Original scientific paper
Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree
Natalie M. Myres
; Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, USA
Kathleen H. Ritchie
; Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, USA
Alice A. Lin
; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, Calif, USA
Robert H. Hughes
; Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, USA
Scott R. Woodward
; Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, USA
Peter A. Underhill
orcid.org/0000-0003-3389-6272
; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, Calif, USA
Abstract
Aim To determine the human Y-chromosome haplogroup
backgrounds of intermediate-sized variant alleles displayed
by short tandem repeat (STR) loci DYS392, DYS449,
and DYS385, and to valuate the potential of each intermediate
variant to 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 medianjoining
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 I1*-M253, and likely represents
a new phylogenetic subdivision in this European
haplogroup. Intermediate variants DYS449.2 and DYS385.2
both occur on multiple haplogroup backgrounds, and
when evaluated within specific haplogroup contexts, delineate
new phylogenetic substructure, with DYS449.2 being
informative within haplogroup A-P97 and DYS385.2
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 STR 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.
Keywords
Y-chromosome; haplogroups, haplotypes; forensics, genealogy; human evolution; population genetics
Hrčak ID:
40672
URI
Publication date:
15.6.2009.
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