Internal diversification of mtDNA haplogroup R0a

Molecular Biology and Evolution, doi:10.1093/molbev/msq178

Internal diversification of mitochondrial haplogroup R0a reveals post-Last Glacial Maximum demographic expansions in South Arabia

Viktor Černý et al.

Abstract

Widespread interest in the first successful Out of Africa dispersal of modern humans 60 – 80 KYA via a southern migration route has overshadowed the study of later periods of South Arabian prehistory. In this work we show that the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial genomes (71 being newly presented here) for haplogroup R0a – the most frequent and widespread haplogroup in Arabia. Additionally, two geographically specific clades (R0a1a1a and R0a2f1) have been identified in non-Arabic speaking peoples such as the Soqotri and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence for seafaring activity in the peninsula in the sixth millennium BC.

Link

More on Henn et al. on time-dependent evolutionary mutation rate

Brenna Henn, lead author of the recent study I commented on earlier has a guest post at the Spittoon on her paper. Here is the actionable bit:

To date, the timing of most population events in human evolutionary genetics was estimated has used a rate close to the slower one we see for older lineages, before the end of the Ice Age. So our understanding of the genetic history of early human evolution shouldn’t change very much. But the timing of the splits between mitochondrial lineages associated with relatively recent events, such as agricultural expansions, may need revision. Using our newly calibrated mitochondrial mutation rates, researchers will be better able to correlate genetic, archaeological and linguistic data, leading to a more accurate understanding of human prehistory.

Thus, event ages have been systematically underestimated in the literature whenever a slower "evolutionary" mutation rate, derived from calibration has been used.

For example, according to the recent paper on Soqotra:

For calculation of time to most recent common ancestor (TMRCA), q statistics (mean divergence from inferred ancestral haplotype) were used with a HVS-I mutation rate of one transition per 20,180 years (Forster et al., 1996).

Forster et al. (1996):

Therefore, we use ρ as an appropriate measure for time depth (table 2), yielding a rate of one transition per 20,180 + 1,000 years in the mtDNA control region (np 16090-16365).

Thus, this rate is equivalent to 0.28/bp/My (assuming a generation length of 20 years).

But from Henn et al.:

The average of ρ-based rate estimates for events younger than 5,000 years is 0.895/bp/My, virtually identical to the pedigree-based average and well within the confidence interval calculated by Howell et al. (2003).

Hence, the 6,000-year old estimate for the novel lineages identified by Cerny et al. for Soqotra should be downgraded to around ~2,000 years, making them more likely to be quite recent founder lineages, rather than Holocene lineages associated with the early settlement of the island.

Y chromosomes and mtDNA from Soqotra

UPDATE (18/11): see a related post on the age of the new mtDNA lineages [end update]

Soqotra is an island in the Indian Ocean which belongs to Yemen. What is most interesting -to me- about this paper, is that 71.4% of the Y-chromosomes belong to haplogroup J*(xJ1, J2) which is found at trace frequencies elsewhere. Interestingly, haplogroup J2 is not found in this isolated region, while haplogroup J1 is found at a frequency of 14.3%.

The authors write:

For the perspective of the Y-chromosome data, a high
frequency of haplogroup J1 in Soqotra is consistent with
a gradient of this haplogroup in the Arabian Peninsula
(Cadenas et al., 2008). These authors estimated ages for
J1 in Arabia (9.7 +/ 2.4 in Yemen, 7.4 +/- 2.3 in Qatar and
6.4 +/- 1.4 KYBP in UAE), consistent with a Neolithic
expansion from the north (where Y-chromosome STR diversity
is higher). However, we report a much higher frequency
of J* (lack of M267 and M172) in Soqotra. Since
this lineage was not found by Cadenas et al. (2008) in
the Arabian Peninsula, this raises the possibility of an
earlier input for these lineages or more probably very
strong genetic drift of a low frequency Arabian lineage
in the Y-chromosome gene pool of Soqotra.

The early dates from Cadenas et al. are due to the use of an evolutionary mutation rate, and thus need to be downgraded to about ~1,000BC onwards, coinciding (within wide confidence intervals) with the formation of the earliest Arabian kingdoms. It seems probable that J*(xJ1, J2) was commoner in the past, and contributed to the population of Soqotra, but this population was later overwhelmed by the expansion of J1-carriers who dominate the Arabian peninsula to this day.

It is unfortunate that apparently many J2 downstream markers were typed even though there is no J2 on the island, whereas haplogroup E, occurring at a frequency of 9.5% was not further resolved. This underscores the need for a more flexible typing stratgy; at this level it is not clear whether this E came to the island from Africa or from Arabia.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20960

Out of Arabia - The settlement of Island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity

Viktor Cerny et al.

Abstract

The Soqotra archipelago is one of the most isolated landmasses in the world, situated at the mouth of the Gulf of Aden between the Horn of Africa and southern Arabia. The main island of Soqotra lies not far from the proposed southern migration route of anatomically modern humans out of Africa 60,000 years ago (kya), suggesting the island may harbor traces of that first dispersal. Nothing is known about the timing and origin of the first Soqotri settlers. The oldest historical visitors to the island in the 15th century reported only the presence of an ancient population. We collected samples throughout the island and analyzed mitochondrial DNA and Y-chromosomal variation. We found little African influence among the indigenous people of the island. Although the island population likely experienced founder effects, links to the Arabian Peninsula or southwestern Asia can still be found. In comparison with datasets from neighboring regions, the Soqotri population shows evidence of long-term isolation and autochthonous evolution of several mitochondrial haplogroups. Specifically, we identified two high-frequency founder lineages that have not been detected in any other populations and classified them as a new R0a1a1 subclade. Recent expansion of the novel lineages is consistent with a Holocene settlement of the island ~6 kya.

Link