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North African populations carry the signature of admixture with Neandertals - PubMed

North African populations carry the signature of admixture with Neandertals

Federico Sánchez-Quinto et al. PLoS One. 2012.

Abstract

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Results of the ADMIXTURE analysis (k = 4) with North African populations.

ADMIXTURE was performed on a set of European, North African, Near Eastern and Sub-Saharan populations in order to account for the different admixture proportions in North Africa. Tunisians and Saharawi are the North African populations with highest proportion of autochthonous component, whereas the rest of the populations have greater amounts of admixture with neighboring populations.

Figure 2
Figure 2. PCA analysis of North African, Sub-Saharan, European and Asian populations.

Upper right box: PCA analysis with the African populations (dark blue, Sub-Saharan, light blue, North African), along with three outgroups: chimpanzee, Neandertal and Denisovan. It can be seen that North African populations are placed in the direction of the Neandertal. In the population analysis, the North African groups tend to be placed in an intermediate position between Sub-Saharan and non-African human populations. Population abbreviations are the same as in Table 2.

Figure 3
Figure 3. Neandertal genetic introgression in North African populations as a fraction of that found in Europeans.

Relative proportion of Neandertal ancestry for each population is presented as the dark blue section of the pies on a map of North Africa. Additionally, each population is also represented as a barplot of the different geographic genetic components; in red: North African, in blue: Sub-Saharan, in green: European, in yellow: Near East. Populations are shown as having Neandertal ancestry if the estimates are more than two standard errors from zero. Full name descriptions of these population labels are found in Table 2.

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Grants and funding

FS-Q, SC, CA and CL-F are supported by a grant from the Ministerio de Ciencia e Innovación of Spain (BFU2009-06974) and CGL2010-14944/BOS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.