Improved phylogenetic resolution within Y-haplogroup R1a1

Here is the table of haplogroup frequencies:

I have written before that I envision R1a1 to have been anciently distributed in the wide arc of "flatlands" north and east of the Caspian sea, complementing R-M269 whose distribution is suggestive of the short arc of "highlands" west and south of it.

The current distribution is strongly geographically bimodal, with peaks in eastern Europe and South Asia. The phylogeny of this group is continuously refined, but one of the problems with the "commercial" studies of haplogroups is that they tend to consist of samples drawn primarily of the groups of people who are likely to have heard of DNA testing, and this excludes large regions within the Eurasian heartland. For example, Z280 is listed as "Central and Eastern Europe Western Asia" in the R1a1a and subclades project, but here makes up 2/9 R-M198 related samples from the Central Asian Uzbek sample. Similarly, M458 is listed as Central Europe, but occurs in 1/9 Uzbek. We can't know for sure which SNP occurs where until we test large representative samples.

There are various aspects of the problem that need to be considered: the absence of R1a-related lineages in pre-Copper Age Europe, and of the distant R1b relative, together with the firm rooting of the R1 clade in Asia indicate that the lineage leading to R1a1 traces its ancestry to a migration into Europe. How and when that migration occurred is an open problem. The paucity of SNP diversity in South Asia, at least in the available samples, indicates that a migration into South Asia also occurred. So, I agree with the authors "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."

My working hypothesis is that the bimodal distribution of R1a1-related lineages in Eurasia can be explained on the basis of two expansions involving largely Z283 in Europe and Z93 in Asia. The source of those expansions may have been Central Asia, and the relative scarcity of R1a1 in that region (relative to Europe and South Asia) may be the result of a subsequent movement of East Eurasians into it, at the same time as the expansion of Altaic speakers. The Uzbek sample in this paper give us a strong hint about the existence of an overlap zone in Central Asia, but the SNP diversity is little studied in the populations of the -stan states, and ancient DNA samples are missing.

The issue of time depth is also relevant, as it will anchor in time the evolutionary relationships between different populations of R1a1 descendants. This can be achieved both by (i) typing ancient samples for the relevant markers, which will provide -assuming a positive result- a terminus ante quem for the appearance of particular SNP, and (ii) sequencing modern Y-chromosomes to determine their TMRCA.

AJPA DOI: 10.1002/ajpa.22167

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

Horolma Pamjav et al.

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.

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