Brief communication: New Y‐chromosome binary markers improve phylogenetic resolution within haplogroup R1a1

Abstract

Haplogroup R1a1-M198 is a major clade of Y chromosomal haplogroups which is distributed all across Eurasia. To this date, many efforts have been made to identify large SNP-based subgroups and migration patterns of this haplogroup. The origin and spread of R1a1 chromosomes in Eurasia has, however, remained unknown due to the lack of downstream SNPs within the R1a1 haplogroup. Since the discovery of R1a1-M458, this is the first scientific attempt to divide haplogroup R1a1-M198 into multiple SNP-based sub-haplogroups. We have genotyped 217 R1a1-M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the "1000 Genomes Project". The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub-haplogroups. R1a1-M458 and R1a1-Z280 were typical for the Hungarian population groups, whereas R1a1-Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages. This pattern implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a-M82 is their only discernible paternal lineage of Indian heritage.

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

“…The group also occurs at 43% in some Iranian populations and is present at 430% in Roma from Croatia and Hungary, consistent with previous studies reporting the presence of R1a-Z93 in Roma. 31,51 Finally, the rare R1a-M560 was only observed in four samples: two Burushaski speakers from north Pakistan, one Hazara from Afghanistan, and one Iranian Azeri.…”

“…31 Both of these haplogroups were found among Near/Middle East and Caucasus populations comprising 560 samples.…”

“…22,[26][27][28][29][30] However, with the discovery of the Z280 and Z93 substitutions within Phase 1 1000 Genomes Project data 1 and subsequent genotyping of these SNPs in B200 samples, a schism between European and Asian R1a chromosomes has emerged. 31 We have evaluated this division in a larger panel of populations, estimated the split time, and mapped the distributions of downstream sub-hgs within seven regions: Western/Northern Europe, Eastern Europe, Central/South Europe, the Near/Middle East, the Caucasus, South Asia, and Central Asia/Southern Siberia.…”

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

“…The Y-chromosome [159], however, is present with only one copy per normal cell, and has higher diversity than mtDNA in addition to an increasing number of Y-STRs [9, 155,160] completed by rapidly mutating (RM) markers [155,[160][161][162], Y-SNPs [155,160,[163][164][165] and insertion/deletion polymorph (Indel) markers [166,167]. Although, the analysis of Ychromosomal markers can provide complementary information in addition to an autosomal genetic profile [168], the most common application of Y-STRs is in cases of sexual assault, when the female component can greatly overshadow the male component, making autosomal STR profiling frequently difficult, unclear or impossible.…”

Genetic and Cultural Reconstruction of the Migration of an Ancient Lineage

“…These new insights have established the dominant clade of R1a1 in the Iran-Afghanistan migration corridor to South Asia as carrying the defining SNPs Z93 and L342.2. In this group, the L657 branch is most abundant [1, 2]. …”