Skip to main content

Advertisement

SpringerLink
Log in

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

  • Original Article
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Weimin Zhou LT (2018) Hainan general history (in Chinese). People’s Publishing House

  2. Yan G (2013) History and culture of Hainan (in Chinese). Social Sciences Academic Press Beijing

  3. Zhong Y (2010) Historical Hainan (in Chinese). Hainan Publishing House Hainan

  4. J Y. (2008) Eco-environmental changes in Hainan Island. Science Press Beijing

  5. Xia XM (2015) Environmental conditions of Hainan marine resources. Ocean Press Hainan

  6. Huang ZGZW, Chai FX, Xu QH (1995) On the lowest sea level during the culmination of the lastest glacial period in South China. Acta Geogr Sin 50:385–393

    Google Scholar 

  7. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB (2008) Climate change and postglacial human dispersals in southeast Asia. Mol Biol Evol 25:1209–1218. https://doi.org/10.1093/molbev/msn068

    Article  CAS  PubMed  Google Scholar 

  8. Zhu H (2016) Biogeographical evidences help revealing the origin of Hainan Island. PLoS One 11:e0151941. https://doi.org/10.1371/journal.pone.0151941

  9. Zhang TY (1974) Ming Shi (The history of Ming Dynasty, Volume three hundred and four). Zhonghua Book Company Beijing

  10. Du RYV (1993) Ethnic groups in China. Science Press Beijing

  11. He G, Wang Z, Guo J, Wang M, Zou X, Tang R, Liu J, Zhang H, Li Y, Hu R, Wei LH, Chen G, Wang CC, Hou Y (2020) Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping. Eur J Hum Genet. 28:1111–1123. https://doi.org/10.1038/s41431-020-0599-7

  12. Li D, Li H, Ou C, Lu Y, Sun Y, Yang B, Qin Z, Zhou Z, Li S, Jin L (2008) Paternal genetic structure of Hainan aborigines isolated at the entrance to East Asia. PLoS One 3:e2168. https://doi.org/10.1371/journal.pone.0002168

  13. Li D, Sun Y, Lu Y, Mustavich LF, Ou C, Zhou Z, Li S, Jin L, Li H (2010) Genetic origin of Kadai-speaking Gelong people on Hainan island viewed from Y chromosomes. J Hum Genet 55:462–468. https://doi.org/10.1038/jhg.2010.50

  14. Li DN, Wang CC, Yang K et al (2013) Substitution of Hainan indigenous genetic lineage in the Utsat people, exiles of the Champa kingdom. J Syst Evol 51:287–294. https://doi.org/10.1111/jse.12000

  15. Peng MS, He JD, Liu HX, Zhang YP (2011) Tracing the legacy of the early Hainan islanders--a perspective from mitochondrial DNA. BMC Evol Biol 11:46. https://doi.org/10.1186/1471-2148-11-46

  16. Song M, Wang Z, Zhang Y, Zhao C, Lang M, Xie M, Qian X, Wang M, Hou Y (2019) Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China. Forensic Sci Int Genet 39:e14–e20. https://doi.org/10.1016/j.fsigen.2018.11.016

  17. Sun YYB, Ou C, Chen L, Su Z, Li D (2007) Investigation into the origin of Li ethnic group in China by genetic analysis of Y chromosome single nucleotide polymorphism. China Trop Med 7:1527–1529

  18. Sun YYB, Ou C, Zhou Z, Su Z, Li D (2007) Origins of the three minority populations in Hainan Island as seen from Y-SNP. Sci &Technol Rev 25:44–47

  19. Yang BLD, Sun Y, Ou C, Ying D (2007) Genetic analysis of Y-chromosomal single nucleotide polymorphoism in three banches of Li ethnic groups in Hainan Province. China Trop Med 7:341–356

  20. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM (2009) The Last Glacial Maximum. Science 325:710–714. https://doi.org/10.1126/science.1172873

  21. Yao YTHJ, Meyer M, Zhan WH (2009) Reconstruction of paleocoastlines for the northwestern South China Sea since the Last Glacial Maximum. Sci China Ser D-Earth Sci 52:1127–1136

  22. Hao SDHB (1998) Sanya Luobidong Site. Southern Press Guangzhou

  23. Hao SDWD (2003) Retrospection and prospection of archaeology in Hainan. Archaeology (in Chinese) 4:291–299

  24. HP W (1990) The Neolithic archaeological discoveries and researches in Hainan. J Hainan Normal Univ:81–89

  25. Li CRLZ, Wang DX, Hao SD, Wang MZ, Jiang B, Huang ZX, Fang XL (2008) Some stone artifacts discovered in Changjiang, Hainan. Acta Anthropol Sin 27:66–69

    CAS  Google Scholar 

  26. Li ZLC, Wang DX (2008) Paleolithic archaeology in Hainan Province. In: Dong W (ed) Proceedings of the Eleventh Annual Meeting of the Chinese Society of Vertebrate Paleontology. China Ocean Press, Beijing

    Google Scholar 

  27. Zhao HTWL, Yuan JY (2007) Origin and time of Qiongzhou Strait. Mar Geol & Quaternary Geol 27:33–40

    CAS  Google Scholar 

  28. Liang G (2013) Eight major evidence of Hainan island's spinning drift apart from China’s Beibu Gulf (in Chinese). ACTA GEOLOGICA SINICA 7(supplementary issue):73–76

    Google Scholar 

  29. Ge JXWS, Chao SJ (1997) Zhongguo yimin shi (The migration history of China). Fujian People’s Publishing House Fuzhou, China

    Google Scholar 

  30. XT F (1999) The pattern of diversity in unity of the Chinese nation. Central Univ. for Nationalities Press Beijing

  31. PK N (2015) A phonological reconstruction of Proto-Hlai. Brill Leiden/Boston

  32. Wang XPWJ, Xing GY (2004) China Hlai. The Ethnic Publishing House Beijing

  33. Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Arch Med Sadowej Kryminol 65:260–271. https://doi.org/10.5114/amsik.2015.61029

  34. Borsting C, Morling N (2015) Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 18:78–89. https://doi.org/10.1016/j.fsigen.2015.02.002

  35. Bruijns B, Tiggelaar R, Gardeniers H (2018) Massively parallel sequencing techniques for forensics: a review. Electrophoresis 39:2642–2654. https://doi.org/10.1002/elps.201800082

  36. de Knijff P (2019) From next generation sequencing to now generation sequencing in forensics. Forensic Sci Int Genet 38:175–180. https://doi.org/10.1016/j.fsigen.2018.10.017

  37. Minogue TD, Koehler JW, Stefan CP, Conrad TA (2019) Next-generation sequencing for biodefense: biothreat detection, forensics, and the clinic. Clin Chem 65:383–392. https://doi.org/10.1373/clinchem.2016.266536

  38. van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426. https://doi.org/10.1016/j.tig.2014.07.001

  39. Yang Y, Xie B, Yan J (2014) Application of next-generation sequencing technology in forensic science. Genomics Proteomics Bioinformatics 12:190–197. https://doi.org/10.1016/j.gpb.2014.09.001

  40. Guo F, Yu J, Zhang L, Li J (2017) Massively parallel sequencing of forensic STRs and SNPs using the Illumina((R)) ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Forensic Sci Int Genet 31:135–148. https://doi.org/10.1016/j.fsigen.2017.09.003

  41. Hollard C, Ausset L, Chantrel Y, Jullien S, Clot M, Faivre M, Suzanne É, Pène L, Laurent FX (2019) Automation and developmental validation of the ForenSeq() DNA Signature Preparation kit for high-throughput analysis in forensic laboratories. Forensic Sci Int Genet 40:37–45. https://doi.org/10.1016/j.fsigen.2019.01.010

  42. Jager AC, Alvarez ML, Davis CP et al (2017) Developmental validation of the MiSeq FGx Forensic Genomics System for targeted next generation sequencing in forensic DNA casework and database laboratories. Forensic Sci Int Genet 28:52–70. https://doi.org/10.1016/j.fsigen.2017.01.011

  43. Kocher S, Muller P, Berger B et al (2018) Inter-laboratory validation study of the ForenSeq DNA Signature Prep Kit. Forensic Sci Int Genet 36:77–85. https://doi.org/10.1016/j.fsigen.2018.05.007

  44. Mehta B, Venables S, Roffey P (2018) Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping. Int J Legal Med 132:125–132. https://doi.org/10.1007/s00414-017-1591-9

  45. Muller P, Sell C, Hadrys T et al (2020) Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA. Int J Legal Med 134:185–198. https://doi.org/10.1007/s00414-019-02201-2

  46. Sharma V, Chow HY, Siegel D, Wurmbach E (2017) Qualitative and quantitative assessment of Illumina’s forensic STR and SNP kits on MiSeq FGx. PLoS One 12:e0187932. https://doi.org/10.1371/journal.pone.0187932

  47. Xavier C, Parson W (2017) Evaluation of the Illumina ForenSeq DNA Signature Prep Kit - MPS forensic application for the MiSeq FGx benchtop sequencer. Forensic Sci Int Genet 28:188–194. https://doi.org/10.1016/j.fsigen.2017.02.018

  48. Carrasco P, Inostroza C, Didier M, Godoy M, Holt CL, Tabak J, Loftus A (2020) Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing. Int J Legal Med 134:79–91. https://doi.org/10.1007/s00414-019-02124-y

  49. Fattorini P, Previdere C, Carboni I et al (2017) Performance of the ForenSeq(TM) DNA Signature Prep kit on highly degraded samples. Electrophoresis 38:1163–1174. https://doi.org/10.1002/elps.201600290

    Article  CAS  PubMed  Google Scholar 

  50. Hwa HL, Wu MY, Chung WC, Ko TM, Lin CP, Yin HI, Lee TT, Lee JCI (2019) Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq system in combination with EuroForMix software. Int J Legal Med 133:25–37. https://doi.org/10.1007/s00414-018-1961-y

    Article  PubMed  Google Scholar 

  51. Zubakov D, Kokmeijer I, Ralf A, Rajagopalan N, Calandro L, Wootton S, Langit R, Chang C, Lagace R, Kayser M (2015) Towards simultaneous individual and tissue identification: a proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM. Forensic Sci Int Genet 17:122–128. https://doi.org/10.1016/j.fsigen.2015.04.002

    Article  CAS  PubMed  Google Scholar 

  52. Ambers AD, Churchill JD, King JL, Stoljarova M, Gill-King H, Assidi M, Abu-Elmagd M, Buhmeida A, al-Qahtani M, Budowle B (2016) More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing. BMC Genomics 17:750. https://doi.org/10.1186/s12864-016-3087-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Elwick K, Bus MM, King JL, Chang J, Hughes-Stamm S, Budowle B (2019) Utility of the Ion S5 and MiSeq FGx sequencing platforms to characterize challenging human remains. Leg Med (Tokyo) 41:101623. https://doi.org/10.1016/j.legalmed.2019.08.001

    Article  CAS  Google Scholar 

  54. Zeng X, Elwick K, Mayes C, Takahashi M, King JL, Gangitano D, Budowle B, Hughes-Stamm S (2019) Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success. Int J Legal Med 133:51–58. https://doi.org/10.1007/s00414-018-1955-9

    Article  PubMed  Google Scholar 

  55. Szargut M, Diepenbroek M, Zielinska G et al (2019) Is MPS always the answer? Use of two PCR-based methods for Y-chromosomal haplotyping in highly and moderately degraded bone material. Forensic Sci Int Genet 42:181–189. https://doi.org/10.1016/j.fsigen.2019.07.016

    Article  CAS  PubMed  Google Scholar 

  56. Wu J, Li JL, Wang ML, Li JP, Zhao ZC, Wang Q, Yang SD, Xiong X, Yang JL, Deng YJ (2019) Evaluation of the MiSeq FGx system for use in forensic casework. Int J Legal Med 133:689–697. https://doi.org/10.1007/s00414-018-01987-x

    Article  PubMed  Google Scholar 

  57. Moreno LI, Galusha MB, Just R (2018) A closer look at Verogen’s Forenseq DNA Signature Prep kit autosomal and Y-STR data for streamlined analysis of routine reference samples. Electrophoresis 39:2685–2693. https://doi.org/10.1002/elps.201800087

    Article  CAS  PubMed  Google Scholar 

  58. Churchill JD, Schmedes SE, King JL, Budowle B (2016) Evaluation of the Illumina((R)) Beta Version ForenSeq DNA Signature Prep Kit for use in genetic profiling. Forensic Sci Int Genet 20:20–29. https://doi.org/10.1016/j.fsigen.2015.09.009

    Article  CAS  PubMed  Google Scholar 

  59. Just RS, Moreno LI, Smerick JB, Irwin JA (2017) Performance and concordance of the ForenSeq system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. Forensic Sci Int Genet 28:1–9. https://doi.org/10.1016/j.fsigen.2017.01.001

    Article  CAS  PubMed  Google Scholar 

  60. King JL, Churchill JD, Novroski NMM, Zeng X, Warshauer DH, Seah LH, Budowle B (2018) Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq DNA Signature Prep Kit. Forensic Sci Int Genet 36:60–76. https://doi.org/10.1016/j.fsigen.2018.06.005

    Article  CAS  PubMed  Google Scholar 

  61. Li R, Wu R, Li H, Zhang Y, Peng D, Wang N, Shen X, Wang Z, Sun H (2020) Characterizing stutter variants in forensic STRs with massively parallel sequencing. Forensic Sci Int Genet 45:102225. https://doi.org/10.1016/j.fsigen.2019.102225

    Article  CAS  PubMed  Google Scholar 

  62. Alonso A, Barrio PA, Muller P et al (2018) Current state-of-art of STR sequencing in forensic genetics. Electrophoresis 39:2655–2668. https://doi.org/10.1002/elps.201800030

    Article  CAS  PubMed  Google Scholar 

  63. McCord B, Lee SB (2018) Novel applications of massively parallel sequencing (MPS) in forensic analysis. Electrophoresis 39:2639–2641. https://doi.org/10.1002/elps.201870175

    Article  CAS  PubMed  Google Scholar 

  64. Xue J, Wu R, Pan Y, Wang S, Qu B, Qin Y, Shi Y, Zhang C, Li R, Zhang L, Zhou C, Sun H (2018) Integrated massively parallel sequencing of 15 autosomal STRs and amelogenin using a simplified library preparation approach. Electrophoresis 39:1466–1473. https://doi.org/10.1002/elps.201700429

    Article  CAS  PubMed  Google Scholar 

  65. Kostrzewa G, Konarzewska M, Pepinski W (2017) Application of massively parallel sequencing (MPS) in paternity testing - case report. Arch Med Sadowej Kryminol 67:61–67. https://doi.org/10.5114/amsik.2017.70338

    Article  PubMed  Google Scholar 

  66. Li R, Li H, Peng D, Hao B, Wang Z, Huang E, Wu R, Sun H (2019) Improved pairwise kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 38:77–85. https://doi.org/10.1016/j.fsigen.2018.10.006

    Article  CAS  PubMed  Google Scholar 

  67. Ma Y, Kuang JZ, Nie TG, Zhu W, Yang Z (2016) Next generation sequencing: improved resolution for paternal/maternal duos analysis. Forensic Sci Int Genet 24:83–85. https://doi.org/10.1016/j.fsigen.2016.05.015

    Article  CAS  PubMed  Google Scholar 

  68. Xu M, Du Q, Ma G et al (2019) Utility of ForenSeq DNA Signature Prep Kit in the research of pairwise 2nd-degree kinship identification. Int J Legal Med 133:1641–1650. https://doi.org/10.1007/s00414-019-02003-6

    Article  PubMed  Google Scholar 

  69. Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M, Pryce TO, Willis A, Matsumura H, Buckley H, Domett K, Nguyen GH, Trinh HH, Kyaw AA, Win TT, Pradier B, Broomandkhoshbacht N, Candilio F, Changmai P, Fernandes D, Ferry M, Gamarra B, Harney E, Kampuansai J, Kutanan W, Michel M, Novak M, Oppenheimer J, Sirak K, Stewardson K, Zhang Z, Flegontov P, Pinhasi R, Reich D (2018) Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science 361:92–95. https://doi.org/10.1126/science.aat3188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Jin L, Su B (2000) Natives or immigrants: modern human origin in east Asia. Nat Rev Genet 1:126–133. https://doi.org/10.1038/35038565

    Article  CAS  PubMed  Google Scholar 

  71. Yew CW, Lu D, Deng L, Wong LP, Ong RTH, Lu Y, Wang X, Yunus Y, Aghakhanian F, Mokhtar SS, Hoque MZ, Voo CLY, Abdul Rahman T, Bhak J, Phipps ME, Xu S, Teo YY, Kumar SV, Hoh BP (2018) Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Hum Genet 137:161–173. https://doi.org/10.1007/s00439-018-1869-0

    Article  CAS  PubMed  Google Scholar 

  72. Tian JY, Li YC, Kong QP, Zhang YP (2018) The origin and evolution history of East Asian populations from genetic perspectives (in Chinese). Yi Chuan 40:814–824. https://doi.org/10.16288/j.yczz.18-202

    Article  PubMed  Google Scholar 

  73. Stoneking M, Delfin F (2010) The human genetic history of East Asia: weaving a complex tapestry. Curr Biol 20:R188–R193. https://doi.org/10.1016/j.cub.2009.11.052

    Article  CAS  PubMed  Google Scholar 

  74. Consortium HP-AS, Abdulla MA, Ahmed I et al (2009) Mapping human genetic diversity in Asia. Science 326:1541–1545. https://doi.org/10.1126/science.1177074

    Article  CAS  Google Scholar 

  75. Wen SQ, Tong XZ, Li H (2016) Y-chromosome-based genetic pattern in East Asia affected by Neolithic transition. Quatern Int 426:50–55. https://doi.org/10.1016/j.quaint.2016.03.027

    Article  Google Scholar 

  76. (2015) Illumina Inc. ForenSeqTM DNA Signature Prep Reference Guide.

    Google Scholar 

  77. (2015) Illumina Inc. MiSeq FGxTM Instrument Reference Guide.

    Google Scholar 

  78. (2004) Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods. 1-13.

  79. (2015) Illumina Inc. ForenSeqTM Universal Analysis Software User Guide.

    Google Scholar 

  80. Woerner AE, King JL, Budowle B (2017) Fast STR allele identification with STRait Razor 3.0. Forensic Sci Int Genet 30:18–23. https://doi.org/10.1016/j.fsigen.2017.05.008

    Article  CAS  PubMed  Google Scholar 

  81. Parson W, Ballard D, Budowle B, Butler JM, Gettings KB, Gill P, Gusmão L, Hares DR, Irwin JA, King JL, Knijff P, Morling N, Prinz M, Schneider PM, Neste CV, Willuweit S, Phillips C (2016) Massively parallel sequencing of forensic STRs: considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. Forensic Sci Int Genet 22:54–63. https://doi.org/10.1016/j.fsigen.2016.01.009

    Article  CAS  PubMed  Google Scholar 

  82. Phillips C, Gettings KB, King JL, Ballard D, Bodner M, Borsuk L, Parson W (2018) “The devil’s in the detail”: release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide. Forensic Sci Int Genet 34:162–169. https://doi.org/10.1016/j.fsigen.2018.02.017

    Article  CAS  PubMed  Google Scholar 

  83. Gettings KB, Borsuk LA, Ballard D, Bodner M, Budowle B, Devesse L, King J, Parson W, Phillips C, Vallone PM (2017) STRSeq: a catalog of sequence diversity at human identification short tandem repeat loci. Forensic Sci Int Genet 31:111–117. https://doi.org/10.1016/j.fsigen.2017.08.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Borsuk LA, Gettings KB, Steffen CR, Kiesler KM, Vallone PM (2018) Sequence-based US population data for the SE33 locus. Electrophoresis 39:2694–2701. https://doi.org/10.1002/elps.201800091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Devesse L, Ballard D, Davenport L, Riethorst I, Mason-Buck G, Syndercombe Court D (2018) Concordance of the ForenSeq system and characterisation of sequence-specific autosomal STR alleles across two major population groups. Forensic Sci Int Genet 34:57–61. https://doi.org/10.1016/j.fsigen.2017.10.012

    Article  CAS  PubMed  Google Scholar 

  86. Gettings KB, Borsuk LA, Steffen CR, Kiesler KM, Vallone PM (2018) Sequence-based U.S. population data for 27 autosomal STR loci. Forensic Sci Int Genet 37:106–115. https://doi.org/10.1016/j.fsigen.2018.07.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Novroski NMM, King JL, Churchill JD, Seah LH, Budowle B (2016) Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 25:214–226. https://doi.org/10.1016/j.fsigen.2016.09.007

    Article  CAS  PubMed  Google Scholar 

  88. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x

    Article  PubMed  Google Scholar 

  89. Fan H, Wang X, Chen H, Long R, Liang A, Li W, Chen J, Wang W, Qu Y, Song T, Zhang P, Deng J (2018) The evaluation of forensic characteristics and the phylogenetic analysis of the Ong Be language-speaking population based on Y-STR. Forensic Sci Int Genet 37:e6–e11. https://doi.org/10.1016/j.fsigen.2018.09.008

    Article  CAS  PubMed  Google Scholar 

  90. Fan H, Wang X, Chen H, Zhang X, Huang P, Long R, Liang A, Song T, Deng J (2018) Population analysis of 27 Y-chromosomal STRs in the Li ethnic minority from Hainan Province, southernmost China. Forensic Sci Int Genet 34:e20–ee2. https://doi.org/10.1016/j.fsigen.2018.01.007

    Article  CAS  PubMed  Google Scholar 

  91. Fan H, Zhang X, Wang X, Ren Z, Li W, Long R, Liang A, Chen J, Song T, Qu Y, Deng J (2018) Genetic analysis of 27 Y-STR loci in Han population from Hainan Province, southernmost China. Forensic Sci Int Genet 33:e9–e10. https://doi.org/10.1016/j.fsigen.2017.12.009

    Article  CAS  PubMed  Google Scholar 

  92. Nei M (1987) Molecular evolutionary genetics. Columbia University Press New York

  93. Gouy A, Zieger M (2017) STRAF-A convenient online tool for STR data evaluation in forensic genetics. Forensic Sci Int Genet 30:148–151. https://doi.org/10.1016/j.fsigen.2017.07.007

    Article  CAS  PubMed  Google Scholar 

  94. Hansen J (2000) Using SPSS for Windows and Macintosh: analyzing and understanding data. Amer Statistician 59:113

    Article  Google Scholar 

  95. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70:3321–3323. https://doi.org/10.1073/pnas.70.12.3321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Nei M (1977) F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet 41:225–233. https://doi.org/10.1111/j.1469-1809.1977.tb01918.x

    Article  CAS  PubMed  Google Scholar 

  97. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  98. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

  99. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578. https://doi.org/10.1111/j.1471-8286.2007.01758.x

  100. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

  101. D.A. Earl BMV (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

  102. Rosenberg NA (2003) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

  103. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

  104. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    Article  CAS  PubMed  Google Scholar 

  106. Excoffier L, Smouse PE (1994) Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136:343–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Letunic I, Bork P (2019) Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:W256–W2W9. https://doi.org/10.1093/nar/gkz239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Fan H, Wang X, Chen H, Li W, Wang W, Deng J (2019) The Ong Be language-speaking population in Hainan Island: genetic diversity, phylogenetic characteristics and reflections on ethnicity. Mol Biol Rep 46:4095–4103. https://doi.org/10.1007/s11033-019-04859-8

    Article  CAS  PubMed  Google Scholar 

  110. Fan H, Wang X, Ren Z, He G, Long R, Liang A, Song T, Deng J (2019) Population data of 19 autosomal STR loci in the Li population from Hainan Province in southernmost China. Int J Legal Med 133:429–431. https://doi.org/10.1007/s00414-018-1828-2

    Article  PubMed  Google Scholar 

  111. Barrio PA, Martin P, Alonso A et al (2019) Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power. Forensic Sci Int Genet 42:49–55. https://doi.org/10.1016/j.fsigen.2019.06.009

    Article  CAS  PubMed  Google Scholar 

  112. Churchill JD, Novroski NMM, King JL, Seah LH, Budowle B (2017) Population and performance analyses of four major populations with Illumina’s FGx Forensic Genomics System. Forensic Sci Int Genet 30:81–92. https://doi.org/10.1016/j.fsigen.2017.06.004

    Article  CAS  PubMed  Google Scholar 

  113. Hussing C, Bytyci R, Huber C, Morling N, Borsting C (2019) The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq DNA Signature Prep Kit. Int J Legal Med 133:325–334. https://doi.org/10.1007/s00414-018-1854-0

    Article  CAS  PubMed  Google Scholar 

  114. Khubrani YM, Hallast P, Jobling MA, Wetton JH (2019) Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia. Forensic Sci Int Genet 43:102164. https://doi.org/10.1016/j.fsigen.2019.102164

    Article  CAS  PubMed  Google Scholar 

  115. Wu R, Li R, Wang N, Peng D, Li H, Zhang Y, Zheng C, Sun H (2019) Genetic polymorphism and population structure of Torghut Mongols and comparison with a Mongolian population 3000 kilometers away. Forensic Sci Int Genet 42:235–243. https://doi.org/10.1016/j.fsigen.2019.07.017

    Article  CAS  PubMed  Google Scholar 

  116. Bodner M, Bastisch I, Butler JM, Fimmers R, Gill P, Gusmão L, Morling N, Phillips C, Prinz M, Schneider PM, Parson W (2016) Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER). Forensic Sci Int-Gen 24:97–102. https://doi.org/10.1016/j.fsigen.2016.06.008

    Article  CAS  Google Scholar 

  117. Houston R, Mayes C, King JL, Hughes-Stamm S, Gangitano D (2018) Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa. Electrophoresis 39:2906–2911. https://doi.org/10.1002/elps.201800152

    Article  CAS  PubMed  Google Scholar 

  118. Kim EH, Lee HY, Yang IS, Jung SE, Yang WI, Shin KJ (2016) Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Sci Int Genet 22:1–7. https://doi.org/10.1016/j.fsigen.2016.01.001

    Article  CAS  PubMed  Google Scholar 

  119. Kim SY, Lee HC, Chung U, Ham SK, Lee HY, Park SJ, Roh YJ, Lee SH (2018) Massive parallel sequencing of short tandem repeats in the Korean population. Electrophoresis 39:2702–2707. https://doi.org/10.1002/elps.201800090

    Article  CAS  PubMed  Google Scholar 

  120. Kwon SY, Lee HY, Kim EH, Lee EY, Shin KJ (2016) Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. Forensic Sci Int Genet 25:132–141. https://doi.org/10.1016/j.fsigen.2016.08.010

    Article  CAS  PubMed  Google Scholar 

  121. Phillips C, Devesse L, Ballard D, van Weert L, de la Puente M, Melis S, Álvarez Iglesias V, Freire-Aradas A, Oldroyd N, Holt C, Syndercombe Court D, Carracedo Á, Lareu MV (2018) Global patterns of STR sequence variation: sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis 39:2708–2724. https://doi.org/10.1002/elps.201800117

    Article  CAS  PubMed  Google Scholar 

  122. Salvador JM, Apaga DLT, Delfin FC, Calacal GC, Dennis SE, De Ungria MCA (2018) Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet 36:e8–e12. https://doi.org/10.1016/j.fsigen.2018.06.008

    Article  CAS  PubMed  Google Scholar 

  123. Wendt FR, King JL, Novroski NMM, Churchill JD, Ng J, Oldt RF, McCulloh KL, Weise JA, Smith DG, Kanthaswamy S, Budowle B (2017) Flanking region variation of ForenSeq DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. Forensic Sci Int Genet 28:146–154. https://doi.org/10.1016/j.fsigen.2017.02.014

    Article  CAS  PubMed  Google Scholar 

  124. Wendt FR, Novroski NM (2019) Identity informative SNP associations in the UK Biobank. Forensic Sci Int Genet 42:45–48. https://doi.org/10.1016/j.fsigen.2019.06.007

    Article  CAS  PubMed  Google Scholar 

  125. Zhang QX, Yang M, Pan YJ, Zhao J, Qu BW, Cheng F, Yang YR, Jiao ZP, Liu L, Yan JW (2018) Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis 39:2725–2731. https://doi.org/10.1002/elps.201800071

    Article  CAS  PubMed  Google Scholar 

  126. Siva N (2008) 1000 Genomes project. Nat Biotechnol 26:256. https://doi.org/10.1038/nbt0308-256b

    Article  PubMed  Google Scholar 

  127. Genomes Project C, Auton A, Brooks LD et al (2015) A global reference for human genetic variation. Nature 526:68–74. https://doi.org/10.1038/nature15393

    Article  CAS  Google Scholar 

  128. Sudmant PH, Rausch T, Gardner EJ et al (2015) An integrated map of structural variation in 2504 human genomes. Nature 526:75–81. https://doi.org/10.1038/nature15394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Birney E, Soranzo N (2015) Human genomics: the end of the start for population sequencing. Nature 526:52–53. https://doi.org/10.1038/526052a

    Article  CAS  PubMed  Google Scholar 

  130. Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans. Science 239:1263–1268. https://doi.org/10.1126/science.3125610

    Article  CAS  PubMed  Google Scholar 

  131. Hedges SB (2000) Human evolution. A start for population genomics. Nature 408:652–653. https://doi.org/10.1038/35047193

    Article  CAS  PubMed  Google Scholar 

  132. Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713. https://doi.org/10.1038/35047064

    Article  CAS  PubMed  Google Scholar 

  133. King MC, Motulsky AG (2002) Human genetics. Mapping human history. Science 298:2342–2343. https://doi.org/10.1126/science.1080373

    Article  CAS  PubMed  Google Scholar 

  134. Bae CJ, Douka K, Petraglia MD (2017) On the origin of modern humans: Asian perspectives. Science 358:eaai9067. https://doi.org/10.1126/science.aai9067

    Article  CAS  PubMed  Google Scholar 

  135. Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee SS, Kalsbeek AMF, Petersen DC, Rautenbach H, Förtsch HEA, Bornman MSR, Hayes VM (2019) Human origins in a Southern African palaeo-wetland and first migrations. Nature 575:185–189. https://doi.org/10.1038/s41586-019-1714-1

    Article  CAS  PubMed  Google Scholar 

  136. Dennell R (2015) Palaeoanthropology: Homo sapiens in China 80,000 years ago. Nature 526:647–648. https://doi.org/10.1038/nature15640

    Article  CAS  PubMed  Google Scholar 

  137. Liu W, Martinon-Torres M, Cai YJ et al (2015) The earliest unequivocally modern humans in southern China. Nature 526:696–699. https://doi.org/10.1038/nature15696

    Article  CAS  PubMed  Google Scholar 

  138. Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, Xue Y, Haber M, Ekong R, Oljira T, Mekonnen E, Luiselli D, Bradman N, Bekele E, Zalloua P, Durbin R, Kivisild T, Tyler-Smith C (2015) Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am J Hum Genet 96:986–991. https://doi.org/10.1016/j.ajhg.2015.04.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381–2385. https://doi.org/10.1126/science.1078311

    Article  CAS  PubMed  Google Scholar 

  140. Tattersall I (2009) Out of Africa: modern human origins special feature: human origins: out of Africa. Proc Natl Acad Sci U S A 106:16018–16021. https://doi.org/10.1073/pnas.0903207106

    Article  PubMed  PubMed Central  Google Scholar 

  141. Weaver TD (2014) Tracing the paths of modern humans from Africa. Proc Natl Acad Sci U S A 111:7170–7171. https://doi.org/10.1073/pnas.1405852111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Zuccala E (2015) Evolution: filling gaps in early human history. Nat Rev Genet 16:686–687. https://doi.org/10.1038/nrg4039

    Article  CAS  PubMed  Google Scholar 

  143. Zhilin J (2001) Columbus and the “New Continent”. Journal of Capital Normal University (Social Sciences Edition) 6:27–31. https://doi.org/10.3969/j.issn.1004-9142.2001.06.005

    Article  Google Scholar 

  144. Cheng S (1982) Columbus’ first voyage to America. Journal of Latin American Studies 5:20–26

    Google Scholar 

  145. Qipan Y (1992) The influence of Columbus’ discovery of the New World on the population development of Latin America. Journal of Hebei University (Social Sciences Edition) 2:47–51

    Google Scholar 

  146. Xuefen W (2016) The historical influence of Columbus’ discovery of America. New Silk Road 24:254. https://doi.org/10.19312/j.cnki.61-1499/c.2016.12.196

    Article  Google Scholar 

  147. Yuling Z (1989) The immigration activities and characteristics of the Americas started by Columbus (in Chinese). World History 5:136–140

    Google Scholar 

  148. Chen P, Han Y, He G, Luo H, Gao T, Song F, Wan D, Yu J, Hou Y (2018) Genetic diversity and phylogenetic study of the Chinese Gelao ethnic minority via 23 Y-STR loci. Int J Legal Med 132:1093–1096. https://doi.org/10.1007/s00414-017-1743-y

    Article  PubMed  Google Scholar 

  149. Fan GY, An YR, Peng CX, Deng JL, Pan LP, Ye Y (2019) Forensic and phylogenetic analyses among three Yi populations in Southwest China with 27 Y chromosomal STR loci. Int J Legal Med 133:795–797. https://doi.org/10.1007/s00414-018-1984-4

    Article  PubMed  Google Scholar 

  150. Hu L, Gu T, Fan X, Yuan X, Rao M, Pang J, Nie A, du L, Zhang X, Nie S (2017) Genetic polymorphisms of 24 Y-STR loci in Hani ethnic minority from Yunnan Province, Southwest China. Int J Legal Med 131:1235–1237. https://doi.org/10.1007/s00414-017-1543-4

    Article  PubMed  Google Scholar 

  151. Ji J, Ren Z, Zhang H, Wang Q, Wang J, Kong Z, Xu C, Tian M, Huang J (2017) Genetic profile of 23 Y chromosomal STR loci in Guizhou Shui population, southwest China. Forensic Sci Int Genet 28:e16–ee7. https://doi.org/10.1016/j.fsigen.2017.01.010

    Article  CAS  PubMed  Google Scholar 

  152. Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, Huang J, Xie M, Chen S, Song M, Zhang Y, Qian X, Yuan T, Wang Z, Liu Y, Wang M, Liu Y, Liu J, Hou Y (2019) Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population. Forensic Sci Int Genet 42:e13–e20. https://doi.org/10.1016/j.fsigen.2019.07.011

    Article  CAS  PubMed  Google Scholar 

  153. Liao Y, Chen L, Huang R, Wu W, Liu D, Sun H (2019) Genomic portrait of Guangdong Liannan Yao population based on 15 autosomal STRs and 19 Y-STRs. Sci Rep 9:2141. https://doi.org/10.1038/s41598-018-36262-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Liu C, Han X, Min Y, Liu H, Xu Q, Yang X, Huang S, Chen Z, Liu C (2018) Genetic polymorphism analysis of 40 Y-chromosomal STR loci in seven populations from South China. Forensic Sci Int 291:109–114. https://doi.org/10.1016/j.forsciint.2018.08.003

    Article  CAS  PubMed  Google Scholar 

  155. Shu L, Li L, Yu G, Yu B, Liu Y, Li S, Jin L, Yan S (2015) Genetic analysis of 17 Y-STR loci in Han, Dong, Miao and Tujia populations from Hunan Province, central-southern China. Forensic Sci Int Genet 19:250–251. https://doi.org/10.1016/j.fsigen.2015.07.007

    Article  CAS  PubMed  Google Scholar 

  156. Song F, Xie M, Xie B, Wang S, Liao M, Luo H (2020) Genetic diversity and phylogenetic analysis of 29 Y-STR loci in the Tibetan population from Sichuan Province, Southwest China. Int J Legal Med 134:513–516. https://doi.org/10.1007/s00414-019-02043-y

    Article  PubMed  Google Scholar 

  157. Xie M, Song F, Li J, Lang M, Luo H, Wang Z, Wu J, Li C, Tian C, Wang W, Ma H, Song Z, Fan Y, Hou Y (2019) Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs. Forensic Sci Int Genet 41:11–18. https://doi.org/10.1016/j.fsigen.2019.03.022

    Article  CAS  PubMed  Google Scholar 

  158. Zhang X, Gu T, Yao J, Yang C, du L, Pang J, Rao M, Nie A, Hu L, Nie S (2017) Genetic analysis of 24 Y-STR loci in the Miao ethnic minority from Yunnan Province, southwestern China. Forensic Sci Int Genet 28:e30–ee2. https://doi.org/10.1016/j.fsigen.2017.02.006

    Article  CAS  PubMed  Google Scholar 

  159. Zhou H, Ren Z, Zhang H, Wang J, Huang J (2016) Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China. Forensic Sci Int Genet 25:e6–e7. https://doi.org/10.1016/j.fsigen.2016.05.010

    Article  CAS  PubMed  Google Scholar 

  160. Chang YM, Perumal R, Keat PY, Kuehn DL (2007) Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia. Forensic Sci Int 167:70–76. https://doi.org/10.1016/j.forsciint.2006.01.002

    Article  CAS  PubMed  Google Scholar 

  161. Miranda-Barros F, Romanini C, Perez LA et al (2016) Y Chromosome STR haplotypes in different ethnic groups of Vietnam. Forensic Sci Int Genet 22:e18–e20. https://doi.org/10.1016/j.fsigen.2016.02.007

    Article  CAS  PubMed  Google Scholar 

  162. Souto L, Gusmao L, Ferreira E, Amorim A, Corte-Real F, Vieira DN (2006) Y-chromosome STR haplotypes in East Timor: forensic evaluation and population data. Forensic Sci Int 156:261–265. https://doi.org/10.1016/j.forsciint.2005.02.015

    Article  CAS  PubMed  Google Scholar 

  163. Yong RY, Lee LK, Yap EP (2006) Y-chromosome STR haplotype diversity in three ethnic populations in Singapore. Forensic Sci Int 159:244–257. https://doi.org/10.1016/j.forsciint.2005.05.010

    Article  CAS  PubMed  Google Scholar 

  164. Henry J, Dao H, Scandrett L, Taylor D (2019) Population genetic analysis of Yfiler((R)) plus haplotype data for three South Australian populations. Forensic Sci Int Genet 41:e23–ee5. https://doi.org/10.1016/j.fsigen.2019.03.021

    Article  CAS  PubMed  Google Scholar 

  165. Ke Y, Su B, Xiao J, Chen H, Huang W, Chen Z, Chu J, Tan J, Jin L, Lu D (2001) Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians. Sci China C Life Sci 44:225–232. https://doi.org/10.1007/BF02879329

    Article  CAS  PubMed  Google Scholar 

  166. Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, Gao Y, Mao X, Zhang L, Qian J, Tan J, Jin J, Huang W, Deka R, Su B, Chakraborty R, Jin L (2004) Genetic evidence supports demic diffusion of Han culture. Nature 431:302–305. https://doi.org/10.1038/nature02878

    Article  CAS  PubMed  Google Scholar 

  167. L M. (1997) A study of Lingao. Shanghai Far Eastern Publishing House Shanghai

  168. Weera O (1998) A mainland Bê language. J Chin Ling 26:338–344

    Google Scholar 

  169. Yl C (2015) Obstruents in Proto-Ong-Be: a reconstruction. Paper presented at the 25th Annual Meeting of the Southeast Asian Linguistics Society (SEALS), May 27–29 (2015) at Payap University Chiang Mai, Thailand.

  170. Burusphat S (2007) A comparison of general classifiers in Tai-Kadai languages. Mon-Khmer studies: J. Southeast Asian Lang. Cultures 37:129–153

    Google Scholar 

  171. GT (1994) Tai-Kadai and Austronesian: the nature of the historical relationship. Oceanic Linguistics 33: 345– 368.

  172. LM Z (1996) An introduction to the Kam-Tai languages. China Soc Sci Acad Press, Beijing

    Google Scholar 

  173. M. Liang JRZ. (1996) An overview of the language family of Dong Tai: the primitive common language constructs of the Dong Tai Language.

  174. W O (2005) Kra-Dai and Austronesian: notes on phonological correspondences and vocabulary distribution. In: Sagart L, Blench R, Sanchez-Mazas A (eds) The peopling of East Asia: putting together archaeology, linguistics and genetics. RoutledgeCurzon, London and New York

    Google Scholar 

  175. Weera O (2017) Kra-Dai in Southern China. Invited talk in the Nankai University Tianjin

  176. J.S. O (1998) An ethnohistorical dictionary of China. Greenwood Publishing Group Westport

  177. H C (2008) Variation in the grammaticalization of complementizers from verba dicendi in Sinitic languages. Ling Typol 12: 45–98.

  178. Wang CC, Wang LX, Shrestha R, Wen S, Zhang M, Tong X, Jin L, Li H (2015) Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction. J Genet Genomics 42:403–407. https://doi.org/10.1016/j.jgg.2015.03.008

    Article  CAS  PubMed  Google Scholar 

  179. Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H, the Genographic Consortium (2011) Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS One 6:e24282. https://doi.org/10.1371/journal.pone.0024282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Gan RJ, Pan SL, Mustavich LF et al (2008) Pinghua population as an exception of Han Chinese’s coherent genetic structure. J Hum Genet 53:303–313. https://doi.org/10.1007/s10038-008-0250-x

    Article  PubMed  Google Scholar 

  181. Li H, Wen B, Chen SJ, Su B, Pramoonjago P, Liu Y, Pan S, Qin Z, Liu W, Cheng X, Yang N, Li X, Tran D, Lu D, Hsu MT, Deka R, Marzuki S, Tan CC, Jin L (2008) Paternal genetic affinity between Western Austronesians and Daic populations. BMC Evol Biol 8:146. https://doi.org/10.1186/1471-2148-8-146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Qiong-Ying Deng C-CW, Wang X-Q, Wang L-X, Wang Z-Y, Wu W-J, Li H, the Genographic Consortium (2013) Genetic affinity between the Kam-Sui speaking Chadong and Mulam people. Journal of Systematics and Evolution 51:263–270. https://doi.org/10.1111/jse.12009

    Article  Google Scholar 

  183. Chaubey G, Metspalu M, Choi Y, Magi R, Romero IG, Soares P, van Oven M, Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Reddy AG, Metspalu E, van Driem G, Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T (2011) Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture. Mol Biol Evol 28:1013–1024. https://doi.org/10.1093/molbev/msq288

    Article  CAS  PubMed  Google Scholar 

  184. Ganesh Prasad Arunkumar LHW, Kavitha VJ, Syama A, Arun VS, Sathua S, Sahoo R, Balakrishnan R, Riba T, Chakravarthy J, Chaudhury B, Panda P, Das PK, Nayak PK, Li H, Pitchappan R, The Genographic Consortium (2015) A late Neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west. J Syst Evol 53:546–560

    Article  Google Scholar 

  185. Majumder PP (2010) The human genetic history of South Asia. Curr Biol 20:R184–R187. https://doi.org/10.1016/j.cub.2009.11.053

    Article  CAS  PubMed  Google Scholar 

  186. Zhang X, Liao S, Qi X, Liu J, Kampuansai J, Zhang H, Yang Z, Serey B, Sovannary T, Bunnath L, Seang Aun H, Samnom H, Kangwanpong D, Shi H, Su B (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. https://doi.org/10.1038/srep15486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Kumar V, Reddy AN, Babu JP et al (2007) Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations. BMC Evol Biol 7:47. https://doi.org/10.1186/1471-2148-7-47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, du R, Fu S, Li P, Hurles ME, Yang H, Tyler-Smith C (2006) Male demography in East Asia: a north-south contrast in human population expansion times. Genetics 172:2431–2439. https://doi.org/10.1534/genetics.105.054270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, Hammer MF (2010) Major east-west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol 27:1833–1844. https://doi.org/10.1093/molbev/msq063

    Article  CAS  PubMed  Google Scholar 

  190. Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, Halos SC, Gunnarsdóttir E, Myles S, Hughes DA, Xu S, Jin L, Lao O, Kayser M, Hurles ME, Stoneking M, de Ungria MCA (2011) The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. Eur J Hum Genet 19:224–230. https://doi.org/10.1038/ejhg.2010.162

    Article  PubMed  Google Scholar 

  191. Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, Jin L, Su B (2005) Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet 77:408–419. https://doi.org/10.1086/444436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Yan S, Wang CC, Zheng HX, Wang W, Qin ZD, Wei LH, Wang Y, Pan XD, Fu WQ, He YG, Xiong LJ, Jin WF, Li SL, An Y, Li H, Jin L (2014) Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers. PLoS One 9:e105691. https://doi.org/10.1371/journal.pone.0105691

    Article  PubMed  PubMed Central  Google Scholar 

  193. Wen SQTX, Li H (2016) Y-chromosome-based genetic pattern in East Asia affected by Neolithic transition. Quatern Int:S1040618215302299

  194. Yan S, Wang CC, Li H, Li SL, Jin L, Genographic C (2011) An updated tree of Y-chromosome haplogroup O and revised phylogenetic positions of mutations P164 and PK4. Eur J Hum Genet 19:1013–1015. https://doi.org/10.1038/ejhg.2011.64

    Article  PubMed  PubMed Central  Google Scholar 

  195. Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H, The Genographic Consortium (2012) Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas. Ann Hum Genet 76:92–99. https://doi.org/10.1111/j.1469-1809.2011.00690.x

    Article  PubMed  Google Scholar 

  196. Tarling N (2003) The Cambridge history of Southeast Asia. Yunnan People’s Publishing House Yunnan

  197. Yingming L (2010) The history of Southeast Asia (in Chinese). People’s Publishing House Beijing

  198. Osborne M (2012) Southeast Asia: an introductory history. The Commercial Press Beijing

  199. Wu Yuqin QS (2011) World history: ancient history. Higher Education Press Beijing

  200. Bao Maohong LY, Bao W (2014) A collection of studies on the history and culture of southeast Asia. Xiamen University Press Fujian

  201. Liang Zhiming LM, Yang B (2013) The ancient history of Southeast Asia. Peking University Press Beijing

  202. Mou L (2007) The formation and distribution of ethnic minorities in Southeast Asia (in Chinese). Southeast 2:47–59

  203. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494. https://doi.org/10.1038/nature08365

  204. Thangaraj K, Chaubey G, Kivisild T et al (2005) Reconstructing the origin of Andaman Islanders. Science 308:996. https://doi.org/10.1126/science.1109987

  205. Pala M, Achilli A, Olivieri A, Kashani BH, Perego UA, Sanna D, Metspalu E, Tambets K, Tamm E, Accetturo M, Carossa V, Lancioni H, Panara F, Zimmermann B, Huber G, al-Zahery N, Brisighelli F, Woodward SR, Francalacci P, Parson W, Salas A, Behar DM, Villems R, Semino O, Bandelt HJ, Torroni A (2009) Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. Am J Hum Genet 84:814–821. https://doi.org/10.1016/j.ajhg.2009.05.004

  206. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru MF, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang HM, Lyons R, Tarrier B, Gresham JB, Li B, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen MB, Uzzau S, Jones C, Schlessinger D, Abecasis GR, Sanna S, Sidore C, Cucca F (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341:565–569. https://doi.org/10.1126/science.1237947

  207. Sidore C, Busonero F, Maschio A, Porcu E, Naitza S, Zoledziewska M, Mulas A, Pistis G, Steri M, Danjou F, Kwong A, Ortega del Vecchyo VD, Chiang CWK, Bragg-Gresham J, Pitzalis M, Nagaraja R, Tarrier B, Brennan C, Uzzau S, Fuchsberger C, Atzeni R, Reinier F, Berutti R, Huang J, Timpson NJ, Toniolo D, Gasparini P, Malerba G, Dedoussis G, Zeggini E, Soranzo N, Jones C, Lyons R, Angius A, Kang HM, Novembre J, Sanna S, Schlessinger D, Cucca F, Abecasis GR (2015) Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat Genet 47:1272–1281. https://doi.org/10.1038/ng.3368

  208. Regueiro M, Stanojevic A, Chennakrishnaiah S, Rivera L, Varljen T, Alempijevic D, Stojkovic O, Simms T, Gayden T, Herrera RJ (2011) Divergent patrilineal signals in three Roma populations. Am J Phys Anthropol 144:80–91. https://doi.org/10.1002/ajpa.21372

  209. Mendizabal I, Lao O, Marigorta UM, Wollstein A, Gusmão L, Ferak V, Ioana M, Jordanova A, Kaneva R, Kouvatsi A, Kučinskas V, Makukh H, Metspalu A, Netea MG, de Pablo R, Pamjav H, Radojkovic D, Rolleston SJH, Sertic J, Macek M Jr, Comas D, Kayser M (2012) Reconstructing the population history of European Romani from genome-wide data. Curr Biol 22:2342–2349. https://doi.org/10.1016/j.cub.2012.10.039

  210. Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, Tzur S, Pereira L, Amorim A, Quintana-Murci L, Majamaa K, Herrnstadt C, Howell N, Balanovsky O, Kutuev I, Pshenichnov A, Gurwitz D, Bonne-Tamir B, Torroni A, Villems R, Skorecki K (2006) The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78:487–497. https://doi.org/10.1086/500307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Hammer MF, Behar DM, Karafet TM, Mendez FL, Hallmark B, Erez T, Zhivotovsky LA, Rosset S, Skorecki K (2009) Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood. Hum Genet 126:707–717. https://doi.org/10.1007/s00439-009-0727-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, Khusnutdinova EK, Balanovsky O, Semino O, Pereira L, Comas D, Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer MF, Skorecki K, Villems R (2010) The genome-wide structure of the Jewish people. Nature 466:238–242. https://doi.org/10.1038/nature09103

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank all the volunteers who contributed samples for this study and Henan Shenyou Medical Laboratory Co. Ltd. for providing the research platform. Especially, we would like to express our sincere gratitude to Miss Lijuan Yang for the image processing of Fig. 1.

Data and materials availability

The raw data of this article are available from the supplementary information files.

Code availability

Not applicable

Funding

This study was supported by the Program of Hainan Association for Science and Technology Plans to Youth R&D Innovation (QCXM201705), the National Undergraduate Innovation and Entrepreneurship Training Program (No. 201911810008 and No. 201911810023), the National Natural Science Foundation of China (NSFC, No. 81671865 and No.81525015), and GDUPS (2017).

Author information

Authors and Affiliations

  1. School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China

    Haoliang Fan, Bofeng Zhu & Pingming Qiu

  2. School of Basic Medicine and Life Science, Hainan Medical University, Haikou, 571199, China

    Haoliang Fan

  3. First Clinical Medical College, Hainan Medical University, Haikou, 571199, China

    Zhengming Du, Fenfen Wang, Shengping Cao, Zhenming Luo & Peiyu Huang

  4. Department of Psychiatry, The First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, China

    Xiao Wang

  5. Institute of Archaeological Science, Fudan University, Shanghai, 200433, China

    Shao-Qing Wen & Lingxiang Wang

  6. MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China

    Panxin Du

  7. Division of the Criminal Investigation Department, Henan Provincial Public Security Bureau, Zhengzhou, 450003, China

    Hai Liu

  8. School of Traditional Chinese Medicine, Hainan Medical University, Haikou, 571199, China

    Bingbing Han

Authors
  1. Haoliang Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhengming Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fenfen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shao-Qing Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lingxiang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Panxin Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hai Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Shengping Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Zhenming Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Bingbing Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Peiyu Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Bofeng Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Pingming Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Haoliang Fan, Bofeng Zhu or Pingming Qiu.

Ethics declarations

Ethics approval

This study was approved by the Institutional Review Boards of Hainan Medical University and the Medical Ethics Committee of Hainan Medical University (No. HYLL-2020-012).

Consent to participate

All participants had signed the informed consent form.

Consent for publication

Not applicable.

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Highlights

1. It is the first batch of DNA profiling for Hainan Li population using the MPS-based ForenSeq™ DNA Signature Prep Kit to characterize the forensic genetic polymorphism landscape.

2. Three datasets were set up, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately by different bioinformatic methods and the phylogenetic analyses from different perspectives.

3. The sequence-based genetic markers featured more genetic diversity of loci and improved the system efficiency compared with the length-based markers.

4. The phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively, which experienced limited gene flows with surrounding populations by virtue of geography, history, and culture.

Supplementary Information

ESM 1

(DOCX 12359 kb)

ESM 2

(XLSX 1109 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fan, H., Du, Z., Wang, F. et al. The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 135, 1295–1317 (2021). https://doi.org/10.1007/s00414-021-02590-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-021-02590-3

Keywords

Search

Navigation