TITLE

V-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree

AUTHOR(S)
Myres, Natalie M.; Ritchie, Kathleen H.; Lin, Alice A.; Hughes, Robert H.; Woodward, Scott R.; Underhill, Peter A.
PUB. DATE
June 2009
SOURCE
Croatian Medical Journal;Jun2009, Vol. 50 Issue 3, p239
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Aim To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (SIR) loci DY5392, DY5449, and DY5385, and to valuate the potential of each intermediate variant elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. Results We show that DYS392.2 occurs on a single haplogroup background, specifically l1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DY5385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DY5449.2 being informative within haplogroup A-P97 and DYS38S.2 in haplogroups D-M145, E1b1a-M2, and R1b-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Conclusions Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and SIR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.
ACCESSION #
43256348

 

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