Advanced search
Publication Cover
Annals of Human Biology Volume 50, 2023 - Issue 1
Submit an article Journal homepage
1,274
Views
1
CrossRef citations to date
0
Altmetric
Human Genetics

Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China

Guang-Yao Fana Forensic Center, College of Medicine, Shaoxing University, Shaoxing, ChinaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0003-4297-7883View further author information
ORCID Icon,
De-Zhi Jiangb Criminal Technology Department, Qingdao Public Security Bureau, Shandong, ChinaView further author information
,
Yao-Heng Jiangb Criminal Technology Department, Qingdao Public Security Bureau, Shandong, ChinaView further author information
,
Wei Songb Criminal Technology Department, Qingdao Public Security Bureau, Shandong, ChinaView further author information
,
Ying-Yun Hec Ningbo Health Gene Technologies Co. Ltd, Ningbo, ChinaView further author information
&
Nixon Austin Wuod College of Life Sciences, Shaoxing University, Shaoxing, ChinaView further author information
Pages 35-41 | Received 24 May 2022, Accepted 05 Dec 2022, Published online: 06 Mar 2023

References

  • Altman NS. 1992. An introduction to kernel and nearest-neighbor nonparametric regression. Am Stat. 46(3):175–185.
  • Fan G, Pan L, Tang P, Zhou Y, Liu M, Luo X. 2021. Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples. Int J Legal Med. 135(2):409–419.
  • Fan GY. 2022. Assessing the factors influencing the performance of machine learning for classifying haplogroups from Y-STR haplotypes. Forensic Sci Int. 340:111466.
  • Gu Z, Eils R, Schlesner M. 2016. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 32(18):2847–2849.
  • Hansen J. 2005. Using SPSS for Windows and Macintosh: analyzing and understanding data. Amer Stat. 59(1):113–113.
  • Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, et al. 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.
  • Liu J, Zeng W, Sun B, Mao X, Zhao Y, Wang F, Li Z, et al. 2021. Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago. Sci bull. 66(11):1129–1135.
  • Nei M, Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics. 97(1):145–163.
  • Retief JD. 2000. Phylogenetic analysis using PHYLIP. Methods Mol Biol. 132:243–258.
  • Reynolds J, Weir BS, Cockerham CC. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics. 105(3):767–779.
  • Song M, Wang Z, Zhang Y, Zhao C, Lang M, Xie M, Qian X, et al. 2019a. 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.
  • Song M, Zhao C, Wang Z, Hou Y. 2019b. Applying machine learning algorithms to a real forensic case to predict Y-SNP haplogroup based on Y-STR haplotype. Forensic Sci Int Genet Suppl Ser. 7(1):637–638.
  • Subramanian B, Gao S, Lercher MJ, Hu S, Chen WH. 2019. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Res. 47(W1):270–275.
  • Takezaki N, Nei M. 1996. Genetic distances and reconstruction of phylogenetic trees from Microsatellite DNA. Genetics. 144(1):389–399.
  • Venables WN, Ripley BD, Fernández C. 2002. Modern Applied Statistics with S-PLUS. New Jersey: Blackwell Publishers. p. 302–303.
  • Wang L, Oota H, Saitou N, Jin F, Matsushita T, Ueda S. 2000. Genetic structure of a 2,500-year-old human population in China and its spatiotemporal changes. Mol Biol Evol. 17(9):1396–1400.
  • Yao J, Wang B. 2016. Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China. Plos One. 11 (8):e160415.
  • Yin C, He Z, Wang Y, He X, Zhang X, Xia M, Zhai D, et al. 2022. Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: a pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet. 57:102659–102659.
  • Yin C, Su K, He Z, Zhai D, Guo K, Chen X, Jin L, Li S. 2020. Genetic reconstruction and forensic analysis of chinese shandong and yunnan han populations by co-analyzing Y chromosomal STRs and SNPs. Genes. 11(7):743.
  • Young FW. 1970. Nonmetric multidimensional scaling: recovery of metric information. Psychometrika. 35(4):455–473.
  • Zhang J, Tao R, Zhong J, Sun D, Qiao L, Shan S, Yang Z, et al. 2019. Genetic polymorphisms of 27 Y-STR loci in the Dezhou Han population from Shandong province, Eastern China. Forensic Sci Int Genet. 39:e26–e28.
  • Zhang Y, Zhang R, Li M, Luo L, Zhang J, Ding J, Zhang S, et al. 2020. Genetic polymorphism of both 29 Y-STRs and 213 Y-SNPs in Han populations from Shandong Province, China. Leg Med (Tokyo)). 47:101738–101738.
  • Zhang Z. 2016. Introduction to machine learning: k-nearest neighbors. Ann Transl Med. 4(11):218–218.
  • Zhou Y, Huang L, Liu H, Liu M, Fan G. 2021. Population genetic characteristic for populations on the Shandong peninsula revealed by autosomal STR. Ann Hum Biol. 48(2):157–159.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.