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. 2007 Aug;48(4):450-9.

Y-chromosome short tandem repeat DYS458.2 non-consensus alleles occur independently in both binary haplogroups J1-M267 and R1b3-M405

Natalie M Myres  1 , Jayne E Ekins, Alice A Lin, L Luca Cavalli-Sforza, Scott R Woodward, Peter A Underhill
Affiliations

Y-chromosome short tandem repeat DYS458.2 non-consensus alleles occur independently in both binary haplogroups J1-M267 and R1b3-M405

Natalie M Myres et al. Croat Med J. 2007 Aug.

Abstract

Aim: To determine the human Y-chromosome haplogroup backgrounds of non-consensus DYS458.2 short tandem repeat alleles and evaluate their phylogenetic substructure and frequency in representative samples from the Middle East, Europe, and Pakistan.

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, including DYS388 to construct haplotypes. DNA sequencing of the DYS458 locus and median-joining network analyses were used to evaluate Y-chromosome lineages displaying the DYS458.2 motif.

Results: We showed that the DYS458.2 allelic innovation arose independently on at least two distinctive binary haplogroup backgrounds and possibly a third as well. The partial allele length pattern was fixed in all haplogroup J1 chromosomes examined, including its known rare sub-haplogroups. Within the alternative R1b3 associated M405 defined sub-haplogroup, both DYS458.0 and DYS458.2 allele classes occurred. A single chromosome also allocated to the R1b3-M269*(xM405) classification. The physical position of the partial insertion/deletion occurrence within the normal tetramer tract differed distinctly in each haplogroup context.

Conclusions: While unusual DYS458.2 alleles are informative, additional information for other linked polymorphic loci is required when using such non-conforming alleles to infer haplogroup background and common ancestry.

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Figures

Figure 1
Figure 1
DYS458 allele frequency distribution normalized for total sample counts.
Figure 2
Figure 2
Median-joining network analysis of 192 chromosomes with non-consensus DYS458.2 alleles using loci: DYS388, 389I, 389B, 390, 391, 392, 393, 394, 437, 439, 445, 448, 454, 456, 460, 461, 462, GGAAT1B07, YGATA-A10, YGATA-C4, YGATA-H4.1 (all equally weighted).
Figure 3
Figure 3
DYS388 allele frequency distribution in DYS458.2 demarcated chromosomes normalized for total sample counts.
Figure 4
Figure 4
Phylogenetic relationships of DYS458.2 chromosomes in panel A) haplogroup J1 and panel B) haplogroup R1b3.
See this image and copyright information in PMC

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