African Y chromosome news (E1b1a and R-V88)

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.176

Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people

Naser Ansari Pour1, Christopher A Plaster1 and Neil Bradman1

Abstract

The expansion of the Bantu-speaking people (EBSP) during the past 3000–5000 years is an event of great importance in the history of humanity. Anthropology, archaeology, linguistics and, in recent decades, genetics have been used to elucidate some of the events and processes involved. Although it is generally accepted that the EBSP has its origin in the so-called Bantu Homeland situated in the area of the border between Nigeria and the Grassfields of Cameroon, and that it followed both western and eastern routes, much less is known about the number and dates of those expansions, if more than one. Mitochondrial, Y-chromosome and autosomal DNA analyses have been carried out in attempts to understand the demographic events that have taken place. There is an increasing evidence that the expansion was a more complex process than originally thought and that neither a single demographic event nor an early split between western and eastern groups occurred. In this study, we analysed unique event polymorphism and short tandem repeat variation in non-recombining Y-chromosome haplogroups contained within the E1b1a haplogroup, which is exclusive to individuals of recent African ancestry, in a large, geographically widely distributed, set of sub-Saharan Africans (groups=43, n=2757), all of whom, except one Nilo-Saharan-speaking group, spoke a Niger-Congo language and most a Bantu tongue. Analysis of diversity and rough estimates of times to the most recent common ancestors of haplogroups provide evidence of multiple expansions along eastern and western routes and a late, exclusively eastern route, expansion.

Link

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.167

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

Miguel González1, Verónica Gomes1,2, Ana Maria López-Parra3, António Amorim1,4, Ángel Carracedo2, Paula Sánchez-Diz2, Eduardo Arroyo-Pardo3 and Leonor Gusmão1

Abstract

Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a ‘back-to-Africa’ migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene.

Link

R-V88 and migration of Chadic speakers across the Sahara

The presence of R1b chromosomes in Africa is one of a few Y-chromosome phylogeographic anomalies I noted long ago. This new paper offers an insight into the migration of these chromosomes along with the Chadic branch of Afroasiatic from Asia to Europe. More on this after I read the paper.

UPDATE (8/1/10):

The paper, to its credit acknowledges that the "effective mutation rate" depends on population growth history as I have argued a year and a half ago. The authors write:

Owing to the uncertainties associated with the estimate of the evolutionary effective microsatellite mutationrates, depending on the haplogroup demographic history,³⁷ we considered two different population models: (1) a constant size population and (2) a single rate of m=0.01 for exponential population growth. After calibration for the specificmicrosatellites used in this study,¹³ we found evolutionary effective mutationrates of 7.9x10^-4 and 1.3x10^-3, respectively.

and:

As an upper limit, we used the coalescence time of the R-M343/P25 haplogroup (12.9 ky, 95% CI=11.6–14.3 ky, under a conservative scenario of constant population size), which, on the basis of the accumulated nucleotide and microsatellite diversity (Table 1; Figure 2), most likely originated outside Africa. The coalescence time of the seemingly African-specific haplogroup R-V69 (6.0 ky, 95% CI=4.2–8.2 ky, under the hypothesis of an expanding population) was used as a lower limit.

As I noted in haplogroup sizes and observation selection effects haplogroup sizes provide a sanity check to assumptions about population growth history:

Haplogroups do not reach commonly-observed present-day sizes under the assumption of constant population size. Inferences of age based on such an assumption are a very conservative upper limit. However, the assumption of m=0.01 also does not result in "large" present day haplogroups (see previous link).

Thus, I suppose that the age of R-V88 is younger than 4.2–8.2 ky, and could be as young as ~3-4ky in a rapidly expanding population. To determine how fast R-V88 actually grew, we must take into account its present-day demographic size (how many people in the world now possess it). The final estimate must be consistent with both the demographic size and the current Y-STR variance.

I don't have data on R-V88 prevalence today, but it really doesn't take a very large haplogroup in order to infer a very fast growth rate, and a Y-STR variance accumulation rate (effective rate) close to the germline one. Therefore, I am guessing that R-V88 is also one of a growing palette of haplogroups that expanded during the Bronze Age.

European Journal of Human Genetics doi:10.1038/ejhg.2009.231

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Fulvio Cruciani et al.

Abstract

Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25* and about half of the few European/west Asian R-P25* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

Link

Tishkoff et al. on genetic structure of Africans and African Americans

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(Updated May 1)

The importance of this new paper from the Tishkoff Lab cannot be emphasized enough. It is probably the most comprehensive study of African genetic variation to date. The supplementary material (pdf) is itself 102 pages long and should keep you busy reading for a while (free for non-subscribers).

What this study has found in a nutshell is that "black" Africans belong to 14 distinct clusters. Black Americans belong overwhelmingly to the Niger-Kordofanian cluster, consistent with their origin largely from Western Africa.

The paper covers the levels of diversity in different African populations, finding that:

Within Africa, genetic diversity estimated from expected heterozygosity significantly correlates with estimates from microsatellite variance (fig. S4) (4) and varies by linguistic, geographic, and subsistence classifications (fig. S5). Three hunter-gatherer populations (Baka and Bakola Pygmies and San) were among the five populations with the highest levels of genetic diversity based on variance estimates (fig. S2A) (4). In addition, more private alleles exist in Africa than other regions (fig. S6A). Consistent with bi-directional gene flow (14), African and Middle Eastern populations shared the greatest number of alleles absent from all other populations(fig. S6B). Within Africa, the most private alleles were in southern Africa, reflecting those in southern African Khoesan (SAK) San and !Xun/Khwe populations (fig. S6C) (12). Eastern and Saharan Africans shared the most alleles absent from other African populations examined (fig. S6D).

As I have stated many times before, Bantu speakers have recently expanded from their cradle and contributed genetically to almost all other Africans, while remaining relatively pure in their own homeland:

High levels of heterogeneous ancestry (i.e. multiple cluster assignments) were observed in nearly all African individuals, with the exception of western and central African Niger-Kordofanian speakers (medium orange), who are relatively homogeneous at large K values (Fig. 5C and fig. S13). Considerable Niger-Kordofanian ancestry (shades of orange) was observed in nearly all populations, reflecting the recent spread of Bantu-speakers across equatorial, eastern, and southern Africa (26) and subsequent admixture with local populations (27).

Similarly, the high levels of diversity in East Africa are attributable in part to the multiple waves of migration into the region, which occurred in the last 5,000 years, long after the ancestral Eurasians left the continent:

East Africa, the hypothesized origin of the migration of modern humans out of Africa, has a remarkable degree of ethnic and linguistic diversity, as reflected by the greatest level of regional substructure in Africa (figs. S13, S14, and S17 to S19). The diversity among populations from this region reflects the proposed long-term presence of click-speaking Hadza and Sandawe hunter-gatherers and successive waves of immigration of Cushitic, Nilotic, and Bantu populations within the past 5,000 years (4, 28, 31, 37, 38).

The 14 clusters are: Mbugu, Chadic, Saharan Cushitic, Eastern Bantu, NiloSaharan, Saharan/Dogon, Fulani, Western Bantu, S.African Khoesan/Mbuti, Niger Kordofanian, Sandawe, Central Sudanic, Hadza, W.Pygmy.

Table S8 in the supplementary material also allows us to measure the extra-African influences in African populations (and vice versa). Mozabites, for example, from the Sahara are 60.2% "European" reflecting their substantial Caucasoid influence. The Beja possess about a third of this "European" element, the Dogon about 45%. Conversely, low-level African admixture in the Near East consists primarily of the "Cushitic" cluster.

UPDATE I (May 1):

The results of the STRUCTURE analysis on a global level (Figure S10 in the supplementary material provide a visual display of global diversity when seen in an African context. At K=14, there are 10 African and 4 non-African clusters (European, Indian, East Asian, Native American). Contrast between Central-Western and Eastern Africa is the most salient feature of the broad picture, punctuated by interesting mini-clusters formed by Pygmies, Khoi-San and Hadza.

An interesting quote from the paper (AAC=Associated Ancestral Clusters):

The Fulani and Cushitic (an eastern Afroasiatic subfamily) AACs, which likely reflect Saharan African and East African ancestry, respectively, are closest to the non-African AACs, consistent with an East African migration of modern humans out of Africa or a back-migration of non-Africans into Saharan and Eastern Africa.

I had pretty much argued as much in the old Dodona forum, that the intermediacy of certain African people between Sub-Saharan Africans and Eurasians was due both to the fact that (a) Eurasians did not originate from Africa in general, but from a specific subset of Africans that was already differentiated from the rest of Africans, and (b) there were back-migrations of Eurasians into Africa.

Related:

• Campbell & Tishkoff review paper on African genetic diversity
• Click language speakers share deep not recent common ancestry
• Male and female genomic contributions to African Americans

Science doi:10.1126/science.1172257

The Genetic Structure and History of Africans and African Americans

Sarah A. Tishkoff et al.

Abstract

Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, 4 African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observe high levels of mixed ancestry in most populations, reflecting historic migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan-speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (~71%), European (~13%), and other African (~8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

Link

mtDNA of Chad Basin populations

Annals of Human Genetics (OnlineEarly Articles)

A Bidirectional Corridor in the Sahel-Sudan Belt and the Distinctive Features of the Chad Basin Populations: A History Revealed by the Mitochondrial DNA Genome

V. Černý et al.

Summary

The Chad Basin was sparsely inhabited during the Stone Age, and its continual settlement began with the Holocene. The role played by Lake Chad in the history and migration patterns of Africa is still unclear. We studied the mitochondrial DNA (mtDNA) variability in 448 individuals from 12 ethnically and/or economically (agricultural/pastoral) different populations from Cameroon, Chad, Niger and Nigeria. The data indicate the importance of this region as a corridor connecting East and West Africa; however, this bidirectional flow of people in the Sahel-Sudan Belt did not erase features peculiar to the original Chad Basin populations. A new sub-clade, L3f2, is described, which together with L3e5 is most probably autochthonous in the Chad Basin. The phylogeography of these two sub-haplogroups seems to indicate prehistoric expansion events in the Chad Basin around 28,950 and 11,400 Y.B.P., respectively. The distribution of L3f2 is virtually restricted to the Chad Basin alone, and in particular to Chadic speaking populations, while L3e5 shows evidence for diffusion into North Africa at about 7,100 Y.B.P. The absence of L3f2 and L3e5 in African-Americans, and the limited number of L-haplotypes shared between the Chad Basin populations and African-Americans, indicate the low contribution of the Chad region to the Atlantic slave trade.

Link