Contrasting patterns of Y chromosome and mtDNA variation in Africa: Evidence for sex-biased demographic processes

Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.
European Journal of HumanGenetics (Impact Factor: 4.35). 08/2005; 13(7):867-76. DOI: 10.1038/sj.ejhg.5201408
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ABSTRACT To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

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Available from: Giovanni Destro Bisol, Sep 26, 2015
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    • "Batai et al. 2013; Beleza et al. 2005; Castri et al. 2009; Coia et al. 2005; Gonder et al. 2007; Plaza et al. 2004; Quintana-Murci et al. 2008; Richards et al. 2004; Salas et al. 2002; Scozzari et al. 1994). Several also studied populations speaking Nilo-Saharan languages (Krings et al. 1999; Poloni et al. 2009; Tishkoff et al. 2007, 2009; Watson et al. 1996; Wood et al. 2005) and Afroasiatic languages (Boattini et al. 2013), and a substantial genome-wide dataset from Ethiopia points to significant differentiation amongst speakers of the different language phyla (Pagani et al. 2012). Studies of mtDNA in Bantu-and Nilotic-speaking groups in Kenya have shown that they have much in common, but that they can nevertheless be differentiated phylogeographically by language phylum (Castri et al. 2008), and that even distinct Bantu-speaking groups can differ significantly genetically, possibly depending on the extent of assimilation of local lineages (Batai et al. 2013). "
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    ABSTRACT: The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
    Human Genetics 07/2015; 134(9). DOI:10.1007/s00439-015-1583-0 · 4.82 Impact Factor
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    • "More importantly, our results indicate substantial differences among regional groups in the between-group variance for the NRY versus mtDNA (Figure 2) as well as in overall levels of NRY versus mtDNA diversity (Figure 2, Table 1). Thus, focusing on global patterns of variation misses this important regional variation, which (as discussed in more detail above in the Results) likely reflects differences in the paternal versus maternal demographic history of specific human populations (for example, the large impact of the Bantu expansion on African NRY diversity [59,60], and of the Austronesian expansion on Oceanic mtDNA diversity [63,65]). "
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    ABSTRACT: Background Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. Conclusions The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
    Investigative Genetics 09/2014; 5(1):13. DOI:10.1186/2041-2223-5-13
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    • " feature of the Cushitic way of life since the proto - Cushitic period ( Ehret 1979 ) . An eastern Bantu migration through East Africa appears to have occurred around 2 , 000 years ago as evidenced by both Y - chromosome and mitochondrial DNA variation ( Pereira et al . 2001 ; Salas et al . 2002 ; Scheinfeldt et al . 2010 ; Tishkoff et al . 2009 ; Wood et al . 2005 ) . The expansions of pastoral and farming groups across East Africa likely resulted in the large - scale demise or incorporation of the incumbent click - speaking populations ( Diamond and Bellwood 2003 ) , though the exact nature of their disappear - ance remains to be ascertained . The Sandawe have experienced gene flow with neighbou"
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    ABSTRACT: This paper examines intersections between different societies occupying the Nyali Coast region of southern Kenya from the late first millennium ad to the mid-second millennium ad. We explore interaction between societies at three scales: between hunter-gatherers and farmers in the coastal hinterland, between the hinterland and the coast and between the coast and the wider Indian Ocean. The patterns indicate that local intersections in the hinterland between hunter-gatherers and farmers went hand-in-hand with both the emergence of larger settlements in the hinterland and on the coast, and participation in a pan-Indian Ocean trade network.
    African Archaeological Review 12/2013; 30(4). DOI:10.1007/s10437-013-9140-5
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