Mitochondrial genomes (N = 2074) from the Central Eurasia for comparative analyses.

(XLSX)</p

Map of Jetisuu and the sampling sites.

1. Engbekshi Kazak; 2. Talghar; 3. Ile; 4. Almati; 5. Karasay; 6. Jambil; 7. Balkash; 8. Karatal; 9. Köksuu; 10. Taldikorghan; 11. Eskeldi; 12. Kerbulak; 13. Panfilov; 14. Kegen; 15. Rayimbek.</p

Schematic phylogenetic tree for the haplotype T2b.

Note: Kaz: Kazak; Hu: Hungarian; Rus: Russian; Tat: Tatar; Uyg: Uyghur; SU006 and SH105 are Jetisuu sequences; EU007872 and JQ798066 are sequences from the Phylotree Build 17.0 [46].</p

Information on whole mitochondrial genome sequences which used for comparison.

Information on whole mitochondrial genome sequences which used for comparison.</p

Information on the Jetisuu samples genotyped via the GenoChip microarray (N = 80).

(XLSX)</p

Sample ID List of the mitochondrial genomes (N = 1155) used for the second round mtGenome analysis.

Ethnicity and GenBank ID information of the samples can be found in S2–S4 Tables. (XLSX)</p

Geographic distribution of the human populations and the mtDNA control region haplogroup frequency based PCA.

Notes on Fig 2: Jeti_AL [Alban (N = 35)], Jeti_JA [Jalayir (N = 76)], Jeti_SH [Shapirashti (N = 59)], and Jeti_SU [Suan (N = 26] are the four Kazak populations from Jetisuu, Kazakhstan; Jeti_KZ [Four populations from Jetisuu combined, plus 4 individuals with ambiguous clan identity (N = 200)]; Altaian [Altaians (N = 490) from the Altay Republic, Russia] [25]; AltKaz_a [Kazaks (N = 237) from the Altay Republic, Russia] [12]; AltKaz_b [Kazaks (N = 98) from the Altay Republic, Russia] [15]; Barghut [Barghuts (N = 149) from Hulunbuir, Inner Mongolia, China][15]; IM_Mon [Mongols (N = 48) from Inner Mongolia, China] [26]; KZ_Uyg [Uyghurs (N = 55) from Penjim, Panfilov, Almati, Kazakhstan], KG_KirT [Kirghiz (N = 48) from Talas, Kirghizstan], KG_KirS [Kirghiz (N = 47) from Sari-Tash, Kirghizstan], KZ_Kaz [Kazaks (N = 55) from Kegen, Almati, Kazakhstan] [13]; Tibetan [Tibetans (N = 6109) from across Tibet, China] [27]; XJ_Hui [Dungans (Hui) (N = 45)], XJ_Mon_a [Mongols (N = 49)], XJ_Kaz_a [Kazaks (N = 53)], XJ_Uzb [Uzbeks (N = 58)], XJ_Uyg [Uyghurs (N = 47)], and XJ_Han [Han Chinese (N = 47)] [All six populations from Xinjinag, China] [17]; XJ_Kaz_b [Kazaks (N = 151) from several locations in Xinjiang, China, including b.1: Altay, b.2: Ile (Kulja), b.3: Buratala, and b.4: Urumqi, Sanji, and Kumul] [16]; XJ_Mon_b [Mongols (N = 106) from Xinjiang, China, but exact sampling site is unknown] [28].</p

Schematic phylogenetic tree for the haplogroup A mitochondrial genomes.

Note: Alt: Altaian; Uyg: Uyghur; Kir: Kirghiz; Hu: Hungarian.</p

Geographic distribution of the human populations included in the analysis of mitochondrial genomes from Central Eurasia and the mtGenome pairwise F_ST value based PCA.

Notes on Fig 4: Populations having more than 30 sequences were included in the PCA analysis, and thus the dataset contained 1954 sequences from previous studies (Table 3) and 120 Kazak mtGenome sequences from Jetisuu. Sample IDs of the sequences were given in S7 Table. The pseudo-mtGenomes (N = 80) were excluded from the PCA analysis. Kazak [Kazaks from Jetisuu, Kazakhstan, i.e., Jeti_Kaz on the map]; Alt_Kaz [Kazaks from the Altay Republic, Russia]; Buryat [Buryats from the Buryat Republic, Russia]; Hungarian [Hungarians from Hungary]; Kirghiz [Kirghiz from Xinjiang, China (TJ_Kir) and Kirghiz from Tajikistan (TJ_Kir)]; Russian [Russians from Russia]; Sherpa [Sherpas from Zhangmu, Tibet, China]; Tajik [Tajiks from Xinjiang, China (XJ_Taj) and Tajiks from Tajikistan (TJ_Taj)]; Tatar [Tatars from the Tatar Republic, Russia]; Tibetan [Ethnic Tibetans and other ethnic groups from Tibet, China (Tib_1–5)]; Tuba [Tubas from the Tuba/Tuva Republic, Russia]; Uyghur [Uyghurs from Xinjiang, China (Uyg_1–2)].</p

Schematic phylogenetic tree for the haplogroup C4a1 mitochondrial genomes.

Note: Alt: Altaian; Bur: Buryat; Uyg: Uyghur; Kir: Kirghiz; Tib: Tibetan.</p