The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

Underhill, Peter A.; Passarino, Giuseppe; Lin, Alice A.; Shen, Peidong; Lahr, Marta Mirazón; Foley, Robert; Oefner, Peter J.; Cavalli-Sforza, Luigi Luca

doi:10.1046/j.1469-1809.2001.6510043.x

Cited by 695 publications

(575 citation statements)

References 53 publications

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“…Most of the binary markers have been described in the literature. 9,35,36 A novel informative polymorphism (ss4bp, rs41352448) defining a newly found Y-haplogroup Q sublineage (Q5), presently restricted to India, 37 was also typed. These samples were also genotyped for seven Y-microsatellite markers (Y-STRs): DYS 389I, DYS 389II, DYS390, DYS391, DYS392, DYS19/394 and DYS448, to estimate the haplotype variation within the HG defined by binary markers (Y-STR haplotypes data are available through personal communication).…”

Section: Screening Of Y-chromosomal Polymorphismsmentioning

confidence: 99%

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system

et al. 2009

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Many major rival models of the origin of the Hindu caste system co-exist despite extensive studies, each with associated genetic evidences. One of the major factors that has still kept the origin of the Indian caste system obscure is the unresolved question of the origin of Y-haplogroup R1a1*, at times associated with a male-mediated major genetic influx from Central Asia or Eurasia, which has contributed to the higher castes in India. Y-haplogroup R1a1* has a widespread distribution and high frequency across Eurasia, Central Asia and the Indian subcontinent, with scanty reports of its ancestral (R*, R1* and R1a*) and derived lineages (R1a1a, R1a1b and R1a1c). To resolve these issues, we screened 621 Y-chromosomes (of Brahmins occupying the upper-most caste position and schedule castes/tribals occupying the lower-most positions) with 55 Y-chromosomal binary markers and seven Y-microsatellite markers and compiled an extensive dataset of 2809 Y-chromosomes (681 Brahmins, and 2128 tribals and schedule castes) for conclusions. A peculiar observation of the highest frequency (up to 72.22%) of Yhaplogroup R1a1* in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1* in different tribal population groups, existence of Y-haplogroup R1a* in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1* haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1* and confirm the present conclusions.

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Section: Screening Of Y-chromosomal Polymorphismsmentioning

confidence: 99%

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system

et al. 2009

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“…In addition, M91, a defining mutation in the A clade, shows variation in the number of T repeats (9T→8T), and has been used as a binary marker in the YCH Tree. 7,20 Therefore, we propose assignment of these mutations as haplogroup markers.…”

Section: Population Studymentioning

confidence: 99%

Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

et al. 2013

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The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic, but also archeological and forensic studies. The

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“…We followed a hierarchical genotyping strategy identifying the major haplogroups first and then the downstream mutations along the haplogroup tree. The nomenclature followed for the Y-haplogrouping is as recommended by Y Chromosome Consortium 22 and Karafet et al 23 The primer and sequence information for the insertion, deletion as well as single-nucleotide polymorphisms (SNPs) genotyped by denaturing high-performance liquid chromatography and direct sequencing were taken from Underhill et al 24 and Karafet et al 23 For the SNPs genotyped by the GenomeLab SNPstream genotyping system, we have used 12-plex format and performed the multiplex PCR as well as extension reactions following manufacturer's recommendations. Genotyping was carried out in an automated multiplexed system that employed oligonucleotide microarrays manufactured in a 384-well format on a glass-bottomed plate.…”

Section: Y-chromosome Haplogroupingmentioning

confidence: 99%

Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India

et al. 2011

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The sub-Himalayan Terai and Duars, the important outermost zones comprising the plains of East India, are known as the reservoirs of ethnic diversity. Analysis of the paternal genetic diversity of the populations inhabiting these regions and their genetic relationships with adjacent Himalayan and other Asian populations has not been addressed empirically. In the present investigation, we undertook a Y-chromosome phylogeographic study on 10 populations (n¼375) representing four different linguistic groups from the sub-Himalayan Terai and Duars regions of East India. The high-resolution analysis of Y-chromosome haplogroup variations based on 76 binary markers revealed that the sub-Himalayan paternal gene pool is extremely heterogeneous. Three major haplogroups, namely H, O and R, are shared across the four linguistic groups. The Indo-European-speaking castes exhibit more haplogroup diversity than the tribal groups. The findings of the present investigation suggest that the sub-Himalayan gene pools have received predominant Southeast Asian contribution. In addition, the presence of Northeast and South Asian signatures illustrate multiple events of population migrations as well as extensive genetic admixture amongst the linguistic groups.

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The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

Cited by 695 publications

References 53 publications

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system

The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system

Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India

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