December 04, 2012

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:
The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].
A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:
Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.
Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234

Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.

We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.

Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.



clusteredmaps said...

A ANCIENT ibero-maurisian cave was studied it was western eurasn and either U or H was the core, but it lacked U6 and M1.

wagg said...

@ clusteredmaps: I assume you're talking of Kefi et al. 2005 about the Taforalt, but there were actually some U6 and a lineage that was either L3, M or N and we can suppose it was M1. But it's true that both U6 and M1 were a little minority in the whole pool though.

andrew said...

Great analysis.

So, we have an LGM era introgression of U6 from Iberia to NW Africa across the Strait of Gibralter where it thrives and continues to be present through the language shift of the local populations to first the Berber and later the Arabic languages. This never really thrives outside NW Africa, despite small blogs of it in Ethiopia and Oman.

Thus, U6, rather than looking like a cousin to M1, really looks like closer kin to mtDNA haplogroup V and some Iberian leaning mtDNA haplogroup H subtypes that are found in NW Africa. This also fits the European distribution of haplogroup E which shows SW European E having one set of subhaplogroups with an affinity to NW Africa, and SE European and SW Asian E having an affinity to NE Africa.

In contrast, we have M1 present in current highest frequencies right next to the two main candidates for Out of Africa migrations into SW Asia, a later expansion date (with an inferred demographic history showing an effective population surge right around 10,000 to 7,000 BP when the Neolithic revolution reaches Egypt), and a distribution strongly coincident with that of the Afro-Asiatic languages and a suggested East African origin.

An East African place of expansion is consistent with M1 coinciding with Y-DNA E more than any Eurasian Y-DNA haplogroup. The distribution pattern appears to not have reached any "wet Sahara" territory and instead of follow pretty closely the North African coast, the Nile and Blue Nile, and the East African coast. Within Ethiopia, there is a highlands rather than lowland distribution. These look like farmers or sedentary pastoralists, not nomadic pastoralists like the Berbers or Chadic people or Nilo-Saharans.

Somehow, a community of M1 carriers manages to migrate to the Pontic-Caspian Steppe at some point (my first instinct would be Egyptians, perhaps in the Bronze Age).

It also looks like Niger-Congo linguistic communities were coherent enough to prevent demic intrusion of AA or pre-AA NW African peoples into their turf at the time of the expansions of these mtDNA haplogroups, and that the M1 in Tanzania could be a legacy of maritime trade or Bantu expansion that had incorporated formerly AA speaking populations.

South Central Haplo said...

The graph mimics Y haplo T spread .
All these area has no other South west Asian male presence. Except in Arab dominated areas due to recent influx.

andrew said...

Y-DNA hg T is in Egypt and the Horn of Africa, but it is more or less absent from the North African coast and has a lot of presence in SW Asia centered on Mesopotamia, a thin but consistent presence across Europe (particularly Italy, Greece and coastal Germanic areas), and a pretty strong spike in eastern India (especially Andhra Pradesh, West Bengal, Madhya Pradesh, Uttar Pradesh and Kashmir). Also notable is a high frequency of Y-DNA T among Sasun Armenians.

wagg said...

"Somehow, a community of M1 carriers manages to migrate to the Pontic-Caspian Steppe at some point (my first instinct would be Egyptians, perhaps in the Bronze Age)."

Strange Idea. Are you thinking of this because Herodotus claimed that the population of Colchis was (partly?) of Egyptian origin?

"For example, Herodotus states that the Colchians, with the Egyptians and the Ethiopians, were the first to practice circumcision, a custom which he claims (without historical proof) that the Colchians inherited from remnants of the army of Pharaoh Sesostris. Herodotus thus erroneously regarded the Colchians as Egyptians. Apollonius of Rhodes states that the Egyptians of Colchis preserved as heirlooms a number of wooden tablets, which show, with considerable accuracy, seas and highways."

andrew said...

Wagg, I was not thinking of Herodotus, although that is an interesting data point. My reasoning was as follows:

That M1 women arrived there is fact. So, somebody on the M1 map must have traveled there. Who among the candidates is most likely? The Ethiopians? The Moroccans? The Tunisians (aka Cathagians?) The Nubians? The desert Arabs? Or the Egyptians?

Egypt's dominion extended roughly as far as modern day Lebanon at its Bronze Age peak and had diplomatic relations with the Bronze Age Hittites (and their predecessors) that involved bride exchanges. It wouldn't be implausible that there could have been brides exchanged with other principalities beyond Anatolia either by the Egyptian Pharonic state or by families engaged in Egyptian long distance maritime trade that escaped the Egyptian historical record (the peoples of the Pontic-Caspian steppe were illiterate at the time and hence left no contemporaneous written historical texts).

Egypt's dominion hasn't been closer to the Caucusus Mountains before or after this time period. There are also cave wall painting of boats probably from the Bronze Age on the shores of the Caspian Sea that superficially look quite similar to Egyptian boats (I've seen photos from ca. the 1940s to 1960s and a discussion of the find from sometime after the Cold War online by a Russian researcher but don't have a reference at hand - the researcher did not himself make the leap to conclude that this was an Egyptian style boat). No other East Africa or North African source seems more plausible.

There was a later diasporic migration of Jews to that general region who could also have been a source, but Jews are far less rich in M1 than Egyptians, and if they were one would expect a thin trace of M1 all across Ashkenazi Jewish descendants from Europe rather than the distribution seen.