 |
| [62] | Moreno-Mayar JV, Potter BA, Vinner L, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans[J]. Nature, 2018,553(7687):203-207 |
| [63] | Shinde V, Narasimhan VM, Rohland N, et al. An ancient Harappan genome lacks ancestry from Steppe pastoralists or Iranian farmers[J]. Cell, 2019, 179(3): 729-735.e10 |
| [64] | Ding M, Wang T, Ko AMS, et al. Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans[J]. Proceedings of the Royal Society B, 2020,287(1923):20192968 |
| [65] | Bhandari S, Zhang X, Cui C, et al. Genetic evidence of a recent Tibetan ancestry to Sherpas in the Himalayan region[J]. Scientific reports, 2015,5:16249 |
| [66] | Chandrasekar A, Kumar S, Sreenath J, et al. Updating phylogeny of mitochondrial DNA macrohaplogroup M in India: dispersal of modern human in South Asian corridor[J]. PloS one, 2009,4(10):e7447 |
| [67] | Duong NT, Macholdt E, Ton ND, et al. Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia[J]. Scientific reports, 2018,8(1):1-13 |
| [68] | Fornarino S, Pala M, Battaglia V, et al. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation[J]. BMC Evolutionary Biology, 2009,9(1):154 |
| [69] | Kang L, Zheng H X, Zhang M, et al. MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders[J]. Scientific reports, 2016,6(1):1-11 |
| [70] | Kutanan W, Kampuansai J, Srikummool M, et al. Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages[J]. Human genetics, 2017,136(1):85-98 |
| [71] | Li YC, Wang HW, Tian JY, et al. Ancient inland human dispersals from Myanmar into interior East Asia since the Late Pleistocene[J]. Scientific reports, 2015,5:9473 |
| [72] | Lippold S, Xu H, Ko A, et al. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences[J]. Investigative genetics, 2014,5(1):13 |
| [73] | Peng MS, Palanichamy MG, Yao YG, et al. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b[J]. BMC biology, 2011,9(1):2 |
| [74] | Peng MS, Xu W, Song JJ, et al. Mitochondrial genomes uncover the maternal history of the Pamir populations[J]. European Journal of Human Genetics, 2018,26(1):124-136 |
| [75] | Qin Z, Yang Y, Kang L, et al. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum[J]. American Journal of Physical Anthropology, 2010,143(4):555-569 |
| [76] | Summerer M, Horst J, Erhart G, et al. Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar[J]. BMC evolutionary biology, 2014,14(1):1-12 |
| [77] | Wang HW, Li YC, Sun F, et al. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes[J]. Journal of human genetics, 2012,57(4):228-234 |
| [78] | Renaud G, Stenzel U, Kelso J. leeHom: adaptor trimming and merging for Illumina sequencing reads[J]. Nucleic acids research, 2014,42(18):e141-e141 |
| [79] | Renaud G, Stenzel U, Maricic T, et al. deML: robust demultiplexing of Illumina sequences using a likelihood-based approach[J]. Bioinformatics, 2015,31(5):770-772 |
| [80] | Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. bioinformatics, 2009,25(14):1754-1760 |
| [81] | Andrews RM, Kubacka I, Chinnery PF, et al. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA[J]. Nature genetics, 1999,23(2):147 |
| [82] | Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009,25(16):2078-2079 |
| [83] | Patterson N, Moorjani P, Luo Y, et al. Ancient admixture in human history[J]. Genetics, 2012,192(3):1065-1093 |
| [84] | Fu QM, Mittnik A, Johnson PLF, et al. A revised timescale for human evolution based on ancient mitochondrial genomes[J]. Current biology, 2013,23(7):553-559 |
| [85] | Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity[J]. BMC bioinformatics, 2004,5(1):113 |
| [86] | Kloss-Brandst?tter A, Pacher D, Sch?nherr S, et al. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups[J]. Human mutation, 2011,32(1):25-32 |
| [87] | Van Oven M. PhyloTree Build 17: Growing the human mitochondrial DNA tree[J]. Forensic Science International: Genetics Supplement Series, 2015,5:e392-e394 |
| [88] | Van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[J]. Human mutation, 2009,30(2):E386-E394 |
| [89] | Bandelt H J, Forster P, R?hl A. Median-joining networks for inferring intraspecific phylogenies[J]. Molecular biology and evolution, 1999,16(1):37-48 |
| [90] | Leigh JW, Bryant D, Nakagawa S. PopART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 2015,6(9):1110-1116 |
/
| 〈 |
|
〉 |
京ICP证05002819号-3