September 13, 2014

Ancient mtDNA from southern Africa related to San

Genome Biol Evol (2014) doi: 10.1093/gbe/evu202

First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African

Alan G. Morris et al.

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of Southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semi-desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-pastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330 year old male skeleton, confirmed via osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that pre-pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

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9 comments:

Grey said...

This also shows the importance of the coast as an early vector of expansion. A population moving into a new inland ecosystem would have to adapt to it all at once to survive whereas a population adapted to maritime (or large river) foraging could move into a new ecosystem along those vectors because they had the sea or river food as a fail safe giving them time to adapt to the new ecosystem's other plants and animals.

I can imagine San like people spreading all around the coasts (both along the west coast up to Scandinavia and the east coast all the way to China) but then being mostly displaced by later expansions leaving larger or smaller traces of DNA in the various modern populations.

Grognard said...

From 2300 years back it doesn't really prove much of anything.

Rokus said...

'Providing the first genomic evidence that pre‐pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.'

While it may be true that Southern Africa has some of the most divergent surviving strains of mtDNA, I am not so sure this new evidence attests this divergence to extend into the past. All the contrary, the pre-pastoral sample shows that the local mtDNA origin of immigrant pastoralist Khoe-speakers (and most current San) remains to be seen - thus suggesting that L0d2c1a and L0d2c1b of Khoe may originate from geographic distances that are difficult to reconcile with the genetic closeness of some surviving pre-pastoralist L0d2c1c still found in San. Actually, this study may cast an unexpected glimpse on an amazing degree of extinct mtDNA homozygosity that extended potentially between Tanzania and the west coast and south coast of Africa.

terryt said...

"From 2300 years back it doesn't really prove much of anything".

Certainly not the conclusions Grey jumps to:

"This also shows the importance of the coast as an early vector of expansion".

It perhaps shows the importance of the coast as a vector 2300 years ago but is hardly relevant to any early human expansions.

"A population moving into a new inland ecosystem would have to adapt to it all at once to survive whereas a population adapted to maritime (or large river) foraging could move into a new ecosystem along those vectors because they had the sea or river food as a fail safe giving them time to adapt to the new ecosystem's other plants and animals".

Not correct at all. Coastal environments are extremely varied
whereas savannah environments are widespread and, certainly at times, connected. Adaptation to a grassland environment with clumps of trees scattered through it was probably the preferred early human environment anyway. On occasions such habitat would stretch all the way from much of Africa through much of Central Asia to Northern China. Further to that, from the abstract:

"Khoesan are today largely restricted to the semi-desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal"

A 'broader southerly dispersal' certainly does not at all imply 'coastal'. In fact a coastal population finishing up in semi-desert, inland regions is extremely unlikely.

terryt said...

"L0d2c1a and L0d2c1b of Khoe may originate from geographic distances that are difficult to reconcile with the genetic closeness of some surviving pre-pastoralist L0d2c1c still found in San".

I think the data doesn't show 'migration' of L0d2c1 haplogroups but rather the 'adoption' of these haplogroups by incoming pastoralists. Just some Khoi-San joined the pastoralists while others remained as independent 'pre-pastoralists'.

"Actually, this study may cast an unexpected glimpse on an amazing degree of extinct mtDNA homozygosity that extended potentially between Tanzania and the west coast and south coast of Africa".

To me that is highly likely, and is what I have long believed. The Bantu, and now it seems the pastoralist, expansions overly an earlier L0 presence through the region. The later expansions are responsible for mt-DNA haplogroups other than L0.

Rokus said...

'I think the data doesn't show 'migration' of L0d2c1 haplogroups but rather the 'adoption' of these haplogroups by incoming pastoralists. Just some Khoi-San joined the pastoralists while others remained as independent 'pre-pastoralists'.'

Inconsistent with this picture is that L0d2c1 today is limited to a few hunter-gatherer individuals, and absent in the pastoralist group. The pastoralists have an abundance of two quite closely related haplogroups. Since it has long be suspected these pastoralists were long distance immigrants, this absence of divergent defining haplogroups for the immigrants is amazing. So far there is no evidence the pastoralists acquired their mtDNA from locals. If anything, it seems the gene flow of one of these pastoralist haplogroups rather went into the opposite direction. For sure this didn't apply to L0d2c1, though. My question now is how this apparent pre-pastoralist regional homogeneity could be reconciled with the OOA assumption of high African diversity. Instead, the latter tends to imply lots of extinct and divergent mtDNA, so where it is?

terryt said...

"Inconsistent with this picture is that L0d2c1 today is limited to a few hunter-gatherer individuals, and absent in the pastoralist group".

How is the inconsistent with the somewhat random absorption of pre-existing L0d2c lines? Surely it is shows that not all L0d2c1 lineages were absorbed by incoming pastoralists. As some confirmation of the idea that L0d2c1 is an indigenous southern African haplogroup is the fact that L0d as a whole is basically a southern African haplogroup and so must have first formed somewhere in that region, presumably from some earlier wider L0 expansion. In that sense the comment from the abstract: 'Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-pastoral arrival' is not strictly correct. The 'population' is extinct but the L0 haplogroup as a whole is just such a survivor.

"Since it has long be suspected these pastoralists were long distance immigrants"

But it has also long been accepted that at least the Bantu mixed with pre-existing local populations. From this paper it becomes apparent that the first pastoralists did too.

"this absence of divergent defining haplogroups for the immigrants is amazing".

Hang on a minute. L0d is by no means the only southern African mt-DNA haplogroup. South African L0a, L0f and L0k, for example, are unlikely to be as ancient in southern Africa as are the L0d haplogroups and could have come in with pastoralists. Other L haplogroups are more likely to have come with the Bantu.

"My question now is how this apparent pre-pastoralist regional homogeneity could be reconciled with the OOA assumption of high African diversity".

The 'regional homogeneity' covered in the paper refers only to ancient Africa south of the Zambezi. It says nothing about regions north of there. It makes complete sense to me that Africa south of the Zambezi was relatively isolated from the rest of Africa.

terryt said...

A clarification:

"Since it has long be suspected these pastoralists were long distance immigrants, this absence of divergent defining haplogroups for the immigrants is amazing. So far there is no evidence the pastoralists acquired their mtDNA from locals".

But what element of the pastoralists were long distance immigrants?

The paper just says:

"Archeological evidence suggests
herding migrants with sheep and
goats entered northern Namibia
around 2,200 ya migrating southwards along the western coast
(Robbins et al. 2005; Pleurdeau et
al. 2012), reaching the southeastern Cape by 2,000 ya."

So did the 'herding migrants' consist of something similar to the familiar story of Moses and the Israelites crossing the Red Sea, or was it more like small groups of males with a few goats and sheep? I suspect something in between, groups quite capable of absorbing members of resident populations.

Marianne Luban said...

Some years ago, I read a paper about an Egyptian mummy whose DNA surprised researchers by having what is known as an "Iberian allele". Can anyone remember that paper and its title or authors. I also made some remarks at my own blog about another mummy[unless she was the same one as in the paper]. It's "Thuya--Black or Jewish. Would appreciate some comments. http://thetimetravelerreststop.blogspot.com/