- Email: [email protected]
Genetic polymorphisms and haplotypic structure analysis of the Guizhou Gelao ethnic group based on 35 Y-STR loci
Legal Medicine 43 (2020) 101666
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Genetic polymorphisms and haplotypic structure analysis of the Guizhou Gelao ethnic group based on 35 Y-STR loci
T
Xiaojuan Wanga,b,1, Li Jiangb,1, Enfang Qiana,b,c, Fei Longd, Wei Cuib,e, Anquan Jib, ⁎ ⁎ Fangshun Zhangf, Kang Zoug, Jiang Huanga, , Caixia Lib, a
Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China c Forensic identification center, Guizhou Provincial People’s Hospital, Guiyang 550002, China d Zunyi Public Security Bureau, Zunyi 563000, China e Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China f Zunyi Medical and Pharmaceutical College, Zunyi 563000, China g Wuchuan County Public Security Bureau, Zunyi 564300, China b
A R T I C LE I N FO
A B S T R A C T
Keywords: Genetic polymorphisms Y-STR Guizhou Gelao Haplotypes
In this research, 35 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 286 unrelated healthy Gelao male individuals from Guizhou Province, China. Allelic and haplotype frequencies, haplotype diversity (HD), haplotype match probability (HMP), and discrimination capacity (DC) values were computed. Pairwise Rst values were assessed by AMOVA analysis and visualized through multidimensional scaling and neighbor-joining tree construction. A total of 609 alleles were detected at the 35 Y-STR loci, and the allelic frequencies ranged from 0.0035 to 0.8322. The HD, HMP, and DC were 0.9999, 0.0036, and 0.9825, respectively. A total of 281 haplotypes were found at 35 loci in the 286 Gelao individuals, 98.25% of which were unique. Related forensic parameters revealed that this panel of 35 loci had a high level of genetic polymorphisms in the Gelao group. However, the use of multi-copy and rapidly mutating Y-STR loci could significantly increase the discrimination power of a common Y-STR panel. Analyses of population differentiation with the same set of common Y-STR loci demonstrated that the Gelao group has a closer genetic relationship with the Guizhou Han and Guizhou Miao groups than other groups.
1. Introduction The Gelao are one of the most ancient ethnic groups in southwestern China. According to the latest census in 2010 [1], the Gelao group has a population of 550,746, almost 90% of which resides in Guizhou Province. Many Chinese scholars believe that the Gelao language belongs to Tai–Kadai language. Gelaos have frequent contacts with neighboring groups, such as the Han and Miao groups, and most of them speak and write Chinese [2]. With their male-specific inheritance patterns and relatively low mutation rate [3], Y-chromosomal short tandem repeats (Y-STRs) have been widely applied in the field of forensics, population genetic studies of paternal immigration routes, and to determine ethnic origin in recent decades. As a specific type of Y-STR loci, multi-copy (MC) loci generally contain 2–4 copies and display high genetic polymorphisms [4].
Analogously, rapidly mutating (RM) loci with high mutation rates also demonstrate higher discrimination power for differentiating paternal lineages [5]. Therefore, the application of MC and RM Y-STR loci can be an important addendum to the current technology. Recently, several papers have reported Y chromosome haplotype diversity for Y-STR loci in the Gelao group [6–8], and only a few of these Y-STR loci were MC and/or RM Y-STR loci. Thus, it is valuable to further explore the genetic polymorphisms of the Gelao group using multiple types of Y-STR loci. In this study, blood stain samples from 286 unrelated healthy Gelao individuals were collected from Guizhou Province. All of the samples were obtained with informed consent and self-declared ancestry information. Ethical clearance was obtained from the Ethics Committee of the Institute of Forensic Science of China. Samples collection and all experiment procedures were in accordance with the requirements of the ethics committee.
⁎
Corresponding authors. E-mail addresses: [email protected] (J. Huang), [email protected] (C. Li). 1 Xiaojuan Wang and Li Jiang are equally contributed to this work. https://doi.org/10.1016/j.legalmed.2019.101666 Received 14 May 2019; Received in revised form 4 November 2019; Accepted 29 December 2019 Available online 07 January 2020 1344-6223/ © 2020 Elsevier B.V. All rights reserved.
Legal Medicine 43 (2020) 101666
X. Wang, et al.
Table 1 Haplotype numbers and forensic parameters of different panels.
Yfiler RM + MC Yfiler + RM Yfiler + MC 35 Y-STR loci
Number of haplotypes
Percentage of unique haplotypes
Haplotype diversity
Haplotype match probability
Discrimination capacity
232 277 278 274 281
89.22% 97.11% 97.84% 97.45% 98.58%
0.9968 0.9998 0.9997 0.9995 0.9999
0.0067 0.0037 0.0038 0.0040 0.0036
0.8112 0.9685 0.9720 0.9580 0.9825
Notes: RM, rapidly mutating loci; MC, multi-copy loci.
2. DNA extraction and PCR
single-copy loci (DYS391, DYS508, DYS437, DYS456, and DYS438) displayed a low level of genetic polymorphisms, with a GD value < 0.5. GD values for MC and RM loci ranged from 0.6947 to 0.9906 and 0.7794 to 0.9379, respectively, which demonstrated that these loci had high levels of genetic polymorphisms. The HD, HMP, and DC values were 0.9999, 0.0036, and 0.9825, respectively. In total, 281 haplotypes were found at 35 loci in 286 Gelao individuals, 98.25% of which were unique (Table S2). Among them, one haplotype (H20) was shared by three individuals, and three haplotypes (H32, H56, and H155) were shared by two other individuals. Tracing back the residence information of these samples, we inferred individuals with shared haplotypes may have a common paternal ancestry without being aware of it. We also evaluated the forensic statistical parameters of Yfiler loci and other Y-STR combinations (Table 1). Compared to common Y-STR loci, the combined use of MC and RM loci had high genetic polymorphisms in the Gelao group, which is of great value for improving the discrimination of Y-STR typing systems and can be expected to separate male relatives from the same paternal lineage. Based on the pairwise RST values, a NJ tree was constructed and plotted, as shown in Fig. 1. The Guizhou Gelao group and other groups in Guizhou Province, including the Guizhou Han and Guizhou Miao, were clustered in the middle portion of the tree. In the MDS plot (Fig. 2), the Guizhou Gelao group displays a closer genetic relationship with the Guizhou Han and Guizhou Miao groups than the other groups. This result is also supported by other genetic makers, including X-STRs, autosomal STRs, and mitochondrial DNA [13–15]. Many factors may result in the close relationship among these groups. With the rapid development of economy and society, the Guizhou Gelao group and other neighboring groups have experienced migration, mixed living situations, and genetic fusion, resulting in a closer relationship among these groups. We also found that there was a relatively large genetic distance between the Guizhou Gelao and Guangxi Gelao groups. According to census data, the Guangxi Gelao is composed of approximately 3000 people, a small ethnic group residing in northwestern Guangxi Province. The mountains of the Yunnan-Kweichow Plateau are natural geographical barriers, resulting in geographical and genetic isolation, which caused this genetic differentiation between the Guangxi Gelao and Guizhou Gelao. With deeper ethnic and historical studies in future, more about the origin and migration of the Gelao group can be learned.
DNA extraction was executed from blood stain samples using a MagAttract® M48 DNA Manual Kit (Qiagen, Hilden, Germany), and PCR of the 35 Y-STR loci was performed using a Mastercycler ProS (Eppendorf, Hamburg, Germany) following the instructions of the DNATyperTM Y29 and DNATyperTM MCY amplification kits (Ministry of Public Security, Beijing, China). The 35 studied Y-STR loci contained 20 common Y-STR loci, seven RM loci, and 12 MC loci (four were both RM and MC loci). 3. Genotyping and quality control Amplification products were electrophoresed on an ABI Genetic Analyzer 3500xL (Thermo Fisher Scientific, Waltham, MA, USA). The 9948 control DNA and double-distilled water (ddH2O) were analyzed as positive and negative controls, respectively. Genotyping data were analyzed using GeneMapper ID-X Analysis Software (Thermo Fisher Scientific). Haplotype data were submitted to the Y-chromosome Haplotype Reference Database with the population accession number YA004593. 4. Statistical analysis The direct counting method was used to evaluate allelic and haplotype frequencies. Genetic diversity (GD) was calculated using the formula: GD = (n/n − 1) (1 − ∑ Pi2), where n is the total number of samples, and Pi is the frequency of the ith allele. Haplotype diversity (HD) was calculated using the formula: HD = (n/n − 1) (1 − ∑ Pi2), where n is the total number of samples, and Pi is the frequency of the ith haplotype. Haplotype match probability (HMP) was calculated according to MP = ∑ Pi2, where Pi is the frequency of the haplotype. Discrimination capacity (DC) was calculated based on the formula: DC = k/Σ(Pi × N), where k is the number of haplotypes, Pi is the frequency of the ith haplotype, and N is the total number of individuals. To evaluate the population genetic relationships between the Gelao group and other Chinese groups, we compared data from the 17 Yfiler haplotypes of the Gelao group with 13 neighboring populations (including Han [9], Yi (YP001344), Miao (YP001249), Shui (YP001172), and Qiannan Bouyei (YP001182) of Guizhou Province; Bai (YP000902), Hani [10], Xishuangbanna Dai (YP000903), and Lijiang Mosuo (YP001334) of Yunnan Province; and Gelao (YA004286), Gin (YP001166), Maonan (YP001168), and Miao (YP001169) of Guangxi Province). All of the reference groups were obtained from the Y-STR Haplotype Reference Database (YHRD) website [11]. Pairwise genetic distances (RST) and p values were calculated by analysis of molecular variance (AMOVA) and visualized in multidimensional scaling (MDS) plots using the AMOVA & MDS tool on the YHRD website. MEGA 6.0 [12] was used to construct a phylogenetic tree using the neighborjoining (NJ) method based on the RST values.
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgments This study was funded in part by the National Key Research and Development Program of China (2017YFC0803501), the basic research project (2017JB027), and the Key Laboratory of Forensic Genetics Open Project (2017FGKFKT02). Biological samples from the Caixia laboratory were funded by the National Infrastructure of Chinese Genetic Resources (NICGR: YCZYPT [2017]01-3) and the basic research project
5. Results and discussion As shown in Table S1, a total of 609 alleles were detected at 35 YSTR loci, and the allelic frequencies ranged from 0.0035 to 0.8322. Five 2
Legal Medicine 43 (2020) 101666
X. Wang, et al.
Fig. 1. Neighbor-joining phylogenetic tree constructed by MEGA based on the RST values. Pairwise RST values were calculated using the AMOVA & MDS tools on the YHRD website.
Fig. 2. Multidimensional scaling plot of Gelao and 13 reference groups constructed using the AMOVA & MDS tools on the YHRD website. 3
Legal Medicine 43 (2020) 101666
X. Wang, et al.
(2017JB025).
[5] A. Boattini, S. Sarno, C. Bini, V. Pesci, C. Barbieri, F.S. De, A. Quagliariello, L. Pagani, Q. Ayub, G. Ferri, Mutation rates and discriminating power for 13 rapidly-mutating Y-STRs between related and unrelated individuals, PLoS ONE 11 (11) (2016) e0165678. [6] P. Chen, Y. Han, G. He, H. Luo, T. Gao, F. Song, D. Wan, J. Yu, Y. Hou, Genetic diversity and phylogenetic study of the Chinese Gelao ethnic minority via 23 Y-STR loci, Int. J. Legal Med. 132 (4) (2018) 1093–1096. [7] Y. Liu, C. Wang, W. Zhou, X.B. Li, M. Shi, R. Bai, S. Ma, Haplotypes of 27 Y-STRs analyzed in Gelao and Miao ethnic minorities from Guizhou Province, Southwest China, Forensic Sci. Int. Genet. 40 (2019) e264–e267. [8] C. Liu, X. Han, Y. Min, H. Liu, Q. Xu, X. Yang, S. Huang, Z. Chen, C. Liu, Genetic polymorphism analysis of 40 Y-chromosomal STR loci in seven populations from South China, Forensic Sci. Int. 291 (2018) 109–114. [9] H. Zhou, Z. Ren, H. Zhang, J. Wang, J. Huang, Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China, Forensic Sci. Int.: Genetics 25 (2016) e6–e7. [10] L. Hu, T. Gu, X. Fan, X. Yuan, M. Rao, J.B. Pang, A. Nie, L. Du, X. Zhang, S. Nie, Genetic polymorphisms of 24 Y-STR loci in Hani ethnic minority from Yunnan Province, Southwest China, Int. J. Legal Med. 131 (5) (2017) 1–3. [11] http://www.yhrd.org/. [12] B.G. Hall, Building phylogenetic trees from molecular data with MEGA, Mol. Biol. Evol. 30 (5) (2013) 1229–1235. [13] P. Chen, G. He, X. Zou, M. Wang, H. Luo, L. Yu, X. Hu, M. Xia, H. Gao, J. Yu, Y. Hou, Y. Han, Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers, Sci. Rep. 8 (1) (2018) 14585. [14] L. Yang, Y. Zhao, C. Liu, D.W.T. Chan, M. Chan, M. He, Allele frequencies of 15 STRs in five ethnic groups (Han, Gelao, Jing, Shui and Zhuang) in South China, Forensic Sci. Int.: Genetics 7 (1) (2013) e9–e14. [15] C. Liu, S.-Y. Wang, M. Zhao, Z.-Y. Xu, Y.-H. Hu, F. Chen, R.-Z. Zhang, G.-F. Gao, Y.S. Yu, Q.-P. Kong, Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China, Forensic Sci. Int.: Genetics 5 (1) (2011) e4–e10.
Compliance with ethical standards This research was approved by the Ethics Committee of the Institute of Forensic Science, Ministry of Public Security, People’s Republic of China. Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.legalmed.2019.101666. References [1] http://www.stats.gov.cn/tjsj/pcsj/rkpc/6rp/indexch.htm. [2] J. Li, C. Jiayou, Genetic Diversity of the Chinese Nation, Shanghai Science and Technology Press, Shanghai, 2006. [3] H. Skaletsky, T. Kuroda-Kawaguchi, P.J. Minx, H.S. Cordum, L. Hillier, L.G. Brown, S. Repping, T. Pyntikova, J. Ali, T. Bieri, A. Chinwalla, A. Delehaunty, K. Delehaunty, H. Du, G. Fewell, L. Fulton, R. Fulton, T. Graves, S.-F. Hou, P. Latrielle, S. Leonard, E. Mardis, R. Maupin, J. McPherson, T. Miner, W. Nash, C. Nguyen, P. Ozersky, K. Pepin, S. Rock, T. Rohlfing, K. Scott, B. Schultz, C. Strong, A. Tin-Wollam, S.-P. Yang, R.H. Waterston, R.K. Wilson, S. Rozen, D.C. Page, The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes, Nature 423 (2003) 825. [4] M. Jacobs, L. Janssen, N. Vanderheyden, B. Bekaert, W.V.D. Voorde, R. Decorte, Development and evaluation of multiplex Y-STR assays for application in molecular genealogy, Forensic Sci. Int. Genet. Suppl. 2 (1) (2009) 57–59.
4
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Genetic polymorphisms and haplotypic structure analysis of the Guizhou Gelao ethnic group based on 35 Y-STR loci
T
Xiaojuan Wanga,b,1, Li Jiangb,1, Enfang Qiana,b,c, Fei Longd, Wei Cuib,e, Anquan Jib, ⁎ ⁎ Fangshun Zhangf, Kang Zoug, Jiang Huanga, , Caixia Lib, a
Department of Forensic Genetics, Guizhou Medical University, Guiyang 550004, Guizhou, China Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China c Forensic identification center, Guizhou Provincial People’s Hospital, Guiyang 550002, China d Zunyi Public Security Bureau, Zunyi 563000, China e Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China f Zunyi Medical and Pharmaceutical College, Zunyi 563000, China g Wuchuan County Public Security Bureau, Zunyi 564300, China b
A R T I C LE I N FO
A B S T R A C T
Keywords: Genetic polymorphisms Y-STR Guizhou Gelao Haplotypes
In this research, 35 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 286 unrelated healthy Gelao male individuals from Guizhou Province, China. Allelic and haplotype frequencies, haplotype diversity (HD), haplotype match probability (HMP), and discrimination capacity (DC) values were computed. Pairwise Rst values were assessed by AMOVA analysis and visualized through multidimensional scaling and neighbor-joining tree construction. A total of 609 alleles were detected at the 35 Y-STR loci, and the allelic frequencies ranged from 0.0035 to 0.8322. The HD, HMP, and DC were 0.9999, 0.0036, and 0.9825, respectively. A total of 281 haplotypes were found at 35 loci in the 286 Gelao individuals, 98.25% of which were unique. Related forensic parameters revealed that this panel of 35 loci had a high level of genetic polymorphisms in the Gelao group. However, the use of multi-copy and rapidly mutating Y-STR loci could significantly increase the discrimination power of a common Y-STR panel. Analyses of population differentiation with the same set of common Y-STR loci demonstrated that the Gelao group has a closer genetic relationship with the Guizhou Han and Guizhou Miao groups than other groups.
1. Introduction The Gelao are one of the most ancient ethnic groups in southwestern China. According to the latest census in 2010 [1], the Gelao group has a population of 550,746, almost 90% of which resides in Guizhou Province. Many Chinese scholars believe that the Gelao language belongs to Tai–Kadai language. Gelaos have frequent contacts with neighboring groups, such as the Han and Miao groups, and most of them speak and write Chinese [2]. With their male-specific inheritance patterns and relatively low mutation rate [3], Y-chromosomal short tandem repeats (Y-STRs) have been widely applied in the field of forensics, population genetic studies of paternal immigration routes, and to determine ethnic origin in recent decades. As a specific type of Y-STR loci, multi-copy (MC) loci generally contain 2–4 copies and display high genetic polymorphisms [4].
Analogously, rapidly mutating (RM) loci with high mutation rates also demonstrate higher discrimination power for differentiating paternal lineages [5]. Therefore, the application of MC and RM Y-STR loci can be an important addendum to the current technology. Recently, several papers have reported Y chromosome haplotype diversity for Y-STR loci in the Gelao group [6–8], and only a few of these Y-STR loci were MC and/or RM Y-STR loci. Thus, it is valuable to further explore the genetic polymorphisms of the Gelao group using multiple types of Y-STR loci. In this study, blood stain samples from 286 unrelated healthy Gelao individuals were collected from Guizhou Province. All of the samples were obtained with informed consent and self-declared ancestry information. Ethical clearance was obtained from the Ethics Committee of the Institute of Forensic Science of China. Samples collection and all experiment procedures were in accordance with the requirements of the ethics committee.
⁎
Corresponding authors. E-mail addresses: [email protected] (J. Huang), [email protected] (C. Li). 1 Xiaojuan Wang and Li Jiang are equally contributed to this work. https://doi.org/10.1016/j.legalmed.2019.101666 Received 14 May 2019; Received in revised form 4 November 2019; Accepted 29 December 2019 Available online 07 January 2020 1344-6223/ © 2020 Elsevier B.V. All rights reserved.
Legal Medicine 43 (2020) 101666
X. Wang, et al.
Table 1 Haplotype numbers and forensic parameters of different panels.
Yfiler RM + MC Yfiler + RM Yfiler + MC 35 Y-STR loci
Number of haplotypes
Percentage of unique haplotypes
Haplotype diversity
Haplotype match probability
Discrimination capacity
232 277 278 274 281
89.22% 97.11% 97.84% 97.45% 98.58%
0.9968 0.9998 0.9997 0.9995 0.9999
0.0067 0.0037 0.0038 0.0040 0.0036
0.8112 0.9685 0.9720 0.9580 0.9825
Notes: RM, rapidly mutating loci; MC, multi-copy loci.
2. DNA extraction and PCR
single-copy loci (DYS391, DYS508, DYS437, DYS456, and DYS438) displayed a low level of genetic polymorphisms, with a GD value < 0.5. GD values for MC and RM loci ranged from 0.6947 to 0.9906 and 0.7794 to 0.9379, respectively, which demonstrated that these loci had high levels of genetic polymorphisms. The HD, HMP, and DC values were 0.9999, 0.0036, and 0.9825, respectively. In total, 281 haplotypes were found at 35 loci in 286 Gelao individuals, 98.25% of which were unique (Table S2). Among them, one haplotype (H20) was shared by three individuals, and three haplotypes (H32, H56, and H155) were shared by two other individuals. Tracing back the residence information of these samples, we inferred individuals with shared haplotypes may have a common paternal ancestry without being aware of it. We also evaluated the forensic statistical parameters of Yfiler loci and other Y-STR combinations (Table 1). Compared to common Y-STR loci, the combined use of MC and RM loci had high genetic polymorphisms in the Gelao group, which is of great value for improving the discrimination of Y-STR typing systems and can be expected to separate male relatives from the same paternal lineage. Based on the pairwise RST values, a NJ tree was constructed and plotted, as shown in Fig. 1. The Guizhou Gelao group and other groups in Guizhou Province, including the Guizhou Han and Guizhou Miao, were clustered in the middle portion of the tree. In the MDS plot (Fig. 2), the Guizhou Gelao group displays a closer genetic relationship with the Guizhou Han and Guizhou Miao groups than the other groups. This result is also supported by other genetic makers, including X-STRs, autosomal STRs, and mitochondrial DNA [13–15]. Many factors may result in the close relationship among these groups. With the rapid development of economy and society, the Guizhou Gelao group and other neighboring groups have experienced migration, mixed living situations, and genetic fusion, resulting in a closer relationship among these groups. We also found that there was a relatively large genetic distance between the Guizhou Gelao and Guangxi Gelao groups. According to census data, the Guangxi Gelao is composed of approximately 3000 people, a small ethnic group residing in northwestern Guangxi Province. The mountains of the Yunnan-Kweichow Plateau are natural geographical barriers, resulting in geographical and genetic isolation, which caused this genetic differentiation between the Guangxi Gelao and Guizhou Gelao. With deeper ethnic and historical studies in future, more about the origin and migration of the Gelao group can be learned.
DNA extraction was executed from blood stain samples using a MagAttract® M48 DNA Manual Kit (Qiagen, Hilden, Germany), and PCR of the 35 Y-STR loci was performed using a Mastercycler ProS (Eppendorf, Hamburg, Germany) following the instructions of the DNATyperTM Y29 and DNATyperTM MCY amplification kits (Ministry of Public Security, Beijing, China). The 35 studied Y-STR loci contained 20 common Y-STR loci, seven RM loci, and 12 MC loci (four were both RM and MC loci). 3. Genotyping and quality control Amplification products were electrophoresed on an ABI Genetic Analyzer 3500xL (Thermo Fisher Scientific, Waltham, MA, USA). The 9948 control DNA and double-distilled water (ddH2O) were analyzed as positive and negative controls, respectively. Genotyping data were analyzed using GeneMapper ID-X Analysis Software (Thermo Fisher Scientific). Haplotype data were submitted to the Y-chromosome Haplotype Reference Database with the population accession number YA004593. 4. Statistical analysis The direct counting method was used to evaluate allelic and haplotype frequencies. Genetic diversity (GD) was calculated using the formula: GD = (n/n − 1) (1 − ∑ Pi2), where n is the total number of samples, and Pi is the frequency of the ith allele. Haplotype diversity (HD) was calculated using the formula: HD = (n/n − 1) (1 − ∑ Pi2), where n is the total number of samples, and Pi is the frequency of the ith haplotype. Haplotype match probability (HMP) was calculated according to MP = ∑ Pi2, where Pi is the frequency of the haplotype. Discrimination capacity (DC) was calculated based on the formula: DC = k/Σ(Pi × N), where k is the number of haplotypes, Pi is the frequency of the ith haplotype, and N is the total number of individuals. To evaluate the population genetic relationships between the Gelao group and other Chinese groups, we compared data from the 17 Yfiler haplotypes of the Gelao group with 13 neighboring populations (including Han [9], Yi (YP001344), Miao (YP001249), Shui (YP001172), and Qiannan Bouyei (YP001182) of Guizhou Province; Bai (YP000902), Hani [10], Xishuangbanna Dai (YP000903), and Lijiang Mosuo (YP001334) of Yunnan Province; and Gelao (YA004286), Gin (YP001166), Maonan (YP001168), and Miao (YP001169) of Guangxi Province). All of the reference groups were obtained from the Y-STR Haplotype Reference Database (YHRD) website [11]. Pairwise genetic distances (RST) and p values were calculated by analysis of molecular variance (AMOVA) and visualized in multidimensional scaling (MDS) plots using the AMOVA & MDS tool on the YHRD website. MEGA 6.0 [12] was used to construct a phylogenetic tree using the neighborjoining (NJ) method based on the RST values.
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgments This study was funded in part by the National Key Research and Development Program of China (2017YFC0803501), the basic research project (2017JB027), and the Key Laboratory of Forensic Genetics Open Project (2017FGKFKT02). Biological samples from the Caixia laboratory were funded by the National Infrastructure of Chinese Genetic Resources (NICGR: YCZYPT [2017]01-3) and the basic research project
5. Results and discussion As shown in Table S1, a total of 609 alleles were detected at 35 YSTR loci, and the allelic frequencies ranged from 0.0035 to 0.8322. Five 2
Legal Medicine 43 (2020) 101666
X. Wang, et al.
Fig. 1. Neighbor-joining phylogenetic tree constructed by MEGA based on the RST values. Pairwise RST values were calculated using the AMOVA & MDS tools on the YHRD website.
Fig. 2. Multidimensional scaling plot of Gelao and 13 reference groups constructed using the AMOVA & MDS tools on the YHRD website. 3
Legal Medicine 43 (2020) 101666
X. Wang, et al.
(2017JB025).
[5] A. Boattini, S. Sarno, C. Bini, V. Pesci, C. Barbieri, F.S. De, A. Quagliariello, L. Pagani, Q. Ayub, G. Ferri, Mutation rates and discriminating power for 13 rapidly-mutating Y-STRs between related and unrelated individuals, PLoS ONE 11 (11) (2016) e0165678. [6] P. Chen, Y. Han, G. He, H. Luo, T. Gao, F. Song, D. Wan, J. Yu, Y. Hou, Genetic diversity and phylogenetic study of the Chinese Gelao ethnic minority via 23 Y-STR loci, Int. J. Legal Med. 132 (4) (2018) 1093–1096. [7] Y. Liu, C. Wang, W. Zhou, X.B. Li, M. Shi, R. Bai, S. Ma, Haplotypes of 27 Y-STRs analyzed in Gelao and Miao ethnic minorities from Guizhou Province, Southwest China, Forensic Sci. Int. Genet. 40 (2019) e264–e267. [8] C. Liu, X. Han, Y. Min, H. Liu, Q. Xu, X. Yang, S. Huang, Z. Chen, C. Liu, Genetic polymorphism analysis of 40 Y-chromosomal STR loci in seven populations from South China, Forensic Sci. Int. 291 (2018) 109–114. [9] H. Zhou, Z. Ren, H. Zhang, J. Wang, J. Huang, Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China, Forensic Sci. Int.: Genetics 25 (2016) e6–e7. [10] L. Hu, T. Gu, X. Fan, X. Yuan, M. Rao, J.B. Pang, A. Nie, L. Du, X. Zhang, S. Nie, Genetic polymorphisms of 24 Y-STR loci in Hani ethnic minority from Yunnan Province, Southwest China, Int. J. Legal Med. 131 (5) (2017) 1–3. [11] http://www.yhrd.org/. [12] B.G. Hall, Building phylogenetic trees from molecular data with MEGA, Mol. Biol. Evol. 30 (5) (2013) 1229–1235. [13] P. Chen, G. He, X. Zou, M. Wang, H. Luo, L. Yu, X. Hu, M. Xia, H. Gao, J. Yu, Y. Hou, Y. Han, Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers, Sci. Rep. 8 (1) (2018) 14585. [14] L. Yang, Y. Zhao, C. Liu, D.W.T. Chan, M. Chan, M. He, Allele frequencies of 15 STRs in five ethnic groups (Han, Gelao, Jing, Shui and Zhuang) in South China, Forensic Sci. Int.: Genetics 7 (1) (2013) e9–e14. [15] C. Liu, S.-Y. Wang, M. Zhao, Z.-Y. Xu, Y.-H. Hu, F. Chen, R.-Z. Zhang, G.-F. Gao, Y.S. Yu, Q.-P. Kong, Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China, Forensic Sci. Int.: Genetics 5 (1) (2011) e4–e10.
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