Mol Biol Evol (2010) doi: 10.1093/molbev/msq312
Y-chromosomal variation in Sub-Saharan Africa: insights into the history of Niger-Congo groups
Cesare de Filippo et al.
Abstract
Technological and cultural innovations, as well as climate changes, are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼10,000 years ago. The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼5,000 years ago represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sub-lineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, D.R.C, and Zambia). With the inclusion of published data, we analyzed 2736 individuals from 26 groups representing all linguistic phyla and covering a large portion of Sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using Linear Discriminant Analysis on STR haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggest that their expansion throughout Sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.
Link
Cesare de Filippo et al.
Abstract
Technological and cultural innovations, as well as climate changes, are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼10,000 years ago. The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼5,000 years ago represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sub-lineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, D.R.C, and Zambia). With the inclusion of published data, we analyzed 2736 individuals from 26 groups representing all linguistic phyla and covering a large portion of Sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using Linear Discriminant Analysis on STR haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggest that their expansion throughout Sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.
Link
6 comments:
Does anyone have access to this paper? It might help explain the frequency of R1b1a in places better . My email is aegrthy@aol.com.
The findings reported in the abstract are unremarkable, given the already detailed understanding we have from other lines of evidence regarding Bantu expansion. Given the prolog, I'd hoped for answers to the more interesting and largely unresolved question of what happened in the expansion of mtDNA L2 and L3, and in the expansion of E1b1 associated with Niger-Congo language speakers generally.
Are these markers of the expansion of Sahel agriculture (we know the tropical agriculture was largely a Bantu invention and came later)? Was there a dual expansion, with one set of farmers expanding from the West and the other from Ethiopia with different sets of crops that converged into a common culture (as suggested by the mtDNA L2 and L3 clines)? If so, did one come first and another second, or were they more or less simultaneous, and which expansion is most closely associated with the Niger-Congo languages?
Were mtDNA L2 and L3 and parallel Y-DNA E haplogroups the result of single expansions with Sahel farming or some other development that gave their bearers an advantage, or are one or both of them part of a much older substrate, perhaps from an original Out of East Africa expansion that may have replaced archaic hominins in West Africa?
Was there a compact homeland of the Niger-Congo languages, or was it a sprachbund? If there was a combat homeland, was it closer to Senegal or Cameroon?
Are the Kordofani language speakers relicts of an East African branch of Niger-Congo languages that was replaced linguistically and/or demographically by Afro-Asiatic languages/peoples? Or are the exiles who ended up far removed from their homes in a single demographic event? There are indications that some of the Afro-Asiatic languages (in addition to the Ethio-Semitic languages which are known to be young and invasive in the historic era) are relatively young and may date to the introduction of Near Eastern pastoralism to Africa. Ethiopia, for example, has both an Ethio-Semitic language strata and an older Afro-Asiatic language strata that may still have roots only in the last seven thousand years or so. What can genetics tell us about the pre-Afro-Asiatic Ethiopians? We care about pre-Afro-Asiatic Ethiopians a lot, since modern Ethiopians have the closest genetic affinities to the common ancestors of all Eurasians (even after parsing out the impact of recent admixture) and that Eurasian population existed in an era that probably predates all or almost all of the contemporary Afro-Asiatic language families. It is fair to guess that the ancestor population of Eurasia once spoke a common language and that Pre-Babel Eurasian populations (to use the metaphor in a less than literal sense) probably spoke a language also spoken in pre-Afro-Asiatic Ethiopia. The direction and sources of ancient West African population expansions tell us if it is more or less likely that pre-Afro-Asiatic Ethiopian languages were similar to Kordofani, more like something else, or lost to the sands of time when it went extinct many thousands of years ago.
There seems to be suggestive evidence that there was a Pygmy language family whose language died in the Bantu expansion and may have been related more strongly to the Khoisan languages than the Niger-Congo languages. Did the hunter-gathers have West Africa have a language family that now leaves no trace? Did the East Africans?
A 2010 open access paper by some of the same authors regarding the population genetics of Eastern Zambia (Y-DNA, mtDNA and biallelic markers), concluding that there was very little admixture of Bantu and hunter-gatherer populations there despite a 1700 year co-existence, may be of interest. There don't appear to be any R1b1a instances in that sample or other samples referenced from prior studies in the region (a summary is on the seventh page of the paper).
"their expansion throughout Sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations".
A process that I believe has been very common during our evolution and expansion. Once a population has managed to reach a previously unexploited environment the improved technolgy or culture that allowed that entry has also allowed an effective back-migration. If we care to look we can discern many other possible examples.
"We care about pre-Afro-Asiatic Ethiopians a lot, since modern Ethiopians have the closest genetic affinities to the common ancestors of all Eurasians (even after parsing out the impact of recent admixture)"
And possibly that close genetic affinity is quite largely a product of that recent admixture. To me the distribution of mtDNA haplogroups suggests a settlement of Ethiopia quite some time after the OoA. No mtDNA haplogroup seems obviously indigenous Ethiopian, which is strange. We would expect the first haplogroup into the mountains to have come to dominate, but instead we find representatives of any number of downstream L haplogroups. Most of the L haplogroup branches in fact. What's more, none of the Ethiopian mtDNA haplogroups show an ancient diversification within that region. They are all close relatives of haplogroups from outside Ethiopia. Just because pre-human fossils are present in Ethiopia from ancient times it doesn't automatically follow that modern humans started their great expansion from there.
"it doesn't automatically follow that modern humans started their great expansion from there."
The Out of Africa journey could have begun, given the boat technology available the, only from the Suez, the Gate of Tears, or Gibralter. There is no evidence to support a Gibralter crossing by AMH in that time frame. AMHs were in Israel ca. 100,000 yrs BP, disappeared ca. 80,000 yrs BP, and didn't return to the Levant until ca. 50,000 yrs BP. Thus, there was a Suez Out of Africa route, but its timing is wrong to be the main Out of Africa event. It follwos that the main Out of Africa route to Asia was the Gate of Tears. You can't get to the Gate of Tears from anywhere else in Africa without going through Ethiopia. We don't know for sure how long the Eurasian ancestor population lived there, but we can be almost certain that they did live in Ethiopia before leaving Africa. This is consistent with the fact that Ethiopia has archaeologically attested AMHs throughout the Out of Africa dates (100,000 years to 50,000 years BP), a time frame also supported by mutation clocks even with substantial error in those dates.
The literature has been able to distinguish clearly Eurasian haplogroups of Y-DNA (C, D, F) and mtDNA (M, N (xL)), from predominantly African Y-DNA (A, B and E) and mtDNA (L) haplogroups within the Ethiopian population. This shows that most Eurasian admixture came from Ethio-Semitic language bearers (ca. 2600 years ago), with a probable earlier wave of Eurasian/North African admixture earlier, probably in the last 12,000 years. The exceptions (e.g. Y-DNA E in Europe, Y-DNA R1b and T in Africa, mtDNA L in Mediterranean coastal areas and South Asia, mtDNA M1 and U6 in Africa) show strong signs of being either African migration to Europe since the Neolithic, or Eurasian back-migration to Africa, probably in the same time frame (given the reasonably link between linguistic populations and populations with high levels of Eurasian haplogroups).
mtDNA L3* is phylogenically the branch of African mtDNA from which all Eurasians descend. L3* was almost absent from Southern Africa and tropical Africa prior to Bantu expansion with which it is linked there, and has been rare in North Africa at least as far back as 12,000 years old ancient DNA.
L3* and its most phylogenically close African haplogroups exibit a distinct cline that peaks in the general vicinity of Ethiopia, and declines as one move West. L2 has the opposite cline. If L3*, which was at some point shared by all matriline ancestors of modern Eurasians, didn't arise in or around Ethiopia, it had to have arisen in West Africa, where L3 is currently much more rare, and L2 is currently more common, without any serious evidence that this flip really happened. Thus, the conclusion that Eurasians have roots in or around Ethiopia is most parsimonious.
The current L2 and L3 mix may derive from separate populations (L2 in West Africa and L3 in Ethiopia) that each surged towards their midpoint around Lake Chad and Southern Sudan close in time in the early African Neolithic (ca. 8,000 to 12,000 years ago), due to a changing climate favoring agriculture in the Sahel. Some Sahel crops have West African origns, some have East African origns. Neither provided the complete diet of mature Sahel farming until the two agricultural cultures fused, that is probably when L2 and L3 admixed, particularly in the middle of the range. So, Out of Africa Ethiopia was probably more strongly L3 than it is now. Since only the mtDNA haplogroups lucky enough to be associated with food producing parts of local populations would have expanded, sister mtDNA L clades of late adopters of food production were probably greatly diminished as a share of the total mtDNA mix then.
I agree with much of what you say. However some of your comments do not add up.
"The Out of Africa journey could have begun, given the boat technology available the, only from the Suez, the Gate of Tears, or Gibralter".
Really only the Suez. Boat technology was presumably very primitive at the time because relatively easily reached islands in the Mediterranean were not substantiually occupied till much later. And the Gate of tears is treacherous at the best of times, although some research suggests it may have been dry land at one time.
"AMHs were in Israel ca. 100,000 yrs BP, disappeared ca. 80,000 yrs BP, and didn't return to the Levant until ca. 50,000 yrs BP. Thus, there was a Suez Out of Africa route, but its timing is wrong to be the main Out of Africa event".
The timing is reasonably correct if we accept dates for mitochondrial DNA diversity literally. As far as I know 80,000 years fits fairly closely the estimated time for the expansion of haplogroup L3.
"We don't know for sure how long the Eurasian ancestor population lived there, but we can be almost certain that they did live in Ethiopia before leaving Africa".
Maju concocted a marvelous digram of mtDNA L at his Leherensuge blog. He may be able to direct you to it. I count 35 mtDNA L haplogroups in Ethiopia. But his diagram shows that no specifically Ethiopian mtDNA haplogroups appear there until after the 23 mutation level (which he takes as the expansion of L3), and most Ethiopian-specific haplogroups are much younger even. And they have close relations outside Ethiopia. L3a is the earliest single Ethiopian-specific haplogroup, at 24 mutations. It looks very much as if the occupation of Ethiopia coincides with the L3 expansion. It is not the source of it. All the other 34 Ethiopian haplogroups appear to have arrived with the expansion of their particular haplogroup, from outside Ethiopia.
"The current L2 and L3 mix may derive from separate populations (L2 in West Africa and L3 in Ethiopia)"
Except I wouldn't place L3 specifically in Ethiopia. East of Lake Chad would be sufficient, somewhere on the Sahel, perhasp as far north as Egypt and south into Kenya.
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