Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: Isolation and drift in the Himalayas

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Abstract

Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).

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Most cited references 12

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A nomenclature system for the tree of human Y-chromosomal binary haplogroups.

Fabricio Santos (2002)

The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.

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Y-chromosomal DNA variation in Pakistan.

Atika Mansoor, Agnar Helgason, Raheel Qamar … (2002)

Eighteen binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci from the nonrecombining portion of the human Y chromosome were typed in 718 male subjects belonging to 12 ethnic groups of Pakistan. These identified 11 stable haplogroups and 503 combination binary marker/STR haplotypes. Haplogroup frequencies were generally similar to those in neighboring geographical areas, and the Pakistani populations speaking a language isolate (the Burushos), a Dravidian language (the Brahui), or a Sino-Tibetan language (the Balti) resembled the Indo-European-speaking majority. Nevertheless, median-joining networks of haplotypes revealed considerable substructuring of Y variation within Pakistan, with many populations showing distinct clusters of haplotypes. These patterns can be accounted for by a common pool of Y lineages, with substantial isolation between populations and drift in the smaller ones. Few comparative genetic or historical data are available for most populations, but the results can be compared with oral traditions about origins. The Y data support the well-established origin of the Parsis in Iran, the suggested descent of the Hazaras from Genghis Khan's army, and the origin of the Negroid Makrani in Africa, but do not support traditions of Tibetan, Syrian, Greek, or Jewish origins for other populations.

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DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis.

L Gusmão, J M Butler, A Carracedo … (2006)

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and a numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods.

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Author and article information

Journal

Journal ID (nlm-ta): Forensic Sci Int

Journal ID (iso-abbrev): Forensic Sci. Int

Title: Forensic Science International

Publisher: Elsevier Science Ireland

ISSN (Print): 0379-0738

ISSN (Electronic): 1872-6283

Publication date PMC-release: 02 March 2007

Publication date (Print): 02 March 2007

Volume: 166

Issue: 2-3

Pages: 176-181

Affiliations

[a ]Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK

[b ]MGC-Department of Human and Clinical Genetics, Leiden University Medical Centre, The Netherlands

[c ]Himalayan Languages Project, Leiden University, The Netherlands

[d ]Centre for Nepal and Asian Studies (CNAS) of Tribhuvan University (TU), Kirtipur, Nepal

Author notes

[* ]Corresponding author. Tel.: +44 116 252 3427; fax: +44 116 252 3378. maj4@ 123456leicester.ac.uk

Article

Publisher ID: FSI4829

DOI: 10.1016/j.forsciint.2006.05.007

PMC ID: 2627361

PubMed ID: 16781103

SO-VID: 0aba90ec-ad5d-4328-8c88-ddce0c24bb30

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This document may be redistributed and reused, subject to certain conditions.

History

Date received : 30 March 2006

Date revision received : 8 May 2006

Date accepted : 9 May 2006

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