Legal Medicine 16 (2014) 390–395

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Announcement of Population Data

Mitochondrial DNA variation in Tajiks living in Tajikistan Igor V. Ovchinnikov ⇑, Mathew J. Malek, Kenneth Drees, Olga I. Kholina Department of Biology and Forensic Science Program, University of North Dakota, Grand Forks, ND 58202, USA

a r t i c l e

i n f o

Article history: Received 23 March 2014 Received in revised form 31 July 2014 Accepted 31 July 2014 Available online 10 August 2014 Keywords: Mitochondrial DNA Control region Tajiks Tajikistan Central Asia

a b s t r a c t This study aimed to characterize mtDNA control region (positions 16,024–576) of unrelated Tajiks living in Tajikistan. DNA was isolated from saliva specimens stored on FTA cards. The mtDNA fragments were amplified and directly sequenced in forward and reverse directions. Haplogroups were determined using HaploGrep and the diagnostic polymorphisms in the coding region of mtDNA. The Tajik mtDNA pool was characterized by substantial admixture of western and eastern Eurasian haplogroups, 62.6% and 26.4% sequences, respectively. It also contained 9.9% of South Asian and 1.1% of African haplotypes. The Tajik mtDNA sequences belonged to 90 different haplotypes defined by 148 transitions and 13 transversions in 156 of 1122 nucleotide sites. The Tajik mtDNA pool demonstrated the high genetic variation with genetic diversity of 0.999 ± 0.002, nucleotide diversity of 0.014 ± 0.007, and the mean number of pairwise nucleotide differences of 15.38 ± 6.93. The random match probability and the power of discrimination were 0.0112 and 0.9888, respectively. Ethno-territorial groups of Tajiks demonstrated significant genetic differentiation with 2.67% of the genetic variance explained by differences between subpopulations. This study provides the insight into the mtDNA pool of Tajiks living in Tajikistan. The data should be taken into account in forensic identifications based on mtDNA. Ó 2014 Elsevier Ireland Ltd. All rights reserved.

Population: Tajikistan is a country in the southeastern part of Central Asia, a vast geographic region in the Eurasian heartland bordered by the Caspian Sea on the West and the Gobi desert on the East. The chronology of the occupation of this region by anatomically modern humans is not well understood. It appears that a major demographic growth of modern humans in Central Asia began shortly after 50,000 years ago, resulting in migrations that contributed to the occupation of Europe, South Asia, and the Americas [1–3]. During the antiquity and the medieval times, Central Asia became one of the world’s main centers where civilization and culture had formed and flourished. Early urbanization and the development of agriculture and farming in the region provided favorable conditions for transmission and exchange of artifacts, innovations, technologies and ideas along the Silk Road which had connected the Near East and Europe with East Asia for centuries. Political processes including births and collapses of states as well as military invasions and conquests over several millennia led to short- and long-term migrations of people across Eurasia [4,5]. All these historic events must have inevitably reshaped the genetics of people ⇑ Corresponding author. Address: Department of Biology, University of North Dakota, 10 Cornell St., Starcher Hall, Stop 9019, Grand Forks, ND 58202, USA. Tel.: +1 701 777 4471; fax: +1 701 777 2623. E-mail address: [email protected] (I.V. Ovchinnikov). http://dx.doi.org/10.1016/j.legalmed.2014.07.009 1344-6223/Ó 2014 Elsevier Ireland Ltd. All rights reserved.

living in Central Asia and influenced the genetic landscape in the entire Eurasia. However, despite the important role of Central Asia in the history of humankind, our knowledge about the genetic variation in numerous ethnic groups that inhabit different parts of Central Asia remains incomplete. The first study of mitochondrial DNA (mtDNA) of people inhabiting Central Asia was carried out on the samples of Uighurs, Kazakhs, and Kyrghyz from eastern Kazakhstan and Kyrghyzstan. It discovered the highest mtDNA diversity in the mtDNA hypervariable region I (HVI) among all other populations in Eurasia. Such a level of diversity was mostly explained by extensive admixture between the western Eurasian and eastern Eurasian mtDNA lineages [6]. It was found that the populations inhabiting Central Asia also contained a low percentage of the mtDNA lineages of south Asian and African origin [7,8]. Further genetic studies demonstrated three characteristics of the Central Asian populations, including similar mtDNA diversity in the highland and lowland populations and in the pastoral and farmer populations as well as a higher migration rate among females than males [9,10]. While some human populations living in Central Asia have been intensively sampled and analyzed [7,11], other ethnic groups remain underrepresented in genetic studies. Tajikistan provides one of such examples. A limited number of DNA samples from Tajikistan have been collected for the large-scale study of the mtDNA variation in Central Asia and considered together with other

I.V. Ovchinnikov et al. / Legal Medicine 16 (2014) 390–395

populations. These samples included three groups of 31, 35, and 32 Tajiks from the Gharm district in Region of Republican Subordination [12] as well as 20 Yagnobi and 44 Shugnans, two small ethnic groups living in north Tajikistan and the Pamir Mountains, respectively [8,9,13]. The mtDNA variation in Tajiks living in Tajikistan was only described for a small sample of 44 Tajiks from an unspecified location in Tajikistan [14]. It was shown that the Tajiks have a number of western Eurasian mtDNA haplogroups typical for South Asia such as W, N2, R0a, R2, HV0a, HV2, U1, U2b, and U7a. The proportion of eastern Eurasian haplogroups in that Tajik sample was 31.8%. The 44 Tajiks from Tajikistan demonstrated the highest diversity values in mtDNA hypervariable regions HVI and HVII among 18 autochthonous populations of northern, central, eastern, and southwestern Asia [14]. The mtDNA diversity in Tajik communities living in neighboring Uzbekistan was more thoroughly studied. The low but statistically significant genetic variance (1.97%; P < 0.001) among Tajik subpopulations collected from five locations in Uzbekistan was explained by an endogamy in which males get married with females from the same large family or living in the same village [15]. Residents living within a single location in Uzbekistan with a direct ancestry to Tajikistan had a higher mean pairwise difference (13 for the entire mtDNA control region) than other populations in Uzbekistan due to the presence of highly divergent lineages within the Tajiks. This Tajik population harbored almost

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equal proportions of the western Eurasian and eastern Eurasian mtDNA haplotypes [7]. Additional small groups of Tajiks living outside Tajikistan were also included to the comparison of demographic parameters of sedentary and nomadic populations (24 Tajiks from Boukhara in Uzbekistan) and the study of ethnic groups living in the Afghanistan provinces including Badakhshan (37 samples), Balkh (57 samples), Samangan (16 samples), and Takhar (37 samples) [16,17]. Our saliva specimens were collected from 91 unrelated adult Tajiks in 1997. The DNA samples came from all four administrative regions of Tajikistan, including Sughd Province (24 samples), Region of Republican Subordination (RRS; 31 samples), Khatlon Province (15 samples), and Gorno-Badakhshan (Pamir) Province (10 samples). A small set of samples was received from Tajiks living in Uzbekistan (11 samples) (Fig. 1). The main aim of this study is to characterize the genetic variation in the mtDNA control region in the Tajik population sampled across Tajikistan. Informed consent and information about birthplace were obtained from all persons. All analyses were performed anonymously. The study and procedures were approved by the Institutional Review Board at the University of North Dakota (Protocol No. IRB- IRB-201307009). DNA extraction: The saliva specimens were transferred to the FTA cards. Total DNA was extracted from the FTA disks with a diameter of 2 mm using the FTA purification solution (Whatman).

Fig. 1. Geographic map of Central Asia (top) and the map of Tajikistan indicating four administrative provinces (bottom).

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PCR: Due to the degraded nature of the archaic DNA samples, an approach based on the primary and secondary nested PCR was used. For the analysis of the mtDNA control region sequences, the primary PCRs were performed to amplify the mtDNA fragment between positions 15,350 and 815. Primary PCR products were used as the templates for the nested PCRs with the secondary primers that flanked the inner regions between positions 15,897– 16,526 and 16,514–786, respectively [18]. The combinations of primers for primary and secondary PCRs according to [18], were also used for the analysis of polymorphisms in the mtDNA coding region in order to validate the main haplogroups. PCR amplifications were performed in 25 ll of the PCR mixture according to the manufacturer’s recommendations for GoTaq DNA polymerase (Promega). Sequencing: The PCR fragments were purified using the DNA Clean and Concentrator-5 columns (Zymo Research) and sequenced in both directions using the Big-Dye termination sequencing kit (Life Technologies) on a 3100 Genetic Analyzer (Applied Biosystems). Each nucleotide was sequenced twice. The 50 and 30 DNA sequences near the poly-C stretches (16,184– 16,193 and 309–315) leading to the displacement of the DNA polymerase were sequenced twice as well. Analysis of the data: Visual inspection of the mtDNA sequences using BioEdit [19], and alignment of the mtDNA sequences utilizing MEGA5 [20] were performed by two researchers independently. The combined mtDNA sequences included the entire control region between positions 16,024–576. The mtDNA haplogroups were determined using HaploGrep, a web-based java application for determination of mtDNA haplogroups updated to Phylotree Build 16 [21,22], and the diagnostic polymorphisms of the main haplogroups identified in the coding region (Supplementary material). The geographic origin of mtDNA haplogroups was determined according to [8,23–26]. Forensically important population values, such as number of transitions, transversions, and polymorphic sites, genetic and nucleotide diversity, pairwise nucleotide differences were determined using Arlequin 3.5 [27]. The random match probability and the power of discrimination were counted according to [28]. Analysis of molecular variance (AMOVA) in Arlequin 3.5 was used to evaluate the Tajik population structure. The following parameters were applied to the AMOVA test including 1000 permutations, a transition/transversion ratio of 10:1, an alpha value of 0.3, and the Kimura 2 model of nucleotide evolution. Results: The control region sequence profiles and assigned mtDNA haplogroups along with their regional distribution in Tajikistan are shown in Table 1. The 91 Tajik mtDNA sequences belonged to 90 different haplotypes based on the control region sequences that constitute 98.9% of the population sample size. One haplotype with motif ‘‘16299G, 16519C, 150T, 263G, 309.1C, 315.1C’’ was found twice while all other mtDNA sequences were unique in the Tajik sample (Table 1). The low proportion of shared haplotypes corresponded to the high genetic diversity of 0.999 ± 0.002. The random match probability and the power of discrimination were counted to be 0.0112 and 0.9888, respectively. The mtDNA haplotypes found in the Tajiks were defined by 148 transitions and 13 transversions in 156 of 1122 sites. Both types of mutations (transitions and transversions) were found in four positions, 16,129, 16,318, 195, and 295 including two transversions at position 16,318. Parallel mutations were already observed at all these positions [29]. To estimate nucleotide diversity and pairwise nucleotide difference, only transitions and transversions were taken into account. The Tajik sample harbored the nucleotide diversity of 0.014 ± 0.007 and the mean number of pairwise nucleotide differences in the entire control region of 15.38 ± 6.93. Some of the Tajik mtDNA sequences had insertions of a cytosine after positions 16,193 (one cytosine in 6 sequences, two cytosines

in 1 sequence), 44 (one cytosine in one sequence), 309 (one cytosine in 38 sequences, two cytosines in 19 sequences), and 315 (one cytosine in 86 sequences and three cytosines in 2 sequences) as well as a thymine insertion after positions 16,192 (one sequence) and 60 (one sequence). The insertion of GCAC after position 514 and the insertions of AC and ACAC after position 524 were only detected in one sequence each. Deletions of a cytosine at position 459 and an adenine at positions 248 and 249 were observed in two, three and two haplotypes, respectively. The rare 105–110 deletion of segment CGGAGC and the 523–524 deletion of AC were correspondingly described in one and 13 sequences (Table 1). Tajik mtDNA sequences are distributed unevenly between the haplogroups of different origins; 62.6% (57 sequences) belong to the western Eurasian haplogroups, 26.4% (24 sequences) to the eastern Eurasian haplogroups, 9.9% (9 sequences) to the south Asian haplogroups, and 1.1% (1 sequence) to the North African haplogroup. The western Eurasian component is represented by haplogroups HV⁄, HV0, H, J, K, T, and U of the macrohaplogroup R, and haplogroups I and W of the macrohaplogroup N [22]. Haplogroup H is predominant in the Tajik sample with twenty-one mtDNA sequences (23.1%). Among the H sub-clades, H2 displays the highest percentage (4 sequences; 4.4%). A few sequences were assigned to other branches of H such as H1 (1 sequence; 1.1%), H5 (1 sequence; 1.1%), H6 (1 sequence; 1.1%), H8 (1 sequence; 1.1%), H15 (2 sequences; 2.2%), H22 (1 sequence; 1.1%), H39 (3 sequences; 3.3%), H41 (1 sequence; 1.1%), and H57 (1 sequence; 1.1%). We were unable to arrange subhaplogroups for five H sequences (5.5%). Four (4.4%) and one (1.1%) Tajik mtDNA sequences were assigned to HV⁄ and HV0, respectively. Haplogroup U is the second most frequent in the Tajik population (14 sequences; 15.4%) and includes 13 samples belonging to the western Eurasian subhaplogroups U2e1’2’3 (3 sequences; 3.3%), U3b3 (1 sequence; 1.1%), U4 (3 sequences; 3.3%), U5a (2 sequences; 2.2%), and U7a (4 sequences; 4.4%), and one sample to the Indian subhaplogroup U2b2 (1.1%). Haplogroup K, a branch of haplogroup U8, was identified in four Tajik samples (4.4%). Haplogroup T accounted for eight mtDNA sequences (8.8%) that were equally distributed between the T1a1’3 and T2b branches. Other western Eurasian lineages in the Tajiks were assigned to haplogroups I (1 sequence; 1.1%), J1 (2 sequences; 2.2%), and W1 (3 sequences; 3.3%). The eastern Eurasian component is represented by haplogroups M8, M10, C, Z, D, G of the macrohaplogroup M, haplogroups A and Y1 of the macrohaplogroup N, and haplogroup B of the macrohaplogroup R [22]. There is no predominant mtDNA haplogroup in the eastern Eurasian pool. Three Tajik mtDNA sequences (3.3%) fell into haplogroup A. Five mtDNA samples were assigned to haplogroup C (5.5%), specifically to different lineages of C4a. Six mtDNA sequences belonged to haplogroup D (6.6%) specifically to subhaplogroup D4. Three mtDNA sequences of haplogroup G (3.3%) were divided among subhaplogroups G1 (1 sequence) and G2 (2 sequences). Other eastern Eurasian haplogroups such as Y1 (2.2%), B5b2a1b (1.1%), Z3a (1.1%), Z3a/Z3b (1.1%), M8a2’3 (1.1%), and M10a2 (1.1%) were represented by one or two mtDNA sequences. The south Asian component is comprised of nine mtDNA sequences (9.9%) belonging to the macrohaplogroups M and R [22]. Two sequences were assigned to main branches of M including M3a1 (1.1%) and M30 (1.1%). Macrohaplogroup R was represented by six mtDNA sequences (6.6%) belonging to R0a (1 sample), R1 (2 samples), R2 (1 sample), and R5a (2 samples). One Tajik mtDNA sequence (1.1%) belonged to aforementioned U2b2, a south Asian autochthonous subhaplogroup of the macrohaplogroup R [25]. One Tajik mtDNA sequence (1.1%) was assigned to subhaplogroup X2j. X2j is considered to be of North African origin [23].

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I.V. Ovchinnikov et al. / Legal Medicine 16 (2014) 390–395 Table 1 The individual Tajik haplotypes and their regional distribution in Tajikistan. Sample

Region

Haplotype

Coding polymorphisms

Hg

91

Sughd

663G, 8794T

A

57 89 52

Sughd Sughd Sughd

663G, 8794T 663G, 8794T 9 bp 8281–8289del

A A B5b2a1b

18 29 14 23

Khatlon RRS Sughd RRS

13263G 13263G 13263G 13263G

C4a1 C4a1 C4a2 C4a2

75 47 42 30 43 20 53 15 101 56 69 87 5 97 4 17 46 24 54 8 55 9 76 77 65 82 73 28 31 67 21 59 64 86 25 58 96 95 61 35 33 37 81 34 2 85 62 83 92

Pamir Sughd RRS Sughd Sughd RRS RRS Pamir Sughd RRS Sughd Sughd Sughd Uzbekistan Uzbekistan RRS RRS Sughd Khatlon RRS Sughd RRS Khatlon Pamir RRS Pamir Sughd Khatlon Pamir Pamir Khatlon Sughd Khatlon Sughd Khatlon Sughd Uzbekistan Pamir Pamir Sughd RRS Pamir Uzbekistan Pamir RRS Sughd Uzbekistan Khatlon Sughd

16189, 16193.1C, 16223, 16290, 16319, 16362, 97T, 105-110del(CGGAGC), 150, 152, 235, 263, 315.1C, 523del, 524del 16223, 16248, 16290, 16319, 16362, 73, 152, 182, 235, 263, 315.1C 16125, 16223, 16290, 16311, 16319, 16362, 73, 152, 235, 263, 315.1C, 438, 523del, 524del, 576 16111G, 16140A, 16182C, 16183C, 16189, 16234, 16243, 73, 131, 204, 207, 263, 309.1C, 309.2C, 315.1C, 523del, 524del 16093, 16129, 16223, 16298, 16327, 16519, 73, 195, 248del, 263, 315.1C, 489 16093, 16129, 16223, 16298, 16327, 16519, 73, 152, 263, 309.1C, 315.1C, 489 16167, 16171, 16223, 16298, 16327, 16344, 16357, 16519, 47, 73, 249del, 263, 309.1C, 315.1C, 489 16167, 16171, 16223, 16298, 16327, 16344, 16357, 16519, 47, 73, 150, 152, 248del, 263, 309.1C, 315.1C, 489 16223, 16239, 16327, 16357, 73, 207, 248del, 263, 309.1C, 315.1C, 489 16223, 16362, 73, 263, 309.1C, 315.1C, 489 16223, 16245, 16362, 16368, 73, 263, 315.1C, 489 16223, 16274, 16362, 73, 196, 263, 298, 309.1C, 309.2C, 315.1C, 489 16223, 16274, 16362, 73, 196, 263, 298, 309.1C, 315.1C, 489 16192, 16223, 73, 195, 263, 309.1C, 315.1C, 489 16223, 16249, 16362, 73, 263, 315.1C, 489 16223, 16325, 16362, 73, 150, 263, 315.1C, 489 16223, 16227, 16278, 16362, 16519, 73, 152, 263, 315.1C, 489, 523del, 524del 16169, 16189, 16223, 16262, 16278, 16294, 16318, 16526, 73, 152, 185, 263, 309.1C, 315.1C, 489 16534, 150, 263, 309.1C, 309.2C, 315.1C 16193, 16311, 263, 309.1C, 309.2C, 480 16309, 146, 263, 309.1C, 309.2C, 315.1C, 487 16092, 263, 309.1C, 315.1C 16298, 72, 263, 309.1C, 315.1C 16360, 16519, 152, 263, 309.1C, 315.1C 16153, 16311, 16385, 151, 152, 263, 309.1C, 309.2C, 315.1C 263, 309.1C, 315.1C 16526, 263, 309.1C, 315.1C 16051, 16092, 16519, 57.1C, 263, 309.1C, 315.1C 16183C, 16189, 16193.1C, 16311, 16356, 125, 127, 263, 309.1, 315.1C 16354, 263, 315.1C 16354, 263, 315.1C 16292, 16354, 263, 315.1C 16354, 263, 309.1C, 309.2C, 315.1C 16304, 72, 263, 309.1C, 315.1C, 456, 523del, 524del 16362, 16482, 239, 263, 309.1C, 315.1C 16288, 16362, 146, 195, 263, 309.1C, 309.2C, 315.1C 16366, 55, 57, 263, 309.1C, 309.2C, 315.1C 16124, 16184, 44.1C, 55, 57, 146, 263, 309.1C, 309.2C, 315.1C 16227, 16325, 263, 309.1C, 309.2C, 315.1C 16299, 16519, 150, 263, 309.1C, 315.1C 16299, 16519, 150, 263, 309.1C, 315.1C 16299, 150, 263, 309.1C, 315.1C 262, 263, 309.1C, 315.1C 16172, 16519, 64, 146, 253, 263, 309.1C, 309.2C, 315.1C 16095, 16129, 16223, 16278, 73, 199, 204, 250, 263, 315.1C, 459del, 524.1A, 524.2C, 524.3A, 524.4C, 574C 16069, 16126, 16145, 16172, 16222, 16261, 73, 146, 242, 263, 295, 309.1C, 309.2C, 315.1C, 462, 489 16069, 16126, 16145, 73, 263, 271, 295, 315.1C, 459del, 462, 489, 523del, 524del 16224, 16311, 16519, 73, 263, 315.1C 16224, 16311, 16519, 73, 263, 280G, 315.1C, 497 16224, 16311, 16519, 73, 263, 280G, 315.1C, 497, 524.1A, 524.2C 16093, 16129, 16224, 16311, 73, 150, 263, 315.1C, 497 16126, 16223, 16519, 73, 204, 263, 315.1C, 482, 489 16184, 16223, 16298, 16319, 73, 263, 315.1C, 489 16066, 16223, 16311, 16519, 73, 152, 200, 263, 315.1C, 489, 574C 16184, 16186, 16223, 16234, 73, 195A, 263, 315.1C, 489, 523del, 524del 16126, 16362, 16519, 60.1T, 64, 263, 309.1C, 309.2C 16174, 16311, 16355, 16519, 73, 263, 295A

C4a4a D4 D4c2a D4g2a D4g2a D4k D4a3 G1a1 G2a G2a3 HV⁄ HV⁄ HV⁄ HV⁄ HV0 H H H H H H1b H2a1 H2a1 H2a1 H2a1 H5 H6 H8 H15 H15a1b H22 H39 H39 H39 H41a H57 I5b1 J1b1a1 J1b1b K K K K1a M3a1 M8a2’3 M10a2 M30 R0a R1a

93

RRS

27

Khatlon

16189, 16192.1T, 16223, 16311, 73, 150, 241, 263, 309.1C, 315.1C, 315.2C, 315.3C, 385, 514.1G, 514.2C, 514.3A, 514.4C 16071, 16362, 16519, 73, 152, 263, 309.1C, 315.1C

66

Uzbekistan

16093, 16266T, 16304, 16519, 16524, 73, 93, 263, 315.1C, 523del, 524del

44

RRS

16266T, 16304, 16311, 16356, 73, 152, 263, 315.1C, 523del, 524del

36 63 74 80

RRS Sughd RRS Khatlon

16126, 16093, 16126, 16126,

13263G 5178A, 14783C 5178A 5178A 5178A 5178A 5178A 4833G 4833G 4833G 7028T, 14766C 7028T, 14766C 7028T, 14766C 7028T, 14766C 4580G 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C 7028C, 5460A 7028C 4529T 12612G 12612G 9055A 9055A 9055A 9055A 14783C 14783C 14783C 14783C 13188T 14766T, 11719A, 12705C 1095C, 11122A, 15940C 14766T, 11719A, 12705C 14766T, 11719A, 12705C 14766T, 11719A, 12705C 10463C 10463C 10463C 10463C

16163, 16126, 16163, 16163,

16186, 16163, 16186, 16186,

16189, 16186, 16189, 16189,

16294, 16189, 16294, 16284,

16519, 16264, 16519, 16294,

73, 152, 195, 263, 309.1C, 315.1C 16294, 16311, 16519, 73, 152, 195, 263, 309.1C, 315.1C 73, 152, 195, 263, 309.1C, 309.2C, 315.1C 16362, 16519, 73, 152, 195, 263, 309.1C, 315.1C

R1b1 R2 R5a1 R5a2 T1a1’3 T1a1’3 T1a1’3 T1a1’3

(continued on next page)

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Table 1 (continued) Sample

Region

Haplotype

Coding polymorphisms

Hg

6 7 38 45 32 68 78 41

RRS RRS RRS RRS RRS Khatlon Khatlon RRS

10463C 10463C 10463C 10463C 1811G, 12308G 1811G, 12308G 1811G, 12308G 1811G, 12308G

T2b T2b T2b T2b U2b2 U2e1’2’3 U2e1’2’3 U2e1’2’3

72 49 70 90 94 60 10 50 12 39 1 84 88 40

Uzbekistan RRS RRS Uzbekistan Uzbekistan Sughd Uzbekistan Khatlon RRS Khatlon RRS RRS RRS Khatlon

4188G 4646C 4646C 4646C 14793G 14793G 10142T, 10142T, 10142T, 10142T, 8994A 8994A 8994A 6371T

U3b3 U4 U4b1a1a1 U4b3 U5a1 U5a2a U7a U7a U7a U7a W1 W1 W1 X2j

71 100 51 3

Uzbekistan RRS RRS Sughd

16126, 16145, 16294, 16296, 16304, 16519, 73, 263, 315.1C 16126, 16192, 16217, 16294, 16296, 16304, 16311, 16519, 41, 73, 263, 309.1C, 309.2C, 315.1C, 319 16126, 16145, 16294, 16296, 16304, 16519, 73, 263, 315.1C 16126, 16201, 16294, 16296, 16304, 16519, 73, 152, 263, 315.1C 16051, 16209, 16239, 16311, 16352, 16353, 73, 146, 152, 153, 195, 234, 263, 309.1C, 315.1C 16051, 16129C, 16183C, 16193.1C, 16362, 16519, 73, 217, 228, 263, 309.1C, 309.2C, 315.1C, 340, 508 16051, 16129C, 16183C, 16189, 16193.1C, 16362, 16519, 73, 152, 217, 263, 309.1C, 315.1C, 508 16051, 16129C, 16183C, 16193.1C, 16278, 16362, 16519, 73, 217, 228, 263, 310, 315.1C, 315.2C, 315.3C, 508 16168, 16183C, 16189, 16193.1C, 16193.2C, 16311, 16343, 16519, 73, 150, 263, 315.1C 16250, 16356, 16519, 73, 195, 263, 309.1C, 315.1C, 499 16356, 16362, 16519, 73, 195, 263, 315.1C, 499 16356, 16519, 73, 195, 215, 263, 309.1C, 315.1C, 499 16129, 16180, 16192, 16218, 16256, 16270, 16291, 16399, 73, 263, 315.1C 16114A, 16192, 16256, 16270, 16294, 16519, 73, 263, 315.1C 16129, 16146, 16318T, 16519, 73, 151, 152, 263, 309.1C, 315.1C, 523del, 524del 16129, 16249, 16309, 16318T, 16519, 73, 151, 152, 263, 309.1C, 309.2C, 315.1C, 523del, 524del 16309, 16318C, 16519, 73, 151, 152, 263, 309.1C, 315.1C, 523del, 524del 16309, 16318C, 16519, 73, 151, 152, 263, 309.1C, 315.1C, 523del, 524del 16223, 16284, 16519, 73, 119, 195, 204, 207, 263, 309.1C, 315.1C 16223, 16284, 16519, 73, 119, 189, 195, 207, 263, 309.1C, 315.1C 16104, 16223, 16284, 16519, 73, 119, 189, 195, 204, 207, 263, 315.1C 16162, 16179, 16183C, 16189, 16193.1C, 16223, 16278, 16357, 16519, 73, 153, 195, 225, 263, 309.1C, 309.2C, 315.1C 16126, 16231, 16266, 16519, 73, 146, 263, 309.1C, 315.1C 16093,16126, 16231, 16266, 16519, 73, 146, 263, 309.1C, 315.1C 16150, 16185, 16223, 16260, 16298, 16311, 16519, 73, 146, 152, 207, 263, 315.1C, 489 16185, 16223, 16234, 16260, 16298, 16311, 16519, 73, 152, 207, 249del, 263, 309.1C, 315.1C, 489

5417A 5417A 8584A 8584A

11467G 11467G 11467G 11467G

Y1 Y1 Z3a/Z3b Z3a

Haplotypes arranged according to assigned haplogroups. Transitions are shown by the nucleotide site coordinates only. The 16266 C ? T transition in the samples 44 and 66 specifies a derived nucleotide because a back mutation is proposed in haplogroup R5a. Transversions also include a derived nucleotide in a mutated position. Deletions are indicated by the coordinates of a deleted nucleotide or a short sequence followed by the abbreviation del. Insertions are displayed by the site coordinate immediately prior to the insertion followed by a point with sequential number and inserted nucleotide. Hg, haplogroup.

To demonstrate that the population structure exists in Tajikistan, we carried out the analysis of molecular variance (AMOVA) for four ethno-territorial groups corresponding to the administrative provinces [30,31]. The AMOVA test demonstrated that 2.67% (P < 0.005) of the genetic variance is defined by differences between ethno-territorial subpopulations and 97.33% of the genetic variance was within these subpopulations. These results showed that the Tajiks in Tajikistan have significant genetic differentiation. This study is specifically focused on the mtDNA diversity in Tajiks living in Tajikistan. The high mtDNA diversity and the significant genetic differentiation occur in the Tajiks. The obtained results are necessary to better understand the challenges of forensic identifications and interpretations in the southeastern part of Central Asia. Acknowledgements This study was supported by the UND faculty start-up awards, the North Dakota EPSCoR award (Project UND0015613), and the ND EPSCoR through NSF Grant #EPS-814442. We thank Zumrat Davlyatbekova for collecting saliva samples in Tajikistan, and Katelyn Kjelland for critical reading of the manuscript. We express gratitude to all volunteers who contributed their saliva specimens to this study. We thank two anonymous reviewers for providing constructive comments that improved this paper and the Editor for the recommendations that helped to revise the manuscript. The authors declare that no conflict of interest occurs. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.legalmed.2014. 07.009.

References [1] Edmonds CA, Lillie AS, Cavalli-Sforza LL. Mutations arising in the wave front of an expanding population. Proc Natl Acad Sci USA 2004;101:975–9. [2] Mukherjee N, Nebel A, Oppenheim A, Majumder PP. High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India. J Genet 2001;80:125–35. [3] Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, et al. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci USA 2001;98:10244–9. [4] Frye RN. The heritage of Central Asia. From antiquity to the Turkish expansion. Princeton: Markus Wiener Publishers; 1996. [5] Baumer C. The history of Central Asia. The age of the steppe warriors. London – New York: I.B. Tauris; 2012. [6] Comas D, Calafell F, Mateu E, Perez-Lezaun A, Bosch E, Martnez-Arias R, et al. Trading genes along the silk road: mtDNA sequences and the origin of Central Asian populations. Am J Hum Genet 1998;63:1824–38. [7] Irwin JA, Ikramov A, Saunier J, Bodner M, Amori S, Rock A, et al. The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns. Int J Legal Med 2010;124:195–204. [8] Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R, et al. Where West meets East: the complex mtDNA landscape of the Southwest and Central Asian corridor. Am J Hum Genet 2004;74:827–45. [9] Chaix R, Quintana-Murci L, Hegay T, Hammer MF, Mobasher Z, Austerlitz F, et al. From social to genetic structures in Central Asia. Curr Biol 2007;17:43–8. [10] Perez-Lezaun A, Calafell F, Comas D, Mateu E, Bosch E, Martinez-Arias R, et al. Sex-specific migration patterns in Central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA. Am J Hum Genet 1999;65:208–19. [11] Rakha A, Shin K-J, Yoon JA, Kim NY, Siddique MH, Yang IS, et al. Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 2011;125:841–8. [12] Segurel L, Martinez-Cruz B, Quintana-Murci L, Balaresque P, Georges M, Hegay T, et al. Sex-specific genetic structure and social organization in Central Asia: insights from a multi-locus study. PLoS Genet 2008;4:e1000200. [13] Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, Calafell F, et al. Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet 2004;12:495–504. [14] Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, et al. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 2007;81:1025–41. [15] Heyer E, Balaresque P, Jobling MA, Quintana-Murci L, Chaix R, Segurel L, et al. Genetic diversity and the emergence of ethnic groups in Central Asia. BMC Genet 2009;10:49.

I.V. Ovchinnikov et al. / Legal Medicine 16 (2014) 390–395 [16] Aime C, Laval G, Patin E, Verdu P, Segurel L, Chaix R, et al. Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming. Mol Biol Evol 2013;30:2629–44. [17] Cristofaro JD, Pennarum E, Mazieres S, Myres NM, Lin AA, Temori SA, et al. Afghan Hindu Kush: where Eurasian sub-continent gene flow converge. PLoS ONE 2013;10:e76748. [18] Taylor RW, Taylor GA, Durham SE, Turnbull DM. The determination of complete human mitochondrial DNA sequences in single cells: implications for the study of somatic mitochondrial DNA point mutations. Nucleic Acids Res 2001;29:e74. [19] Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999;41:95–8. [20] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–9. [21] Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, et al. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat 2011;32:25–32. [22] van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 2008;30:e386–94. [23] Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, et al. The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. Am J Hum Genet 2012;90:347–55.

395

[24] Loogvali E-L, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, et al. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol 2004;21:2012–21. [25] Palanichamy MG, Sun Ch, Agrawal S, Bandelt H-Ju, Kong Q-P, Khan F, et al. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 2004;75:966–78. [26] Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, Fuku N, et al. Mitochondrial genome variation in Eastern Asia and the peopling of Japan. Genome Res 2004;14:1832–50. [27] Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol 2010;10:564–7. [28] Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 1991;48:370–82. [29] Ruiz-Pesini E, Lott M, Procaccio V, Poole JC, Brandon MC, Mishmar D, et al. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 2007;35:D823–8. [30] Breu T, Hurni H. The Tajik Pamirs. Challenges of sustainable development in an isolated mountain region. Berne: Centre for Development and Environment, University of Berne; 2003. [31] Dubovitskiy V. The aspects of ethnic and confessional situation in the Republic of Tajikistan. Moscow: The Centre of Geopolitical Expertise; 2003.

Mitochondrial DNA variation in Tajiks living in Tajikistan.

This study aimed to characterize mtDNA control region (positions 16,024-576) of unrelated Tajiks living in Tajikistan. DNA was isolated from saliva sp...
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