Forensic Science International: Genetics 4 (2010) e129–e130
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Announcement of Population Data
Population genetics of 17 Y-chromosomal STR loci in Yakutia Catherine The`ves a,*, Patricia Balaresque b, Larissa E. Evdokimova c, Innokentevich V. Timofeev c, Anatoly N. Alekseev d, Andre´ Sevin a, Eric Crube´zy a, Morgane Gibert a a
Laboratory AMIS, FRE N82960, CNRS/UPS, 37 alle´es Jules Guesde, 31000 Toulouse, France Department of Genetics, Adrian Building Lab G2,University of Leicester, University Road, Leicester LE17RH, United Kingdom c Hospital of the Viljujsk Ulus, Republic of Sakha, Russia d Yakutsk State University, Republic of Sakha, Russia b
A R T I C L E I N F O
A B S T R A C T
Article history: Received 29 April 2009 Received in revised form 25 January 2010 Accepted 26 January 2010
Haplotype and allele frequencies of 17 Y-chromosomal short tandem repeat (Y-STR) markers in a population sample of 133 Yakut male volunteers from two regions: Central (n = 41) and Western Yakutia (n = 92) were determined using the AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems). A total of 65 haplotypes were identified in the Yakut population, with 15 haplotypes in Central sample and 54 haplotypes in Western sample. Haplotype diversity values of 0.79 and 0.96, and average gene diversity values of 0.14 and 0.41 were calculated for Central and Western samples, respectively. The Fst distances between both our Yakut populations with other Russian, Siberian and Chinese populations were represented by MDS plot. The graphical view demonstrated close distances between most Yakut populations and differences with other Siberian populations. Crown Copyright ß 2010 Published by Elsevier Ireland Ltd. All rights reserved.
Keywords: Y-Chromosomal STR Haplotype AmpFlSTR Yfiler Yakut population
General information on the population under study: The Republic of Sakha (Yakutia) is a wide territory (3,103,200 km2) subdivided into 33 regions or Ulus. From the 2002 census, Yakutia had approximately one million people with 41.15% Slavs and 59.85% autochthonous populations, which included 45.54% Yakuts and 13.31% other minorities (Evenk, Even, Dolgan, Yukaghir and Chukch). In this study, we aim to characterize the Yakut populations. Besides their cultural particularities (Turkic-speakers, cattle/ horse-breeders living among reindeer-breeders, Tungus speakers), previous studies have shown distinctive genetic features. They present a low genetic diversity, possibly due to a population bottleneck or founder effect, and affinities with southern Siberian populations [1–3]. This work proposes to analyze the Yakut population by using, for the first time, 17 Y-STR markers and to compare their haplotypes with those from the surrounding Siberian, Russian and Chinese populations. A sample of 133 male volunteers from Yakutia, unrelated by at least two generations, was collected after obtaining appropriate ethical approval and informed consent. The participants were questioned regarding their ethnic origin including birthplace, nationality and paternal pedigree. Two regions were sampled, one in Central Yakutia (near Yakutsk) and one in the Western Yakutia (in the Viluisk region) (Fig. 1).
* Corresponding author. Tel.: +33 05 61 14 59 82; fax: +33 05 61 14 59 79. E-mail addresses:
[email protected],
[email protected] (C. The`ves).
Extraction: Genomic DNA was extracted from buccal swabs using a standard phenol-chloroform protocol, followed by a purification using a Clean Mix TM kit (Talent). DNA was quantified using a spectrophotometer. PCR: 0.5–2 ng DNA templates were amplified using the AmpF‘STR1 YfilerTM kit amplification kit (Applied Biosystems), following the manufacturer’s instructions. Typing: The PCR fragments were detected with an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems) and sized with GeneScan-600 LIZ internal lane size standard. Data collection was performed with Data Collection v.1.1 software (Applied Biosystems) and the results were analyzed using GeneMapper v.4.0 software (Applied Biosystems). Alleles were designated according to the International Society of Forensic Genetics (ISFG) guidelines for forensic STR analysis but the GATA H4.1 locus alleles were named according to the manufacturer [4,5]. Quality Control: The Quality Control was performed (March 24, 2009) and data submitted to YHRD with the following accession number: YA003499. Data analysis: The per-locus gene diversity averages, haplotype diversity values and pairwise Fst genetic distances were performed using ARLEQUIN software ver. 3.1. [6]. A test implemented by SPAGeDI software [7] was run to choose between Rst and Fst as the most appropriate genetic distance to use. By permuting the allele sizes but not the allelic state, this test evaluates whether the allele size contributes or not to population differentiation. If it does, the Rst is chosen over the Fst. If not, as was in our case, Fst is preferred since Rst has excessive variance for
1872-4973/$ – see front matter . Crown Copyright ß 2010 Published by Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2010.01.018
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population comparisons (see Table 2 in [7]). The graphical view by MDS plot of Fst distances was performed by XL stat.7 ((http:// www.xlstat.com/en/home/). We compared both our Yakut samples with other Siberian populations, using the available Y-STR data in the literature [3,9– 19] and in the YHRD database [8]. We chose to compare the Fst distances for 7 loci (DYS19; DYS389I; DYS389II; DYS390; DYS391; DYS392; DYS393) to standardise with data from Puzyrev et al. (Northeastern Yakuts [13]) and from Kayser et al. (Chinese, Mongol and Inuit [15]). Results: Haplotype frequency data of the 17 Y-STR loci, gene diversities (average and by locus) and haplotype diversity are presented in Table S1. The per-locus gene diversity average for the Central Yakut sample was 0.14 and 0.41 for the Western Yakut sample. The haplotype diversity value was 0.79 0.05 and 0.96 0.01 for the Central and Western samples respectively. It is noted that the gene and haplotype diversities were higher in Western compared to Central Yakutia. A total of 65 Y-STR haplotypes were detected: 15 in the Central Yakut sample and 54 in the Western Yakut sample. Only four 17 YSTR haplotypes were shared by both samples of this study: Ht 1 (12 and 10 subjects), Ht 14 (1 and 15 subjects), Ht 19 (1 subject for each sample) and Ht 23 (15 and 5 subjects) for Central and Western Yakut samples respectively (Table S1). The Fst genetic distances for the 7 loci with their statistical significances, for both the Yakut populations (n = 133) and for the 20 Siberian, Russian and Chinese populations (n = 1288) are shown in Table S2. The graphical view on the MDS plot (Fig. 2) based on Fst distances shows a close distance of our Yakut samples with those studied by Pakendorf et al. [3], but a larger distance is shown with the Yakut population sampled from the settlement of Cheriktei, located 150 km north-east of Yakutsk [13]. This paper have followed and accepted the conditions required for the publication of population genetic papers in the journal [20]. Acknowledgements Our appreciation goes to the populations of the Sakha Republic for their participation, and in particular to Olga Melnichouk. We thank Mark A. Jobling for critical advices, E. Guitard and N. Brucato for providing technical support and Daniel Montagnon for his collected data from the literature. This work was supported by the GIP-ANR (French National Research Agency) JC05_62756 and by EGIDE program. This work was done in collaboration with the MAFSO (French Archaeological Mission in Oriental Siberia). We thank reviewers for their valuable comments to improve this manuscript.
Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2010.01.018.
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