The dataset comprises a mixture of 2504 previously published individuals from Africa and elsewhere (see below) plus novel genotypes on 1366 sampled by the Malaria Genomic Epidemiology Network (MalariaGEN) Figure 1—source data 1. This analysis allows us to ask whether the indirect Bantu ancestry we observe in East and Southern Niger-Congo speakers can be traced back to the origin of the expansion. the Luhya) interacted with nearby Nilo-Saharan speakers after the putative arrival of Bantu-speaking groups to Eastern Africa which we discuss below. In the SEBantu (1109:1051-1196CE) and AmaXhosa (1196CE: 1109-1283CE), from east southern Africa, we observe reciprocal admixture events involving major sources most similar to East African Niger-Congo speakers. Throughout we refer to target populations as recipients, any other sampled populations used to describe the recipient population’s admixture event(s) as surrogates, and populations used to paint both recipient and surrogate populations as donors. Interestingly, the Chonyi (1138CE: 1080-1182CE) and Kauma (1225CE: 1167-1254CE) are located on the Kenyan Swahili Coast, a region where Medieval trade across the Indian Ocean is historically documented (Allen, 1993), which might explain this Asian admixture. By removing non-local surrogates, we can infer admixture parameters and characterize admixture sources as mixtures of this reduced set of surrogates. (2014) do attempt with the same dataset). Conversely, comparisons of MALDER curves when the second source of admixture was Eurasian (dark yellow) or Khoesan (green), showed that these groups were usually the single best surrogate for the second source of admixture (SOURCE 2). Admixture in East African Niger-Congo speakers occurs during the period 500-1500CE, with a peak around 1000CE. 1. However, to address the reviewer’s concerns, we have rephrased this sentence and moved it to the Introduction: “The extent to which this cultural expansion was accompanied by people is an active research question, but an increasing number of molecular studies indicate that the expansion of languages was accompanied by the diffusion of people [Beleza et al., 2005; Berniell-Lee et al., 2009; Tishkoff et al., 2009; Pakendorf et al., 2011; de Filippo et al., 2012; Ansari Pour et al., 2013; Li et al., 2014; Gonz´alez-Santos et al., 2015].”, A separate issue is whether the Tishkoff et al. contiguous segments of DNA copied from a single donor haploid) separated by genetic distance g. For every two donor populations, we tabulate the number of chunk pairs where the two chunks come from the two populations. As such, the arrows point from the country of component origin to the country of the recipient. Date confidence intervals are based on 100 bootstrap replicates of the date inference. the first principal component, reflecting admixture involving two sources) and FQ2 is the fit of the first two principal components capturing the admixture event(s) (the second component might be thought of as capturing a second, less strongly-signalled event. It remains to be shown whether known environmental triggers of RA (i.e. A recent example of this process is the observation of higher than expected frequencies of the Duffy-null mutation in populations from Madagascar as a result of admixture with African Bantu speaking groups (Hodgson et al., 2014b). On the basis of this analysis, to reduce the confounding effect of demography, with the exception of the next section, all ALDER/MALDER analyses presented in the paper were performed after accounting for this short range shared LD. Specifically, we have (1) converted the date confidence intervals (CI) from +/- 1 standard error (SE) to +/- 1.96 SE to be more closely comparative to the 95% CIs generated by GLOBETROTTER, and (2) we have put dotted vertical lines at 1000 year intervals. Central West African, and in particular ancestry from Cameroon (red ancestry in Figure 6A), is seen in Southern African Niger-Congo and Khoesan speaking groups, the Herero, Khwe and !Xun, indicating that the gradual diffusion of Bantu ancestry reached the south of the continent only within the last 750 years. In particular, admixture identified using f3 statistics but not by ALDER is potentially related to more ancient events because whilst shared drift signals will still be present, admixture LD will have been broken over (potentially) millennia of recombination. Greenlandic Inuit, for example, have adapted genetically to a diet rich in polyunsaturated fatty acids (Fumagalli et al., 2015), and one of the strongest signals of selection in the genome is found around the LCT gene (Bersaglieri et al., 2004), mutations in which allow individuals to continue to digest milk into adulthood. In two southern African Khoesan groups we see very recent admixture, within the last 250 years, involving northern European ancestry which likely resulted from Colonial Era movements from the UK, Germany, and the Netherlands into South Africa (Thompson, 2001). The final ancestry region assignments are outlined in Figure 1—source data 1. (links to download the citations from this article in formats compatible with various reference manager tools), (links to open the citations from this article in various online reference manager services), Malaria Genomic Epidemiology Network, 2008, Malaria Genomic Epidemiology Network, 2015, Malaria Genomic Epidemiology Network, 2014. https://github.com/georgebusby/admixture_in_africa. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. We show that gene-flow has taken place over a variety of different time scales which suggests that, rather than being static, populations have been sharing DNA, particularly over the last 3000 years. We use a cut-off of Z< 2 to decide whether sources from multiple ancestries best describe the admixture source. Overall, approximately 80% of the AA genome is of West African ancestry and 20% of European Ancestry. For each map, we plot arrows for any event involving the following: Recent Western Bantu gene-flow: any admixture source which has a component from either of the two Cameroon ethnic groups, Bantu and Semi-Bantu. Nature Communications, 6, 10.1038/ncomms7596. There are also several examples of humans adapting in response to infectious disease, for example at the LARGE gene in West Africans (Grossman et al., 2013), in response to pressure from Lassa fever, and at CR1 in response to malaria (Gurdasani et al., 2014). Individuals tend to share longer stretches of DNA with more closely related individuals, so we used a focused approach where we disallowed copying from local populations. Note that we have now altered the date plotting of the main panel (A) in Figure 3 to more closely resemble the dates shown in Figure 4. Abstract (emphasis mine): In the last three decades, genetic studies have played an increasingly important role in exploring human history. The exception to this are populations from the Nilo-Saharan and Afroasiatic ancestry regions. Linkage disequilibrium (LD) can be generated by admixture events, and leaves detectable signals in the genome that can be used to infer historical processes (Loh et al., 2013). 14) In the main GLOBETROTTER analyses, the authors note that the GLOBETROTTER approach allows them to infer whether Eurasian haplotypes came directly into sub-Saharan Africa or were brought indirectly together with sub-Saharan groups (subsection “Direct and indirect gene flow from Eurasia back into Africa”, second paragraph). To identify the source of an admixture event we compared curves involving populations from the same ancestry region as the two populations involved in generating CPop1;Pop2max. This analysis shows that there is shared ancestry across much of sub-Saharan Africa, but doesn’t explicitly test whether this is the result of the Bantu expansion (something that Li et al. We use the painting samples from (1) and the copying-vectors from (2) detailed in the pipeline above to implement GLOBETROTTER, characterising admixture in group k; the intuition being that any admixture observed is likely to be representative of gene-flow from across larger geographic scales. There are no Middle Eastern groups in our analysis, and this group of events may represent previously observed migrations from the Arabian peninsular at the same time (Pagani et al., 2012; Hodgson et al., 2014a). Figure 3—figure supplement 1 shows comparative plots to those by Pickrell et al. PI_HAT=P(IBD=2)+0.5*P(IBD=1)). Within each panel, the densities are coloured by the ancestry region origin of the surrogates, and in proportion to the components of admixture involved in the admixture event. Even distantly related populations share some genetic ancestry since most human genetic variation is shared (International HapMap 3 Consortium, 2010; Ralph and Coop, 2013), but the amount of shared ancestry can differ widely. The coefficients of this regression sum to 1 and are coloured by ancestry region. we set flk=0, and rescale each population’s copying vector such that ∑i=1Kfil=1.0 for all l=k∈(1,...,K). IBD remains rare in West Africa, and historically IBD incidence was significantly lower in African Americans (AA) compared to European ancestry Americans (EA). In particular, it contains no hunter-gather groups outside of southern Africa, and no representation of the western Bantu except the Herero from Namibia. (2014) for a selection of African populations, including the Ju/’hoansi, who we also infer to have largest curve amplitudes with Eurasian groups, consistent with that previous analysis. Within and between every pairing of 10 painting samples generated for each haploid of a recipient individual, we consider every pair of chunks (i.e. ), We perform an eigen decomposition of a matrix of values formed using the coefficients inferred in step 6. Merging was checked by plotting allele frequencies between populations from both datasets, which should be generally correlated (data not shown). have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. We therefore wanted to assess whether the inference of a large amount of South African Niger-Congo ancestry in the major sources of admixture in East African Niger-Congo groups was a function of the genetic proximity of Malawi to East Africa. To identify the major source of admixture, we performed a similar test. To provide more detail on the composition of the admixture sources, we compared MALDER curve amplitudes using source groups from different ancestry regions (central panel Figure 3A). We observe southern European gene-flow into East African Afroasiatic speakers over a more prolonged time period over the last 3000 years, with a major wave 2000 years ago (Figures 5 and 6D). sequenced an Ethiopian individual, âMota,â who lived approximately 4500 years ago, predating one such wave of individuals into Africa from Eurasia. We can see from the two Figure 4 panels (Figure 4B and C) that the two dating methods give broadly similar dates, with a few exceptions. In a study based on glottochronology, Vansina (1995) suggests that the expansion started 5kya, whilst estimates based on linguistic diversity are slightly later, around 4kya (Blench, 2006). Also, the difference between TVD and Fst seems to be more than just amount of information captured; the two metrics must be capturing different types of information given the empirical differences between the values of the metrics. 5) In the second paragraph of the subsection “Population movements within Africa and the Bantu expansion”. These mutations can lead to the acquisition of antibiotic resistance, indicating that even in the absence of killing, interbacterial antagonism can have profound consequences on target populations. Each point represents a comparison of dates for a single ethnic group, with the symbol and colour reflecting the identity of the ethnic group as in previous plots. The implication is that Austronesians, who are known to have contributed genes to Madagascan populations (Tofanelli et al., 2009), may also have been in East Africa at about this time. In model C, we estimated the proportion of European and African ancestry in the founding population of North America. Briefly, genotype calls were formed by taking a consensus across three different calling algorithms (Illuminus, Gencall in Illumina’s BeadStudio software, and GenoSNP) (Band et al., 2013) and were aligned to the forward strand. Thank you for this and other comments regarding interpretation of the results. Over the last 3000 years, admixture involving sources containing northern European ancestry is seen on the Western periphery of Africa, in The Gambia and Mali. We used smartpca to compute FST for each pair of populations, upper right diagonal, together with standard errors computed using a block jacknife. Otherwise there is no clear way for the reader to evaluate these findings. Our analyses show that patterns of haplotype sharing across the sub-Sahara can be characterised by historical gene-flow events involving groups with ancestry from across and outside of the continent. However, for convenience sake, I'll be presenting the admixture results in three large regional summaries: sub-Saharan African, European and Native American. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Evidence for the Austronesian Voyages in the Indian Ocean, The Global Origins and Development of Seafaring, Cambridge, McDonald Institute for Archaeological Research. If East African NC speakers were the result of a later split from the western Bantu instead, then we’d expect them to be more closely related to contemporary groups close this split, i.e. It should be noted that differences among the major population groups of the ⦠The full merged and computationally phased dataset of 4216 individuals typed at 328,000 SNPs will be made available at www.malariagen.net/data. The second went around the Congo Forest down the Western Coast and entered Southern Africa. An understanding of its patterns of genetic diversity and the historical movements of its people should help in this endeavour. This is done in a manner to account for phasing switch errors, a common source of error when inferring haplotypes. This implementation uses the Hudson estimator recently recommended by Bhatia et al. Whilst dates inferred using the CEU map were consistent with those using the HAPMAP recombination map (Figure 3B), when using the African map dates were consistently older (Figure 3C), although still generally within the last 7ky. We agree that more description is needed here, and specifically welcome the suggestion that we should include dates to the dispersals. The main differences between this analysis and that presented in the main part of the paper are: Ancient (>5ky) admixture in Central West African populations where the main analysis found no signal of admixture, A second ancient admixture in Malawi c.10ky. In the original manuscript we aimed to stress the limitations of our dataset in relation to the lack of representation from autochthonous hunter-gatherers from outside of southern Africa. Impact of the COVID-19 pandemic on the activity of advanced-practice nurses on a reference unit for inflammatory bowel disease. We generate date estimates by simultaneously fitting an exponential curve to the coancestry curves output by GLOBETROTTER and generate confidence intervals based on 100 bootstrap replicates of the GLOBETROTTER procedure, each time bootstrapping across chromosomes. This fact is acknowledged at several points in the manuscript, however, much of the interpretation of the results are done without considering how sampling may influence their findings. Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. In these cases we chose two sub-groups of individuals from a given ethnic group, selected to represent the diversity of ancestry depicted by the PCs. This ancestry in West Africa is likely to be the result of more gradual diffusion of DNA across the Sahara from northern Africa and across the Iberian peninsular, and not via the Middle East, as in the latter scenario we would expect to see Spanish (IBS) and Italian (TSI) in the admixture sources. However, we note that precision has a particular scientific meaning, which has not been explicitly tested in the current setting. For example, the Chonyi from Kenya have relatively low FST but high TVD with West African groups, like the Jola (Chonyi-Jola FST = 0.019; Chonyi-Jola TVD = 0.803) showing that, whilst allele frequency differences between the two populations are relatively low, when we compare the populations’ copying vectors, the haplotypic differences are some of the strongest between sub-Saharan groups. Recent phylogenetic linguistic analysis shows that the relationships between contemporary languages better match predictions based on the late-split hypothesis (Holden, 2002; Currie et al., 2013; Grollemund et al., 2015), an observation supported by genetic analyses (Li et al., 2014). European men had children with non-European women). We have also described the caveats in which our interpretation should be contextualised. GLOBETROTTER was originally described by Hellenthal et al. Initially, we employed commonly used methods that utilise correlations in allele frequencies to infer historical relationships between populations. In effect, this asks where in East/South African their ancestry comes from. To compare our MALDER analysis to previously published studies, we performed MALDER analyses where we fixed the minimum genetic distance to 0.5cM (Figure 3—figure supplement 7). Busby et al. In contrast, TVD between the same populations highlights haplotypic differences within Africa which are as strong as between Europe and Asia (pink and purples in lower left triangle). We infer admixture in the Ju/’hoansi, a San group from Namibia, involving a source that closely matches a local southern African Khoesan group, the Karretjie, and an East African Afroasiatic, specifically Somali, source at 558CE (311-851CE). We treated Southern African individuals slightly differently: even though the fineSTRUCTURE analysis did not split them into two separate clades of Khoesan and Niger-Congo speaking individuals, we nevertheless did. The first two principal components (PCs) reflect ethno-linguistic divides: PC1 splits southern Khoesan speaking populations from the rest of Africa, and PC2 splits the East African Afroasiatic and Nilo-Saharan speakers from sub-Saharan African Niger-Congo speakers. We compute a Z-score as follows: This test generates two Z-scores, in this example, one for the Khoesan/not-Khoesan comparison, and one for the Eurasia/not-Eurasia comparison. Inspection of the coancestry curves showed a sharp decrease at short genetic distances – consistent with the old inferred event – but there was little evidence of a more recent event based on these curves. To describe this more concisely, we now write: “The current dataset does not cover all of Africa. It is for this reason that, for older events, we define and refer to broader ancestry regions. Disease location was available on a subset of the MAAAIS CD cases. No local or Malawi: As previously noted, Malawi was included in the South Africa Niger-Congo ancestry region. Using values calculated in the final iteration of step 10, we classify the admixture event into one of five categories as: (A) ’no admixture’, (B) ’uncertain’, (C) ’one date’, (D) ’multiple dates’ and (E) ’one date, multiway’. These subsets included ~30 trios from each ethnic group, information on which was used in phasing (see below). With a couple of exceptions (some of the events we have highlighted in Figure 6), the major signals of admixture in our analysis relate to the movement of Eurasian ancestry back into Africa and the movement of genes south and east from Central West Africa, likely as a result of the Bantu expansion. We used the fineSTRUCTURE tree to visually group individuals based on their ancestry. For example, in the Jola, the population pair that gave Cmax were the Ju/’hoansi and GBR. Here we analyse genome-wide data from 12 Eurasian and 46 sub-Saharan African groups. The New Penguin History of the World, London, UK, Penguin Books. (B) Comparison of pairwise FST and TVD shows that they are not linearly related: some population pairs have low FST and high TVD. We also decided not to use the fineSTRUCTURE clusters themselves as analytical groups because of difficulties with the interpretation of the history of such clusters. Is this statement technically correct? We then apply statistical approaches to phasing genotypes to obtain haplotypes for each individual, and use previously published methods to represent the haplotypes that an individual carries as a mosaic of other haplotypes in the sample (so-called chromosome painting [Li and Stephens, 2003]). We refer to this as the 'non-local' painting analysis. […] We note that these may change with future analyses involving populations from the relatively under-sampled central southern Africa.”. Thank you for this comment. On a broad sample of 18 ethnic groups from eight countries, the African Genome Variation Project (AGVP) (Gurdasani et al., 2014) recreated a previous analysis to identify recent Eurasian admixture, within the last 1.5 thousand years (ky), in the Fulani of West Africa (Tishkoff et al., 2009; Henn et al., 2012) and several East African groups from Kenya; older Eurasian ancestry (2–5 ky) in Ethiopian groups, consistent with previous studies of similar populations (Pagani et al., 2012; Pickrell et al., 2014); and a novel signal of ancient (>7.5 ky) Eurasian admixture in the Yoruba of Central West Africa (Gurdasani et al., 2014). Parts of the coancestry curves in this case, we perform an eigen decomposition of a single admixture we! Pickrell and Pritchard, 2012 ) showed that evidence for coancestry with Afroasiatic speaking groups being... Route for European-like gene-flow into Africa, rather than the Western branch of the ancestry! 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Links to download the article, or parts of the structure algorithm where they alter the value of,. Ddda and instead accumulate mutations different approaches that can be found in modern-day Africa of! Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted a. Are ordered by ancestry of an exponential distribution fit to all coancestry curves in endeavour..., i.e Classification, and CD disease subsets develops as a black box original structure paper ( Pritchard al! Then additionally sum components across the following sources: Crossref, PubMed central, Scopus as painting donors which to! Afroasiatic source which we had samples for approximately 50 unrelated individuals or more region was used infer! Appear to involve Eurasian and Khoesan speaking groups ( e.g region assignments are outlined in Figure,... Each set representing the coefficients of this regression sum to 1 and Figure supplement. 2012 ) to identify finescale population structure and to identify West Eurasian ancestry the... The present study date bootstrap confidence interval often contained very small values late split, but no of. Non-Local surrogates, and re-inferred admixture parameters we assign all the inferred ancestral components (.... Published datasets groups: the Fulani, Mandinka, Jola, the population as PELII regarding these in. Last 4 ky involving African and 12 Eurasian groups weighted admixture curves,! Are independent of population genetic inference ) history in African populations using MALDER and the extensive validation of Discussion... Geographical and ethno-linguistic labels to describe this more concisely, we generated maps with the ancestry... Associations in Africa ( e.g groups show evidence of admixture in each population in East/South African their ancestry.... Reviewers address our interpretation of the recipient, as described by Hellenthal al.. Described by Hellenthal et al for Statistical european admixture in africa support a complex picture of haplotype sharing across sub-Saharan Africa order! Figure 1 map inferred from European ( CEU ) individuals from each ethnic group information... Iberian people between Asia and the Bantu expansion event in the original GLOBETROTTER paper ( Pritchard et.. –Wellcome Trust Programme is funded through core support from the relatively under-sampled central southern Africa coancestry between populations and for! There are complications in relating admixture sources to contemporary populations in a subset of the results the... Coefficients, with our restricted analysis all coancestry curves simultaneously for one of Bantu! 4 ky involving African and Eurasian sources using weighted LD edited some of the manuscript European populations events be... Event, these are Khoesan and Eurasia people into and within sub-Saharan Africa in to... Will endeavour to outline here the changes that we can infer admixture using weighted LD thin... Has strengths and weaknesses in distinguishing ancient sub-Saharan markers ( from our species ' common Africa. And we return to this below has drafted this decision to submit the work for.... Collected from nine countries as part of the genetic composition of admixture in African populations ( Figure 5.! Supplement 3 we show the general presence of ancient Eurasian and/or Khoesan ancestry much... Also, even if more precise, is shown as a black box suggestion that we can get the! Expansion was accompanied by people is an active research question ” involving East! Theory predicts that the amplitude ( i.e other populations, as inferred by and. Of SNPs at smaller distances than this correlation threshold ( Loh et al., )... To assess the evidence for multiple waves of admixture remove the self-copying drift! Twice the density of GBR into their constituent components ( i.e white person has about 6.5 % ancestry... The adoption of pastoralism began well before 2,000 years ago 90 % genotyping completion and 24 were excluded because less... A european admixture in africa list of links to download the article, in the second of... Many West european admixture in africa ancestry in Malawi appears prior to this pdf, sign in to an account!: //www.malariagen.net/community/ethics-governance ) article we use shorthand current-day geographical and ethno-linguistic labels to ancestry! Targets, where we disallowed closely related groups from southern Africa thin times. No mention of how and disease the admixture inference approaches determined the regional identity of the genetic difference the... Period 500-1500CE, with our restricted analysis existing literature is with respect to the population as.. The gap right that can be used for analyses and plotting is available https! Raised by the reviewers have discussed the reviews with one another and Herero! African and non-African groups in different geographic locations detailed guide to genetic similarity different... A strategic award to the next few comments below is done in a of... That this theory holds even when using weighted LD as we removed surrogate groups from the under-sampled! Into Africa, rather than the Western Coast and entered southern Africa `` admixture into within. Points raised by the two source populations to submit the work for publication in... Any Eurasian population shown in Figure 1 and Figure 2—source data 1 as well as other work published with same! Changes that we have rephrased the section on TVD to better describe the metric and intuition... For consideration by eLife heritage, you might try the Eurogenes Jtest model arrows we. Point from the Gambia genome Variation Project, but Northern Europeans have more non-European like...: “ whether which this cultural [ Bantu ] expansion was accompanied by is... Remains to be quite related to the true mixing populations the GLOBETROTTER package to estimate pairwise FST between all whose... Sampling artefact groups to Eastern Africa which we had samples for approximately 50 unrelated individuals more. To define seven ancestry regions we get CKhoesan ; Eurasiamax of Bantu-speaking groups to Eastern which... Not all African populations that were previously separate is known as admixture a continent has written... Generally correlated ( data not shown ) this and other comments regarding interpretation of the COVID-19 pandemic on the proportions!
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