Fulani from Cameroon show ancestry similar to Afroasiatic speakers from East Africa

sahel-region-fulani

Open access African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, by Fan et al. Genome Biology (2019) 20:82.

Interesting excerpts (emphasis mine):

Introduction

To extend our knowledge of patterns of genomic diversity in Africa, we generated high coverage (> 30×) genome sequencing data from 43 geographically diverse Africans originating from 22 ethnic groups, representing a broad array of ethnic, linguistic, cultural, and geographic diversity (Additional file 1: Table S1). These include a number of populations of anthropological interest that have never previously been characterized for high-coverage genome sequence diversity such as Afroasiatic-speaking El Molo fishermen and Nilo-Saharan-speaking Ogiek hunter-gatherers (Kenya); Afroasiatic-speaking Aari, Agaw, and Amhara agro-pastoralists (Ethiopia); Niger-Congo-speaking Fulani pastoralists (Cameroon); Nilo-Saharan-speaking Kaba (Central African Republic, CAR); and Laka and Bulala (Chad) among others. We integrated this data with 49 whole genome sequences generated as part of the Simons Genome Diversity Project (SGDP) [14] (…)

afroasiatic-samples
Locations of samples included in this study. Each dot is an individual and the color indicates the language classification

Results and discussion

We found that the CRHG populations from central Africa, including the Mbuti from the Demographic Republic of Congo (DRC), Biaka from the CAR, and Baka, Bakola, and Bedzan from Cameroon, also form a basal lineage in the phylogeny. The other two hunter-gatherer populations, Hadza and Sandawe, living in Tanzania, group with populations from eastern Africa (Fig. 2). The two Nilo-Saharan-speaking populations, the Mursi from southern Ethiopia and the Dinka from southern Sudan, group into a single cluster, which is consistent with archeological data indicating that the migration of Nilo-Saharan populations to eastern Africa originated from a source population in southern Sudan in the last 3000 years [4, 23, 24, 25].

phylogenetic-relationship-africans
Phylogenetic relationship of 44 African and 32 west Eurasian populations determined by a neighbor joining analysis assuming no admixture. Here, the dots of each node represent bootstrap values and the color of each branch indicates language usage of each population. Human_AA human ancestral alleles

The Fulani people are traditionally nomadic pastoralists living across a broad geographic range spanning Sudan, the Sahel, Central, and Western Africa. The Fulani in our study, sampled from Cameroon, clustered with the Afroasiatic-speaking populations in East Africa in the phylogenetic analysis, indicating a potential language replacement from Afroasiatic to Niger-Congo in this population (Fig. 2). Prior studies suggest a complex history of the Fulani; analyses of Y chromosome variation suggest a shared ancestry with Nilo-Saharan and Afroasiatic populations [24], whereas mtDNA indicates a West African origin [26]. An analysis based on autosomal markers found traces of West Eurasian-related ancestry in this population [4], which suggests a North African or East African origin (as North and East Africans also have such ancestry likely related to expansions of farmers and herders from the Near East) and is consistent with the presence at moderate frequency of the −13,910T variant associated with lactose tolerance in European populations [15, 16].

Phylogenetic reconstruction of the relationship of African individuals under a model allowing for migration using TREEMIX [27] largely recapitulates the NJ phylogeny with the exception of the Fulani who cluster near neighboring Niger-Congo-speaking populations with whom they have admixed (Additional file 2: Figure S1). Interestingly, TREEMIX analysis indicates evidence for gene flow between the Hadza and the ancestors of the Ju|‘hoan and Khomani San, supporting genetic, linguistic, and archeological evidence that Khoesan-speaking populations may have originated in Eastern Africa [28, 29, 30].

afroasiatic-niger-congo-admixture
ADMIXTURE analysis of 92 African and 62 West Eurasian individuals. Each bar is an individual and colors represent the proportion of inferred ancestry from K ancestral populations. The bottom bar shows the language classification of each individual. With the increasing of K, the populations are largely grouped by their current language usage

About the Fulani, this is what the referenced study of Y‐chromosome variation among 15 Sudanese populations by Hassan et al. (2008), had to say:

  • Haplogroups A-M13 and B-M60 are present at high frequencies in Nilo-Saharan groups except Nubians, with low frequencies in Afro-Asiatic groups although notable frequencies of B-M60 were found in Hausa (15.6%) and Copts (15.2%).
  • Haplogroup E (four different haplotypes) accounts for the majority (34.4%) of the chromosome and is widespread in the Sudan. E-M78 represents 74.5% of haplogroup E, the highest frequencies observed in Masalit and Fur populations. E-M33 (5.2%) is largely confined to Fulani and Hausa, whereas E-M2 is restricted to Hausa. E-M215 was found to occur more in Nilo-Saharan rather than Afro-Asiatic speaking groups.
  • In contrast, haplogroups F-M89, I-M170, J-12f2, and JM172 were found to be more frequent in the Afro-Asiatic speaking groups. J-12f2 and J-M172 represents 94% and 6%, respectively, of haplogroup J with high frequencies among Nubians, Copts, and Arabs.
  • Haplogroup K-M9 is restricted to Hausa and Gaalien with low frequencies and is absent in Nilo-Saharan and Niger-Congo.
  • Haplogroup R-M173 appears to be the most frequent haplogroup in Fulani, and haplogroup R-P25 has the highest frequency in Hausa and Copts and is present at lower frequencies in north, east, and western Sudan.
  • Haplogroups A-M51, A-M23, D-M174, H-M52, L-M11, OM175, and P-M74 were completely absent from the populations analyzed.
fulfulde-fulani-language
Image modified from “Fulfulde Language Family Report” Author: Annette Harrison; Cartographer: Irene Tucker; SIL International 2003.

This is what David Reich will talk about in the seminar Insights into language expansions from ancient DNA:

In this talk, I will describe how the new science of genome-wide ancient DNA can provide insights into past spreads of language and culture. I will discuss five examples: (1) the spread of Indo-European languages to Europe and South Asia in association with Steppe pastoralist ancestry, (2) the spread of Austronesian languages to the open Pacific islands in association with Taiwanese aboriginal-associated ancestry, (3) the spread of Austroasiatic languages through southeast Asia in association with the characteristic ancestry type that is also represented in western Indonesia suggesting that these languages were once widespread there, (4) the spread of Afroasiastic languages through in East Africa as part of the Pastoral Neolithic farming expansion, and (5) the spread of Na-Dene languages in North America in association with Proto-Paleoeskimo ancestry. I will highlight the ways that ancient DNA can meaningfully contribute to our understanding of language expansions—increasing the plausibility of some scenarios while decreasing the plausibility of others—while emphasizing that with genetic data by itself we can never definitively determine what languages ancient people spoke.

EDIT (3 MAY 2019): Apparently, there was not much to take from the talk:

neolithic-pastoralist-africa
Pastoralist Neolithic in Africa, through a pale-green Sahelo-Sudanian steppe corridor. See full map.

This seminar (and maybe some new paper on the Neolithic expansion in Africa) could shed light on population movements that may be related to the spread of Afroasiatic dialects. Until now, it seems that Bantu peoples have been more interesting for linguistics and archaeology, and South and East Africans for anthropology.

Archaeology in Africa appears to be in its infancy, as is population genomics. From the latest publication by Carina Schlebusch, Population migration and adaptation during the African Holocene: A genetic perspective, a chapter from Modern Human Origins and Dispersal (2019):

The process behind the introduction and development of farming in Africa is still unclear. It is not known how many independent invention events there were in the continent and to which extent the various first instances of farming in northern Africa are linked. Based on the archeological record, it was proposed that at least three regions in Africa may have developed agriculture independently: the Sahara/Sahel (around 7 ka), the Ethiopian highlands (7-4 ka), and western Africa (5-3 ka). In addition to these developments, the Nile River Valley is thought to have adopted agriculture (around 7.2 ka), from the Neolithic Revolution in the Middle East (Chapter 12 – Jobling et al. 2014; Chapter 35, 37 – Mitchell and Lane 2013). From these diverse centers of origin, farmers or farming practices spread to the rest of Africa, with domesticate animals reaching the southern tip of Africa ~2 ka and crop farming ~1,8 ka (Mitchell 2002; Huffman 2007)

african-popularion-movements
Schematic representation of possible migration routes related to the expansion of herders and crop farmers during Holocene times. Arrow color indicate source populations; Brown-Eurasian, Green-western African, Blue-eastern African.

Similar to the case in Europe and the 1990s-2000s wrong haplogroup history based on the modern distribution of R1b, R1a, N, or I2, it is possible that neither of the most often mentioned haplogroups linked to the Afroasiatic expansion, E and J, were responsible for its early spread within Africa, despite their widespread distribution in certain modern Afroasiatic-speaking areas. The fact that such assessments include implausible glottochronological dates spanning up to 20,000 years for the parent language, combined with regional language continuities despite archaeological changes, makes them even more suspicious.

Similar to the case with Indo-Europeans and the “steppe ancestry” concept of the 2010s, it may be that the often-looked-for West Eurasian ancestry among Africans is the effect of recent migrations, unrelated to the Afroasiatic expansion. The results of this paper could be offering another sign of how this ancestry may have expanded only quite recently westwards from East Africa through the Sahel, after the Semitic expansion to the south:

1. From approximately 1000 BC, accompanying Nilo-Saharan peoples.

2. From approximately AD 1500, with the different population movements related to the nomadic Fulani:

sahel-nomadic-sedentary
Image from Sahel in West African History – Oxford Research Encyclopedia of African History.
  • Arguably, since the Fulani caste system wasn’t as elaborate in northern Nigeria, eastern Niger, and Cameroon, these specific groups would be a good example of the admixture with eastern populations, based on the (proportionally) huge amount of slaves they dealt with.
  • Similarly, it could be argued that the castes-based social stratification in most other territories (including Sudan) would have helped them keep a genetic make-up similar to their region of origin in terms of ancient lineages, hence similar to Chadic populations from west to east.

Reich’s assertion of the association of the language expansion with the spread of Pastoral Neolithic is still too vague, but – based on previous publications of ancient DNA in Africa and the Levant – I don’t have high hopes for a revolutionary paper in the near future. Without many samples and proper temporal transects, we are stuck with speculations based on modern distributions and scarce historical data.

fula-people-distribution
A distribution map of Fula people. Dark green: a major ethnic group; Medium: significant; Light: minor. Modified from image by Sarah Welch at Wikipedia.

About the potential genetic make-up of Cameroon before the arrival of the Neolithic, from the recent SAA 84th Annual Meeting (Abstracts in PDF):

Lipson, Mark (Harvard Medical School), Mary Prendergast (Harvard University), Isabelle Ribot (Université de Montréal), Carles Lalueza-Fox (Institute of Evolutionary Biology CSIC-UPF) and David Reich (Harvard Medical School)

[253] Ancient Human DNA from Shum Laka (Cameroon) in the Context of African Population History We generated genome-wide DNA data from four people buried at the site of Shum Laka in Cameroon between 8000–3000 years ago. One individual carried the deeply divergent Y chromosome haplogroup A00 found at low frequencies among some present-day Niger-Congo speakers, but the genome-wide ancestry profiles for all four individuals are very different from the majority of West Africans today and instead are more similar to West-Central African hunter-gatherers. Thus, despite the geographic proximity of Shum Laka to the hypothesized birthplace of Bantu languages and the temporal range of our samples bookending the initial Bantu expansion, these individuals are not representative of a Bantu source population. We present a phylogenetic model including Shum Laka that features three major radiations within Africa: one phase early in the history of modern humans, one close to the time of the migration giving rise to non-Africans, and one in the past several thousand years. Present-day West Africans and some East Africans, in addition to Central and Southern African hunter-gatherers, retain ancestry from the first phase, which is therefore still represented throughout the majority of human diversity in Africa today.

Related

Genetic ancestry of Hadza and Sandawe peoples reveals ancient population structure in Africa

Open access paper Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa, by Shriner, Tekola-Ayele, Adeyemo, & Rotimi, GBE (2018).

Abstract (emphasis mine):

The Hadza and Sandawe populations in present-day Tanzania speak languages containing click sounds and therefore thought to be distantly related to southern African Khoisan languages. We analyzed genome-wide genotype data for individuals sampled from the Hadza and Sandawe populations in the context of a global data set of 3,528 individuals from 163 ethno-linguistic groups. We found that Hadza and Sandawe individuals share ancestry distinct from and most closely related to Omotic ancestry; share Khoisan ancestry with populations such as ≠Khomani, Karretjie, and Ju/’hoansi in southern Africa; share Niger-Congo ancestry with populations such as Yoruba from Nigeria and Luhya from Kenya, consistent with migration associated with the Bantu Expansion; and share Cushitic ancestry with Somali, multiple Ethiopian populations, the Maasai population in Kenya, and the Nama population in Namibia. We detected evidence for low levels of Arabian, Nilo-Saharan, and Pygmy ancestries in a minority of individuals. Our results indicate that west Eurasian ancestry in eastern Africa is more precisely the Arabian parent of Cushitic ancestry. Relative to the Out-of-Africa migrations, Hadza ancestry emerged early whereas Sandawe ancestry emerged late.

Excerpts:

Introduction
In the Hadza population, the distribution of Y chromosomes includes mostly B2 haplogroups, with a smaller number of E1b1a haplogroups, which are common in Niger-Congo-speaking populations, and E1b1b haplogroups, which are common in Cushitic populations (Tishkoff, et al. 2007). In the Sandawe population, E1b1a and E1b1b haplogroups are more common, with lower frequencies of B2 and A3b2 haplogroups (Tishkoff, et al. 2007).

Conclusion
We found that Hadza ancestry diverged early, rather than late. We found evidence for contributions of Cushitic and Niger-Congo ancestries in Tanzania, consistent with the movements of herding and cultivating Cushitic speakers ~4,000 years ago and agricultural Niger-Congo speakers ~2,500 years ago (Newman 1995). However, we did not find evidence of a substantial contribution of Nilo-Saharan ancestry that might have resulted from movement of pastoralist Nilo-Saharan speakers (Newman 1995). We also identified west Eurasian ancestry in eastern and southern African populations more precisely as the Arabian parent of Cushitic ancestry. Finally, our ancestry analyses support the hypothesis that Omotic, Hadza, and Sandawe languages group together, rather than Omotic languages belonging to the Afroasiatic family and Hadza and Sandawe languages belonging to the Khoisan family.

I don’t like linguistic assumptions from admixture analysis; especially from scarce modern samples, as in this case.

Nevertheless, these papers may help clarify the different nature of Omotic and Cushitic among Afroasiatic languages, and thus leave the origin of Afroasiatic either:

a) To the east, with the traditionalist Afroasiatic – Semitic/Hamitic homeland association.

afroasiatic-homeland
Expansion of Afroasiatic

b) To the west, near modern Chadic languages (associated with the expansion of R1b-V88 subclades through a Green Sahara), as I suggested.

Related:

Human ancestry solves language questions? New admixture citebait

human_ancestry

A paper at Scientific Reports, Human ancestry correlates with language and reveals that race is not an objective genomic classifier, by Baker, Rotimi, and Shriner (2017).

Abstract (emphasis mine):

Genetic and archaeological studies have established a sub-Saharan African origin for anatomically modern humans with subsequent migrations out of Africa. Using the largest multi-locus data set known to date, we investigated genetic differentiation of early modern humans, human admixture and migration events, and relationships among ancestries and language groups. We compiled publicly available genome-wide genotype data on 5,966 individuals from 282 global samples, representing 30 primary language families. The best evidence supports 21 ancestries that delineate genetic structure of present-day human populations. Independent of self-identified ethno-linguistic labels, the vast majority (97.3%) of individuals have mixed ancestry, with evidence of multiple ancestries in 96.8% of samples and on all continents. The data indicate that continents, ethno-linguistic groups, races, ethnicities, and individuals all show substantial ancestral heterogeneity. We estimated correlation coefficients ranging from 0.522 to 0.962 between ancestries and language families or branches. Ancestry data support the grouping of Kwadi-Khoe, Kx’a, and Tuu languages, support the exclusion of Omotic languages from the Afroasiatic language family, and do not support the proposed Dené-Yeniseian language family as a genetically valid grouping. Ancestry data yield insight into a deeper past than linguistic data can, while linguistic data provide clarity to ancestry data.

Regarding European ancestry:

Southern European ancestry correlates with both Italic and Basque speakers (r = 0.764, p = 6.34 × 10−49). Northern European ancestry correlates with Germanic and Balto-Slavic branches of the Indo-European language family as well as Finno-Ugric and Mordvinic languages of the Uralic family (r = 0.672, p = 4.67 × 10−34). Italic, Germanic, and Balto-Slavic are all branches of the Indo-European language family, while the correlation with languages of the Uralic family is consistent with an ancient migration event from Northern Asia into Northern Europe. Kalash ancestry is widely spread but is the majority ancestry only in the Kalash people (Table S3). The Kalasha language is classified within the Indo-Iranian branch of the Indo-European language family.

Sure, admixture analysis came to save the day. Yet again. Now it’s not just Archaeology related to language anymore, it’s Linguistics; all modern languages and their classification, no less. Because why the hell not? Why would anyone study languages, history, archaeology, etc. when you can run certain algorithms on free datasets of modern populations to explain everything?

What I am criticising here, as always, is not the study per se, its methods (PCA, the use of Admixture or any other tools), or its results, which might be quite interesting – even regarding the origin or position of certain languages (or more precisely their speakers) within their linguistic groups; it’s the many broad, unsupported, striking conclusions (read the article if you want to see more wishful thinking).

This is obviously simplistic citebait – that benefits only journals and authors, and it is therefore tacitly encouraged -, but not knowledge, because it is not supported by any linguistic or archaeological data or expertise.

Is anyone with a minimum knowledge of languages, or general anthropology, actually reviewing these articles?

Related:

Featured image: Ancestry analysis of the global data set, from the article.

Potential Afroasiatic Urheimat near Lake Megachad

palaeolithic-migrations

The publication of new ancient DNA samples from Africa is near, according to people at the SMBE meeting. As reported by Anthropology.net, a group by Pontus Skoglund has analysed new samples (complementing the study made by Carina Schlebusch), so we will have ancient samples of Africans from 300 to 6,000 years ago. They have been compared to the data of modern African populations, and among their likely conclusions (to be published):

  • Several thousand years ago, likely Tanzanian herders migrated far and wide, reaching Southern Africa centuries before the first farmers.
  • West Africans were likely early contributors to the gene pool of sub-Saharan Africans.
  • One ancient African herder showed influence from even farther abroad, with 38% of their DNA coming from outside Africa. 9-22% of the DNA of modern farmers, including the southern Khoe-San, comes from East Africans and Eurasian herders
  • Modern farmers, the ones as old as 500 years old, did have Bantu DNA in their genomes, but the ancient hunter-gatherers predated the spread of the Bantu.

Razib Khan, asked about the Afroasiatic homeland by David Reich, has taken this opportunity to publish his own hypothesis on the expansion of Afroasiatic, given the known Admixture analyses, using Y-DNA phylogeography, and with reasonable assumptions. He concludes that Afroasiatic expansion might also be associated with the western expansion of E1b1b subclades from a Levantine (“Natufian”) homeland.

I think it is necessary to remind everyone of the many problems unsolved by Indo-European studies – a much older discipline (and with more research published) than Afroasiatic studies. It is already quite revealing that we can’t still trace back Proto-Semitic to its homeland, and that Proto-Semitic is probably as old as Late Proto-Indo-European. We are talking, then, about an ancient proto-language – Afroasiatic – possibly older than Middle Indo-European (or Indo-Hittite), and whose dialects are still not well studied – but for the Semitic and Egyptian branches. Linguistic guesstimates or phylogenetic speculation date the proto-language (and thus the homeland) within a wide range, from 15,000 to 6,000 years ago.

There is an obvious trend (probably driven by Semitic and Egyptian researchers) to place the Afroasiatic Homeland near one of the many proposed Semitic homelands, i.e. in East Africa. This is similar to the trend seen in the first half of the 20th century in Indo-European studies, with most proposals locating the Proto-Indo-European homeland in Europe. European languages were the best known, and only the perceived antiquity of Vedic Sanskrit made some propose South Asian origins for the proto-language. However, it was only careful interpretation of linguistic finds, combined with archaeological data, what eventually yielded the Kurgan hypothesis, which has been since refined.

afroasiatic-homeland
A model for the homeland and expansion of Afroasiatic, from Wikipedia

Razib Khan’s proposal makes sense in that it fits what others have proposed before, i.e. an east African or Middle Eastern Afroasiatic homeland, and that it links it with the expansion of farming. However, we have to keep in mind that until 5,000 years ago the Sahara was not the desert we know: it had certain important green corridors, humid areas between megalakes. The Sahara might not have been exactly green 10,000 to 5,000 years ago (roughly the time when Afroasiatic must have been spoken), but it had certain regions that allowed for an east-west migration. However, it also allowed for a west-east migration, and – perhaps more importantly – for a sizeable population expansion in central Saharan territory. To forget that is to allow for potentially wrong assumptions to be made.

What we expect from the next papers on ancient African DNA samples are the result of certain (more recent) population – and thus potentially ethnolinguistic – movements, but they probably won’t solve the question of the Afroasiatic homeland, which has an older time span than the samples studied. There is a wide void in African prehistory – compared with Near Eastern history – and this research will be closing that gap, just like European samples are helping close the gap in the prehistory of western, northern, and eastern Europe, compared to the history of the eastern Mediterranean regions.

palaeolithic-europe-africa
Diachronic map of Paleolithic migrations of R1b lineages in Europe and Africa

I already wrote, regarding the potential ethnolinguistic link between Indo-European and Afroasiatic, that a close look at the migration of R1b-V88 lineages from Europe (through southern Italy?) into the Sahara – through the Fezzan-Chad-Chotts, and Chad-Chotts-Ahnet-Moyer megalake green corridors – could have been the key to the successful expansion of Afrasians.

Interesting aspects to take into account are the distribution of R1b-V88 lineages, compared to the location of Chadic languages (probably the most divergent and least known of the group) and to the potential North Afroasiatic (composed by Egyptian, Berber, and Semitic) and South Afroasiatic group (made of Cushitic and Omotic). Chadic has been argued to be connected variously to North Afroasiatic, or to the Berber branch, but the Northern group has also been argued to be connected with Cushitic, with Omotic as an independent branch. Also interesting would then be the potential connection between Indo-European (or Indo-Uralic) and Afroasiatic.

r1b-map
Modern distribution of haplogroup R1b, from Wikipedia

We could speculatively place the potential primary Afroasiatic homeland in the south-central Sahara, near the Megachad lake (i.e. near the peak of R1b-V88 lineages), with a secondary homeland in eastern Africa (as in the map above) – and maybe a tertiary homeland (of North Afroasiatic) in the Middle East, associated with the expansion of “Natufians” and E1b1b subclades. The identification of the spread of Afroasiatic languages with the expansion of R1b-V88 lineages needs an anthropological context (linguistic and archaeological) that is obviously lacking today.

It is important to keep all possibilities in sight when reviewing genetic analyses.

Related:

EDIT (16/7/2017): Added link to Neby’s post on a potential Semitic homeland, and Nature article on Schlebusch and Skoglund research.