Andrews, R.M., Kubacka, I., Chinnery, P.F., Lightowlers, R.N., Turnbull, D.M., Howell, N., 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147-147.
|
Bai, F., Zhang, X., Ji, X., Cao, P., Feng, X., Yang, R., Peng, M., Pei, S., Fu, Q., 2020. Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes. J. Hum. Genet. 65, 1125-1128.
|
Briggs, A.W., Stenzel, U., Johnson, P.L.F., Green, R.E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M.T., Lachmann, M., et al., 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U. S. A. 104, 14616-14621.
|
Chen, M., 1989a. A review of research on Hanging Coffin (in Chinese). Ethno-National Stud. 1, 98-103.
|
Chen, M., 1989b. A study of the comparison between hanging coffin and cave burial in southern China (in Chinese). J. Minzu Univ. China (Phil. Soc. Sci. Ed.) 5, 42-49.
|
China National Center for Bioinformation, National Genomics Data Center Members and Partners, 2020. Database resources of the national genomics data center, China national center for bioinformation in 2021. Nucleic Acids Res. 49, D18eD28.
|
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al., 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 110, 15758-15763.
|
Dabney, J., Meyer, M., 2012. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87-94.
|
Derenko, M., Malyarchuk, B., Grzybowski, T., Denisova, G., Rogalla, U., Perkova, M., Dambueva, I., Zakharov, I., 2010. Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLoS One 5, e15214.
|
Ding, M., Wang, T., Ko, A.M.-S., Chen, H., Wang, H., Dong, G., Lu, H., He, W., Wangdue, S., Yuan, H., et al., 2020. Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans. Proc. Biol. Sci. 287, 20192968.
|
Duong, N.T., Macholdt, E., Ton, N.D., Arias, L., Schröder, R., Van Phong, N., Thi Bich Thuy, V., Ha, N.H., Thi Thu Hue, H., Thi Xuan, N., et al., 2018. Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia. Sci. Rep. 8, 11651.
|
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H.A., Kelso, J., Pääbo, S., 2013a. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. U. S. A. 110, 2223-2227.
|
Fu, Q., Mittnik, A., Johnson, Philip L.F., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., et al., 2013b. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553-559.
|
Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., et al., 2016. The genetic history of ice age Europe. Nature 534, 200-205.
|
Fu, X., 1988. On stepped adze and shoulder stone tools (in Chinese). Acta Archaeol. Sinica 1, 1-36.
|
Gansauge, M.-T., Meyer, M., 2013. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737-748.
|
Ji, X., Kuman, K., Clarke, R.J., Forestier, H., Li, Y., Ma, J., Qiu, K., Li, H., Wu, Y., 2016. The oldest Hoabinhian technocomplex in Asia (43.5 ka) at Xiaodong rockshelter, Yunnan Province, southwest China. Quat. Int. 400, 166-174.
|
Kircher, M., Sawyer, S., Meyer, M., 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3.
|
Ko, Albert M.-S., Chen, C.-Y., Fu, Q., Delfin, F., Li, M., Chiu, H.-L., Stoneking, M., Ko, Y.-C., 2014. Early Austronesians: into and out of Taiwan. Am. J. Hum. Genet. 94, 426-436.
|
Kong, Q.-P., Sun, C., Wang, H.-W., Zhao, M., Wang, W.-Z., Zhong, L., Hao, X.-D., Pan, H., Wang, S.-Y., Cheng, Y.-T., et al., 2011. Large-scale mtDNA screening reveals a surprising matrilineal complexity in East Asia and its implications to the peopling of the region. Mol. Biol. Evol. 28, 513-522.
|
Kutanan, W., Kampuansai, J., Srikummool, M., Kangwanpong, D., Ghirotto, S., Brunelli, A., Stoneking, M., 2017. 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. Hum. Genet. 136, 85-98.
|
Kutanan, W., Shoocongdej, R., Srikummool, M., Hübner, A., Suttipai, T., Srithawong, S., Kampuansai, J., Stoneking, M., 2020. Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand. Eur. J. Hum. Genet. 28, 1563-1579.
|
Lahr, M.M., Foley, R., 1994. Multiple dispersals and modern human origins. Evol. Anthropol. Issues News Rev. 3, 48-60.
|
Larruga, J.M., Marrero, P., Abu-Amero, K.K., Golubenko, M.V., Cabrera, V.M., 2017. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol. Biol. 17, 115-115.
|
Leigh, J.W., Bryant, D., 2015. popart: full-feature software for haplotype network construction. Meth. Ecol. Evol. 6, 1110-1116.
|
Li, H., Durbin, R., 2009. Fast and accurate short read alignment with BurrowsWheeler transform. Bioinformatics 25, 1754-1760.
|
Lin, Z., Wu, Y., Lin, Z., Mei, H., 1980. A brief report on the clearance of Baiyan hanging coffin in Wuyi mountain, Chong ’an, Fujian (in Chinese). Cult. Relics 14-22.
|
Liu, J., Zeng, W., Sun, B., Mao, X., Zhao, Y., Wang, F., Li, Z., Luan, F., Guo, J., Zhu, C., et al., 2021. Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago. Sci. Bull. 66, 1129-1135.
|
Luo, E., 2000. Cave burial in southern China (in Chinese). Archaeology 6, 79-87.
|
Matsumura, H., Hung, H.-c., Higham, C., Zhang, C., Yamagata, M., Nguyen, L.C., Li, Z., Fan, X.-c., Simanjuntak, T., Oktaviana, A.A., et al., 2019. Craniometrics reveal “two layers” of prehistoric human dispersal in eastern Eurasia. Sci. Rep. 9, 1451.
|
McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J.V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al., 2018. The prehistoric peopling of Southeast Asia. Science 361, 88.
|
Mei, H., 1989. On the pottery pots unearthed in Fujian, guangdong and Guangxi (in Chinese). Archaeology 11, 1022-1026.
|
O’Connell, J.F., Allen, J., Williams, M.A.J., Williams, A.N., Turney, C.S.M., Spooner, N.A., Kamminga, J., Brown, G., Cooper, A., 2018. When did Homo sapiens first reach Southeast Asia and Sahul? Proc. Natl. Acad. Sci. U. S. A. 115, 8482-8490.
|
Peng, C., 2001. Preliminary study on early cave burials in Guangxi (in Chinese). Guangxi Ethnic Stud. 84-90.
|
Rambaut, A., Drummond, A.J., Xie, D., Baele, G., Suchard, M.A., 2018. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Syst. Biol. 67, 901-904.
|
Renaud, G., Stenzel, U., Kelso, J., 2014. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141.
|
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., Reich, D., 2015. Partial uracileDNAeglycosylase treatment for screening of ancient DNA. Phil. Trans. Biol. Sci. 370, 20130624.
|
Skoglund, P., Northoff, B.H., Shunkov, M.V., Derevianko, A.P., Pääbo, S., Krause, J., Jakobsson, M., 2014. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl. Acad. Sci. U. S. A. 111, 2229.
|
Soares, P., Trejaut, J.A., Loo, J.-H., Hill, C., Mormina, M., Lee, C.-L., Chen, Y.-M., Hudjashov, G., Forster, P., Macaulay, V., et al., 2008. Climate change and postglacial human dispersals in Southeast Asia. Mol. Biol. Evol. 25, 1209-1218.
|
Stoneking, M., Delfin, F., 2010. The human genetic history of East Asia: Weaving a complex tapestry. Curr. Biol. 20, R188-R193.
|
Suchard, M.A., Lemey, P., Baele, G., Ayres, D.L., Drummond, A.J., Rambaut, A., 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016.
|
Tanaka, M., Cabrera, V.M., González, A.M., Larruga, J.M., Takeyasu, T., Fuku, N., Guo, L.J., Hirose, R., Fujita, Y., Kurata, M., et al., 2004. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 14, 1832-1850.
|
Tofanelli, S., Bertoncini, S., Castrì, L., Luiselli, D., Calafell, F., Donati, G., Paoli, G., 2009. On the origins and admixture of Malagasy: new evidence from highresolution analyses of paternal and maternal lineages. Mol. Biol. Evol. 26, 2109-2124.
|
van Oven, M., Kayser, M., 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386-E394.
|
Wall, J.D., Stawiski, E.W., Ratan, A., Kim, H.L., Kim, C., Gupta, R., Suryamohan, K., Gusareva, E.S., Purbojati, R.W., Bhangale, T., et al., 2019. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576, 106-111.
|
Wang, T., Wang, W., Xie, G., Li, Z., Fan, X., Yang, Q., Wu, X., Cao, P., Liu, Y., Yang, R., et al., 2021. Human population history at the crossroads of East and Southeast Asia since 11,000 years ago. Cell 184, 3829-3841. e3821.
|
Wang, C.-C., Yeh, H.-Y., Popov, A.N., Zhang, H.-Q., Matsumura, H., Sirak, K., Cheronet, O., Kovalev, A., Rohland, N., Kim, A.M., et al., 2021. Genomic insights into the formation of human populations in East Asia. Nature 591, 413-419.
|
Weissensteiner, H., Pacher, D., Kloss-Brandstätter, A., Forer, L., Specht, G., Bandelt, H.J., Kronenberg, F., Salas, A., Schönherr, S., 2016. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58-W63.
|
Wen, B., Li, H., Gao, S., Mao, X., Gao, Y., Li, F., Zhang, F., He, Y., Dong, Y., Zhang, Y., et al., 2004. Genetic structure of Hmong-mien speaking populations in East Asia as revealed by mtDNA lineages. Mol. Biol. Evol. 22, 725-734.
|
Yang, M.A., Fan, X., Sun, B., Chen, C., Lang, J., Ko, Y.-C., Tsang, C.-h., Chiu, H., Wang, T., Bao, Q., et al., 2020. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science 369, 282-288.
|
Yao, Y.G., Kong, Q.P., Bandelt, H.J., Kivisild, T., Zhang, Y.P., 2002. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am. J. Hum. Genet. 70, 635-651.
|
Zhang, M., Fu, Q., 2020. Human evolutionary history in Eastern Eurasia using insights from ancient DNA. Curr. Opin. Genet. Dev. 62, 78-84.
|
Zhang, X., Liao, S., Qi, X., Liu, J., Kampuansai, J., Zhang, H., Yang, Z., Serey, B., Sovannary, T., Bunnath, L., et al., 2015. Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci. Rep. 5, 15486.
|