- Email: [email protected]
Haplotype diversity of 22 Y-chromosomal STRs in a southeast China population sample (Chaoshan area)
Available online at www.sciencedirect.com
Forensic Science International: Genetics 3 (2009) e45–e47 www.elsevier.com/locate/fsig
Announcement of Population Data
Haplotype diversity of 22 Y-chromosomal STRs in a southeast China population sample (Chaoshan area) Meisen Shi a,*, Rufeng Bai a, Xiaojun Yu b, Junyao Lv b, Bo Hu b a
Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Eduction 25 Xitucheng Road, Haidian District, Beijing 100088, PR China b Department of Forensic Medicine, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong 515031, PR China Received 24 December 2007; received in revised form 25 March 2008; accepted 13 May 2008
Abstract In this study, 22 Y-specific STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS461, DYS481, DYS504, DYS505, DYS508, DYS533, DYS576, DYS588, DYS607, DYS634, and DYS643) were analyzed in 216 unrelated male individuals from southeast China (Chaoshan area) by three multiplex PCR systems. The haplotype diversity using the classical set of Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS385; PowerPlexY Systems) was 0.9908. For the same population sample, the haplotype diversity using the new sets of 11 novel Y-STRs (DYS461, DYS481, DYS504, DYS505, DYS508, DYS533, DYS576, DYS588, DYS607, DYS634, and DYS643; multiplex I and II) was 0.9917. By combining the allelic states of the 22 Y-STR loci we could construct highly informative haplotypes that allowed the discrimination of 99.1% (214 out of 216) of the samples tested and the overall haplotype diversity of 0.9999. These results, including the haplotype data at 22 Y-STR loci in the present study, provide useful information for forensic practice in the Chaoshan population in southeast China. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosomal STR; Haplotype; Southeast China (Chaoshan area)
Population: Chaoshan is a littoral area located in the southeast of mainland China with its south facing the South China Sea and its east bordering on Fujian Province, which stands opposite to Taiwan across the Taiwan Strait (Fig. S1). The whole area covers the cities of Shantou, Chaozhou, and Jieyang, and the population is 4,846,000. It is one of the five major Special Economic Zones and open coastal cities of China. With the innumerable overseas Chinese of Chaoshan origin, Chaoshan area has been one of the largest emigration ports in modern Chinese history and the famous hometown of returned overseas Chinese: more than 3 million are overseas Chinese and compatriots of Hong Kong, Macau and Taiwan, spread over approximately 40 countries and regions, and over 2 million are returned overseas Chinese, family members of overseas Chinese and compatriots of Hong Kong, Macau and Taiwan. People residing in this area speak in a unique dialect and have a distinct lifestyle. Blood samples were obtained from 216 unrelated males of native Chaoshanese. All participants
* Corresponding author. E-mail address: [email protected] (M. Shi). 1872-4973/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2008.05.009
signed the informed consent and provided information about birthplace, parents and grandparents. Their ancestors had lived in the region for at least three generations. Extraction: DNA was extracted using the Chelex-100 and proteinase K protocol [1]. The quantity of recovered DNA was determined spectrophotometrically. PCR: Amplification of the classical Y-STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS385) was performed in fluorescence-based multiplex reaction using PowerPlexY Systems (Promega, Madison, WI, USA) following the manufacturer’s recommendations. PCR primer sequences of the 11 novel Y-STR loci used in this study were those presented in the Genome Database (GDB; http://www.gdb.org). Fluorescent dyes 6-FAM, HEX, or TAMRA were included on the 50 -end of the forward primers to create blue, green, or yellow-labeled PCR products. The reverse primers included an extra six base tail (gttctt) to promote non-template addition. Amplification was carried out using the multiplex PCR: (I) DYS505, DYS533, DYS576, DYS588, DYS634, and DYS643; (II) DYS461, DYS481, DYS504, DYS508, and DYS607. Each PCR multiplex was performed in a total volume of 37.5 ml containing
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M. Shi et al. / Forensic Science International: Genetics 3 (2009) e45–e47
1–2 ng genomic DNA, 1 GeneAmp PCR buffer (containing 1.5 mM MgCl2), 200 mmol/L deoxynucleotide triphosphates (dNTPs; Promega Corporation, Madison, WI), each primer set, and 1.5 U of AmpliTaq Gold DNA polymerase (5 U/ml, Applied Biosystems, USA). Thermal cycling was conducted on a PTC-200 DNA engine (MJ Research, Waltham, MA) using the following conditions (i.e., ramp speeds of 1 8C/s): 95 8C for 10 min; 10 cycles of (94 8C for 30 s, 58 8C for 1 min, 72 8C for 50 s); 22 cycles of (90 8C for 30 s, 60 8C for 40 s, 72 8C for 30 s); 65 8C for 45 min; and 4 8C until removed from thermal cycler. Typing: ABI PRISM 310 genetic analyzer (Applied Biosystems, Foster City, CA, USA) and GeneScan software 3.7 (Applied Biosystems, Foster City, CA, USA); the genotyping of PCR products at each of the 11 novel YSTR loci was carried out based on sequenced allelic ladder using Genotyper 3.7 software (Applied Biosystems, CA, USA). Allelic ladders were constructed by combining all observed alleles from each locus. At least two different alleles for each Y-STR locus were sequenced on an ABI PRISM 310 genetic analyzer using a BigDye Terminator Cycle Sequencing v2.0 Ready Reaction kit (Applied Biosystems, Foster City, CA, USA) to aid calibration of observed size to repeat number and to assist in nomenclature decisions. Allele designation was established according to the International Society of Forensic Genetics (ISFG) guidelines for forensic STR analysis [2]. Quality control: Quality assurance standards as stipulated by the Scientific Working Group on DNA Analysis Methods (SWGDAM) were followed. Laboratory internal control standards and 25 random samples (>10% of all 216 samples) were genotyped twice to further ensure result reproducibility and accuracy. Analysis of data: Haplotype and allele frequencies were estimated by gene counting. Observed gene and haplotype diversities were calculated according to the formula of Hou et al. [3]. The discrimination capacity was calculated as the proportion of different haplotypes in the sample. Analysis of molecular variance (AMOVA) and exact test of population differentiation were performed using ARLEQUIN software Version 2.000 [4]. In population comparisons, DYS437 was not considered and the number of repeats in DYS389I was subtracted from DYS389II. A neighbor-joining tree was constructed from the distance matrix (Rst) by using the program PHYLIP software [5] to illustrate the relationship between populations. The tree was visualized with the Treeview software [6] (Fig. S2). Results: The haplotypes detected in the Chaoshan population for classical and novel Y-STR loci are shown in Table S1. The allelic frequency distribution and gene diversity values found for each locus are listed in Table S2. The number of different haplotypes and haplotype diversity values found for combinations of 22 loci are shown in Table S3. The Rst values calculated to measure genetic distances between ExtHt haplotypes of 14 reference populations (n = 2697) with the statistical significance are shown in Table S4.
Access to the data: The raw data worksheet and the Arlequin input files are available upon request: shimeisen2000 @yahoo.com.cn. Other remarks: In this study, the 11 novel Y-STR loci examined were all single copy and male-specific markers and thus exhibited only a single peak at each locus. The number of alleles of these 11 STRs detected in the Chaoshan population sample ranged from 4 (DYS533, DYS634) to 11 (DYS481). DYS481 was the most informative loci with gene diversity of 0.8011, while DYS634, which has high and spiked distribution for a single allele frequency above 0.8, was the least informative loci with gene diversity of 0.3299. By combining the allelic states of these 11 novel Y-STRs it was possible to define 166 different haplotypes. The haplotype diversity value was 0.9917 with a discrimination capacity of 0.7685. For the same population sample, a total of 170 different haplotypes were observed using the classical set of ‘ExtHt’ Y-STRs, and the haplotype diversity was calculated as 0.9908 with a discrimination capacity of 0.7870. The combination of the allelic states of the 22 classical and novel Y-STRs allowed us to construct highly informative haplotypes. A total of 214 haplotypes were observed in 216 individuals, of which 212 haplotypes were unique and only 2 haplotypes were observed twice (Table S1). The overall haplotype diversity of 22 Y-STRs set was 0.9999 with a discrimination capacity of 0.9907. These results provide information for the decisions on the inclusion or exclusion of new markers to the established ‘Ext’ haplotype of the present databases. Our present ‘ExtHt’ data were compared with previously published data available for the same set of Y-STR loci in samples from Chaoshan Han Chinese in southeast China [7], from Minnan Han Chinese in southeast China [8], from the Han Chinese population in Singapore [9], from the Han population residing in northeast China [10], from the Chinese population in Hong Kong [11], from the Chinese population in Taiwan [12], from the Chinese Mongol ethnic group [13], from the Chinese Tibetan ethnic group [14], from the Chinese Naxi ethnic group [15], from the Chinese Yi ethnic minority group [16], from the Chinese Uygur ethnic group [17], from the Chinese Korean ethnic group [18], from the southern population in Korea [19], and from the Japanese [20]. The results from AMOVA analysis revealed that variation among individuals within each population and variations among populations were 92.22 and 7.78%, respectively, for the ExtHt data set comparison. Pairwise analysis showed no significant differences (P > 0.05) in the comparison of the Chaoshan population sample with other south China origin populations from Chaoshan, Minnan, Hong Kong, and Singapore (Rst = 0.0024, 0.0030, 0.0031 and 0.0034, respectively). With populations from northeast China and Taiwan, although significant, low Rst values were obtained (0.0109 and 0.0124, respectively). In comparison to the remaining Chinese minority ethnic groups and two Asian populations, highly significant distances were observed (P = 0.0000). Fig. S2 shows neighbor-joining trees built from the Rst distance matrices between the 14 reference populations, where the Chaoshan population clusters with south China origin populations, confirming their historical ancestry, and
M. Shi et al. / Forensic Science International: Genetics 3 (2009) e45–e47
stands far apart from the Chinese minority ethnic groups, South Korea, and Japan populations. Our ‘ExtHt’ data were also compared against the data available in YHRD, which currently includes 23,979 haplotypes in a set of 221 populations worldwide for an extended haplotype (extHt, minHt + DYS438, 439) data set (http:// www.yhrd.org, last update 10 August 2007). One hundred and thirty-two (77.6%) haplotypes detected in the southeast China population are in zero matches in YHRD with the ‘ExtHt’ database. In conclusion, combining with the novel Y-STRs, our Y-STR data in the Chaoshan population in southeast China could be useful as a regional specific and prerequisite reference for forensic investigation and human evolution. Future studies will address optimal loci in terms of haplotype resolution and mutation rates as well as development of new large multiplexes to enable simultaneous amplification of the better performing loci in various populations. This paper follows the guidelines for publication of population data requested by the journal [21]. Acknowledgements We would like to thank Mr. Junyao Lv for collecting DNA samples during the course of this work. Special thanks go to volunteers for providing DNA samples. This study was supported by the Natural Science Foundation of Guangdong Province (No. D6301091). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2008.05.009. References [1] B.S. Walsh, D.A. Petzger, R. Higuchi, Chelex-100 as medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [2] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [3] Y.P. Hou, J. Zhang, Y.B. Li, J. Wu, S. Zhang, M. Prinz, Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population, Forensic Sci. Int. 118 (2001) 147–152.
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[4] S. Schneider, D. Roessli, L. Excoffier, Arlequin: A Software for Population Genetics Data Analysis. Version 2.000, Genetics and Biometry Lab, Department of Anthropology, University of Geneva, 2000. [5] J. Felsenstein, PHYLIP: phylogeny inference package (version 3.2), Cladistics 5 (1989) 164–166. [6] R.D.M. Page, Treeview: an application to display phylogenetic trees on personal computers, Comput. Appl. Biosci. 12 (1996) 357–358. [7] S.P. Hu, Genetic polymorphism of 12 Y-chromosomal STR loci in the Minnan Han Chinese in Southeast China, Forensic Sci. Int. 159 (2006) 77–82. [8] S.P. Hu, Polymorphism of Y-chromosomal STR haplotypes in the Chaoshan Han Chinese in south China, Forensic Sci. Int. 158 (2006) 80–85. [9] J.S. Tang, H.Y. Wong, C.K. Syn, W.F. Tan-Siew, S.T. Chow, B. Budowle, Population study of 11 Y-chromosomal STR loci in Singapore Chinese, Forensic Sci. Int. 158 (2006) 65–71. [10] B.Q. Yang, M.B. Gu, G. Wang, X.P. Li, Y.C. Liu, W.S. Yang, Population data for 11 Y-chromosome STRs in northeast China Han, Forensic Sci. Int. 164 (2006) 65–71. [11] S.M. Yeung, L.M. Wong, B.K.K. Cheung, K.Y. To, Allele frequencies and haplotypes of 12 Y-STR loci for the local Chinese population in Hong Kong, Forensic Sci. Int. 162 (2006) 55–63. [12] T.Y. Huang, Y.T. Hsu, J.M. Li, J.H. Chung, C.T. Shun, Polymorphism of 17 Y-STR loci in Taiwan population, Forensic Sci. Int. 174 (2–3) (2007) 249–254. [13] B.F. Zhu, X.S. Li, Z.Y. Wang, H.Y. Wu, Y.F. He, J. Zhao, Y. Liu, Y-STRs haplotypes of Chinese Mongol ethnic group using Y-PLEXTM12, Forensic Sci. Int. 153 (2005) 260–263. [14] B.F. Zhu, S.Z. Liu, D. Ci, J.F. Huang, Y.C. Wang, L.P. Chen, J. Zhu, Y.C. Xu, Q.Z. Zhao, S.B. Li, Y. Liu, Population genetics for Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group in Tibet, Forensic Sci. Int. 161 (2006) 78–83. [15] N. Xin, T. Chen, B. Yu, S.B. Li, 12 Y-STRs haplotypes in Chinese Naxi ethnic minority group, Forensic Sci. Int. 174 (2008) 244–248. [16] B.F. Zhu, C.M. Shen, G.L. Qian, R.Y. Shi, Y.H. Dang, J. Zhu, P. Huang, Y.C. Xu, Q.Z. Zhao, J. Ma, Y. Liu, Genetic polymorphisms for eleven YSTRs haplotypes of Chinese Yi ethnic minority group, Forensic Sci. Int. 158 (2006) 229–233. [17] B.F. Zhu, Z.Y. Wang, C.H. Yang, X.S. Li, J. Zhu, G. Yang, P. Huang, Y. Liu, Y-chromosomal STR haplotypes in Chinese Uigur ethnic group, Int. J. Legal Med. 119 (2005) 306–309. [18] Y.J. Zhang, H.J. Zhang, Y. Cui, H. Cui, Q.S. Xu, S. Sun, L.P. Sun, J.B. Lee, Population genetics for Y-chromosomal STRs haplotypes of Chinese Korean ethnic group in northeastern China, Forensic Sci. Int. 173 (2007) 197–203. [19] B.W. Chun, S.C. Shin, Y.J. Kim, K.S. Kim, D.H. Choi, K.H. Kim, J.Y. Kim, H.S. Kang, Allele frequencies and haplotypes of the STR loci of the PowerPlex Y-system in southern populations from Korea, Forensic Sci. Int. 148 (2005) 225–231. [20] M. Hashiyada, T. Nagashima, Y. Itakura, J. Sakai, Y. Kanawaku, J. Kanetake, M. Nata, M. Funayama, 12 Y-chromosomal STR haplotypes in Japanese, Forensic Sci. Int. 158 (2006) 204–212. [21] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Forensic Science International: Genetics 3 (2009) e45–e47 www.elsevier.com/locate/fsig
Announcement of Population Data
Haplotype diversity of 22 Y-chromosomal STRs in a southeast China population sample (Chaoshan area) Meisen Shi a,*, Rufeng Bai a, Xiaojun Yu b, Junyao Lv b, Bo Hu b a
Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Eduction 25 Xitucheng Road, Haidian District, Beijing 100088, PR China b Department of Forensic Medicine, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong 515031, PR China Received 24 December 2007; received in revised form 25 March 2008; accepted 13 May 2008
Abstract In this study, 22 Y-specific STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS461, DYS481, DYS504, DYS505, DYS508, DYS533, DYS576, DYS588, DYS607, DYS634, and DYS643) were analyzed in 216 unrelated male individuals from southeast China (Chaoshan area) by three multiplex PCR systems. The haplotype diversity using the classical set of Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS385; PowerPlexY Systems) was 0.9908. For the same population sample, the haplotype diversity using the new sets of 11 novel Y-STRs (DYS461, DYS481, DYS504, DYS505, DYS508, DYS533, DYS576, DYS588, DYS607, DYS634, and DYS643; multiplex I and II) was 0.9917. By combining the allelic states of the 22 Y-STR loci we could construct highly informative haplotypes that allowed the discrimination of 99.1% (214 out of 216) of the samples tested and the overall haplotype diversity of 0.9999. These results, including the haplotype data at 22 Y-STR loci in the present study, provide useful information for forensic practice in the Chaoshan population in southeast China. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosomal STR; Haplotype; Southeast China (Chaoshan area)
Population: Chaoshan is a littoral area located in the southeast of mainland China with its south facing the South China Sea and its east bordering on Fujian Province, which stands opposite to Taiwan across the Taiwan Strait (Fig. S1). The whole area covers the cities of Shantou, Chaozhou, and Jieyang, and the population is 4,846,000. It is one of the five major Special Economic Zones and open coastal cities of China. With the innumerable overseas Chinese of Chaoshan origin, Chaoshan area has been one of the largest emigration ports in modern Chinese history and the famous hometown of returned overseas Chinese: more than 3 million are overseas Chinese and compatriots of Hong Kong, Macau and Taiwan, spread over approximately 40 countries and regions, and over 2 million are returned overseas Chinese, family members of overseas Chinese and compatriots of Hong Kong, Macau and Taiwan. People residing in this area speak in a unique dialect and have a distinct lifestyle. Blood samples were obtained from 216 unrelated males of native Chaoshanese. All participants
* Corresponding author. E-mail address: [email protected] (M. Shi). 1872-4973/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2008.05.009
signed the informed consent and provided information about birthplace, parents and grandparents. Their ancestors had lived in the region for at least three generations. Extraction: DNA was extracted using the Chelex-100 and proteinase K protocol [1]. The quantity of recovered DNA was determined spectrophotometrically. PCR: Amplification of the classical Y-STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, and DYS385) was performed in fluorescence-based multiplex reaction using PowerPlexY Systems (Promega, Madison, WI, USA) following the manufacturer’s recommendations. PCR primer sequences of the 11 novel Y-STR loci used in this study were those presented in the Genome Database (GDB; http://www.gdb.org). Fluorescent dyes 6-FAM, HEX, or TAMRA were included on the 50 -end of the forward primers to create blue, green, or yellow-labeled PCR products. The reverse primers included an extra six base tail (gttctt) to promote non-template addition. Amplification was carried out using the multiplex PCR: (I) DYS505, DYS533, DYS576, DYS588, DYS634, and DYS643; (II) DYS461, DYS481, DYS504, DYS508, and DYS607. Each PCR multiplex was performed in a total volume of 37.5 ml containing
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M. Shi et al. / Forensic Science International: Genetics 3 (2009) e45–e47
1–2 ng genomic DNA, 1 GeneAmp PCR buffer (containing 1.5 mM MgCl2), 200 mmol/L deoxynucleotide triphosphates (dNTPs; Promega Corporation, Madison, WI), each primer set, and 1.5 U of AmpliTaq Gold DNA polymerase (5 U/ml, Applied Biosystems, USA). Thermal cycling was conducted on a PTC-200 DNA engine (MJ Research, Waltham, MA) using the following conditions (i.e., ramp speeds of 1 8C/s): 95 8C for 10 min; 10 cycles of (94 8C for 30 s, 58 8C for 1 min, 72 8C for 50 s); 22 cycles of (90 8C for 30 s, 60 8C for 40 s, 72 8C for 30 s); 65 8C for 45 min; and 4 8C until removed from thermal cycler. Typing: ABI PRISM 310 genetic analyzer (Applied Biosystems, Foster City, CA, USA) and GeneScan software 3.7 (Applied Biosystems, Foster City, CA, USA); the genotyping of PCR products at each of the 11 novel YSTR loci was carried out based on sequenced allelic ladder using Genotyper 3.7 software (Applied Biosystems, CA, USA). Allelic ladders were constructed by combining all observed alleles from each locus. At least two different alleles for each Y-STR locus were sequenced on an ABI PRISM 310 genetic analyzer using a BigDye Terminator Cycle Sequencing v2.0 Ready Reaction kit (Applied Biosystems, Foster City, CA, USA) to aid calibration of observed size to repeat number and to assist in nomenclature decisions. Allele designation was established according to the International Society of Forensic Genetics (ISFG) guidelines for forensic STR analysis [2]. Quality control: Quality assurance standards as stipulated by the Scientific Working Group on DNA Analysis Methods (SWGDAM) were followed. Laboratory internal control standards and 25 random samples (>10% of all 216 samples) were genotyped twice to further ensure result reproducibility and accuracy. Analysis of data: Haplotype and allele frequencies were estimated by gene counting. Observed gene and haplotype diversities were calculated according to the formula of Hou et al. [3]. The discrimination capacity was calculated as the proportion of different haplotypes in the sample. Analysis of molecular variance (AMOVA) and exact test of population differentiation were performed using ARLEQUIN software Version 2.000 [4]. In population comparisons, DYS437 was not considered and the number of repeats in DYS389I was subtracted from DYS389II. A neighbor-joining tree was constructed from the distance matrix (Rst) by using the program PHYLIP software [5] to illustrate the relationship between populations. The tree was visualized with the Treeview software [6] (Fig. S2). Results: The haplotypes detected in the Chaoshan population for classical and novel Y-STR loci are shown in Table S1. The allelic frequency distribution and gene diversity values found for each locus are listed in Table S2. The number of different haplotypes and haplotype diversity values found for combinations of 22 loci are shown in Table S3. The Rst values calculated to measure genetic distances between ExtHt haplotypes of 14 reference populations (n = 2697) with the statistical significance are shown in Table S4.
Access to the data: The raw data worksheet and the Arlequin input files are available upon request: shimeisen2000 @yahoo.com.cn. Other remarks: In this study, the 11 novel Y-STR loci examined were all single copy and male-specific markers and thus exhibited only a single peak at each locus. The number of alleles of these 11 STRs detected in the Chaoshan population sample ranged from 4 (DYS533, DYS634) to 11 (DYS481). DYS481 was the most informative loci with gene diversity of 0.8011, while DYS634, which has high and spiked distribution for a single allele frequency above 0.8, was the least informative loci with gene diversity of 0.3299. By combining the allelic states of these 11 novel Y-STRs it was possible to define 166 different haplotypes. The haplotype diversity value was 0.9917 with a discrimination capacity of 0.7685. For the same population sample, a total of 170 different haplotypes were observed using the classical set of ‘ExtHt’ Y-STRs, and the haplotype diversity was calculated as 0.9908 with a discrimination capacity of 0.7870. The combination of the allelic states of the 22 classical and novel Y-STRs allowed us to construct highly informative haplotypes. A total of 214 haplotypes were observed in 216 individuals, of which 212 haplotypes were unique and only 2 haplotypes were observed twice (Table S1). The overall haplotype diversity of 22 Y-STRs set was 0.9999 with a discrimination capacity of 0.9907. These results provide information for the decisions on the inclusion or exclusion of new markers to the established ‘Ext’ haplotype of the present databases. Our present ‘ExtHt’ data were compared with previously published data available for the same set of Y-STR loci in samples from Chaoshan Han Chinese in southeast China [7], from Minnan Han Chinese in southeast China [8], from the Han Chinese population in Singapore [9], from the Han population residing in northeast China [10], from the Chinese population in Hong Kong [11], from the Chinese population in Taiwan [12], from the Chinese Mongol ethnic group [13], from the Chinese Tibetan ethnic group [14], from the Chinese Naxi ethnic group [15], from the Chinese Yi ethnic minority group [16], from the Chinese Uygur ethnic group [17], from the Chinese Korean ethnic group [18], from the southern population in Korea [19], and from the Japanese [20]. The results from AMOVA analysis revealed that variation among individuals within each population and variations among populations were 92.22 and 7.78%, respectively, for the ExtHt data set comparison. Pairwise analysis showed no significant differences (P > 0.05) in the comparison of the Chaoshan population sample with other south China origin populations from Chaoshan, Minnan, Hong Kong, and Singapore (Rst = 0.0024, 0.0030, 0.0031 and 0.0034, respectively). With populations from northeast China and Taiwan, although significant, low Rst values were obtained (0.0109 and 0.0124, respectively). In comparison to the remaining Chinese minority ethnic groups and two Asian populations, highly significant distances were observed (P = 0.0000). Fig. S2 shows neighbor-joining trees built from the Rst distance matrices between the 14 reference populations, where the Chaoshan population clusters with south China origin populations, confirming their historical ancestry, and
M. Shi et al. / Forensic Science International: Genetics 3 (2009) e45–e47
stands far apart from the Chinese minority ethnic groups, South Korea, and Japan populations. Our ‘ExtHt’ data were also compared against the data available in YHRD, which currently includes 23,979 haplotypes in a set of 221 populations worldwide for an extended haplotype (extHt, minHt + DYS438, 439) data set (http:// www.yhrd.org, last update 10 August 2007). One hundred and thirty-two (77.6%) haplotypes detected in the southeast China population are in zero matches in YHRD with the ‘ExtHt’ database. In conclusion, combining with the novel Y-STRs, our Y-STR data in the Chaoshan population in southeast China could be useful as a regional specific and prerequisite reference for forensic investigation and human evolution. Future studies will address optimal loci in terms of haplotype resolution and mutation rates as well as development of new large multiplexes to enable simultaneous amplification of the better performing loci in various populations. This paper follows the guidelines for publication of population data requested by the journal [21]. Acknowledgements We would like to thank Mr. Junyao Lv for collecting DNA samples during the course of this work. Special thanks go to volunteers for providing DNA samples. This study was supported by the Natural Science Foundation of Guangdong Province (No. D6301091). Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2008.05.009. References [1] B.S. Walsh, D.A. Petzger, R. Higuchi, Chelex-100 as medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [2] L. Gusmao, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [3] Y.P. Hou, J. Zhang, Y.B. Li, J. Wu, S. Zhang, M. Prinz, Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population, Forensic Sci. Int. 118 (2001) 147–152.
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