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Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China.
Ann Hum Biol. 2023 Feb; 50(1):35-41.AH

Abstract

BACKGROUND

Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered.

AIM

This investigation intends to provide light on Qingdao's paternal genetic diversity and its evolutionary connections to other Han subgroups.

SUBJECTS AND METHODS

The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype.

RESULTS

The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups.

CONCLUSIONS

This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.

Links

Publisher Full Text (DOI)

Authors+Show Affiliations

Fan GY
Forensic Center, College of Medicine, Shaoxing University, Shaoxing, China.
Jiang DZ
Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China.
Jiang YH
Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China.
Song W
Criminal Technology Department, Qingdao Public Security Bureau, Shandong, China.
He YY
Ningbo Health Gene Technologies Co. Ltd, Ningbo, China.
Wuo NA
College of Life Sciences, Shaoxing University, Shaoxing, China.

MeSH

HumansGenetics, PopulationPhylogenyEthnicityChromosomes, Human, YHaplotypesChinaMicrosatellite RepeatsGene Frequency

Pub Type(s)

Journal Article

Language

eng

PubMed ID

36636009

Citation

Fan, Guang-Yao, et al. "Phylogenetic Analyses of 41 Y-STRs and Machine Learning-based Haplogroup Prediction in the Qingdao Han Population From Shandong Province, Eastern China." Annals of Human Biology, vol. 50, no. 1, 2023, pp. 35-41.
Fan GY, Jiang DZ, Jiang YH, et al. Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China. Ann Hum Biol. 2023;50(1):35-41.
Fan, G. Y., Jiang, D. Z., Jiang, Y. H., Song, W., He, Y. Y., & Wuo, N. A. (2023). Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China. Annals of Human Biology, 50(1), 35-41. https://doi.org/10.1080/03014460.2023.2168057
Fan GY, et al. Phylogenetic Analyses of 41 Y-STRs and Machine Learning-based Haplogroup Prediction in the Qingdao Han Population From Shandong Province, Eastern China. Ann Hum Biol. 2023;50(1):35-41. PubMed PMID: 36636009.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China. AU - Fan,Guang-Yao, AU - Jiang,De-Zhi, AU - Jiang,Yao-Heng, AU - Song,Wei, AU - He,Ying-Yun, AU - Wuo,Nixon Austin, PY - 2023/1/14/pubmed PY - 2023/3/9/medline PY - 2023/1/13/entrez KW - Qingdao Han KW - Y-STR KW - machine learning KW - patrilineal history KW - phylogeny SP - 35 EP - 41 JF - Annals of human biology JO - Ann Hum Biol VL - 50 IS - 1 N2 - BACKGROUND: Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. AIM: This investigation intends to provide light on Qingdao's paternal genetic diversity and its evolutionary connections to other Han subgroups. SUBJECTS AND METHODS: The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. RESULTS: The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. CONCLUSIONS: This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database. SN - 1464-5033 UR - https://www.unboundmedicine.com/medline/citation/36636009/Phylogenetic_analyses_of_41_Y_STRs_and_machine_learning_based_haplogroup_prediction_in_the_Qingdao_Han_population_from_Shandong_province_Eastern_China_ DB - PRIME DP - Unbound Medicine ER -