Monday, March 13, 2017

Central African Hunter-Gatherer Ancient DNA Is Distinctive

Malawi is along the Great Rift Valley that divides Eastern and Central Africa. 
In 1950, J. Desmond Clark led excavations at a Later Stone Age rockshelter at Hora Mountain, a large inselberg overlooking a modern floodplain in the Mzimba District of northern Malawi. At the Hora 1 site, he recovered two human skeletons, one male and one female, along with a rich—but superficially described and undated—cultural sequence. In 2016, our renewed excavations recovered a wealth of lithic, faunal, and other materials such as mollusk shell beads and ochre. Our reexamination of the skeletons also produced the first ancient DNA from the central African region, which together with previous morphological analysis demonstrates that the LSA foragers of the area cannot be readily fit within the known genetic and phenotypic parameters of living foragers. The significance of the Hora 1 site was made further clear by the relocation of several previously known sites also at the mountain, the discovery of four new rock art sites, and the discovery of four very rich new archaeological sites in the mountains adjacent to the floodplain. Here, we describe our renewed work and how it fits with the original findings to offer unprecedented promise for understanding the lifeways of Holocene foragers in central Africa.
Jessica Thompson, et al., "The Forgotten Significance of the Later Stone Age Sites near Hora Mountain, Mzimba District, Malawi" (Forthcoming, SAA 2017 Conference Paper).

The late stone age site, most notably, precedes Bantu expansion.

This seems to be of a piece with the face that the substrate population in Mozambique (where Bantu populations have click consonants) likewise does not correspond to any modern African population. As previously noted at this blog in that link:
A 2010 article in the European Journal of Human Genetics found genetic traces of a substrate population in Mozambique that was an ancestral component distinct from any of the other ancestral populations of Africa. As the body text in that open access article explains (citations omitted):
The southeastern Bantu from Mozambique are remarkably differentiated from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and also differentiated from geographically closer Eastern Bantu samples, such as Luhya. 
These results suggest that the Bantu expansion of languages, which started ~5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology, was not a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people. 
The complexity of the expansion of Bantu languages to the south (with an eastern and a western route), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists. 
Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with.
In other words, there is genetic evidence that there was an entire "lost race" in Mozambique, distinct from Khoisans, Pygmies, East Africans and West Africans, with no pure blooded remaining members that disappeared when it was subsumed into the population of Bantus expanding into the area.

Those Bantus had a linguistic and cultural legacy from a quite precisely identified small region near the coastal border of Nigeria and Cameroon, but had assimilated a mish mash of Africans peoples into their genetic melting pot, including the ancestral peoples of Mozambique, on their way to Southeast Africa.


DDeden said...

Malawi is Central Africa?

andrew said...

The authors of the paper describe it that way, so I followed their lead. Obviously, Malawi is where Malawi is and you are free to call it anything you like. Using the Great Rift Valley to distinguish Central Africa from East Africa would not be uncommon.

DDeden said...

Yes, but...

The Malawi Chichewa Bantu who surround Lake Malawi have a oral history of their arrival there and finding Aka Fula Pygmies living around the lake, and mixing with them.

Aka Pygmies are mostly in Central and West Central Congo (Cameroon) rainforest, but there are also Aka Bea Pygmies in Andaman Islands.

Pygmies use powdered red wood in their body & barkcloth painting, not ochre. I think ochre usage was not culturally ritualized until people moved out of the tropical rainforest, separating from the Pygmy populations, and adapting new housing and technology based on new microclimates (exposure to wind, direct sun, cold, drought) which left physical remains which Pygmies' wood crafting did not, such as stone crafting, ceramic & metal technology. The article mentions finding mollusk shell beads and ochre.

andrew said...

There is no genetic or linguistic commonality between indigenous Andamanese populations and Africa pygmy populations. Any similarities are purely products of convergent evolution. The fact that an indigenous tribe of the Andaman islands (the Aka Bea) was given the same name as a pygmy population of central Africa by European colonialists is no more meaningful than the fact that Native Americans were named after people from India, or that Romani who migrated from India to Europe were named after people from Egypt.

andrew said...

Put another way, the Andamanese are closer genetically to Japanese people or Greek people than they are to African Pygmies, a population that did not participate in the Out of Africa migration.

andrew said...

See also and and and and

Central African pygmies were ancestrally Y-DNA B2b4 and mtDNA L1c1a and were closest in autosomal DNA to the Khoisan people of South Africa. They diverged genetically from other Africans ca. 60,000 years ago and from Western Pygmies about 20,000 years ago.

The Andamanese are all Y-DNA D-M174 and all have either M31or M32 mtDNA, subgroups of M which are unique to Andamanese people, and have similarities in autosomal DNA to indigenous people of Southern India and Malaysia. They have Neanderthal ancestry as levels similar to other non-Africans. There is a controversial claim that they and some other Southeast Asians have a small percentage of ancestry from an archaic hominin species other than Neadnerthals and Denisovans. None of these archaic hominin genes are found in Africans and "The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size."

DDeden said...

"at" (Oko Juwoi) fire (Andamans) (Oko = Aka)
"apa" (Mbuti) fire (Central Africa)

"aka" (Aka Bea) prefix for things related to the tongue.
(wiki: aka-bea language)

(Please inform your readers when you're guessing. "Aka" has nothing to do with recent European name-calling.)