Abstract 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. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. 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. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.
Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture.
Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations.
As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. 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. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa.
Introduction
Advances in DNA analysis technology and the drive to understand the genetic basis of human phenotypes has led to a rapid growth in the amount of genomic data that is available for analysis. Whilst tens of thousands of genetic variants have been associated with different diseases in populations of European descent (Welter et al., 2014), less progress has been made in studies of important diseases in Africa (Need and Goldstein, 2009). Several consortia are beginning to focus on understanding the genetic basis of infectious and non-communicable disease specifically in Africa (Malaria Genomic Epidemiology Network, 2008; 2015; H3Africa Consortium, 2014; Gurdasani et al., 2014), and a number of recent studies have described patterns of genetic variation across the continent (Campbell and Tishkoff, 2008; Tishkoff et al., 2009; Gurdasani et al., 2014). Analyses of the structure of genetic variation are important in the design, analysis, and interpretation of genetic epidemiology studies – which aim to uncover novel relationships between genes, the environment, and disease (Malaria Genomic Epidemiology Network, 2015) – and provide an opportunity to relate patterns of association to historical connections between different human populations.
Admixture occurs when genetically differentiated ancestral groups come together and mix, a process which is increasingly regarded as a common feature of human populations across the globe (Patterson et al., 2012; Hellenthal et al., 2014; Busby et al., 2015). Genome-wide analyses of African populations are refining previous models of the continent’s history and its impact on genetic diversity. One insight is the identification of clear, but complex, evidence for the movement of Eurasian ancestry back into the continent as a result of admixture over a variety of timescales (Pagani et al., 2012; Pickrell et al., 2014; Gurdasani et al., 2014; Hodgson et al., 2014a; Llorente et al., 2015). 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). Comparisons of contemporary sub-Saharan African populations with the first ancient genome from within Africa, a 4.5 ky Ethiopian individual (Llorente et al., 2015), provide additional support for limited migration of Eurasian ancestry back into East Africa within the last 3000 years.
Within this timescale, the major demographic change within Africa was the transition from hunting and gathering to pastoralist and agricultural lifestyles (Diamond and Bellwood, 2003; Smith, 2005; Barham and Mitchell, 2008; Li et al., 2014). This shift was long and complex and occurred at different speeds, instigating contrasting interactions between the agriculturalist pioneers and the inhabitant people (Mitchell, 2002; Marks et al., 2014). The change was initialised by the spread of pastoralism (i.e. the raising and herding of livestock) across Africa and the subsequent movement east and south from Central West Africa of agricultural technology together with the branch of Niger-Congo languages known as Bantu (Mitchell, 2002; Barham and Mitchell, 2008). 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; González-Santos et al., 2015).
The AGVP also found evidence of widespread hunter-gatherer ancestry in African populations, including ancient (9 ky) Khoesan ancestry in the Igbo from Nigeria, and more recent hunter-gatherer ancestry in eastern (2.5–4.5 ky) and southern (0.9–4 ky) African populations (Gurdasani et al., 2014). The identification of hunter-gatherer ancestry in non-hunter-gatherer populations together with the timing of these latter events is consistent with the known expansion of Bantu languages across Africa within the last 3 ky (Mitchell, 2002; Diamond and Bellwood, 2003; Smith, 2005; Barham and Mitchell, 2008; Marks et al., 2014; Li et al., 2014). These studies have described the novel and important influence of both Eurasian and hunter-gatherer ancestry on the population genetic history of sub-Saharan Africa and provide an important description of the movement of alleles and haplotypes into and within the continent, but questions remain of the extent and timing of key events, and their impact on contemporary populations.
Here we analyse genome-wide data from 12 Eurasian and 46 sub-Saharan African groups. Half (23) of the African groups represent subsets of samples collected from nine countries as part of the MalariaGEN consortium. Details on the recruitment of samples in relation to studying malaria genetics are published elsewhere (Malaria Genomic Epidemiology Network, 2014; 2015). The remaining 23 groups are from publicly available datasets from a further eight sub-Saharan African countries (Pagani et al., 2012; Schlebusch et al., 2012; Petersen et al., 2013) and the 1000 Genomes Project (1KGP), with Eurasian groups from the latter included to help understand the genetic contribution from outside of the continent (Figure 1—figure supplement 1). With the exception of Austronesian in Madagascar, African languages can be broadly classified into four major macro-families: Afroasiatic, Nilo-Saharan, Niger-Congo, and Khoesan (Blench, 2006); and although we have representative groups from each (Supplementary file 1), our sample represents a significant proportion of the sub-Saharan population in terms of number, but not does not equate to a complete picture of African ethnic diversity. We created an integrated dataset of genotypes at 328,000 high-quality SNPs and use established approaches for comparing population allele frequencies across groups to provide a baseline view of historical gene-flow. 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 present a detailed picture of haplotype sharing across sub-Saharan Africa using a model-based clustering approach that groups individuals using haplotype information alone. The inferred groups reflect broad-scale geographic patterns. At finer scales, our analysis reveals smaller groups, and often differentiates closely related populations consistent with self-reported ancestry (Tishkoff et al., 2009; Bryc et al., 2010; Hodgson et al., 2014a). We describe these patterns by measuring gene-flow between populations and relate them to potential historical movements of people into and within sub-Saharan Africa. Understanding the extent to which individuals share haplotypes (which we call coancestry), rather than independent markers, can provide a rich description of ancestral relationships and population history (Lawson et al., 2012; Leslie et al., 2015). For each group we use the latest analytical tools to characterise the populations as mixtures of haplotypes and provide estimates for the date of admixture events (Lawson et al., 2012; Hellenthal et al., 2014; Leslie et al., 2015; Montinaro et al., 2015). As well as providing a quantitative measure of the coancestry between groups, we identify the dominant events which have shaped current genetic diversity in sub-Saharan Africa. We close by discussing the relevance of these observations to studying genotype-phenotype associations in Africa.
Results
Broad-scale population structure reflects geography and language
Throughout this article we use shorthand current-day geographical and ethno-linguistic labels to describe ancestry. For example we write “Eurasian ancestry in East African Niger-Congo speakers”, where the more precise definition would be “ancestry originating from groups currently living in Eurasia in groups currently living in East Africa that speak Niger-Congo languages” (Pickrell et al., 2014). We also stress that the use of Khoesan in the current setting refers to groups with shared linguistic characteristics which does not necessarily imply shared close genealogical relationships (Güldemann and Fehn, 2014). Our combined dataset included 3283 individuals from 46 sub-Saharan different African ethnic groups and 12 non-African populations (Figure 1A and Figure 1—figure supplement 1). An initial fineSTRUCTURE analysis (outlined below and in Figure 1—figure supplement 2 and Figure 1—figure supplement 3) demonstrated sub-structure in two of the African ethnic groups, the Fula and Mandinka, so we split both of these populations into two groups, giving a final set of 48 African groups for all analysis.
Many West African groups show evidence of admixture within the last 4 ky involving African and Eurasian sources. The Mossi from Burkina Faso have the oldest inferred date of admixture, at roughly 5000BCE. Across East Africa Niger-Congo speakers (orange) we infer admixture within the last 4 ky (and often within the last 1 ky) involving Eurasian sources on the one hand, and African sources containing ancestry from other Niger-Congo speaking African groups from the west, on the other. Despite events between African and Eurasian sources appearing older in the Nilo-Saharan and Afroasiatic speakers from East Africa, we see a similar signal of very recent Central West African ancestry in a number of Khoesan groups from Southern Africa, such as the Khwe and /Gui //Gana, together with Malawi-like (brown) sources of ancestry in recent admixture events in East African Niger-Congo speakers.
The Fulani represent the best-matching surrogate to the minor source of recent admixture in the Jola and Manjago, which we interpret as resulting not from specific admixture from them into these groups, but because the mix of African and Eurasian ancestries in contemporary Fulani is the best proxy for the minor sources of admixture in this region. With the exception of the Fulani themselves, the major admixture source in groups across this region is a similar mixture of African ancestries that most closely matches contemporary Gambian and Malian surrogates (Jola, Serere, Serehule, and Malinke), suggesting ancestry from a common West African group within the last 3000 years. The Ghana Empire flourished in West Africa between 300 and 1200CE, and is one of the earliest recorded African states (Roberts, 2007). Whilst its origins are uncertain, it is clear that trade in gold, salt, and slaves across the Sahara, perhaps from as early as the Roman Period, as well as evolving agricultural technologies, were the driving forces behind its development (Oliver and Fagan, 1975; Roberts, 2007). It is possible these interactions through North Africa, catalysed by trade across the Sahara, allowed gene-flow from Europe and North Africa back into West Africa.
We infer more direct admixture from Eurasian sources in two populations from Kenya, where specifically South Asian populations (GIH, KHV) are the most closely matched surrogates to the minor sources of admixture (Figure 5). 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. Alternatively, Blench (2010) notes that the expansion of Arab shipping down the east Coast of Africa in the 10th Century CE masked the Austronesian (i.e. Oceania and Asia) influence of the resident coastal culture. 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. Further work on these groups will help to understand whether the events we observed in the Chonyi and Kauma represent the first evidence of an Austronesian impact in mainland Africa.
In the Kambe, the third group from coastal Kenya, we infer two events, the more recent one involving local groups, and the earlier event involving a European-like source (GBR, 761CE: 461BCE-1053CE). In Tanzanian groups from the same ancestry region, we infer admixture during the same period, this time involving minor admixture sources with Afroasiatic ancestry: in the Giriama (1196CE: 1138-1254CE), Wasambaa (1312CE: 1254-1341CE), and Mzigua (1080: 1007-1138CE). Although the proportions of admixture from these minor sources differ, the major sources of admixture in East African Niger-Congo speakers are similar, containing a mix of Southern Niger-Congo (Malawi), Central West African, Afroasiatic, and Nilo-Saharan ancestries. These events may be an indirect route for European-like gene-flow into East Africa.
In the Afroasiatic speaking populations of East Africa, we infer admixture involving sources containing mostly Eurasian ancestry, which most closely matches the Tuscans (TSI, Figure 4). Visualising the temporal distribution of admixture contributions shows that this ancestry appears to have entered the Horn of Africa in two waves (at c. 1800 and 0CE in Figure 5) as result of admixture into the Afar (326CE: 7-587CE), Wolayta (268CE: 8BCE-602CE), Tigray (36CE: 196BCE-240CE), and Ari (689BCE:965-297BCE). 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).
Although Afroasiatic and Nilo-Saharan speakers were sampled from the same part of East Africa, the ancestry of the major sources of admixture of the former do not contain much Nilo-Saharan ancestry and are predominantly Afroasiatic (pink). In Nilo-Saharan speaking groups (purple), the Sudanese (1341CE: 1225–1660), Gumuz (1544CE: 1384–1718), Anuak (703: 427-1037CE), and Maasai (1646CE: 1584-1743CE), we infer greater proportions of West (blue) and East (orange) African Niger-Congo speaking surrogates in the major sources of admixture, indicating both that the Eurasian admixture occurred into groups with mixed Niger-Congo and Nilo-Saharan/Afroasiatic ancestry, and a clear recent link with Central and West African groups.
Lastly, in two Khoesan speaking groups from South Africa, the ≠Khomani and Karretjie, we infer very recent direct admixture involving Eurasian groups most similar to Northern European populations, with dates aligning to European colonial period settlement in Southern Africa (c. 5 generations or 225 years ago; Figure 5) (Hellenthal et al., 2014). Taken together, and in addition the MALDER analysis above, these observations suggest that gene-flow back into Africa from Eurasia has been common around the edges of the continent, has been sustained over the last 3000 years, and can often be attributed to specific and different historical time periods.
Population movements within Africa and the Bantu expansion
Before discussing the impact of the Bantu expansion, we highlight three inferred admixture events involving sources unconnected to that migration. 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). Another, older, event in the Maasai (254BCE: 764BCE-239CE) also involves an Afroasiatic source. In contrast the minor source in the event inferred in the Luhya (1486: 1428-1573CE) most closely matches Nilo-Saharan groups. The recent date of this event implies that Eastern Niger-Congo speaking groups (e.g. the Luhya) interacted with nearby Nilo-Saharan speakers after the putative arrival of Bantu-speaking groups to Eastern Africa which we discuss below.
Most of the sampled groups in this study, and indeed most sub-Saharan Africans, speak a language belonging to the Niger Congo linguistic phylum (Greenberg, 1972; Nurse and Philippson, 2003). A sub-branch of this group are the so-called 'Bantu' languages – a group of approximately 500 very closely related languages – that are of particular interest because they are spoken by the vast majority of Africans south of the line between Southern Nigeria/Cameroon and Somalia (Pakendorf et al., 2011). Given their high similarity and broad geographic range, it is likely that Bantu languages spread across Africa quickly. Bantu languages can themselves be divided into three major groups: northwestern, which are spoken by groups near to the proto-Bantu heartland of Nigeria/Cameroon; western Bantu languages, spoken by groups situated down the west coast of Africa; and eastern, which are spoken across East and Central Africa (Li et al., 2014).
Whilst there is linguistic and archaeological consensus that the Bantu heartland was in the general region of southern Nigeria and Cameroon (Nurse and Philippson, 2003), it is unclear whether eastern Bantu languages were a primary branch that split off before the western groups began to spread south (the early-split hypothesis), or whether this occurred after the start of the movement south (the late-split hypothesis) (Pakendorf et al., 2011). 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). This latter date agrees well with the breakthrough of Neolithic technologies, such as tools and pottery, in the archaeology of the Cameroon proto-Bantu heartlands (Bostoen, 2007) and perhaps further south (Lavachery, 2001), linking the spread of technology and farming with the Bantu expansion.
The early split hypothesis suggests that the eastern Bantu migrated directly east from Cameroon, 3–2.5 kya (Nurse and Philippson, 2003) along the border north of the Congo rainforest, to the Great Lakes Region of East Africa (Pakendorf et al., 2011). The late-split hypothesis, on the other hand, suggests that there was an initial spread south, through the equatorial rainforest, with a sub-group splitting east under the rainforest, arriving later in East Africa, potentially around 2kya (Vansina, 1995). Regardless of the exact route, the expansion spread south, arriving in southern Africa by the late first millennium CE (Nurse and Philippson, 2003). 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).
The current dataset does not cover all of Africa. In particular, it contains no hunter-gather groups outside of southern Africa, and no representation of the western Bantu except the Herero from Namibia. Nevertheless, we explored whether our admixture approach could be used to gain insight into the Bantu expansion. Specifically, we wanted to see whether the dates of admixture and composition of admixture sources were consistent with either of the two major models of the Bantu expansion. In the remaining discussion, we make the following assumption: when we observe ancestry from contemporary groups residing in Cameroon (Semi-Bantu and Bantu) this is a proxy for direct gene-flow from the origin of the Bantu expansion. Alternatively, higher proportions of ancestry from Southern or Eastern Niger-Congo speakers are the result of subsequent indirect gene-flow through these groups, which we use together with the time of admixture to relate to the Bantu expansion. We note that our interpretation may change with future analyses involving populations from the relatively under-sampled central southern Africa.
The major sources of admixture in East African Niger-Congo speakers have both Central West and Southern Niger-Congo ancestry, although it is predominantly the latter (Figure 4). If admixture in Eastern Niger-Congo speakers results from early movements directly from Central West Africa (Cameroon surrogates) then we would expect to see sources with predominantly Central West African ancestry. However, all East African Niger-Congo speakers that we sampled have admixture ancestry from a Southern group (Malawi) within the last 2000 years, suggesting that Malawi is more closely related to their Bantu ancestors than Central West Africans on their own. 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. In west southern Africa, on the other hand, we infer two admixture events in the Herero (1834CE: 1805-1892CE and 674CE: 124BCE-979CE), and a single date in the Khoesan-speaking Khwe (1312; 1152-1399CE), both of which involve sources with higher proportions of ancestry from Cameroon (Figure 4—source data 1). In a third west southern African group, the !Xun (1312CE: 1254-1385CE) from Angola, who do not speak a Bantu language, we also infer admixture from a Cameroon-like source at around the same time as the Khwe. The putative Bantu admixture events in Malawi and the Herero occur before those in the !Xun and Khwe (Figure 4). This suggests a separate, more recent, arrival for Bantu ancestry in west southern compared to east southern Africa, with the former coming directly down the west coast of Africa and the latter from earlier interactions in central southern Africa (de Filippo et al., 2012; Li et al., 2014).
In individuals from Malawi we infer a multi-way event with an older date (471: 340-631CE) involving a minor source which mostly contains ancestry from Cameroon, which is, as mentioned, at a similar date to the event seen in the Herero from Namibia. This Bantu admixture appears to have preceded that in other southern Africans by a few hundred years. Given that ancestry from Malawi is often observed in large proportions in the admixture sources of East and Southern African Niger-Congo speakers, and its position between eastern and the most southern groups, Malawi represents the closest proxy in our dataset for the intermediate group that split from the western Bantu. We also see an admixture source in Malawi with a significant proportion of non-Bantu (green) ancestry (2nd event, minor source in Figure 4), ancestry which we do not observe in the mixture model analysis, but which is also evident in the other east Southern Niger-Congo speakers (the AmaXhosa and SEBantu) implying that gene-flow must have occurred between the expanding Bantus and the resident hunter-gatherer groups (Marks et al., 2014).
In summary, the early date of Bantu admixture in Malawi, its presence as an admixture surrogate across eastern and southern Africa, and the observation of later direct Central West African (Bantu) admixture in western south African groups, highlight the complex dynamics, and multiple waves of migration associated with the movement of Bantu agriculturists from the region around Cameroon into southern and eastern Africa. Moreover, our analysis – in addition to evidence from linguistic phylogenetics (Currie et al., 2013; Grollemund et al., 2015) – provides genetic support for the late-split hypothesis, suggesting that the agriculturist Bantus migrated south around the Congo rainforest before travelling east.
A haplotype-based model of gene-flow in sub-Saharan Africa
Our haplotype-based analyses support a complex picture of recent historical gene-flow in Africa (Figure 6). Using genetics to infer historical demography will always depend on the available samples and methods used to infer population relationships. Our aim here is to highlight the key gene-flow events that chromosome painting allows us to detect, and to describe their affect on the structure of coancestry:
Discussion
We have presented an in-depth analysis of the genetic history of sub-Saharan Africa in order to characterise its impact on present day diversity. 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. An important question in African history is how contemporary populations relate to those present in Africa before the transition to pastoralism that began in the Nile Valley some 9kya. The f3f3 and MALDER analyses show evidence for deep Eurasian and some hunter-gatherer ancestry across Africa, to which our GLOBETROTTER analysis (Figure 4) provides further clarity on the composition of the admixture sources, as well as the timing of events and their impact on groups in our analysis (Figure 6). On the basis of our analysis, none of the African populations in our study has remained isolated and unchanged over the last 4000 years.
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. The transition from foraging to pastoralism and agriculture in Africa is likely to have been complex, with its impact on existing populations varying substantially. Our analysis provides an estimate of the timing of this expansion (Figure 5). It is important to note that dates of admixture inferred through genetics will always be more recent than the date at which two populations have come together. Our dataset is not an exhaustive sample of African populations, and there are likely to be other events than those reported here that have been important in generating the current genetic landscape of Africa.
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. We have identified gene-flow across Africa, implying that haplotypes have been moving over (potentially large) distances in a relatively short amount of time. As a rough estimate, given that events in southern African groups involving Bantu sources have occurred within the last 2000 years (Figure 6) and the distance between Cameroon and south-east Africa is around 4000km, haplotypes have moved across and into different environments at a rate of roughly 2 km/year.
Interpreting haplotype similarity as historical admixture
Analyses that model the correlations in allele frequencies (such as those performed here in the Allele frequency differences show widespread evidence for admixture section) provided initial evidence that the presence of Eurasian DNA across sub-Saharan Africa is the result of gene-flow back into the continent within the last 10,000 years (Gurdasani et al., 2014; Pickrell et al., 2014; Hodgson et al., 2014a), and that some groups have ancient (over 5 kya) shared ancestry with hunter-gather groups (Figure 3) (Gurdasani et al., 2014). Whilst the weighted admixture LD decay curves between pairs of populations used by MALDER suggests that this admixture involved particular groups, the interpretation of such events is difficult. Firstly, because our dataset includes closely related groups, it is not always possible to identify a single best matching reference, implying that sub-Saharan African groups share some ancestry with many different extant groups. On the basis of these analyses alone, it is not possible to characterise the composition of admixture sources. Secondly, when ancient events are identified with MALDER, such as in the Mossi from Burkina Faso, where we estimate admixture around 5000 years ago between a Eurasian (GBR) and a Khoesan speaking group (/Gui //Gana), we know that modern haplotypes are likely to only be an approximation of ancestral diversity (Pickrell and Reich, 2014). Even the Ju/’hoansi, a San group from southern Africa traditionally thought to have undergone limited recent admixture, has experienced gene-flow from non-Khoesan groups within this timeframe (Figure 4) (Pickrell et al., 2012; 2014).
There are complications in relating admixture sources to contemporary populations. For example, our analyses indicate that the Mossi share deep ancestry with Eurasian and Khoesan groups (Figure 3), but any description of the historical event leading to this observation is potentially biased by the discontinuity between extant populations and those present in Africa in the past. It is for this reason that, for older events, we define and refer to broader ancestry regions. So in this case, we describe Eurasian ancestry in general moving back into Africa, rather than British DNA in particular. GLOBETROTTER provides an alternative approach by characterising admixture as occurring between sources that themselves are mixtures of ancestry from contemporary groups. In the situation where no sample group provides a good representation of the admixture source, this additional complexity is likely to be a closer approximation to the truth, with the downside that it is not always possible to assign a specific population label to mixed admixture sources. Using contemporary populations as proxies for ancient groups is not the perfect approach and would be improved by DNA from significant numbers of ancient human individuals, at sufficient quality, with which to calibrate temporal changes in population genetics.
Spread of genes within Africa
When new haplotypes are introduced into a population by gene-flow their fate will be partly be determined by the selective advantage they confer, as well as the chance effects of genetic drift. Selection can occur in response to a number of different factors. 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. Responding to changes in their environment, populations living at high altitudes have adapted convergently at different genes involved in hypoxic response: at BHLHE41 in Ethiopians (Huerta-Sánchez et al., 2013); EPAS1 and EGLN1 in Tibetans (Yi et al., 2010); and at a separate loci within EGLN1 in Andean groups (Bigham et al., 2010). 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). Diseases such as malaria are caused by highly polymorphic parasites and movement into new environments might lead to exposure to new strains. An implication of widespread gene-flow is that it can provide a route for potentially beneficial novel mutations to enter populations allowing them to adapt to such change.
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). The spread of the Duffy-null allele, an ancient mutation which is thought to have arose at least 30,000 years ago (Hamblin and Di Rienzo, 2000; Hamblin et al., 2002) and confers resistance to Plasmodium vivax malaria, throughout Africa is only possible through contact and gene-flow between populations right across the sub-Sahara. Conversely, the mutation responsible for the sickle cell phenotype, which offers protection against P. falciparum malaria, appears to have recently occurred five times independently in Africa, causing multiple distinct haplotypes to be observed (Hedrick, 2011). These mutations are young, within the order of 250–1750 years old (Currat et al., 2002; Modiano et al., 2008), so will have had limited opportunity to have been moved around by the gene-flow events that we describe. Further work is needed to understand the role of admixture in facilitating adaptation.
Admixture and genetic epidemiology
Epidemiology is the process of identifying the mechanisms that lead to changes in disease prevalence that could result from different environments, behaviours, or genetic backgrounds. Our study helps address these questions by providing a detailed guide to genetic similarity between different ethno-liguistic groups in different geographic locations. This is equally relevant for studies of important infectious disease (such as malaria), as it is for studies of non-communicable diseases which are associated with life-style changes in developing parts of Africa (see Rotimi and Jorde (2010) for a review). As an example, we detect consistent genetic differences between groups in Central West Africa (e.g. the Akans and Namkam/Kasem from Ghana in Figure 2—figure supplement 1), but not in groups from the West and East Africa Niger-Congo ancestry regions (The Gambia and Kenya; Figure 1—figure supplement 3). Within these groups we see individuals with a spectrum of different ancestral backgrounds. These observations are specific to groups in our analysis, and cannot be extended to other groups from similar populations; the seven ethnic groups from The Gambia were all collected in and around Banjul in the Western District, whereas the three ethnic groups from Ghana were collected from two hospitals in the north (Navrongo) and centre (Kumasi) of the country. Nonetheless, the potential for genetic differences to underlie difference in disease should be guided by analyses of haplotype sharing between groups.
Chromosome painting approaches also provide a quantitative measure of the extent to which self-reported ethnic labels capture genetic relationships, which is also important for controlling for the potential confounding effects of population structure (Marchini et al., 2004; Price et al., 2006), when genome-wide data are unavailable. We see that this can vary extensively from one population to the next (Figure 1—figure supplement 3); some individuals who report as coming from the same ethnic group cluster into different groups and other individuals from different ethnicities cluster together. We also show that there are differences in the inferred relationship between populations using analyses genotype based approaches such as PCA and FSTFST, and our haplotype based analysis (Figure 1) and TVD (Figure 2). These results suggest that for some groups, haplotype similarity to other ancestries can vary more substantially than allele frequencies alone. In designing genotyping and sequencing studies these differences can be important in ensuring that the breadth of variation in African populations is adequately covered (Kwiatkowski, 2005; Gurdasani et al., 2014). Africa has an exciting and important role in furthering understanding of human biology and disease. An understanding of its patterns of genetic diversity and the historical movements of its people should help in this endeavour.
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There are a few ethnic groups in Africa, who have a oral tradition, telling that they originated from the Arabian Peninsula ("Eurasian"). We have people like Dana Marniche, who writes about this a lot.
Dana Reynolds-Marniche
University of Chicago, Division of the Social Sciences, Alumnus.
And Africa does have old written scripture, known as signs and symbols. The deep meaning of these symbols are known to only a select few (priest).
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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This paper is nonsense. It is found on hypothesis which do not reflect the African reality. Firstly,there is no Afro-Asiatic language family and the Bantu speakers did not originate in West-Central Africa. In addition, there is no discussion of archaeological evidence in support of any of the authors propositions, and as I pointed out in my article A PROTOCOL TO EVALUATE POPULATION GENETICS PAPERS the absence of archaeological data is the major indication that the paper lacks credibility.
Reading this paper is like reading any other racist Eurocentric article written at the turn of the 20th Century perpetuating the Hamitic myth.THE Hamitic myth states that everything of value ever found in Africa was brought there by the Hamites, allegedly a branch of the Caucasian race. Seligman formulated this hypothesis which led researchers to declare that the Fulani and Afro-Asiatic speakers were Hamites. As a result, when this study declares that the Fulani, who are not of Eurasian origin, and the Afro-Asiatic speakers have a high frequency of Eurasian (white) admixture, this paper is just reinforcing a hypothesis that lacks credibility. The results of this paper only perpetuates the Hamitic myth, many researchers had thought was abandoned--but has remained constant by geneticist who dress the hypothesis up in new clothes based on statistics, instead of actual archeaogenetics evidence.
The authors assume that the Bantu migrated out of Cameroon 2,5kya. This is ludicrous because the Bantu had been living in the Nile Valley long before 500BC.
In summary this paper is maintaining the status quo dogma that the Bantu and the rest of the Niger-Congo speakers are true Negroes, and the Afro-Asiatic speakers and Fulani are Hamites, i.e., dark skinned Caucasians. This paper offers nothing new in relation to African genetics, it is a throwback back to the 1930's racist antropological studies.
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die Baldeh • 3 years ago I am a Gambian Fulani... The unique thing of being a Fulani is people get know you are a Fulani where ever you go..i recently travel to Lagos Nigeria for a workshop, what surprise me is people knew i was a Fulani even before speaking to them..just as it happens in the Gambia..i was so amazed.
However according to our oral history, Fulanis or fulas came from the east, some said around India, Egypt or The Magreb to round it all...Meanwhile whilst growing up i remember my parents or family members when talking about the other tribes called them the dark skinned tribes..i wonder aren't we dark? some claim the skins of our ancestors were much lighter..just as most Fulanis in Guinea Conakry..so as such they still refer other as dark skinned people...i am even told of why Fulani leave their land and spread in all of west and other parts of Africa....
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So what about the Africans before 4,000 years ago? Surely he isn't suggesting that those populations that we know were all over Africa just disappeared? This is a stupid paper. Africans have been around longer than any 4000 years and surely those people from prior to that didn't up and disappear. Basically it is sounding like they are claiming those "other" older African groups disappeared and were replaced by Bantus and Eurasians, which is ridiculously stupid. Africans have been moving around in Africa for years and certainly those lineages still exist in some form.
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quote:Originally posted by Doug M: So what about the Africans before 4,000 years ago? Surely he isn't suggesting that those populations that we know were all over Africa just disappeared? This is a stupid paper. Africans have been around longer than any 4000 years and surely those people from prior to that didn't up and disappear. Basically it is sounding like they are claiming those "other" older African groups disappeared and were replaced by Bantus and Eurasians, which is ridiculously stupid. Africans have been moving around in Africa for years and certainly those lineages still exist in some form.
Its not necessarily stupid. They are not saying there were no Africans around until 4000 years ago. Where do you see that? Their findings indicate that some gene flow from areas outside Africa has occurred in sub-Saharan populations over time. Nothing surprising there- given environmental fluctuations of the region over millennia that could spark movement of nomads, etc. None of that supports any mass movement of "incoming" or "wandering Causacoids" into Africa to civilize the natives. In any event the "incoming Eurasians" in many cases would already look like some of today's sub-Saharan Africans. This defeats attempts to use genetic data to recycle "Hamiticism," for the "Hamites" in question would look like some of the much maligned "negro types."
The real problem is how some in the academy throw around the label "Eurasian"- giving it all these broad interpretations but draw the category "sub-Saharan African" as narrowly as possible, as in the classic "true negro" dodge. There is a clear problem with hypocrisy and double standards in the field, as even Keita himself notes. It is not just random commenters or bloggers off the web saying this.
Remember the term "basal Eurasian" and so on- again, using a wider expansive format. Why couldn't they just as well use the term "Afro-Asian transitional" or similar, given various phenotype resemblances to today's "black Africans?" ANd many who talk up "EUrasian influences" in Africa, are reluctant to apply the format to talk about African influences in Europe. If the same "true negro" model applies to Africa, why don't they apply a "true white" model likewise in Europe and call various like Southern Europeans "Mixed race"? But they seldom apply their own race models the other way- the classic hypocritical, double standard, that Diop so well pointed out years ago.
Thankfully some recent scholars have begun to honestly talk about the African influences in Europe. Busby seems more careful than others we have seen here in the past.
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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quote:Originally posted by zarahan- aka Enrique Cardova:
quote:Originally posted by Doug M: So what about the Africans before 4,000 years ago? Surely he isn't suggesting that those populations that we know were all over Africa just disappeared? This is a stupid paper. Africans have been around longer than any 4000 years and surely those people from prior to that didn't up and disappear. Basically it is sounding like they are claiming those "other" older African groups disappeared and were replaced by Bantus and Eurasians, which is ridiculously stupid. Africans have been moving around in Africa for years and certainly those lineages still exist in some form.
Its not necessarily stupid. They are not saying there were no Africans around until 4000 years ago. Where do you see that? Their findings indicate that some gene flow from areas outside Africa has occurred in sub-Saharan populations over time. Nothing surprising there- given environmental fluctuations of the region over millennia that could spark movement of nomads, etc. None of that supports any mass movement of "incoming" or "wandering Causacoids" into Africa to civilize the natives. In any event the "incoming Eurasians" in many cases would already look like some of today's sub-Saharan Africans. This defeats attempts to use genetic data to recycle "Hamiticism," for the "Hamites" in question would look like some of the much maligned "negro types."
I am calling it stupid because of the reasons you mentioned in your posts, but more specifically because of genetic lineages and the use of labels for African populations at various time depths. Firstly, all modern humans originated in Sub Saharan Africa, therefore the idea that "Sub Saharan" lineages and "mixture" among various lineages are only 4000 years old are ridiculous. And more importantly, since humans were moving around IN Africa for most of their 200,000 years in Africa before even leaving, how do you accurately reconstruct the patterns of migrations and movements that have been taking place WITHIN the continent over such a long time? I am not only questioning the labels but the attempts to downplay and minimize the impact of the fact that humans have been in Africa longer than any other part of the planet and therefore have a much more complex genetic history than simple "Sub Saharans" versus "North Africans" or "Bantu" migration labels that constantly get thrown around. Because if you really follow the flow of these papers you would think that the Africans from 200,000 years ago disappeared or were a 'different species' and replaced by later migrants, which is totally stupid. Case in point: blombos cave South Africa or the 100,000 year old jewelry found in North Africa. What happened to all these folks? They just disappeared?
It is all about how you look at the data. If you are looking at Africa solely to determine when "white genes" arrived, which many scholars have been focusing on vis-a-vis ancient Egypt, then you will get one result. But if you are truly looking at the long history of humans in Africa and all the lineages that migrated OUT of Africa at various times, then you will get another picture. And this is the problem in my opinion, because most European scholars are focusing on the former and not the latter. They only care about how far back they can identify "Eurasian" lineages in Africa as a result of "reverse migration" than they are in identifying where said "Eurasian" lineages originated, which if they were going by the latter approach would point out the African origins of many of these lineages.... Ultimately the issue being that Africa is not stagnant, humans are a migratory species and focusing on one small period of time in order to flesh out one piece of the picture doesn't replace the whole picture.
quote: To shed light on the structure of the basal backbone of the human Y chromosome phylogeny, we sequenced about 200 kb of the male-specific region of the human Y chromosome (MSY) from each of seven Y chromosomes belonging to clades A1, A2, A3, and BT. We detected 146 biallelic variant sites through this analysis. We used these variants to construct a patrilineal tree, without taking into account any previously reported information regarding the phylogenetic relationships among the seven Y chromosomes here analyzed. There are several key changes at the basal nodes as compared with the most recent reference Y chromosome tree. A different position of the root was determined, with important implications for the origin of human Y chromosome diversity. An estimate of 142 KY was obtained for the coalescence time of the revised MSY tree, which is earlier than that obtained in previous studies and easier to reconcile with plausible scenarios of modern human origin. The number of deep branchings leading to African-specific clades has doubled, further strengthening the MSY-based evidence for a modern human origin in the African continent. An analysis of 2204 African DNA samples showed that the deepest clades of the revised MSY phylogeny are currently found in central and northwest Africa, opening new perspectives on early human presence in the continent.
And not ironically, we are starting to see more studies that focus on the latter view I mentioned in more detail:
quote: Starting with five migration events, we observed positive log-likelihoods and the range of residuals stopped decreasing (Supplementary Figures S1 and S2). Despite low confidence, we report three additional migration events that may be real: the fifth migration event connects sub-Saharan Africa to an internal node ancestral to Chinese, Japanese, Melanesian, Native American, Siberian, and Southeast Asian ancestries; the sixth migration event connects Siberian and Northern European ancestries; and the seventh migration event connects the Kalash and Levantine-Caucasian ancestries (Supplementary Figure S2).
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..which if they were going by the latter approach would point out the African origins of many of these lineages.... Ultimately the issue being that Africa is not stagnant, humans are a migratory species and focusing on one small period of time in order to flesh out one piece of the picture doesn't replace the whole picture.
True enough. This notion of "static" Africans is still in the minds of many- such as "sub-Saharan" Africans staying meekly behind the "Saharan barrier" like some apartheid line of old South Africa. ANd the Sahara itself is a shifting barrier - with net movement south over the centuries. This means that numerous peoples once "sub-Saharan" become NON "sub-Saharan" as the barrier creeps south. The Kingdom of Kush was a sub-Saharan entity with trade and admin links far south.
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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??? come on! BTW the dating is all screwed up.
“We do NOT have middle Eastern groups in our analysis”. Why? Because their lie will be exposed. If they want to prove Eurasian back migration why not include populations right NEXT to Africa? Lol! Typical! Europeans up to their old tricks. Sleight of hands. Get with the program people. Took me all but 30mins!!
------------------ Quotes:
Many West African groups show evidence of admixture within the last 4 ky involving African and Eurasian sources. The Mossi from Burkina Faso have the oldest inferred date of admixture, at roughly 5000BCE. Across East Africa Niger-Congo speakers (orange) we infer admixture within the last 4 ky (and often within the last 1 ky) involving Eurasian sources on the one hand, and African sour- ces containing ancestry from other Niger-Congo speaking African groups from the west, on the other.
4. Gene-flow across the Sahara. Over the last 3000 years, admixture involving sources contain- ing northern European ancestry is seen on the Western periphery of Africa, in The Gambia and Mali. 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 Mid- dle East, as in the latter scenario we would expect to see Spanish (IBS) and Italian (TSI) in the admixture sources. We do see limited southern European ancestry in West Africa (Figures 5 and 6D) in the Fulani, suggesting that some Eurasian ancestry may also have entered West Africa via North East Africa (Henn et al., 2012).
5. Several waves of Mediterranean / Middle Eastern ancestry into north-east Africa. We observe southern European gene-flow into East African Afroasiatic speakers over a more pro- longed time period over the last 3000 years, with a major wave 2000 years ago (Figures 5 and 6D). We do not have Middle-Eastern groups in our analysis, so the observed Italian ancestry in the minor sources of admixture – the Tuscans are the closest Eurasian group to the Middle East – is consistent with previous results using the same samples (Pagani et al., 2012; Hodgson et al., 2014a), indicating this region as a major route for the back migration of Eur- asian DNA into sub-Saharan Africa (Pagani et al., 2012; Pickrell et al., 2014).
9. Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry. The f3 statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the ubiquitous hunter-gatherer ancestry across the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations.
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-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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To those who can follow. Remember I speculated in that “Aegan origin of Neolithic farmer” thread. That in the pie chart “black” Loschbour would be found in African Hunter Gatherers. Well, there you have it. They refuse to show Khoisan African or SSA in that Aegan paper. Lol! Remember the OOA meta-population were closely related to Asians and Khoisan has greater percentage of “asian” ancestry.
This is so easy! The games they play. Lol!
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I have to admit these Europeans are good. If you are not gullible they give you all the clues. Being bipolar and confused about their place in the world. The truth with lies are embedded within the document. SMH!
Quote: Discussion We have presented an in-depth analysis of the genetic history of sub-Saharan Africa in order to char- acterise its impact on present day diversity. 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. An important question in African history is how contem- Porary(xxyman insert- Eurasian) populations relate to those present in Africa before the transition to pastoralism that began in the Nile Valley some 9kya. The f3 and MALDER analyses show evidence for deep Eurasian and some hunter-gatherer ancestry across Africa, to which our GLOBETROTTER analysis (Figure 4) pro- vides further clarity on the composition of the admixture sources, as well as the timing of events and their impact on groups in our analysis (Figure 6). On the basis of our analysis, none of the African populations in our study has remained isolated and unchanged over the last 4000 years. With a couple of exceptions (some of the events we have highlighted in Figure 6), the major sig- nals 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. The transition from foraging to pastoralism and agriculture in Africa is likely to have been complex, with its impact on existing populations varying substantially. Our analysis provides an esti- mate of the timing of this expansion (Figure 5). It is important to note that dates of admixture inferred through genetics will always be ******more recent than ******the date at which two populations have come together. Our dataset is not an exhaustive sample of African populations, and there are likely to be other events than those reported here that have been important in generating the current genetic landscape of Africa. 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 conti- nent. We have identified gene-flow across Africa, implying that haplotypes have been moving over (potentially large) distances in a relatively short amount of time. As a rough estimate, given that events in southern African groups involving Bantu sources have occurred within the last 2000 years (Figure 6) and the distance between Cameroon and south-east Africa is around 4000km, haplotypes have moved across and into different environments at a rate of roughly 2 km/year.
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Yes, they are playing both sides. They are back to the Nile Valley/Sudan (Sergi) and the advent of Agriculture 9,000years ago. But they are trying to flip it claiming it was back migration accounting for the Eurasian ancestry in Africans. In other words. The back-migrating Basal Eurasians/EEF was responsible for the Neolithic Revolution in Africa and throughout the world. SMH! Is this a pre-emptive strike on Lazaridis latest paper? Lol!
I guess the researchers don’t talk to each other before publishing. lol!
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In short they are trying to “explain away” the presence of European and Asian “LABELLED” genes in Africans and particularly West Africans, the so-called “true Negro”. Lol! But some authors have already identified ‘European’ genes in the true Negro. In fact some authors have identified the ‘European’ genes as being OLDER in the true negro compared to the “Caucasoid Horners’. Which is baffling these researchers. But it is only baffling to them because of their hypocritical views and prejudices. DNATribes in their digest on continental populations had already identified ‘Basque” ie European genes in Central Africa, and it increase in frequency moving away from Central Africans. ie IBD or genetic surfing. Lazaridis and DNATribes also identified archaic genetic material primarily in Khoi-San and Mbuti. This is puzzling the racialist because at first they believed there was no Neanderthal admixture in SSA. Lol! They are hitting roadblocks at every turn.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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lol! AMH never entered Europe from Africa through the Levant but always from Southern Europe via North Africa.
Keep in mind they are labeling Eurasia "ancestry" as the population with the highest frequency. But genetic surfing and/or IBD explains the high frequency...but theY are bone headed and refusing to accept that fact.
T H E Y - W I L L - C O M E - A R O U N D!!
== quote 9. Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry. The f3 statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the ubiquitous hunter-gatherer ancestry across the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by zarahan- aka Enrique Cardova: ..which if they were going by the latter approach would point out the African origins of many of these lineages.... Ultimately the issue being that Africa is not stagnant, humans are a migratory species and focusing on one small period of time in order to flesh out one piece of the picture doesn't replace the whole picture.
True enough. This notion of "static" Africans is still in the minds of many- such as "sub-Saharan" Africans staying meekly behind the "Saharan barrier" like some apartheid line of old South Africa. ANd the Sahara itself is a shifting barrier - with net movement south over the centuries. This means that numerous peoples once "sub-Saharan" become NON "sub-Saharan" as the barrier creeps south. The Kingdom of Kush was a sub-Saharan entity with trade and admin links far south.
This is more than an issue of Nile Valley settlement though. It is an issue of time depth and multiple waves of dispersions within Africa and out of Africa. Imagine how ripples interact within a pond and now put the Omo valley as the source of the ripples with waves radiating out then bouncing around within Africa, with some leaking out. Their view is so simplistic that it doesn't even admit to the fact that Africans have been migrating back and forth within Africa over multiple thousands of years as a result of various climate and environmental changes. This would imply that there have been multiple waves of settlements in various parts of Africa and that "Sub Saharans" is a meaningless term in that the first humans were born in Sub Saharan Africa to begin with so how does that distinction mean anything IN Africa among African populations? And this is where the time depth and diversity of Africans and African lineages come into play because all African populations have tremendous diversity as a result.
Studies like this ignore the 200,000 year history of Africans migrating in and around Africa and create some artificially shallow and arbitrary time depth of African migrations, as if Africans only got to South Africa or any other part of Africa 4,000 years ago.
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XYZ says: The back-migrating Basal Eurasians/EEF was responsible for the Neolithic Revolution in Africa and throughout the world
Yes, but as you have pointed out the "back migration" would be by "basal" types already linked with Africans would it not?
The f3 statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the ubiquitous hunter-gatherer ancestry across the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations.
Wait a minute. SO they are passing off the Khosians as "Eurasians." or saying that the "EUrasian backflowees" mixed with the Khosians? And if so, how are the Khosians/Mbuti the only population in place to meet the putative backflowees? Nobody else was in Africa besides "Khosians" or Mbuti?
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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quote:Originally posted by xyyman: Yes, they are playing both sides. They are back to the Nile Valley/Sudan (Sergi) and the advent of Agriculture 9,000years ago. But they are trying to flip it claiming it was back migration accounting for the Eurasian ancestry in Africans. In other words. The back-migrating Basal Eurasians/EEF was responsible for the Neolithic Revolution in Africa and throughout the world. SMH! Is this a pre-emptive strike on Lazaridis latest paper? Lol!
I guess the researchers don’t talk to each other before publishing. lol!
Well observed, ...
The time I responded, I had not really read this "paper", only glanced over it. But I see the intend here.
quote: An important question in African history is how contemporary populations relate to those present in Africa before the transition to pastoralism that began in the Nile Valley some 9kya.
quote:9) In the first paragraph of the Discussion. The adoption of pastoralism began well before 2,000 years ago. The earliest archaeological evidence of cattle keeping may date to as early as 9kya in the Nile River Valley, and is well established by 6kya (see Boivin et al. 2010). Pastoralists reach the Koobi Fora region of Kenya by 4.5 kya, and are east of Lake Victoria by 3.8 kyat (see Pendergast 2011).
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by zarahan- aka Enrique Cardova: XYZ says: The back-migrating Basal Eurasians/EEF was responsible for the Neolithic Revolution in Africa and throughout the world
Yes, but as you have pointed out the "back migration" would be by "basal" types already linked with Africans would it not?
The f3 statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the ubiquitous hunter-gatherer ancestry across the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations.
Wait a minute. SO they are passing off the Khosians as "Eurasians." or saying that the "EUrasian backflowees" mixed with the Khosians? And if so, how are the Khosians/Mbuti the only population in place to meet the putative backflowees? Nobody else was in Africa besides "Khosians" or Mbuti?
It's ironic because they completely ignore this following data, and let's not forget, Sara Tishkoff has the largest sample collection on Africans, which took her ten years to collect.
quote: According to the current data East Africa is home to nearly 2/3 of the world genetic diversity independent of sampling effect. Similar figure have been suggested for sub-Saharan Africa populations [1]. The antiquity of the east African gene pool could be viewed not only from the perspective of the amount of genetic diversity endowed within it but also by signals of uni-modal distribution in their mitochondrial DNA (Hassan et al., unpublished) usually taken as an indication of populations that have passed through ‘‘recent’’ demographic expansion [33], although in this case, may in fact be considered a sign of extended shared history of in situ evolution where alleles are exchanged between neighboring demes [34].
Figure S1 Neighbor joining (NJ). NJ tree of the world populations based on MT-CO2 sequences. The evolutionary relationship of 171 sequences and evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 0.20401570 is shown. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 543 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4. Red dots: east Africa, Blue: Africa, Green: Asia, Yellow: Australia, Pink: Europe and gray: America. (TIF)
Figure S2 Multidimensional Scaling Plot (MDS). The 2nd and 3rd coordinates of an MDS plot of 848 nuclear microsatellite loci from 469 individuals of 24 world populations. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The figure, besides a separate clustering of east Africans, indicates the substantial contribution of Africans and east Africans to the founding of populations of Europe and Asia. (TIF)
Figure S3 Multidimensional Scaling Plot (MDS). The 3rd and 4th coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The central position of east Africans and some other Africans emphasizes the founding role of east African gene pool and the disparate alignment on coordinates along which the world populations were founded including populations of Aftica aligning along the 4th dimension. (TIF)
Figure 4. Multidimensional Scaling Plot (MDS). A. First and second coordinates of an MDS plot of 848 Microsatellite Marshfield data set across the human genome for 24 populations from Africa, Asia and Europe. MDS plot was constructed from pairwise differences FST generated by Arlequin program (Table S3). B. First and second coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. East Africans cluster to the left of the plot, while Beja (red cluster in the middle), assumes intermediate position. doi:10.1371/journal.pone.0097674.g004
Figure S4 Multidimensional Scaling Plot (MDS). First and second coordinates of an MDS plot based on MT-CO2 data set constructed from pairwise differences FST generated by Arlequin v3.11. Population code as follows: Nara: Nar, Kunama (Kun), Hidarb (Hid), Afar (Afa), Saho (Sah), Bilen (Bil), Tigre (Tgr), Tigrigna (Tig), Rashaida (Rsh), Nilotics (Nil), Beja (Bej), Ethiopians(Eth), Egyptians (Egy), Moroccans (Mor), Southern Africans (Sth), Pygmy (Pyg), Saudi Arabia (Sdi), Asia (Asi), Europe (Eur), Native Americans (NA), Australians (Ast), Nubians (Nub), Nuba (Nba) (TIF)
--Jibril Hirbo, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
PLoS One. 2014; 9(5): e97674. Published online 2014 May 20. doi: 10.1371/journal.pone.0097674
quote:Originally posted by xyyman: In short they are trying to “explain away” the presence of European and Asian “LABELLED” genes in Africans and particularly West Africans, the so-called “true Negro”. Lol! But some authors have already identified ‘European’ genes in the true Negro. In fact some authors have identified the ‘European’ genes as being OLDER in the true negro compared to the “Caucasoid Horners’. Which is baffling these researchers. But it is only baffling to them because of their hypocritical views and prejudices. DNATribes in their digest on continental populations had already identified ‘Basque” ie European genes in Central Africa, and it increase in frequency moving away from Central Africans. ie IBD or genetic surfing. Lazaridis and DNATribes also identified archaic genetic material primarily in Khoi-San and Mbuti. This is puzzling the racialist because at first they believed there was no Neanderthal admixture in SSA. Lol! They are hitting roadblocks at every turn.
Brenna Henn, in this 2014 interview on population genetics and population structure, considering African populations.
“African populations have the most genetic diversity in the world,” Henn said.“If you compared people from the Kalahari Desert to people from Mali, they’d be as different from each other [genetically] as Italians and Chinese people.”
Why are other populations of humans so much less genetically varied than Africans? The answer, Henn explains, lies in our ancestors’ history; the groups of people that migrated out of Africa and spread throughout other continents were smaller subsets of that original, genetically diverse population.
"AND WITHIN EACH OF THESE GROUPS THERE IS AN AMAZING AMOUNT OF DIVERSITY,[...] THE DIVERSITY IS INDIGNIOUS TO AFRICAN POPULATIONS":
Tracing Family Trees, And Human History, With Genetics
Colored dots indicate genetic diversity. Each new group outside of Africa represents a sampling of the genetic diversity present in its founder population. The ancestral population in Africa was sufficiently large to build up and retain substantial genetic diversity.
--Brenna M. Henna, L. L. Cavalli-Sforzaa,1, and Marcus W. Feldmanb,2 Edited by C. Owen Lovejoy, Kent State University, Kent, OH, and approved September 25, 2012 (received for review July 19, 2012)
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quote:Originally posted by zarahan- aka Enrique Cardova: ..which if they were going by the latter approach would point out the African origins of many of these lineages.... Ultimately the issue being that Africa is not stagnant, humans are a migratory species and focusing on one small period of time in order to flesh out one piece of the picture doesn't replace the whole picture.
True enough. This notion of "static" Africans is still in the minds of many- such as "sub-Saharan" Africans staying meekly behind the "Saharan barrier" like some apartheid line of old South Africa. ANd the Sahara itself is a shifting barrier - with net movement south over the centuries. This means that numerous peoples once "sub-Saharan" become NON "sub-Saharan" as the barrier creeps south. The Kingdom of Kush was a sub-Saharan entity with trade and admin links far south.
This is more than an issue of Nile Valley settlement though. It is an issue of time depth and multiple waves of dispersions within Africa and out of Africa. Imagine how ripples interact within a pond and now put the Omo valley as the source of the ripples with waves radiating out then bouncing around within Africa, with some leaking out. Their view is so simplistic that it doesn't even admit to the fact that Africans have been migrating back and forth within Africa over multiple thousands of years as a result of various climate and environmental changes. This would imply that there have been multiple waves of settlements in various parts of Africa and that "Sub Saharans" is a meaningless term in that the first humans were born in Sub Saharan Africa to begin with so how does that distinction mean anything IN Africa among African populations? And this is where the time depth and diversity of Africans and African lineages come into play because all African populations have tremendous diversity as a result.
Studies like this ignore the 200,000 year history of Africans migrating in and around Africa and create some artificially shallow and arbitrary time depth of African migrations, as if Africans only got to South Africa or any other part of Africa 4,000 years ago.
Their proposition indeed has been that Africans are inferior, therefore could not have moved themselves in Africa, from place-to-place. It took magical Eurasians (caucasoids/ whites) to roam all over Africa.
This view is horrendous and racist ideology, which has root in old colonial thinking.
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quote:Originally posted by zarahan- aka Enrique Cardova:
Wait a minute. SO they are passing off the Khosians as "Eurasians."
No, read the article not the xyyman-ization of it
quote:
Despite events between African and Eurasian sources appearing older in the Nilo-Saharan and Afroasiatic speakers from East Africa, we see a similar signal of very recent Central West African ancestry in a number of Khoesan groups from Southern Africa, such as the Khwe and /Gui //Gana, together with Malawi-like (brown) sources of ancestry in recent admixture events in East African Niger-Congo speakers.
quote:Originally posted by zarahan- aka Enrique Cardova:
or saying that the "EUrasian backflowees" mixed with the Khosians?
quote: Lastly, in two Khoesan speaking groups from South Africa, the ≠Khomani and Karretjie, we infer very recent direct admixture involving Eurasian groups most similar to Northern European populations, with dates aligning to European colonial period settlement in Southern Africa (c. 5 generations or 225 years ago; Figure 5) (Hellenthal et al., 2014). Taken together, and in addition the MALDER analysis above, these observations suggest that gene-flow back into Africa from Eurasia has been common around the edges of the continent, has been sustained over the last 3000 years, and can often be attributed to specific and different historical time periods.
quote:Originally posted by zarahan- aka Enrique Cardova:
or saying that the "EUrasian backflowees" mixed with the Khosians?
You act like you're hearing this for the first time. Yours is the first comment on the thread below
Khoisans often have bantu admixture. But keep in perspective the amount of admixture they also have of Eurasian ancestry is on average lower than the average Eurasian admixture in AAs. I think I might have read 7% but don't quote me on that go back to the PDF The reference in this Busby paper is Hellenthal et al article below , 2014 co-authors including Busby Supplement see: "San Khomani" of South Africa. Note the the San of Namibia are less admixed. And keep in mind many San no longer live in the bush, are not the San that people like to photograph far out in the rural areas but I'm not sure the spread of their sampling but it's better to refer to the Pickrell article because that is focused more on the San than the below genetic atlas article
Garrett Hellenthal,1 George B.J. Busby,2 Gavin Band,3 James F. Wilson,4 Cristian Capelli,2 Daniel Falush,#5 and Simon Myers#*,3
4. value used for CHROMOPAINTER’s inferred genome-wide average switching rate (i.e. Ne; see Appendix A.3) For each of 1-4, we provide results for nine populations in Table S13. These populations rep- resent a diverse range of admixture scenarios, including simple events, multiple sources (Maya, Kalash) and multiple dates (San Khomani), with varying admixture proportions (3-37%) and times (e.g. 598BCE in the Kalash to 1670CE in the Maya). These nine populations also repre- sent a variety of inferred admixing source groups, illustrating admixture within Africa (South African Bantu, San Khomani), within Europe (Greek), within Asia (Cambodian, Turkish) and between sources from different continents (Druze, Kalash, Maya, San Khomani, West Sicilian). In the final part of this section below, we also discuss consistency, in particular of admix- ture date inference, using our standard and “NULL” coancestry curves across all our sampled populations. This is motivated particularly by our finding in Note S5.5.3 that very strong bottlenecks following relatively old admixture may affect inference, and also by the fact that if our approach is working satisfactorily, the two types of curve ought to produce dates that approximately agree.
Waves of admixture in Southern Africa The South African Bantu speakers show a genetic contribution from the San (Khomani) dating to 1220CE (1080-1360CE), highlighting genetic influences consistent with the dispersal of Bantu-speaking peoples into southern Africa (61; 62; 63), and placing an upper bound on the arrival time of these peoples in the region consistent with archaeological dates (64; 65). The strongest evidence of complex admixture in the entire dataset of 95 populations is in the Khomani San from the Northern Cape province of South Africa. Here we infer one older event (of very uncertain age prior to 1000CE) between sources more similar to present-day Namibian San and Bantu speakers. Such an event is complementary to, though potentially slightly earlier than, the signal seen in the South Africa Bantu speakers and demonstrates substantial admixture from Bantu-speaking peoples in this San group. A second, more recent (1700-1840CE) admixture episode occurred between the San Khomani and one group with a mixture of inferred ancestries: North European, and South Asian, contributing an estimated 27% of DNA (Figure 2D). This date is consistent with the colonial-period arrival of European settlers (from Britain, Holland, and Germany) and South Asian immigrants (39). We note we do not (attempt to) directly separate more than two recent sources, although the wide geographic separation between Northwest Europe and Central/South Asia, with only small inferred contributions from groups between these locations is perhaps most simply explained by more than one Eurasian group being involved in the recent event. Thus, we observe a likely genetic impact for two distinct waves of settlement into South Africa, one by Bantu and the other by colonial-era migrants (61).
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Yes. Read the article. what do you think "and/or" mean? They are equating Khoisan=ancient European >10,000years ago. So Dr Winter may be right. See the thread on ancient Khoisan in North Africa. I had my doubts about Grimaldi man being Khoisans. But I started to come around when I saw Canary Islanders carry a high frequency of Loschbour ancestry. The author of that study refused to show Central Africans and Khoisan in that study.
--- Quote by Lioness:
Originally posted by zarahan- aka Enrique Cardova:
Wait a minute. SO they are passing off the Khosians as "Eurasians." “No, read the article not the xyyman-ization of it”
---
@ Z-man. They are not saying the Khoisan/MButi are the ONLY Africans with the ancestry. They are equating the source. “and/or”. This >10,0000year old, Hunter gatherer, whether European origin or Khoisan origin are basically related. That is the bottomline. If you look at the Aegan Neolithic thread that is the “black” color in the pie chart. Notice they did not include Khosian in that study. Which was a clue to me. It showed Berbers and Canary Islanders were closely related to Loshcbour. Which was a shocker to me. And we are finding out Berbers and Khoisans are related. Also see my thread on ESR about “Berbers in pictures”. There is definitely a close link between the two groups of Africans.
IIRC Khoisan carry siblings clades within E-215(E1b1b) but NOT on the same branch. Berber also carry their own unique branch of yDNA hg-A. Significance? Ancient connection between North African Berbers and Khoisans. In the words of X. Chicken coming home to roost.
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You got it. They are back to European domination. The back-migrating Europeans (with Khoisan ancestry which they are now calling European ancestry ), were the forbearers of Neolithic technology and was therefore responsible for civilizing the world.
Europeans are still trying to find their place in world history and they will steal or make one up if they have to. Lol!
quote:Originally posted by Ish Gebor:
quote:Originally posted by xyyman: [qb] Yes, they are playing both sides. They are back to the Nile Valley/Sudan (Sergi) and the advent of Agriculture 9,000years ago. But they are trying to flip it claiming it was back migration accounting for the Eurasian ancestry in Africans. In other words. The back-migrating Basal Eurasians/EEF was responsible for the Neolithic Revolution in Africa and throughout the world. SMH! Is this a pre-emptive strike on Lazaridis latest paper? Lol!
I guess the researchers don’t talk to each other before publishing. lol! [/q][/Q]Well observed, ...
The time I responded, I had not really read this "paper", only glanced over it. But I see the intend here.
[QUOTE] An important question in African history is how contemporary populations relate to those present in Africa before the transition to pastoralism that began in the Nile Valley some 9kya.
quote:9) In the first paragraph of the Discussion. The adoption of pastoralism began well before 2,000 years ago. The earliest archaeological evidence of cattle keeping may date to as early as 9kya in the Nile River Valley, and is well established by 6kya (see Boivin et al. 2010). Pastoralists reach the Koobi Fora region of Kenya by 4.5 kya, and are east of Lake Victoria by 3.8 kyat (see Pendergast 2011).
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quote:Originally posted by xyyman: [QB] Yes. Read the article. what do you think "and/or" mean? They are equating Khoisan=ancient European >10,000years ago. So Dr Winter may be right. See the thread on ancient Khoisan in North Africa.
stop spreading confusion Quote the article
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xyz said: @ Z-man. They are not saying the Khoisan/MButi are the ONLY Africans with the ancestry. They are equating the source. “and/or”. This >10,0000year old, Hunter gatherer, whether European origin or Khoisan origin are basically related.
Indeed. SO it seems the putative category "Eurasians" is itself in part related to Khosians, who ironically are themselves "sub-Saharan" Africans.
lioness sez: not the xyyman-ization of it”
Well xyz is not always 100% perfect on all statements made but he has brought forward a ton of valuable data, and is tweaking and rotating various points to present new models, theories and angles, for which he deserves some credit. Ultimately these models and approaches are all testable, and folks here including myself have disagreed with some conclusions as stated, but there has agreement as well on the flip side. Give him props. His batting average has been on the positive side several times.
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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== quote 9. Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry. The f3statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the **ubiquitous** hunter-gatherer ancestry** across** the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations
quote:Originally posted by the lioness,: [
that's wrong, quote the article [/QUOTE]
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quote:Originally posted by zarahan- aka Enrique Cardova:
Indeed. SO it seems the putative category "Eurasians" is itself in part related to Khosians, who ironically are themselves "sub-Saharan" Africans.
that's wrong, quote the article
What's wrong with analyzing and interpreting the article? And what exactly do you mean by p, wrong?
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^^lol.. Some people still can't seem to grasp this..
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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quote:Originally posted by zarahan- aka Enrique Cardova:
Indeed. SO it seems the putative category "Eurasians" is itself in part related to Khosians, who ironically are themselves "sub-Saharan" Africans.
that's wrong, quote the article
quote:Originally posted by xyyman: Khoisan are south of the Sahara. SSA
T H E Y - W I L L - C O M E - A R O U N D!!
== quote 9. Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry. The f3statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the **ubiquitous** hunter-gatherer ancestry** across** the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations
quote:Originally posted by the lioness,:
that's wrong, quote the article
[/QUOTE]
Here's the quote with the original bolding sans xyymanization:
quote: (9) Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry. The MALDER analysis and f3 statistics show the general presence of ancient Eurasian and / or Khoesan ancestry across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia [Hodgson et al., 2014a], with the ubiquitous hunter-gatherer ancestry across the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations.
Again, the theme of the paragraph is bolded:
Ancient Eurasian gene-flow back into Africa and shared hunter-gatherer ancestry.
That is two separate things as the title of the article says:
Admixture into and within sub-Saharan Africa George
"Admixture into" = Eurasian
"within sub-Saharan Africa' = within sub-Saharan Africa'
quote:
5. South African Khoesan. Several Khoesan groups show evidence of specific admixture events involving Central West African donors, in the Khwe, /Gui//Gana, and Xun. When we remove Khoesan groups from being surrogates, interestingly we see that the major sources of admixture now tend to contain ancestry from Southern African Niger-Congo populations, which specifically are not Malawi-like (Fig. 4-figure supplement 2). We also observe a small amount of West African (dark blue) ancestry in these admixture sources, and very little Central West African ancestry (and none from Cameroon). This suggests that the non-Khoesan ancestry in groups from this region is unlikely to be associated with the migrations that spread the Cameroon (Bantu) ancestry into East and South Africa. We also observe a small amount of East African Nilo-Saharan / Afroasiatic ancestry in the major sources of admixture in the non-local analysis.
quote:
The model we present here is therefore unlikely to recapitulate the full history of the continent and will be refined in the future with additional data and methodology. We again caution that we do not have an exhaustive sample of African populations, and in particular lack significant representation from extant hunter-gatherer groups outside of southern Africa. Nevertheless, there are signals in the data that our haplotype-based approach allows us to pick up, and it is therefore possible to highlight the key gene-flow events and sources of coancestry in Africa:
(1) Colonial Era European admixture in the Khoesan.
In two southern African Khoesan groups we see very recent admixture involving northern European ancestry which likely resulted from Colonial Era movements from the UK, Germany, and the Netherlands into South Africa [Thompson, 2001].
(2) The recent arrival of the Western Bantu expansion in southern Africa.
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. Central West African ancestry in Malawi appears to have appeared prior to this event.
(3) Medieval contact between Asia and the East African Swahili Coast.
Specific Asian gene- flow is observed into two coastal Kenyan groups, the Kauma and Chonyi, which represents a distinct route of Eurasian, in this case Asian, ancestry into Africa, perhaps as a result of Medieval trade networks between Asia and the Swahili Coast around 1200CE.
(4) Gene-flow across the Sahara.
Over the last 3,000 years, admixture involving sources containing northern European ancestry is seen on the Western periphery of Africa, in The Gambia and Mali. 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. We do see limited southern European ancestry in West Africa (Figs. 5 and 6D) in the Fulani, suggesting that some Eurasian ancestry may also have entered West Africa via North East Africa [Henn et al., 2012].
Northern European populations, relate closely to Germanic people. Depending on the part of the region.
Thus German, Dutch ... etc. So this does make sense.
Folks like the Vadals are related to Germanic, Nordic Europeans. They invaded Northwest Africa.
quote:Now the Vandals, dwelling about the Maeotic Lake [the Sea of Azov], since they were pressed by hunger, moved to the country of the Germans, who are now called Franks, and the river Rhine, associating with themselves the Alans, a Gothic people [Arkenberg: actually, they were one of the Indo-Iranian peoples].
Ancient History Sourcebook: Procopius of Caesarea: Gaiseric & The Vandal Conquest of North Africa, 406 - 477 CE
The general analysis (based on historical sources, epigraphy and archaeological evidence) focuses on transitions in town and country and economy from Roman to Vandal and to Byzantine rule and observing patterns and facets of continuity and change.
Background: The most recent Alu insertions reveal different series of characteristics such as stability that make them particularly suitable genetic markers for human biological studies.
Subjects and methods: Forty-seven Berbers from Sejnane and 33 from Takrouna were sampled. Alu insertion polymorphism was analysed using PCR with loci specific primers.
Results: A similar level of gene diversity was detected in Sejnane and Takrouna populations. PC results revealed genetic affinities between these two populations and some Eurasian populations ( Germany, Genova and Syria). In contrast, there is a differentiation between these two Berber communities and North African and Iberian populations.
Conclusion: The results of this study confirm the heterogeneity of Berbers in North Africa, which suggests their diverse origins. In the case of Sejnane and Takrouna populations, these results are in line with an ancient Euro Mediterranean background that has already been studied by archaeologists, particularly for the population of Sejnane.
Assessing human genetic diversity in Tunisian Berber populations by Alu insertion polymorphisms
--S. Frigi, H. Ennafaa, M. Ben Amor, L. Cherni and A. Ben Ammar-Elgaaied
"ANCIENT EURASIAN GENE-FLOW BACK INTO AFRICA AND ***SHARED**** HUNTER-GATHERER ANCESTRY"
>10,000 YEARS AGO!!!!!!!!! ie BEFORE NEOLITHIC
lol!!!!
quote:Originally posted by xyyman: [Q] Khoisan are south of the Sahara. SSA
T H E Y - W I L L - C O M E - A R O U N D!!
== quote 9. ***ANCIENT EURASIAN GENE-FLOW BACK INTO AFRICA AND SHARED HUNTER-GATHERER ANCESTRY.*** The f3statistics show the general presence of **ANCIENT** Eurasian and/or Khoesan ancestry (xyyman comment: This is the missing link. WHG are Khoisans) across much of sub-Saharan Africa. We tentatively interpret these results as being consistent with recent research suggesting very old (>10 kya) migrations back into Africa from Eurasia (Hodgson et al., 2014a), with the **ubiquitous** hunter-gatherer ancestry** across** the continent possibly related to the inhabitant populations present across Africa prior to these more recent movements. Future research involving ancient DNA from multiple African populations will help to further characterise these observations
quote:Originally posted by the lioness,: [q] [
that's wrong, quote the article [/q][/QTE] [/Q]
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The FACT is Hunter gatherers Khoi share more ancestry with late Paleolithic Europeans. Now they are trying to explain away this puzzle. They came up with …you guessed it…..”back-migration” during Paleolithic times. What are novel idea(sic). We have Eurasians “back-migrating” during Paleolithic, early Holocene, Neolithic. Did I leave any period out? Lol!
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quote:Originally posted by xyyman: The FACT is Hunter gatherers Khoi share more ancestry with late Paleolithic Europeans. Now they are trying to explain away this puzzle. They came up with …you guessed it…..”back-migration” during Paleolithic times. What are novel idea(sic). We have Eurasians “back-migrating” during Paleolithic, early Holocene, Neolithic. Did I leave any period out? Lol!
lioness is trolling again.
quote: Analyses that model the correlations in allele frequencies (such as those performed here in the Allele frequency differences show widespread evidence for admixture section) provided initial evidence that the presence of Eurasian DNA across sub-Saharan Africa is the result of gene-flow back into the continent within the last 10,000 years (Gurdasani et al., 2014; Pickrell et al., 2014; Hodgson et al., 2014a), and that some groups have ancient (over 5 kya) shared ancestry with hunter-gather groups (Figure 3) (Gurdasani et al., 2014).
All-in-all, they will do anything to claim ancient Egypt. Because that is what this is about. And of course an explanation to civilizations now found in the "sub Sahara". Ain't nothing changed but the weather. It's troll science. Ten years ago there was no Neanderthal DNA found in "sub Sahara Africans", but only in Asians and Europeans. lol Then all of sudden it magically did.
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That is why taking a close look at the populations they sample is very important. When Paabo did his study about ten years ago and concluded that SSA did NOT have any Neanderthal ancestry he used(3 people from ) ONE African population. yes. IIRC only 3!!! He did not use Khoi-san. Khoi is SSA!!! We need to understand the overall approach for these studies. I speculated that Khoi-San will have Neanderthal ancestry because they are closest to the orginal metapopulational that left Africa initially. The Neolithic seems to have originated from relatively isolated or differentiated populations within Africa. Who later admixed as they migrated outwards across Africa, North Africa, Middle East and Europe and into the Harrapan Valley. That explains why Yorubans(West Africans), Natufians, Europeans and Neolithic do NOT carry as much supposed ‘Neanderthal Ancestry”. Of course it is not Neanderthal “mixing” with humans. It is just sub-structure. ie Archaic modern humans are genetically closer to Neanderthal. That is, they are genetically closer to the ancestors of BOTH AMH and Neanderthals.
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quote:Originally posted by xyyman: That is why taking a close look at the populations they sample is very important. When Paabo did his study about ten years ago and concluded that SSA did NOT have any Neanderthal ancestry he used(3 people from ) ONE African population. yes. IIRC only 3!!! He did not use Khoi-san. Khoi is SSA!!! We need to understand the overall approach for these studies. I speculated that Khoi-San will have Neanderthal ancestry because they are closest to the orginal metapopulational that left Africa initially. The Neolithic seems to have originated from relatively isolated or differentiated populations within Africa. Who later admixed as they migrated outwards across Africa, North Africa, Middle East and Europe and into the Harrapan Valley. That explains why Yorubans(West Africans), Natufians, Europeans and Neolithic do NOT carry as much supposed ‘Neanderthal Ancestry”. Of course it is not Neanderthal “mixing” with humans. It is just sub-structure. ie Archaic modern humans are genetically closer to Neanderthal. That is, they are genetically closer to the ancestors of BOTH AMH and Neanderthals.
quote:Originally posted by Ish Gebor:
quote:Originally posted by xyyman: [qb] The FACT is Hunter gatherers Khoi share more ancestry with late Paleolithic Europeans. Now they are trying to explain away this puzzle. They came up with …you guessed it…..”back-migration” during Paleolithic times. What are novel idea(sic). We have Eurasians “back-migrating” during Paleolithic, early Holocene, Neolithic. Did I leave any period out? Lol!
lioness is trolling again.
Ish Gebor could you give us some details on Khoisans sharing more genetic ancestry with late Paleolithic Europeans
Posts: 42921 | From: , | Registered: Jan 2010
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quote:Originally posted by xyyman: That is why taking a close look at the populations they sample is very important. When Paabo did his study about ten years ago and concluded that SSA did NOT have any Neanderthal ancestry he used(3 people from ) ONE African population. yes. IIRC only 3!!! He did not use Khoi-san. Khoi is SSA!!! We need to understand the overall approach for these studies. I speculated that Khoi-San will have Neanderthal ancestry because they are closest to the orginal metapopulational that left Africa initially. The Neolithic seems to have originated from relatively isolated or differentiated populations within Africa. Who later admixed as they migrated outwards across Africa, North Africa, Middle East and Europe and into the Harrapan Valley. That explains why Yorubans(West Africans), Natufians, Europeans and Neolithic do NOT carry as much supposed ‘Neanderthal Ancestry”. Of course it is not Neanderthal “mixing” with humans. It is just sub-structure. ie Archaic modern humans are genetically closer to Neanderthal. That is, they are genetically closer to the ancestors of BOTH AMH and Neanderthals.
quote:Originally posted by Ish Gebor:
quote:Originally posted by xyyman: [qb] The FACT is Hunter gatherers Khoi share more ancestry with late Paleolithic Europeans. Now they are trying to explain away this puzzle. They came up with …you guessed it…..”back-migration” during Paleolithic times. What are novel idea(sic). We have Eurasians “back-migrating” during Paleolithic, early Holocene, Neolithic. Did I leave any period out? Lol!
lioness is trolling again.
Ish Gebor could you give us some details on Khoisans sharing more genetic ancestry with late Paleolithic Europeans
It was already posted a while ago. About one and a half month ago. Or perhaps two.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by xyyman: That is why taking a close look at the populations they sample is very important. When Paabo did his study about ten years ago and concluded that SSA did NOT have any Neanderthal ancestry he used(3 people from ) ONE African population. yes. IIRC only 3!!! He did not use Khoi-san. Khoi is SSA!!! We need to understand the overall approach for these studies. I speculated that Khoi-San will have Neanderthal ancestry because they are closest to the orginal metapopulational that left Africa initially. The Neolithic seems to have originated from relatively isolated or differentiated populations within Africa. Who later admixed as they migrated outwards across Africa, North Africa, Middle East and Europe and into the Harrapan Valley. That explains why Yorubans(West Africans), Natufians, Europeans and Neolithic do NOT carry as much supposed ‘Neanderthal Ancestry”. Of course it is not Neanderthal “mixing” with humans. It is just sub-structure. ie Archaic modern humans are genetically closer to Neanderthal. That is, they are genetically closer to the ancestors of BOTH AMH and Neanderthals.
As we said many times on this site, biased sampling. Over and over.
This is why Tishkoff always comes with new surprising data, she has the actual samples.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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Ish Gebor could you give us some details on Khoisans sharing more genetic ancestry with late Paleolithic Europeans
It was already posted a while ago. About one and a half month ago. Or perhaps two.
what's the link so the readers know you are not making it up ?
I think it was on the Chinese professor. You know. The one by Mindovermatter.
I have no time to look up links now, nor to be repetitive.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:The wider Jewish world began taking more notice of the Ibo in 2012 - filmmaker Jeff Lieberman released a documentary “Re-emerging: The Jews of Nigeria,” and Northeastern University professor William F.S. Miles published “The Jews of Nigeria: An Afro-Judaic Odyssey."
Filmmaker Laurence Gavron is on a journey to document lost Jewish tribes in Africa.
The French-born Gavron, who has made Senegal her home since 1989, says she was immediately taken by the project, which she says combines her passion for Africa with the mystery of rediscovering Judaism.
Laurence Gavron
The film, titled “Black Jews, Juifs noir en Afrique,” focuses on a dozen African tribes – in Nigeria, Ghana, Cameroon and other countries – each with a Jewish story. Some claim to be descendants of the Bible’s 10 Lost Tribes. Others believe that their ancestors were Jews who emigrated from Judea to Yemen looking for gold.
Rabbinical authorities have not accepted any of the groups as Jewish under halachah, Jewish law, although all the tribes strive to be recognized as such at some level or another.
Edith Bruder, who has been studying these Jewish groups for more than a decade and wrote the book “The black Jews of Africa, history, identity, religion,” turned to Gavron for the film, which is expected to be released in the coming months.
“In sub-Saharan Africa, you can find ‘Judaic’ tribes in Ghana, Nigeria, Mali, Uganda, Cameroon, South Africa, Zimbabwe and even in Sao Tome and other countries. There are many of them,” Bruder said. “It is really a vast subject.”
The two women are documenting Sabbath celebrations in remote African villages, Ghanaian Jews practicing circumcision and Jewish-African traditional marriage ceremonies. They have even been deep into the forests filming black Jews preparing their “kosher” meals – in their own tradition, the way the Torah explains it simply – not mixing the meat of the veal with its mother’s cow milk.
Filming a Shabbat service in Ghana was a moving experience, Gavron says.
“At the end, really very touched and almost started crying,” she said.
The French connection between Bruder and Gavron seems almost predestined: Gavron with her fascination for Africa and for her Jewish roots, and Bruder’s researching of “Jewish-related subjects” for most of her academic career. Their producer, too, is French: Anne Schushman of Scuch Productions.
“I am very interested in Jewish people, being one, and in blacks, living in Africa and having become Senegalese,” Gavron said. “So black Jews is something that was more than perfect for me.”
In the introduction to her documentary project, Gavron writes, “Who has the right to proclaim himself a Jew? Who can assert his connection to Judaism? Are these black Jews really a part of the Jewish people? And if not, why do they wish to be included?”
Her own connection to Judaism – a sense of peoplehood and culture – has mostly been background music, she says, and making the film has “rekindled” those feelings.
Gavron, who keeps busy making films, writing detective stories, organizing cultural evenings, making video clips and curating photo expositions, among other pursuits, recently made history in her adopted homeland. In July, she became the first woman toubab – Senegalese naturalized white person – to be on an electoral list for parliament. With a victory, she would have become the first Jewish member of Senegal’s parliament.
Gavron, 57, hadn’t given much thought to political involvement in the Muslim-dominated country until just a few months ago. At a cocktail party in Dakar, the Senegalese capital, she began speaking to Mamadou Lamine Diallo, who heads Tekki, a left-wing party.
“I told him how much I share with him the values defended by his party: transparency, citizenship activism and ethics,” she said. “He immediately asked me if I cared to join as a candidate for the upcoming elections.”
The offer “enchanted me,” Gavron said. “I felt it was a wonderful way to repay this country, which has embraced me without any restraint or hesitation. It is my way to pay my gratitude back to the Senegalese people.
Gavron was able to run only because the Senegalese parliament adopting an equal gender representation act two years ago, obliging political parties to present an equal number of male and female candidates. And although she did not win the election, the experience convinced her to remain politically active – and she believes the results would be different the next time around.
Senegal has undergone significant changes in the past three years, most recently choosing Macky Sall as president over incumbent Abdoulaye Wade, who was criticized for his grandiose living style. That, along with the new laws designed to promote gender equality, may well play in Gavron’s favor in the next elections.
As to her ”home party,” Gavron is the perfect match for what Tekki is striving to achieve, says El Hadrji Sarr, a Tekki leader who supported Gavron’s candidacy.
”Laurence is a Senegalese in every means and ways, even though she is white,” he said. “She has a natural place within our electoral list.”
Gavron has long split her time among France, Africa and Israel. Although a Senegal citizen who makes her permanent home in Dakar, she says that when she visits Paris, she suddenly feels that is home again, as if she never left the place. Israel, meanwhile, remains her spiritual homeland, she says.
Her first visit to Senegal, a former French colony in western Africa, came in 1987 for an international film festival. She continued to go back and forth before making it her permanent home in 2000. Widowed for several years by then, Gavron says she decided it was time for a real change. She became a Senegalese citizen in 2007.
The night before she left Paris for the permanent move to Dakar, Gavron says she was inexplicably drawn to visit the Jewish quarter of Paris.
“I curiously found myself walking towards the Marais,” she recalls, where she bought a mezuzah.
“Being Jewish is important for me, even though I do not practice Judaism every day,” she said. “I am attached to my Jewish identity and to the cultural elements which differentiate me from others.”
quote:Originally posted by the lioness,: Oase is from a Romanian site, why are you posting on Khosians which have virtually no genetic affiliation to the Oase genome?
posted
Liar!!! Up to your tricks again. San weren't included in the study.
I just checked.
-------------- quote: Originally posted by the lioness,: Oase is from a Romanian site, why are you posting on Khosians which have virtually no genetic affiliation to the Oase genome?
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Pg 4 Oase 1
Lying Lioness and Lying Europeans. One and the same? Quote:
This suggests that the Oase 1 individual belonged to a population that did not contribute much, or not at all, to later Europeans.Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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