Original Investigation

Human Genetics

, Volume 114, Issue 2, pp 127-148

Excavating Y-chromosome haplotype strata in Anatolia

  • Cengiz CinnioğluAffiliated withDepartment of Genetics, Stanford University School of MedicineInstitute of Forensic Sciences, Istanbul University
  • , Roy KingAffiliated withDepartment of Psychiatry and Behavioral Sciences, Stanford University
  • , Toomas KivisildAffiliated withEstonian Biocentre and Tartu University
  • , Ersi KalfoğluAffiliated withInstitute of Forensic Sciences, Istanbul University
  • , Sevil AtasoyAffiliated withInstitute of Forensic Sciences, Istanbul University
  • , Gianpiero L. CavalleriAffiliated withDepartment of Genetics, Stanford University School of Medicine
  • , Anita S. LillieAffiliated withDepartment of Genetics, Stanford University School of Medicine
  • , Charles C. RosemanAffiliated withAnthropological Sciences, Stanford University
  • , Alice A. LinAffiliated withDepartment of Genetics, Stanford University School of Medicine
    • , Kristina PrinceAffiliated withDepartment of Genetics, Stanford University School of Medicine
    • , Peter J. OefnerAffiliated withStanford Genome Technology Center
    • , Peidong ShenAffiliated withStanford Genome Technology Center
    • , Ornella SeminoAffiliated withDipartimento di Genetica e Microbiologia, Università di Pavia
    • , L. Luca Cavalli-SforzaAffiliated withDepartment of Genetics, Stanford University School of Medicine
    • , Peter A. UnderhillAffiliated withDepartment of Genetics, Stanford University School of Medicine Email author 

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Abstract

Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat (STR) loci. The major components (haplogroups E3b, G, J, I, L, N, K2, and R1; 94.1%) are shared with European and neighboring Near Eastern populations and contrast with only a minor share of haplogroups related to Central Asian (C, Q and O; 3.4%), Indian (H, R2; 1.5%) and African (A, E3*, E3a; 1%) affinity. The expansion times for 20 haplogroup assemblages was estimated from associated STR diversity. This comprehensive characterization of Y-chromosome heritage addresses many multifaceted aspects of Anatolian prehistory, including: (1) the most frequent haplogroup, J, splits into two sub-clades, one of which (J2) shows decreasing variances with increasing latitude, compatible with a northward expansion; (2) haplogroups G1 and L show affinities with south Caucasus populations in their geographic distribution as well as STR motifs; (3) frequency of haplogroup I, which originated in Europe, declines with increasing longitude, indicating gene flow arriving from Europe; (4) conversely, haplogroup G2 radiates towards Europe; (5) haplogroup E3b3 displays a latitudinal correlation with decreasing frequency northward; (6) haplogroup R1b3 emanates from Turkey towards Southeast Europe and Caucasia and; (7) high resolution SNP analysis provides evidence of a detectable yet weak signal (<9%) of recent paternal gene flow from Central Asia. The variety of Turkish haplotypes is witness to Turkey being both an important source and recipient of gene flow.