The African Genome Variation Project shapes medical genetics in Africa
Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, Konstantinos Hatzikotoulas, Savita Karthikeyan, Louise Iles, Martin O. Pollard, Ananyo Choudhury, Graham R. S. Ritchie, Yali Xue, Jennifer Asimit, Rebecca N. Nsubuga, Elizabeth H. Young, Cristina Pomilla, Katja Kivinen, Kirk Rockett, Anatoli Kamali, Ayo P. Doumatey, Gershim Asiki, Janet Seeley, Fatoumatta Sisay-Joof, Muminatou Jallow, Stephen Tollman et al. AffiliationsContributionsCorresponding authors Nature (2014) doi:10.1038/nature13997 Received 15 July 2014 Accepted 23 October 2014 Published online 03 December 2014
Abstract
Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa. 18 African populations studied in the AGVP including 2 populations from the 1000 Genomes Project. (The term ‘Ethiopia’ encompasses the Oromo, Amhara and Somali ethno-linguistic groups.) b, c, ADMIXTURE analysis of these 18 populations alone (n = 1,481) (b) and in a global context (n = 3,904) (c). Each colour represents a different ancestral cluster, with clusters 2–6 represented along the y-axis in b and clusters 2–18 represented in c. K = 6 and K = 18 were the most likely clusters on ADMIXTURE analysis. ADMIXTURE analysis suggests substructure between North, East, West and South Africa. Studying these populations in the context of Eurasian and African HG populations suggest extensive Eurasian and HG admixture across Africa.
Population structure in SSAIntroduction
Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this variation can provide insights into evolutionary processes that shape both human adaptation and variation in disease susceptibility1. Although the Hapmap Project2 and the 1000 Genomes Project3 have greatly enhanced our understanding of genetic variation globally, the characterization of African populations remains limited. Other efforts examining African genetic diversity have been limited by variant density and sample sizes in individual populations4, or have focused on isolated groups, such as hunter gatherers (HG)5, 6, limiting relevance to more widespread populations across Africa.
The African Genome Variation Project (AGVP) is an international collaboration that expands on these efforts by systematically assessing genetic diversity among 1,481 individuals from 18 ethno-linguistic groups from sub-Saharan Africa (SSA) (Fig. 1 and Supplementary Methods Tables 1 and 2) with the HumanOmni2.5M genotyping array and whole-genome sequences (WGS) from 320 individuals (Supplementary Methods Table 2). Importantly, the AGVP has evolved to help develop local resources for public health and genomic research, including strengthening research capacity, training, and collaboration across the region. We envisage that data from this project will provide a global resource for researchers, as well as facilitate genetic studies in Africa7.
On examining ~2.2 million variants, we found modest differentiation among SSA populations (mean pairwise FST 0.019) (Supplementary Methods and Supplementary Table 1). Differentiation among the Niger-Congo language groups—the predominant linguistic grouping across Africa was noted to be modest (mean pairwise FST 0.009) (Supplementary Table 1), providing evidence for the ‘Bantu expansion’—a recent population expansion and movement throughout SSA originating in West Africa around 3,000 to 5,000 years ago8.
We identified 29.8 million single-nucleotide polymorphisms (SNPs) from Ethiopian, Zulu and Bagandan WGS (Extended Data Fig. 1 and Supplementary Methods). A substantial proportion of unshared (11%–23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations (Extended Data Fig. 1). The high proportion of unshared variation among populations recapitulates the need for large-scale sequencing across Africa, including among genetically divergent populations.
We used principal component analysis to explore relationships among AGVP populations (Extended Data Figs 2, 3, 4, 5, Supplementary Figs 1 and 2). PC1 appeared to represent a cline extending from West and East African populations towards Ethiopian populations, possibly suggesting Eurasian gene flow, while PC2 separated West African and South/East African populations (Extended Data Fig. 2). Inclusion of the 1000 Genomes Project, North African and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3, 4, 5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. ‘Unsupervised’ (that is, without including known information on individual ancestry) ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for substantial Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6).
To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST = 0.027) may be a remnant of East African diversity pre-dating the Bantu expansion10
Population admixture in SSA
Formal tests for admixture (the three population test or f3 statistic)11, confirmed widespread Eurasian and HG admixture in SSA (Supplementary Tables 2 and 3). Quantification of admixture (Supplementary Table 4, Supplementary Methods and Supplementary Notes 3 and 4) indicated substantial Eurasian ancestry in many African populations (ranging from 0% to 50%), with the greatest proportion in East Africa (Fig. 2 and Supplementary Table 4). Similarly, HG admixture ranged from 0% to 23%, being greatest among Zulu and Sotho (Fig. 2 and Supplementary Table 5).
Figure 2: Dating and proportion of Eurasian and HG admixture among African populations.
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. 2 and Supplementary Note 5). Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ~7,500–10,500 years ago), old admixture among Ethiopian populations (~2,400–3,200 years ago) consistent with previous reports10, 12, and more recent complex admixture in some East African populations (~150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.
We also find evidence for complex and regionally distinct HG admixture across SSA (Fig. 2, Extended Data Figs 7 and Supplementary Note 5), with ancient gene flow (~9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5). Given limited archaeological and linguistic evidence for the presence of Khoe-San populations in West Africa, this extant HG admixture might represent ancient populations, consistent with the presence of mass HG graves from the early Holocene period comprising skeletons with distinct morphological features15, and with evidence of HG rock art dating to this period in the western Sahara16, 17. In East Africa, our analyses suggested that Mbuti rainforest HG populations most closely represented ancient HG mixing populations (Supplementary Note 5), with admixture dating to ~3,000 years ago, suggesting that HG ancestry here is likely to be older than previously reported18. The primary source of HG admixture in Zulu and Sotho populations was from Khoe-San populations (Fig. 2 and Supplementary Note 5), consistent with linguistic assimilation of click consonants among these populations.
Positive selection in SSA•
We examined highly differentiated SNPs between European and African populations, as well as among African populations to gain insights into loci that may have undergone selection in response to local adaptive forces (Supplementary Methods). To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry (Supplementary Methods and Supplementary Note 6).
On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift (P = 0.0002). Additionally, we found no evidence for background selection as the primary driver of differentiation among these loci (Supplementary Note 7).
In addition to genes known to be under positive selection (for example, SLC24A5, SLC45A2 and OCA219, 20, LARGE21 and CYP3A4/5) (Supplementary Fig. 3), we found evidence of differentiation in novel gene regions, including one implicated in malaria (for chemokine receptor 1, CR1) (Extended Data Fig. 8). CR1 carries the Knops blood group antigens and has previously been implicated in malaria susceptibility22 and severity23, with evidence suggesting positive selection in malaria-endemic regions24 (Extended Data Fig. 8). We also identified highly differentiated variants within genes involved in osmoregulation (ATP1A1 and AQP2) (Extended Data Fig. 8). Deregulation of AQP2 expression and loss-of-function mutations in ATP1A1 have been associated with essential and secondary hypertension, respectively25, 26. Climatic adaptive changes in these gene regions could potentially provide a biological basis for the high burden of hypertension and differences in salt sensitivity observed in SSA27.
In contrast, overall differentiation among African populations was modest (maximum masked FST = 0.19) (Supplementary Fig. 4) and only 56/1,237 sites remained in the tail distribution after masking (Supplementary Methods, Supplementary Table 6). This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6). Genes known to be under selection were notably enriched among the most differentiated loci after masking of Eurasian ancestry (P = 2.3 × 10−16). Among the 56 loci robust to Eurasian ancestry masking (Supplementary Table 6), we identified several loci known to be under selection (Extended Data Fig. 8), including a highly differentiated variant (rs1378940) in the CSK gene region implicated in hypertension in genome-wide association studies (GWAS)28. The major allele of rs1378940 among Africans was in complete linkage disequilibrium with the risk allele of the GWAS SNP rs1378942 (ref. 29), with the frequency of this allele highly correlated with latitude (r = −0.67), providing support for local adaptation in response to temperature as a possible mechanism for hypertension (Supplementary Fig. 5)30, 31.
Comparing populations residing in endemic and non-endemic infectious disease regions (Supplementary Methods), we identified several loci associated with infectious disease susceptibility and severity. As well as the known sickle-cell locus related to malaria, this approach identified additional signals for genes potentially under selection, including the PKLR region32, RUNX333, the haptoglobin locus, CD16334, IL1035, 36, CFH, and the CD28-ICOS-CLTA4 locus (Supplementary Table 7 and Extended Data Fig. 8)37. Similar comparisons for Lassa fever identified the known LARGE gene, as well as candidates associated with viral entry and immune response, including in the Histocompatibility Leukocyte Antigen region, DC-SIGN/DC-SIGNR38 (also known as CD209/CLEC4M), RNASEL, CXCR6, IFIH139 and OAS2/3 regions (Supplementary Table 7). For trypanosomiasis, we identified APOL140, as well as several loci implicated in immune response and binding to trypanosoma, including FAS, FASLG41, 42, IL23R43, SIGLEC6 and SIGLEC12 (Supplementary Table 7)44. For trachoma, we identified signals in ABCA1 and CXCR6, which may be important for the growth of the parasite and host immune response, respectively (Supplementary Table 7)45, 46.
Designing medical genetics studies in Africa
To inform the design of genomic studies in Africa, we addressed the following questions: (1) How well do current genotype arrays perform in African populations using existing reference panels for imputation? (2) Can these genotype arrays and reference panels identify and fine-map association signals in populations across Africa? (3) Can we improve imputation accuracy in African populations using a new African reference panel? and (4) What are the most cost-effective designs for large-scale GWAS in Africa?
The 1000 Genomes Project phase I integrated panel provided reasonably accurate imputation into the Illumina Omni 2.5M array in all populations (Supplementary Note 10). However, imputation accuracy was lower among Sotho, Zulu and Afro-Asiatic populations, possibly reflecting poor representation of some African haplotypes (including Khoe-San haplotypes) within the 1000 Genomes Project panel. These findings suggest that improvements in imputation accuracy across diverse population groups may require larger and more diverse reference panels.
We assessed the reproducibility and potential for fine-mapping association signals within Africa and globally at several disease susceptibility loci (Supplementary Methods, Supplementary Table 8 and Extended Data Fig. 9). Current genotype arrays and imputation panels allowed for identification of relevant association signals at most loci across populations in SSA, demonstrating that association signals are reproducible across populations in SSA (Extended Data Fig. 9 and Supplementary Figs 7–18). African populations are likely to provide better fine-mapping resolution around the causal locus (Supplementary Table 8). We highlight one example here: the sickle-cell anaemia locus (HBB)47, which is under positive selection owing to the protection the sickle cells confer against severe malaria. This locus showed marked heterogeneity in association signals across populations, reflecting different linkage disequilibrium patterns and allele frequencies among populations in SSA (Supplementary Figs 9 and 10). This pattern is probably the result of independent selection sweeps at this locus in different parts of Africa, leading to differences in hitchhiking rare haplotypes that attained high frequencies among different populations48. This suggests that these signatures are recent and occurred during or after the Bantu expansion, consistent with the hypothesis that the advent of agriculture and increased malaria transmission may have resulted in increased selection pressure49. However, in contrast to previous reports47, we show that association signals even at such highly differentiated loci can be captured with dense genotype data using existing reference panels for imputation, despite individual population groups not being fully represented in these. This suggests that, instead of large-scale population-specific sequencing across Africa, what is needed is a broad sequencing approach, targeted at capturing widespread haplotype diversity.
To assess the utility of a larger and more diverse African reference panel for imputation, we generated a panel integrating the 1000 Genomes Project phase I and AGVP WGS panels (Supplementary Methods and Supplementary Note 9). Using this integrated panel, we observed marked improvements in imputation accuracy across the whole range of the allele frequency spectrum in specific populations poorly represented by the 1000 Genomes Project panel (Fig. 3 and Supplementary Note 11). These findings suggest that even common haplotypes in some SSA populations may not be sufficiently captured by existing panels, limiting our power to examine associations of common variants with disease. Importantly, given the specificity of the improvement in imputation accuracy, we infer that targeted sequencing of divergent populations representing a broad spectrum of haplotypes across Africa, including HG and North/East African haplotypes, rather than widespread population sequencing is likely to provide a more efficient strategy to improve imputation accuracy and a practicable GWAS framework in Africa.
Figure 3: Improvement in imputation accuracy with the AGVP WGS p The substantial improvement in imputation accuracy in some populations (Sotho), compared to minimal improvement in others (Igbo) with the addition of the AGVP WGS reference panel to the 1000 Genomes Project phase I reference panel (‘merged’) suggests poor representation of some haplotypes (for example, Khoe-San haplotypes in Sotho) in the 1000 Genomes Project reference panel alone (‘1000’). r2 is the correlation coefficient, representing the correlation between imputed and genotyped data, on masking each genotyped variant during imputation. MAF, minor allele frequency.
We compared the utility of existing chip designs (2.5M Illumina) and ultralow-coverage WGS designs (0.5×, 1×, 2× coverage) to determine the optimal design for African GWAS. Sensitivity for common variation was >90% at all sequencing depths (Supplementary Note 12). Examining the effective sample size for a fixed budget50, we found the effective sample size was greater for all ultralow-coverage WGS and chip array designs compared with 4× WGS. When computational costs were accounted for (Supplementary Note 12), the HumanOmni2.5M array provided the greatest effective sample size supporting the development and large-scale use of efficient genotype arrays in Africa, where these have been underutilized.
We therefore sought to evaluate a potential chip design to tag common variation across a wider range of African populations (Supplementary Note 13). Importantly, we show that an array with one million genetic variants could capture >80% of common variation (minor allele frequency >5%) across the genome (Extended Data Fig. 10). These analyses suggest that designing a pan-African genotype array to effectively capture common genetic variation across Africa is feasible, and could greatly facilitate large-scale genomic studies in Africa.
Discussion
The marked haplotype diversity within Africa has important implications for the design of large-scale medical genomics studies across the region, as well as studies of population history and evolution. In this context, the AGVP is a resource that will facilitate a broad range of genomic studies in Africa and globally.
Although Africa is the most genetically diverse region in the world, we provide evidence for relatively modest differentiation among populations representing the major sub-populations in SSA, consistent with recent population movement and expansion across the region beginning around 5,000 years ago—the Bantu expansion8. Although the history of the Bantu expansion is probably complex, assessments of population admixture can provide new insights. We note historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA, including ancient HG and Eurasian ancestry in West and East Africa and more recent complex HG admixture in South Africa. As well as explaining genetic differentiation among modern populations in SSA, these admixture patterns provide genetic evidence for early back-to-Africa migrations, the possible existence of extant HG populations in western Africa—compatible with archaeological evidence15, and patterns of gene flow consistent with the Bantu expansion, including genetic assimilation of populations resident across the region.
This admixture also has important implications for the assessment of differentiation and positive selection in Africa. Accounting for these elements, we have identified loci under positive selection that are linked with hypertension, malaria, and other pathogens. This provides a proof-of-concept for the ability of geographically widespread genetic data within Africa to identify loci under selection related to diverse environments.
Our evidence for the broad transferability of genetic association signals and their statistical refinement has important implications for medical genetic research in Africa. Importantly, we highlight that such studies are feasible and can be enabled through the development of more efficient genotype arrays and diverse WGS reference panels for accurate imputation of common variation. In this context, we describe a framework for a new pan-African genotype array that could directly facilitate large-scale genomic studies in Africa.
A critical next step is the large-scale deep sequencing of multiple and diverse populations across Africa, which should be integrated with ancient DNA data. This would enable us to identify and understand signals of ancient admixture, patterns of historical population movements, and to provide a comprehensive resource for medical genomic studies in Africa.
Extended Data Figure 1: Allele sharing between sequenced populations in the AGVP. a, The overlap of SNPs between 4×WGS data from Zulu, Ugandan and Ethiopian individuals (subsampled to 100 samples each). b, The overlap of novel variants (those not in the 1000 Genomes Project phase I integrated call set, ‘1000G’) between the three populations. c, d, The allele frequency spectra of variants in different portions of the Venn diagrams depicted in a and b, respectively. There appear to be a large proportion of unshared (private) variants in each population: between 10% and 23% of the total number of variants in a given population. The proportion of novel variants was high, with Ethiopia showing the greatest proportion of novel variation. Most of the novel variation appears to be unshared and rare.
_________________________ Extended Data Figure 6: ADMIXTURE clustering analysis for AGVP samples combined with the 1000 Genomes Project, Human Genome Diversity Project, North African and Khoe-San samples. Cluster K = 2 shows separation of European and African ancestry, with delineation of Asian and Khoe-San ancestry in cluster K = 4. Subsequent clusters show separation of East, West, North and South African ancestral components n = 3,202.
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Extended Data Figure 7: Dating and source of admixture in the AGVP , The time and most likely sources of admixture with means and 95% confidence intervals for different AGVP populations estimated with MALDER (see Supplementary Note 5). Circular markers with a line drawn around them represent high-probability events, while those with no line around them represent low-probability events. b, The time and most likely sources of admixture estimated with MALDER for the same populations using high-quality imputed data to improve resolution.
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Thank you. However I'm not that deprectaed in recent times., a little yes, not much
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Tukuler
multidisciplinary Black Scholar
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posted
In any event, plenty in that report to fuel a page or three from Ish Gebor, Zarahan, Xyyman, ARtU, and a few others.
I mean interesting comparison to similar reports and general academe assumptions about Fulani, southern vs eastern baNtu, and others.
Interesting like for instance where, I think it was Tishkoff, the genetic home of humankind is SW Africa versus the paleo-archaeology home of E Africa.
Who paid attention or did archaeologist just frown and sigh rather than survey where in Namibia or wherever to dig and maybe make the find of the century, older sapiens bones than heretofore known.
BTW Pagani is the big-name geneticist of the report and, judging from surnames, a few Africans were among this huge team. Gambian team members may explain why we're finally seeing data on Atlantic speakers.
A purported African Genome Variation Project ought to be under African purview anyway. Who knows maybe one day, not too far off, Nature will sponsor an African scientists mag like the one they have for Arabs.
Meanwhile Bass and others in the Niger-Kordofanian thread may want to ponder the southern baNtu of this report in light of those linguists and historians who posit the Bantu Drift may've been more lingual than demic. UNESCO refused to include an African's opinion on Bantu that is not in line with the status quo in the paperback edition and only printed it as a delineated package with caveat in the original print.
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quote:Originally posted by Tukuler: In any event, plenty in that report to fuel a page or three from Ish Gebor, Zarahan, Xyyman, ARtU, and a few others.
Personally, I try to keep my contributions to this forum, to be mostly about Ancient Egypt. Either history/culture or bio-anthropology. I know some other posters like to talk about the "bio-diversity" of all humans in this forum, which is fine, but I'm mostly doing so when it's related to Ancient Egypt.
For example, I like to talk about the genetic distance between populations, or between population clusters, because this is how we calculate the genetic distance between Ancient Egyptians and modern African populations in relations to other modern populations. Considering the BMJ (Ramses=E1b1a), Jama, and DNA Tribes results, it seems Ancient Egyptians are closer to almost any African populations than non-African populations like West Asians and Europeans. In the sense that we know, from current results that Ancient Egyptians were mostly (black indigenous) Africans, but as any populations, albeit less so in ancient times, Ancient Egyptians were admixed (to a low degree) with Hyksos/Aamu conquerors, West Asians nomadic migrants and Kushites migrants. So any analysis of the Ancient Egyptians population history, ethnic affiliations won't be in the absolute but relatively to modern populations. Hence the needs to use the proper metrics to analyse such situation (like pairwise genetic distance between populations, haplogroup distributions, archaeological continuity, etc).
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Tukuler
multidisciplinary Black Scholar
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I guess I just don't want this to go neglected just because the Lioness broached it.
posted
I only saw the paper a couple of days ago on Dienekes. It has a lot on there. I need time to process all the information and what it means.
-------------------- 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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I just started analyzing this paper. But seriously, come on, this interpretation of the data is laughable, HA! HA! HA!.
Where is Swenet(Pagani) when you need someone to stomp on?
Also the dreaded Nigerian Neanderthal now have Neanderthal ancestry . LOL! They can’t help themselves.
So Europeans “back-migrated” to WEST AFRICA before they entered Horners.. This is really hilarious.
Will break it down and post more on ESR …. ------ >>>>>>
Quote: Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ,7,500– 10,500 years ago), old admixture among Ethiopian populations (,2,400– 3,200 years ago) consistent with previous reports10,12, and more recent complex admixture in some East African populations (,150–1,500 years ago) (Fig. 2, Extended Data Fig. 7 and Supplementary Note 5).Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba
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God. The only thing these researchers have in the favor is that they are white. They can write and interpret BS and the media will give them airplay.
dumb fugks!
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quote:Originally posted by xyyman: I only saw the paper a couple of days ago on Dienekes. It has a lot on there. I need time to process all the information and what it means.
The paper is a farce to me. The authors are trying to do what Charlie Bass would call placing all the Africans in the True Negro group, and recreating the Hamitic race.
The authors appear to believe that there was a lot of back migration of "Eurasians" to Africa, to explain the presence of so-called "Eurasian genes. They just can't get the fact that Africans carried the so-called Eurasian genes into Europe and the presence of "Eurasian" genes in Africa is the result, of some of these people staying at home in Africa, rather than a back migration. .
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BTW Sweetness these are the same people who proposed back –migration of Eurasian to Horners and onto South Africans. Now they have included West Africans in their study using the same BS methodology and to their surprise West Africans have “older” Eurasian ancestry than East Africans. But what is alarming is, instead of giving up on the BS theory they dug themselves in deeper. Being white and male(Pagani), they refuse to admit they are wrong(child with the loaded gun). Instead they created an even more illogical more BS story to “explain it away”. They just don’t get it.
-------------------- 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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I agree with you Dr Winters. So far from what I read they are trying to explain away "Eurasian" genes in the dreaded Nigerian Yoruba.
They are such a pitiful stupid people. BTW. It is not so much some Africans "stayed at home" but "genetic drift" further from Africa as reported by Rosenberger. Not all are stupid.
quote:Originally posted by Clyde Winters:
quote:Originally posted by xyyman: I only saw the paper a couple of days ago on Dienekes. It has a lot on there. I need time to process all the information and what it means.
The paper is a farce to me. The authors are trying to do what Charlie Bass would call placing all the Africans in the True Negro group, and recreating the Hamitic race.
The authors appear to believe that there was a lot of back migration of "Eurasians" to Africa, to explain the presence of so-called "Eurasian genes. They just can't get the fact that Africans carried the so-called Eurasian genes into Europe and the presence of "Eurasian" genes in Africa is the result, of some of these people staying at home in Africa, rather than a back migration. .
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quote:Originally posted by xyyman: I agree with you Dr Winters. So far from what I read they are trying to explain away "Eurasian" genes in the dreaded Nigerian Yoruba.
They are such a pitiful stupid people. BTW. It is not so much some Africans "stayed at home" but "genetic drift" further from Africa as reported by Rosenberger. Not all are stupid.
They're not stupid . They're just maintaining the status quo and trying to preserve the idea of European "white supremacy", i.e., even the European genes dominate evolution in Africa. LOL.
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^^^ All the contrary this research is an excellent news for people like us who want to demonstrate the indigenous black African origins of Ancient Egyptians. In fact, this is almost a complete victory for us on that point.
The Eurasian admixtures in North-Eastern Africa is consistent with the previous Pagani and Pickrell studies (see LINK) and locate it between 2,400– 3,200 years ago with another more recent admixture episode with Eurasians between 150–1,500 years ago (page 3 on the document)
3200 years ago for the earliest Eurasian admixture in Northeastern Africa is excellent for us. 3200 minus 2014 equals 1186 BC. Which is excellent.
It means the earliest traces of Eurasian ancestry in northeastern Africa was in 1186 BC, which is much LATER than the foundation of Ancient Egypt around 3000BC and much later than the Naqada, Badarian and Tasian cultures which were the precursors of Ancient Egypt.
1186 BC makes sense since the date is well after the foundation of Ancient Egypt and at a period when Ancient Egypt was becoming more and more cosmopolitan with the impact of nomadic migrants of Asian origins. It's around that time there was the first Hyksos (Aamu) foreign dynasty composed of West Asians people (Aamu), which were expelled by the 18th Dynasty. So everything is consistent which what we know of Ancient Egyptians history.
You can't almost imagine something better than this (beside more aDNA, of course). This is almost a complete victory for us if you consider the study to be accurate.
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^^^Of course current aDNA studies are also excellent for us since Ramses III is said to be E1b1a, the most common haplogroup in Africans and African Americans. While the autosomal STR of the 18th and 20th dynasty Royal families also matches populations in the same E1b1a and E-P2 regions among sub-Saharan Africans. See BMJ study, JAMA study, and DNA Tribes analysis.
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Listen man. Europeans have absolutely NADA connection with ancient Egypt, but that is not the point or discussion.
The authors are making the rediculous assertion that West Africans(~11,000y) have an older connection to Eurasia than Horners(3000y).
THAT, is the absurdity. You are ... "The Forest for the Trees"
Get your head around the big picture.
Dr Winters post should have helped you out.
quote:Originally posted by Amun-Ra The Ultimate: ^^^ All the contrary this research is an excellent news for people like us who want to demonstrate the indigenous black African origins of Ancient Egyptians. In fact, this is almost a complete victory for us on that point.
The Eurasian admixtures in North-Eastern Africa is consistent with the previous Pagani and Pickrell studies (see LINK) and locate it between 2,400– 3,200 years ago with another more recent admixture episode with Eurasians between 150–1,500 years ago (page 3 on the document)
3200 years ago for the earliest Eurasian admixture in Northeastern Africa is excellent for us. 3200 minus 2014 equals 1186 BC. Which is excellent.
It means the earliest traces of Eurasian ancestry in northeastern Africa was in 1186 BC, which is much LATER than the foundation of Ancient Egypt around 3000BC and much later than the Naqada, Badarian and Tasian cultures which were the precursors of Ancient Egypt.
1186 BC makes sense since the date is well after the foundation of Ancient Egypt and at a period when Ancient Egypt was becoming more and more cosmopolitan with the impact of nomadic migrants of Asian origins. It's around that time there was the first Hyksos (Aamu) foreign dynasty composed of West Asians people (Aamu), which were expelled by the 18th Dynasty. So everything is consistent which what we know of Ancient Egyptians history.
You can't almost imagine something better than this (beside more aDNA, of course). This is almost a complete victory for us if you consider the study to be accurate.
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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The authors are making the rediculous assertion that West Africans(~11,000y) have an older connection to Eurasia than Horners(3000y).
Well Eurasian admixture found in West African populations is at a very low level. Probably with Fulani/Fula acting as intermediary. We know there were already Eurasians from the Iberian regions in Northwestern Africa since at least before 10 000BC. Often called Ibero-maurusian, which form part of the ancestry of modern Berbers.
Still, the proportion of Eurasian ancestry is very low.
People can consider Table 4 (on page 5) in the Supplementary Information document.
It is Labelled: Supp Table 4:Proportion of Eurasian ancestry in AGVP populations,
If we take the time to look at the table of Eurasian admixtures in African populations, we can see the Western African populations with the highest level of Eurasian admixtures are without surprise the Fulani (Fula) with a maximum value of 12.39% of Eurasian admixtures. 12.39% is relatively low and inline with what we knew already from uniparentals or autosomal STR/SNP.
On the table we can also see Yoruba with 0.06% of Eurasian admixtures, Igbo with 0.48%, Mandinka with 2.48% and Ga-Adangbe with 0.72%. Those are very low value.
Even among the Fulani with 12.39% this is a low proportion of Eurasian admixtures. It's possible it could have happened during the wet period of the Sahara with Fulani people acting as intermediary between Berber/Iberomaurusian and other West African populations.
About every modern populations are admixed to each others at various degrees nowadays.
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posted
You are thick...but keep banking your head against the wall...it may sink in.
hint: "ancestry" is a label. There was never any Europeans entering Africa prior to 1500's.
-------------------- 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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posted
^^^ xyyman you seem to not know what the term "Eurasian" means. It means anybody of the entire land mass Europe + Asia It could refer to a Chinese person or a European or Middle Eastern person etc etc etc, this whole area It is not specific to Europe
I notice you do this over and over again, somebody speaks of Eurasians and you immediately start talking about Europeans specifically You act like they used the word European That is either you, using a straw man argument or you just dont know the difference
Posts: 42919 | From: , | Registered: Jan 2010
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posted
Xman got a question is the R found in Chad,Cameroon and north Nigeria originated there or came from outside Africa,note I am not implying that even if it did the carriers looked anything like a stereotypical Eurasian today,Kieta said there were no "White" folks back 40kyrs in Europe,and more recent studies said there were no "White"skinned folks upwards of 10-7kyrs b.c so when did R arrived or made itself known in West Africa.
Posts: 6546 | From: japan | Registered: Feb 2009
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quote:Originally posted by Brada-Anansi: Xman got a question is the R found in Chad,Cameroon and north Nigeria originated there or came from outside Africa,note I am not implying that even if it did the carriers looked anything like a stereotypical Eurasian today,Kieta said there were no "White" folks back 40kyrs in Europe,and more recent studies said there were no "White"skinned folks upwards of 10-7kyrs b.c so when did R arrived or made itself known in West Africa.
I just explained xyymans error and brada comes in an does the same thing
There is no such thing as a " stereotypical Eurasian" Eurasia is the whole landmass of Europe and Asia, one continuous piece of land with a wide variety of people on it.
Brada does the same thing, he starts off about Eurasia then in the same sentence says there were no whites in Europe 40 kya -as if the to terms are synonymous
People please stop this "Europe" does not even comprise most of the landmass of Eurasia
The origin of HG R is believed to be Eurasia but not in Europe,
Not necessarily in Siberia, However the oldest remains of R was found there 24Kya (Raghavan 2014) the Mal'ta boy (mtDNA U)
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posted
xyyman didn't Haplogroup R originate outside of Africa ???
( I said outside of Africa not Europe specifically !!!, listen man listen)
and didn't the R clade, the unique V88 come about in Africa at a later date, as a result of a BACK MIGRATION from somewhere in the Eurasian landmass ?? perhaps Central Asia ???
Hold up , wait a mintue, before you say " NO back migration is physically impossible" >>
-what if Haplogroup R originated outside of Africa with dark skinned non-Africans, Black Eurasians?
Or what if they were even black Europeans ???
???
^^
Can't Eurasians have brought HG R into Africa a certified BACK MIGRATION ???
Isn't it O.k. if these people were BLACK ???
Isn't it OK then for a BACK MIGRATION to have occured If it was a BLACK MIGRATION ?
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posted
Lioness maybe I should have put "stereotypical" in quotes for the average Joe, Eurasian conjures up certain physical types mostly through reflex ,off course folks of the Black Islands do not register immediately until pointed out.
Posts: 6546 | From: japan | Registered: Feb 2009
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sides. As I said many times. geography geography geography.
It does not make sense that West Africans have older Eurasian "ancestry" than Horners. Did the "Eurasians" teleport to West Africa by passing East Africa.
-------------------- 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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Any more questions. Hit me up
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posted
To those who don't get it. R1b in Europe is YOUNGER!!!!!!!!
-------------------- 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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posted
1. Keita speculated correctly as the current data shows. There were no white people beyond may be 7000ya. 2. Irregardless to what AMH looked liked in Europe or Africa 7000ya. The data shows that Y hg-R did not ARRIVE FROM anywhere into Africa. Current data shows that R-V88 (R1b) is older in “inner” Africa compared to regions like Morocco and Siwa. My 4 W’s never fails me. When was the paper written, who wrote the paper, What is the premise, where was the data taken. etc.
@ Beyoku. Getting back to that discussion on AMH expansion OOA. The data continuously emerging is that the exit is very very recent. Richard III is another example. BOTH his parents had atypical European lineage. This means the hg-G and hg-J1c played a prominent role in Europe up to about 600ya. aDNA on a few European Medieval Royals also disclosed they were hg-G There was obviously significant population turn over within Europe in the last 1000-5000years.
quote:Originally posted by Brada-Anansi: Xman got a question is the R found in Chad,Cameroon and north Nigeria originated there or came from outside Africa,note I am not implying that even if it did the carriers looked anything like a stereotypical Eurasian today,Kieta said there were no "White" folks back 40kyrs in Europe,and more recent studies said there were no "White"skinned folks upwards of 10-7kyrs b.c so when did R arrived or made itself known in West Africa.
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Someone is in a bad mood.....alriiiigthy then. Africans!!!
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
@ Mike. I know genetics is not your thing but as I said Europeans are a subset of Africans. The author states there is clear differentiation between Europeans and Asians.
@Sage. You got me. That 1/3 2/3 discussion. You question has long been answered.
@ AMRTU – “ancestry” does NOT mean migration FROM Europe. It means shared SNPs. Don’t get hung up on the labels used. DNATribes has stopped use the label “ancestry” for “shared “genes.
@ Dr Winters. The paper is not a farce. The speculation and inferences is BS but the data itself is very revealing. This paper is a keeper. The genetic pattern suuports your thesis of entrance through Iberia from Africa
QUOTE:
Supplementary Methods). A substantial proportion of unshared (11%– 23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations (Extended Data Fig. 1). The high proportion of unshared variation among populations recapitulates the need for large-scale sequencing across Africa, including among genetically divergent populations. We used principal component analysis to explore relationships among AGVP populations (Extended Data Figs 2–5, Supplementary Figs 1 and 2). PC1 appeared to represent a cline extending from West and East African populations TOWARDS Ethiopian populations, possibly suggesting Eurasian gene flow, while PC2 separated West African and South/East African populations (Extended Data Fig. 2).
Inclusion of the 1000 Genomes Project, North African and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3–5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. ‘Unsupervised’ (that is, without including known information on individual ancestry ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for SUBSTANTIAL Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6). To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6).This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST50.027) may be a remnant of East African diversity pre-dating the Bantu expansion10.
Population admixture in SSA Formal tests for admixture (the three population test or f3 statistic)11, confirmed widespread Eurasian and HG-admixture in SSA (Supplementary
-------------------- 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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posted
I solved the origins of Europeans a long time ago. The only enigma is the modem European male. R-M269. It difficult to believe they arrived on the scene within the last 1200years. But this what the data is showing. More work needs to be done on the white male.
-------------------- 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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quote:Originally posted by xyyman: @ Mike. I know genetics is not your thing but as I said Europeans are a subset of Africans. The author states there is clear differentiation between Europeans and Asians.
@Sage. You got me. That 1/3 2/3 discussion. You question has long been answered.
@ AMRTU – “ancestry” does NOT mean migration FROM Europe. It means shared SNPs. Don’t get hung up on the labels used. DNATribes has stopped use the label “ancestry” for “shared “genes.
@ Dr Winters. The paper is not a farce. The speculation and inferences is BS but the data itself is very revealing. This paper is a keeper. The genetic pattern suuports your thesis of entrance through Iberia from Africa
QUOTE:
Supplementary Methods). A substantial proportion of unshared (11%– 23%) and novel (16%–24%) variants were observed, with the highest proportion among Ethiopian populations (Extended Data Fig. 1). The high proportion of unshared variation among populations recapitulates the need for large-scale sequencing across Africa, including among genetically divergent populations. We used principal component analysis to explore relationships among AGVP populations (Extended Data Figs 2–5, Supplementary Figs 1 and 2). PC1 appeared to represent a cline extending from West and East African populations TOWARDS Ethiopian populations, possibly suggesting Eurasian gene flow, while PC2 separated West African and South/East African populations (Extended Data Fig. 2).
Inclusion of the 1000 Genomes Project, North African and Khoe-San (Khoisan) populations in principal component analysis (Extended Data Figs 3–5, and Supplementary Figs 1 and 2) suggested possible HG ancestry among southern Niger-Congo groups—highlighted by clustering towards the Khoe-San, in addition to confirming a cline towards Eurasian populations. ‘Unsupervised’ (that is, without including known information on individual ancestry ADMIXTURE9 (https://www.genetics.ucla.edu/software/admixture/) analysis including the 1000 Genomes Project and Human Origins data sets (Fig. 1), also supported evidence for SUBSTANTIAL Eurasian and HG ancestry in SSA (Fig. 1 and Extended Data Fig. 6). To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6).This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST50.027) may be a remnant of East African diversity pre-dating the Bantu expansion10.
Population admixture in SSA Formal tests for admixture (the three population test or f3 statistic)11, confirmed widespread Eurasian and HG-admixture in SSA (Supplementary
The paper is a farce. The data doesn't matter because most people only read the article, not the supplementary data.
As a result, the authors have already establsihed what the data means in the minds of the average reader so it is almost impossible to get the reader to see what the data really means.
posted
What is false about the article...I see the board ranting and raving about the article but nobody using any science to dispute it.
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007
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posted
What's bad about the article many things but first let's look at what's good. The article is beautiful. The graphics are bright and colorful.
But once you get past the figures the paper is useless. It is full of inferences and "speculations" about the relationships between HG groups and other African groups. It frequenly mentions that all of the diversity in Africa is due to Eurasians making a back migration to Africa. Although, this is the case the authors' fail to explain who these migrants were, the genes they carried and time they came back into Africa.
The authors fail to look at their own evidence. The data indicates that there was a fromer presence of Khoisan in North Africa and West Africa. Instead of taking this to the next level, they make slight comments of whaT THIS MEANS. To these authors the relationship is recent, but if they looked at the relationship between the Khoisan and Berbers, Aurignacian culture entering Iberia from Straits of Gibraltar, and the presence of Khoisan in ancient America we would have a better explanation of the role of the Khoisan in North and West Africa over the past 30ky.
To accomodate the authors' ideas they explain them as being the result of drift and parallel evolution in some cases. These explainations are not necessary if you accept the earlier spread of Khoisan throughout much of Africa, prior to 40kya.
It also talks about the Yoruba connection to the Neanderthal. Instead of imagining this the result of a back migration, we know that the Neanderthals were in Saharan Africa, the place where the Niger-Congo speakers originated and it was there, not West Africa were the ancestors of the Yoruba and Mande interacted with Neanderthal.
Moreover, the authors' point to West Africa as the location for the Bantu migration, when we know Bantu speakers and other Niger-Congo speakers formerly lived in Egypt. An d in addition we see the Mande speakers entering West Africa from the North, as a result, Niger-Congo speakers probably were not indigenous to West Africa.
For these reasons, the article is useless in explain population movements in Africa, or even medical uses for African people.
posted
I agree with most of what you said when I read the paper. But medical sections makes sense. Sarah Tishkoff came to the same conclusions.
quote:Originally posted by Clyde Winters: What's bad about the article many things but first let's look at what's good. The article is beautiful. The graphics are bright and colorful.
But once you get past the figures the paper is useless. It is full of inferences and "speculations" about the relationships between HG groups and other African groups. It frequenly mentions that all of the diversity in Africa is due to Eurasians making a back migration to Africa. Although, this is the case the authors' fail to explain who these migrants were, the genes they carried and time they came back into Africa.
The authors fail to look at their own evidence. The data indicates that there was a fromer presence of Khoisan in North Africa and West Africa. Instead of taking this to the next level, they make slight comments of whaT THIS MEANS. To these authors the relationship is recent, but if they looked at the relationship between the Khoisan and Berbers, Aurignacian culture entering Iberia from Straits of Gibraltar, and the presence of Khoisan in ancient America we would have a better explanation of the role of the Khoisan in North and West Africa over the past 30ky.
To accomodate the authors' ideas they explain them as being the result of drift and parallel evolution in some cases. These explainations are not necessary if you accept the earlier spread of Khoisan throughout much of Africa, prior to 40kya.
It also talks about the Yoruba connection to the Neanderthal. Instead of imagining this the result of a back migration, we know that the Neanderthals were in Saharan Africa, the place where the Niger-Congo speakers originated and it was there, not West Africa were the ancestors of the Yoruba and Mande interacted with Neanderthal.
Moreover, the authors' point to West Africa as the location for the Bantu migration, when we know Bantu speakers and other Niger-Congo speakers formerly lived in Egypt. An d in addition we see the Mande speakers entering West Africa from the North, as a result, Niger-Congo speakers probably were not indigenous to West Africa.
For these reasons, the article is useless in explain population movements in Africa, or even medical uses for African people.
Enjoy
.
. [/QB]
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
45 thousand years ago is probably close to when Eurasians started diverging from each other as they spread in all directions. So, we expect that a human from that time would be "undifferentiated Eurasian" and indeed this seems to be the case.
First the Y-chromosome:
The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today6
quote:Originally posted by the lioness,:
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Researchers discover fragments of Neandertal DNA in the genome of a 45,000-year-old modern human from Siberia
October 22, 2014
The comparison of his genome to the genomes of people that lived later in Europe and Asia show that he lived close in time to when the ancestors of present-day people in Europe and eastern Asia went different ways. Like all present-day people outside Africa the Ust’-Ishim man carried segments of Neandertal DNA in his genome. But these segments were much longer than the ones found in present-day humans and indicate that the admixture with Neandertals took place between 50,000 and 60,000 years ago.
In 2008, a relatively complete human femur was discovered on the banks of the river Irtysh near the village of Ust’-Ishim in western Siberia. Radiocarbon dating of the bone showed it to be about 45,000 years old. “The morphology of the bone suggests that it is an early modern human; that is an individual related to populations that are the direct ancestors of people alive today” says Bence Viola, an anthropologist who analyzed it. “This individual is one of the oldest modern humans found outside the Middle East and Africa” he says.
The research team sequenced this individual’s genome to a very high quality and compared it to the genomes of present-day humans from more than 50 populations. They found that the Ust’-Ishim bone comes from a male individual who is more related to present-day people outside Africa than to Africans thus showing that he is an early representative of the modern population that left Africa. When his genome was compared to people outside Africa, he was found to be approximately equally related to people in East Asia and people that lived in Europe during the Stone Age. “The population to which the Ust’-Ishim individual belonged may have split from the ancestors of present-day West Eurasian and East Eurasian populations before, or at about the same time, when these two first split from each other”
Posts: 42919 | From: , | Registered: Jan 2010
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Can you give us undoctored charts We're not stupid we can find the relevant data as good as you can. Also a correct citation including original date is something we need to make further investigation. Thx Oh, and the actual caption by the involved scientist(s) is required.
Remember, we're "raising the bar!"
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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posted
^^^You probably mean: xyyman. He's the one spamming this thread with doctored charts and silly inputs.
Posts: 2981 | Registered: Jan 2012
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quote:Originally posted by Amun-Ra The Ultimate: ^^^You probably mean: xyyman. He's the one spamming this thread with doctored charts and silly inputs.
yes, the only reason I put up that chart is that xyyman had put up his own earlier doctored version of this chart but he selectively left out information Nothng was said when he put up doctored charts xyyman is immune to bar raising
Posts: 42919 | From: , | Registered: Jan 2010
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posted
First off, my chart is not doctored. 2nd it clearly states R-V88 Cruiciani at the bottom left. And a link was provided. I can always back up what I post. Always!
-------------------- 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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posted
This innocent looking article, without any support for its conclusions is very dangerous and should be vigorously attacked. Its aim is to resurrect the multiregional theory for the raise of anatomically modern man--with Eurasia--as the center for this evolution.
In this article the authors claim that diversity among African genes is the result of Eurasian genes. They contend that the Eurasian genes exist in Africa because of a back migration.
On the surface this seems like a pretty tame theory. In reality this is quite radical. What the authors are saying is, sure Africans are diverse, but this diversity is the result of Eurasians migrating back into Africa.
If you accept this hypothesis, the next step is to claim that the diversity among haplogroups took place in Eurasia, rather than Africa, and that Europe--not Africa--is the center of evolution and genomic diversity. This is just a first step in destroying the out of Africa (OoA) theory and replace it with a multiregional theory that moves Eurasia back into the center for the raise of modern man.
This paper is a call to return to the days of white/European supremacy in world events and history.
.
.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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posted
^Best criticism of this paper to date. The unintended(?) side-effect of aspects of this paper is that after masking so-called "Eurasian" components, there is no more cline of populations in a manner that's predicted by OOA and all African hg and linguistic diversity seizes to make sense (after all, all diversity is just a function of back-migration, right?). As I'm reading this discussion, it baffles me that some waffle on and on about the finding of old Eurasian ancestry in West Africans (which is definitely not a new or erroneous claim) it takes this forum four days of beefing with minutiae and praising the paper, to come up with just one non-trivial criticsm, lol.
But maybe it's not so surprising: Amun-Ra has passionately promoted both ideas; he called for the recognition of any polymorphism with non- African affinity as non-African and claimed Africans were all monoliths, and no one said a thing. Goes to show you how dysfunctional this forum is.
A post made by the Amun Ra troll on 4 Nov conveys both anti-OOA ideas:
quote:Originally posted by Amun-Ra The Ultimate: The results are basically similar: East and West African populations, and African populations in general, are very close to each others. Especially if you remove the more recent Eurasian component from recent post-OOA back migrations by Semitic (ethio-semitic) and Muslim Arabs speakers
posted
Noooo! What you and Dr Winters highlighted is not unique to the paper. Many geneticists account for "Eurasian" genes in West Africans or Africans in general as "back migration", the idea is not novel and new. Lazaridis himself stated "all Africans carry Eurasian ancestry". I am not bothered by such a rediculous idea. Because they can NEVER prove it.
And yes, the biggest revelation, Mr Pagani, is the West Africa has an older connection than Horners.........meaning what?
The 2nd OOA was not through the Horn but through the "Green" Sahara as the author suggested.
Man, I have to explain everything.
Also check out the authors discussion on SLC45A2 and SLC24A5 and SUPPL Fig. 3. Anyone?
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posted
And to the brotha who don't want me to call his name. The one in the bad mood. Did you observe the time- line calculated by the authors for the West African/ European connection?
That's right, beginning of the Neolithic. Baaaaammmm!!! Basal Eurasian/EEF. Here we go again!
ALL data points to another "recent" exodus after the first.
Still haven't connected the dots? Think La Brana, MA1 etc. All ancient populations tested thus far are genetically closer to each other than modern populations. The closest modern population are East Asians ie Onge, Australians, Makrani.
A new African population arrived on the scene. This is not rocket science.
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by Swenet: A post made by the Amun Ra troll on 4 Nov conveys both anti-OOA ideas:
quote:Originally posted by Amun-Ra The Ultimate: The results are basically similar: East and West African populations, and African populations in general, are very close to each others. Especially if you remove the more recent Eurasian component from recent post-OOA back migrations by Semitic (ethio-semitic) and Muslim Arabs speakers
This quote from me is perfectly fine and factual, it's just a good thing if the latest research also agree with me. This research is inline with previous studies and current state of population genetics knowledge.
What this research says and what I'm saying in this quote has no anti-ooa bias, since those relates to events after the OOA migrations.
For example, East and West Africans have their common E-P2 lineage origin AFTER the OOA migrations of non-Africans. Since, E and E-P2, lineages present in over 80% of modern East and West Africans, is downstream (aka older) to CT and DE (the haplogroups of OOA migrants), and thus after the OOA populations left Africa.
For example, we can see here E (M40/M96), the common haplogroup Y-DNA lineage of both East and West Africans is downstream to CT and DE the haplogroups of OOA migrants.
So the common origin of East and West Africans in East Africa is **AFTER** the OOA migrants left Africa.
For example, West African populations like Yoruba share 93% of the CT haplogroup and 45.45% of the mtDNA L3 haplogroups with OOA migrants because they were still in East Africa after they left (the back migrations of OOA migrants in Yoruba populations is negligible at 0.06%).
Modern West Africans left East Africa AFTER the OOA migrants left Africa. So both East and West Africans share a common origin in northeastern Africa after the OOA migrations. Posts: 2981 | Registered: Jan 2012
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Added to that, I just came across a paper on the Vikings. Dienekes sourced it within the last few days. The paper is suggesting there was another significant population turnover between 1500-1000AD in Europe, at least Northern Europe. Around the Viking age. aDNA was tested on Vikings and to their surprise about 25% of the mtDNA haplotypes were NOT found in Europe. And the MFers stopped there. They left it at that. Not disclosing where in the world 25% of the Vikings matched up. Nevertheless from what was disclosed many of the Vikings were J1b. Lioness what did Eupedia say about mtDNA J1b? That’s right…..Some African Tribes still carry mtDNA J1b.
I GOT THIS COVERED.
-------------------- 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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posted
Early, Middle and Late Pleistocene Africans were never isolated. The channel of water separating the southern extremity of Spain and northern tip of Morocco is only 15 km today, and was even narrower during the Pleistocene because of changes in sea-level.
There is anatomical evidence for European Neanderthal gene flow into Morocco, e.g. Jebel Irhoud. Here is a paper that discusses this.
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