Bringing together linguistic and genetic evidence to test the Bantu expansion

The expansion of Bantu languages represents one of the most momentous events in the history of Africa. While it is well accepted that Bantu languages spread from their homeland (Cameroon/Nigeria) approximately 5000 years ago (ya), there is no consensus about the timing and geographical routes underlying this expansion. Two main models of Bantu expansion have been suggested: The 'early-split' model claims that the most recent ancestor of Eastern languages expanded north of the rainforest towards the Great Lakes region approximately 4000 ya, while the 'late-split' model proposes that Eastern languages diversified from Western languages south of the rainforest approximately 2000 ya. Furthermore, it is unclear whether the language dispersal was coupled with the movement of people, raising the question of language shift versus demic diffusion. We use a novel approach taking into account both the spatial and temporal predictions of the two models and formally test these predictions with linguistic and genetic data. Our results show evidence for a demic diffusion in the genetic data, which is confirmed by the correlations between genetic and linguistic distances. While there is little support for the early-split model, the late-split model shows a relatively good fit to the data. Our analyses demonstrate that subsequent contact among languages/populations strongly affected the signal of the initial migration via isolation by distance.     

Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples

The majority of sub-Saharan Africans today speak a number of closely related languages collectively referred to as ‘Bantu’ languages. The current distribution of Bantu-speaking populations has been found to largely be a consequence of the movement of people rather than a diffusion of language alone. Linguistic and single marker genetic studies have generated various hypotheses regarding the timing and the routes of the Bantu expansion, but these hypotheses have not been thoroughly investigated. In this study, we re-analysed microsatellite markers typed for large number of African populations that—owing to their fast mutation rates—capture signatures of recent population history. We confirm the spread of west African people across most of sub-Saharan Africa and estimated the expansion of Bantu-speaking groups, using a Bayesian approach, to around 5600 years ago. We tested four different divergence models for Bantu-speaking populations with a distribution comprising three geographical regions in Africa. We found that the most likely model for the movement of the eastern branch of Bantu-speakers involves migration of Bantu-speaking groups to the east followed by migration to the south. This model, however, is only marginally more likely than other models, which might indicate direct movement from the west and/or significant gene flow with the western Branch of Bantu-speakers. Our study use multi-loci genetic data to explicitly investigate the timing and mode of the Bantu expansion and it demonstrates that west African groups rapidly expanded both in numbers and over a large geographical area, affirming the fact that the Bantu expansion was one of the most dramatic demographic events in human history.     

Insights into the demographic history of African Pygmies from complete mitochondrial genomes

Pygmy populations are among the few hunter-gatherers currently living in sub-Saharan Africa and are mainly represented by two groups, Eastern and Western, according to their current geographical distribution. They are scattered across the Central African belt and surrounded by Bantu-speaking farmers, with whom they have complex social and economic interactions. To investigate the demographic history of Pygmy groups, a population approach was applied to the analysis of 205 complete mitochondrial DNA (mtDNA) sequences from ten central African populations. No sharing of maternal lineages was observed between the two Pygmy groups, with haplogroup L1c being characteristic of the Western group but most of Eastern Pygmy lineages falling into subclades of L0a, L2a, and L5. Demographic inferences based on Bayesian coalescent simulations point to an early split among the maternal ancestors of Pygmies and those of Bantu-speaking farmers (～ 70,000 years ago [ya]). Evidence for population growth in the ancestors of Bantu-speaking farmers has been observed, starting ～ 65,000 ya, well before the diffusion of Bantu languages. Subsequently, the effective population size of the ancestors of Pygmies remained constant over time and ～ 27,000 ya, coincident with the Last Glacial Maximum, Eastern and Western Pygmies diverged, with evidence of subsequent migration only among the Western group and the Bantu-speaking farmers. Western Pygmies show signs of a recent bottleneck 4,000-650 ya, coincident with the diffusion of Bantu languages, whereas Eastern Pygmies seem to have experienced a more ancient decrease in population size (20,000-4,000 ya). In conclusion, the results of this first attempt at analyzing complete mtDNA sequences at the population level in sub-Saharan Africa not only support previous findings but also offer new insights into the demographic history of Pygmy populations, shedding new light on the ancient peopling of the African continent.     

Cultural phylogeography of the Bantu Languages of sub-Saharan Africa

There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees of Bantu languages and map them onto geographical space in order to assess the likely pathway of expansion and test between dispersal scenarios. The results clearly support a scenario in which groups first moved south through the rainforest from a homeland somewhere near the Nigeria–Cameroon border. Emerging on the south side of the rainforest, one branch moved south and west. Another branch moved towards the Great Lakes, eventually giving rise to the monophyletic clade of East Bantu languages that inhabit East and Southeastern Africa. These phylogenies also reveal information about more general processes involved in the diversification of human populations into distinct ethnolinguistic groups. Our study reveals that Bantu languages show a latitudinal gradient in covering greater areas with increasing distance from the equator. Analyses suggest that this pattern reflects a true ecological relationship rather than merely being an artefact of shared history. The study shows how a phylogeographic approach can address questions relating to the specific histories of certain groups, as well as general cultural evolutionary processes.     

Mitochondrial DNA diversity in two ethnic groups in Southeastern Kenya: Perspectives from the northeastern periphery of the bantu expansion

The Bantu languages are widely distributed throughout sub‐Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu‐ and non‐Bantu‐speaking populations in east Africa. The Taita and Mijikenda are Bantu‐speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu‐speaking groups. The non‐Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu‐speaking Taita groups. In contrast, gene flow from non‐Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non‐Bantu interactions varied throughout the area. Am J Phys Anthropol 150:482–491, 2013. © 2013 Wiley Periodicals, Inc.     

On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

Background  

Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations.     

mtDNA variability in two Bantu‐speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub‐Saharan Africa

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu‐speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu‐speaking populations. Moreover, by comparing our data with those from other Niger‐Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub‐Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu‐speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu‐speaking populations, but also between Bantu and non‐Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu‐speakers, with strong interactions between the different lines of Bantu‐speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups

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 (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ～ 5,000 ya 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 sublineage 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 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 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 short tandem repeat (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 suggests 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.     

Genetic perspectives on forager‐farmer interaction in the Luangwa Valley of Zambia

The transformation from a foraging way of life to a reliance on domesticated plants and animals often led to the expansion of agropastoralist populations at the expense of hunter‐gatherers (HGs). In Africa, one of these expansions involved the Niger‐Congo Bantu‐speaking populations that started to spread southwards from Cameroon/Nigeria ～4,000 years ago, bringing agricultural technologies. Genetic studies have shown different degrees of gene flow (sometimes involving sex‐biased migrations) between Bantu agriculturalists and HGs. Although these studies have covered many parts of sub‐Saharan Africa, the central part (e.g. Zambia) was not yet studied, and the interactions between immigrating food‐producers and local HGs are still unclear. Archeological evidence from the Luangwa Valley of Zambia suggests a long period of coexistence (～1,700 years) of early food‐producers and HGs. To investigate if this apparent coexistence was accompanied by genetic admixture, we analyzed the mtDNA control region, Y chromosomal unique event polymorphisms, and 12 associated Y‐ short tandem repeats in two food‐producing groups (Bisa and Kunda) that live today in the Luangwa Valley, and compared these data with available published data on African HGs. Our results suggest that both the Bisa and Kunda experienced at most low levels of admixture with HGs, and these levels do not differ between the maternal and paternal lineages. Coalescent simulations indicate that the genetic data best fit a demographic scenario with a long divergence (62,500 years) and little or no gene flow between the ancestors of the Bisa/Kunda and existing HGs. This scenario contrasts with the archaeological evidence for a long period of coexistence between the two different communities in the Luangwa Valley, and suggests a process of sociocultural boundary maintenance may have characterized their interaction. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Contrasted polymorphism patterns in a large sample of populations from the evolutionary genetics model Drosophila simulans

African populations of Drosophila simulans are thought to be ancestral in this model species and are increasingly used for testing general hypotheses in evolutionary genetics. It is often assumed that African populations are more likely to be at a neutral mutation drift equilibrium than other populations. Here we examine population structuring and the demographic profile in nine populations of D. simulans. We surveyed sequence variation in four X-linked genes (runt, sevenless, Sex-lethal, and vermilion) that have been used in a parallel study in the closely related species D. melanogaster. We found that an eastern group of populations from continental Africa and Indian Ocean islands (Kenya, Tanzania, Madagascar, and Mayotte Island) is widespread, shows little differentiation, and has probably undergone demographic expansion. The other two African populations surveyed (Cameroon and Zimbabwe) show no evidence of population expansion and are markedly differentiated from each other as well as from the populations from the eastern group. Two other populations, Europe and Antilles, are probably recent invaders to these areas. The Antilles population is probably derived from Europe through a substantial bottleneck. The history of these populations should be taken into account when drawing general conclusions from variation patterns.     

Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria

Background  

The Cross River region in Nigeria is an extremely diverse area linguistically with over 60 distinct languages still spoken today. It is also a region of great historical importance, being a) adjacent to the likely homeland from which Bantu-speaking people migrated across most of sub-Saharan Africa 3000-5000 years ago and b) the location of Calabar, one of the largest centres during the Atlantic slave trade. Over 1000 DNA samples from 24 clans representing speakers of the six most prominent languages in the region were collected and typed for Y-chromosome (SNPs and microsatellites) and mtDNA markers (Hypervariable Segment 1) in order to examine whether there has been substantial gene flow between groups speaking different languages in the region. In addition the Cross River region was analysed in the context of a larger geographical scale by comparison to bordering Igbo speaking groups as well as neighbouring Cameroon populations and more distant Ghanaian communities.     

Recent Acquisition of Helicobacter pylori by Baka Pygmies

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors.     

An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data

Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we resequenced a sample of San, Eastern, and Western Pygmies and non-Pygmy NKs individuals at 40 nongenic (～2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ～110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize "pseudo-observed" data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data.     

Ancient Substructure in Early mtDNA Lineages of Southern Africa

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.     

Dual phylogenetic origins of Nigerian lions (Panthera leo)

Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji‐Lake National Park (central northeast and west Nigeria, respectively) were Sanger‐sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum‐likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji‐Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.     

Unraveling the complex maternal history of Southern African Khoisan populations

The Khoisan populations of southern Africa are known to harbor some of the deepest‐rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre‐Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari. Am J Phys Anthropol 153:435–448, 2014. © 2013 Wiley Periodicals, Inc.     

Y chromosomes traveling south: the cohen modal haplotype and the origins of the Lemba--the "Black Jews of Southern Africa"

The Lemba are a traditionally endogamous group speaking a variety of Bantu languages who live in a number of locations in southern Africa. They claim descent from Jews who came to Africa from "Sena." "Sena" is variously identified by them as Sanaa in Yemen, Judea, Egypt, or Ethiopia. A previous study using Y-chromosome markers suggested both a Bantu and a Semitic contribution to the Lemba gene pool, a suggestion that is not inconsistent with Lemba oral tradition. To provide a more detailed picture of the Lemba paternal genetic heritage, we analyzed 399 Y chromosomes for six microsatellites and six biallelic markers in six populations (Lemba, Bantu, Yemeni-Hadramaut, Yemeni-Sena, Sephardic Jews, and Ashkenazic Jews). The high resolution afforded by the markers shows that Lemba Y chromosomes are clearly divided into Semitic and Bantu clades. Interestingly, one of the Lemba clans carries, at a very high frequency, a particular Y-chromosome type termed the "Cohen modal haplotype," which is known to be characteristic of the paternally inherited Jewish priesthood and is thought, more generally, to be a potential signature haplotype of Judaic origin. The Bantu Y-chromosome samples are predominantly (>80%) YAP+ and include a modal haplotype at high frequency. Assuming a rapid expansion of the eastern Bantu, we used variation in microsatellite alleles in YAP+ sY81-G Bantu Y chromosomes to calculate a rough date, 3,000-5,000 years before the present, for the start of their expansion.     

The peopling of sub-Saharan Africa: the case study of Cameroon.

This study analyzes the distribution of ten protein genetic polymorphisms in eighteen populations from the most densely inhabited areas of Cameroon. The languages spoken belong to three different linguistic families [Afro-Asiatic (AA), Nilo-Saharan (NS) and Niger-Kordofanian (NK)]. The analysis of variation of allele frequencies indicates that the level of genetic interpopulation differentiation is rather low (F(st) = 0.011 +/- 0.006) but statistically significant (p < 0.001). This result is not unexpected because of the relatively small geographic area covered by our survey. This value is also significantly lower than the one estimated for other groups of African populations. Among the factors responsible for this, we discuss the possible role of gene flow. There is a considerable genetic differentiation among the AA populations of north Cameroon as is to be expected because they all originated from the first agriculturists of the farming "savanna complex." The Podowko and Uldeme are considerably different from all the other AA groups, probably due to the combined effect of genetic drift and isolation. In the case of the Wandala and Massa, our analyses suggest that genetic admixture with allogeneous groups (especially with the Kanuri) played an important role in determining their genetic differentiation from other AA speaking groups. The Bantu speaking populations (Bakaka, Bamileke Bassa and Ewondo, NK family, Benué Congo subfamily) settled in western and southern Cameroon are more tightly clustered than AA speaking groups. This result shows that the linguistic affinity among these four populations coincides with a substantial genetic similarity despite their different origin. Finally, the Fulbe are genetically distinct from all the populations that belong to their same linguistic phylum (NK), and closer to the neighboring Fali and Tupuri, eastern Adamawa speaking groups of north Cameroon.     

Refining the Y chromosome phylogeny with southern African sequences

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.     

Digging deeper into East African human Y chromosome lineages

The most significant and widely studied remodeling of the African genetic landscape is the Bantu expansion, which led to an almost total replacement of the previous populations from the sub-Saharan region. However, a poor knowledge exists about other population movements, namely, the Nilotic migration, which is a pastoralist dispersal that, contrary to the Bantu expansion, impacted only East African populations. Here, samples from a Ugandan Nilotic-speaking population were studied for 37 Y chromosome-specific SNPs, and the obtained data were compared with those already available for other sub-Saharan population groups. Although Uganda lies on the fringe of both Bantu and Nilotic expansions, a low admixture with Bantu populations was detected, with haplogroups carrying M13, M182 and M75 mutations prevailing in Nilotes together with a low frequency of the main Bantu haplogroups from clade E1b1a-M2. The results of a comparative analysis with data from other population groups allowed a deeper characterization of some lineages in our sample, clarifying some doubts about the origin of some particular Y-SNPs in different ethnic groups, such as M150, M112 and M75. Moreover, it was also possible to identify a new Y-SNP apparently specific to Nilotic groups, as well as the presence of particular haplogroups that characterize Nilotic populations. The detection of a new haplogroup B2a1b defined by G1, could be, therefore, important to differentiate Nilotes from other groups, helping to trace migration and admixture events that occurred in eastern Africa.