Friday, January 17, 2020

(GUARDIAN UK) The African youth boom: what's worrying Bill Gates

COMMMENT - Don't let these population control dirtbags inject anything into your children's veins. They do not mean well. Bill Gates should never have been allowed to turn Windows into a monopoly, and keep tens of billions of dollars of profits. He has been bad for computing, and now he's allowed to unleash American neuroses about being overrun and outnumbered onto the rest of the planet. If anything, Africa is underpopulated because of centuries of colonialism, the slave trade and outright genocide (DRC, Namibia). They're catching up. There are more people in much smaller places like China and India. - MrK

(GUARDIAN UK) The African youth boom: what's worrying Bill Gates
Polly Toynbee
The philanthropist warns that stability in Africa makes a huge difference to the world, and that investing in the health and education of its young people is vital

Polly Toynbee
Tue 18 Sep 2018 05.01 BSTLast modified on Fri 21 Sep 2018 10.51 BST

What worries Bill Gates most? The booming population of Africa looms over his foundation’s latest global survey. By the end of this century there will be 4 billion more people on Earth – and 3 billion of these extra souls will be born in Africa. The challenge, he says, is that “Africa must almost quadruple its agricultural productivity to feed itself. That’s very daunting.”

The philanthropist is torn between sending out a message of hope and a message of fear when I meet him at his foundation’s spacious campus in the heart of his hometown, Seattle.

He is reaching for what works best to revive the west’s faltering conscience in the face of “America first” nationalism and rising pull-up-the-drawbridge populism in Europe. The spirit of generosity is under assault as government aid budgets come under constant sniper fire from right-wing politicians and their media.

Half of the Bill & Melinda Gates Foundation spending goes to Africa. The funds put into the foundation by themselves and fellow philanthropist Warren Buffett now amount to more than than $50bn (£38bn). Until last year Gates, the Microsoft founder, was the world’s richest man. He has now been overtaken by Amazon’s Jeff Bezos.

Gates’ first instinct is optimism. Just consider the astonishing story of how far and how fast people have been brought out of abject poverty in a very short time. Since 2000, a billion people have been taken well over the line of $1.90-a-day wretchedness (£1.45), with the same uplift among those previously living on $3.20 a day.


The foundation’s report bursts with remarkable data – too few people know about the galloping progress of humankind. Take India, where only 18 years ago almost one in five children were not enrolled in primary school – now, 97% attend classes. Look at the indicators on the report’s global scorecard for the UN’s sustainable development goals for 2030, and most things are improving almost everywhere. But there is a marked variation in the future trajectory: progress depends on the level of future investment.

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Today, the west takes some persuading that things are getting better, especially in Europe where countries like Britain have suffered a decade of falling real living standards and eye-watering austerity. The upbeat message of Gates – as well as those in his late friend Hans Rosling’s book Factfulness, and Steven Pinker’s Enlightenment Now – telling us most of the world is on an unprecedented upswing, jars with our reality. Yet it is so: the world has never seen such a rapid rise in prosperity among most of the poor.

Eager to encourage western countries to keep giving aid, Gates is well aware that Britain – as elsewhere – suffers frequent political attacks on its aid budget. The UK, Sweden and Norway are among the few reaching the UN aid spending target of 0.7% of gross national income, and all feel the cold blast of an anti-foreigner political grudge. “If you are saving lives for a very small amount of money, people should feel good about that,” Gates says emphatically, protesting at current cynicism about international aid organisations. Look what can be done, he keeps saying, pointing as an example to the brilliant education system in Vietnam, a poor country whose results outstrip far richer ones.


If Britain needs encouragement, he says, “the data about the impact has been amazing. The UK has been very generous to the vaccine fund, for two miraculous vaccines – one for pneumonia, one for diarrhoea.” These sicknesses are now preventable “at extremely low cost to all the children of the world. The UK led that effort and saved over 10 million lives.” Do people across the UK know that? He admits a failure to spread the good news. “We’re being challenged to explain.” Everyone should know this message of hope. “We’re talking about uplifting the human condition in a fairly dramatic way.”

But if hope doesn’t beat the new nativism infecting the western world, then fear is Gates’ ammunition of last resort. Ignore Africa at your peril. “The stability of Africa makes a huge difference to the entire world.” Here come the threats: “A pandemic like Ebola can spread very fast,” he warns, and many others spread even faster if there are no local health services to contain them.

Migration is the other threat to touch Europe’s politics. Syria was a small country, he reminds us, yet its civil war exodus has “challenged the asylum system”. But watch out because “Africa is another order of magnitude”. The huge African youth boom is a strong theme in the report, where in a world of ageing and shrinking populations, Africa’s demographic bulge could be an asset or a threat. So it would be wise “to make their lives attractive” not just out of “pure human caring”. Invest in Africa’s young, their human capital, health and education, support more productive agriculture, protect subsistence farmers against climate change and see how self-interest blends with good works.

Africa, he always stresses, is not one country. Of its 54 nations, many are leaping ahead, Ghana, Botswana and Rwanda among them. Those causing concern are the Democratic Republic of the Congo and Nigeria. On his recent visit he warned Nigerians against the country’s growing inequality, where oil wealth for a few is leaving millions behind. The foundation has spent $1bn so far on Nigeria. He says: “Their health system is worse than poorer countries, their agricultural advice largely broken down.” Government resources are low because “their level of taxation is one of the lowest in the world”.

He sounds puzzled: “You would think politicians would compete on the basis of, ‘Hey, I’m going to run a primary health system really well, I’m going to get vaccination coverage up, I’m going to save lives …’ But other issues about religion and ethnicity come to the fore.”

Gates is something of a political naif. After all, I point out, look at us in the west. Look at the gross and rising inequality in the US and UK, look at the need for better public services, yet politics is all too often about culture wars and identity issues – Brexit for us, guns and abortion for America. Look at the problem of homelessness, with tent cities on the streets of his rich Seattle, a most liberal city, where only 8% voted Trump. Yes, he’s trying to help the homelessness crisis: he gives £350m a year to US causes.


So we reachthe great blond elephant in the room, President Trump, who has stopped funding family planning organisations that also offer abortions, stalling access to contraception where women need it most. Trump also attacked the foreign aid budget, but “fortunately the Congress, including a lot of Republicans, said no”. How much can Gates influence him? Here, he steps with the caution of a barefoot man crossing broken glass, anxious to say nothing that could further imperil America’s aid budget.

“We have to work with Trump himself and the whole administration on ‘What is your vision for Africa?’ And as a human being who cares about human beings, as a country who doesn’t want to go fight foreign wars or deal with pandemics that are out of control …” Did that pitch work? What helped was the famous warning of Trump’s defence secretary, General James Mattis, that soft power – state department diplomacy and aid – prevents the need for hard power: “If you don’t fully fund the state department then I need to buy more ammunition.”

Is Trump persuadable? Gates pauses to pace a cautious reply: “Yes, one of the things you can say, a plus or minus, is in very few areas does he have a fixed ideology. If there’s something where he feels he can look smart … particularly if it’s doing things in a different way than was done before, then yes, I think he’s open-minded.”

But the truth is that it would be hard to find two mega-wealthy men further apart in their view of the world, their mission or their morality than Trump and Gates. While Trump slashes tax for the rich, Gates constantly calls for the wealthy to be taxed more. “The fact that people aren’t for an estate tax [inheritance tax] is kind of mind-boggling to me.” He says creation of hereditary aristocracies dampens dynamism. “It’s amazing we allow people to have gigantic amounts of money when the state should take more of that.” He wants higher tax on corporate profits too. Famously, he boasts he has paid $6bn in tax, more than anyone on Earth, “and gladly so”.

He sounds perplexed by the forces of darkness that fail to see the need for equality at home and globally, that oppose redistribution through taxes and that sneer at the spirit of philanthropy. Surely, he says at the end of our interview, “the improvement in the world is something people should be excited about”.

The Now generation is a series produced in collaboration with the Bill & Melinda Gates Foundation. You can read more about it here


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Sunday, December 15, 2019

(NATURE) Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

COMMENT - According to the authors, the Khoi-San population was the largest population of all human beings for most of human history. - MrK

(NATURE) Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history
Hie Lim Kim, Aakrosh Ratan, George H. Perry, Alvaro Montenegro, Webb Miller & Stephan C. Schuster
Nature Communications volume 5, Article number: 5692 (2014) Cite this article

Abstract
The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.

Introduction

Following the rise of agriculture in sub-Saharan Africa ~4,000 years ago, Bantu-speaking subsistence agriculturalists spread rapidly throughout much of the sub-Saharan African continent1. Today, the census population sizes of these groups are orders of magnitude larger than those of sub-Saharan African hunter-gatherers, such as the Khoisan-speakers of the Kalahari Desert region in southern Africa2. Yet Khoisan populations have maintained the greatest nuclear-genetic diversity among all human populations3,4,5 and the most ancient Y-chromosome and mitochondrial DNA lineages6,7, implying relatively larger effective population sizes for ancestral Khoisan populations. While clues exist as to recent demographic histories (following the Bantu expansion) and interactions among sub-Saharan subsistence agricultural and hunter-gatherer groups, including evidence of admixture8,9, we know much less about the early (i.e., prior to the Bantu expansion) histories of these populations. In this study, we examine the early history of the ancestral hunter-gatherers and other human populations using analyses of complete-genome sequences from six individuals from southern Africa.

Previously, we reported the complete-genome sequences of a Namibian-Khoisan hunter-gatherer and a Bantu-speaking individual from Southern Africa, along with the exome sequences of three Namibian-Khoisan individuals10. In the current study, we sequence the complete genomes of five Namibian-Khoisan hunter-gatherers and one Bantu speaker, using the Illumina HiSeq platform to an average coverage of ~27–55-fold per individual (see details in Methods). We also include eight publicly available whole-genome sequences in our analysis (Table 1). Our analyses, using the genome sequences, reveal a larger effective population size for the ancestors of Khoisan following their split from non-Khoisan populations ~100–150 kyr ago, with a relatively dramatic population decline for the non-Khoisan populations. The divergent-population histories may be explained by concomitant-paleoclimate changes across Africa.

Table 1 The 14 complete-genome sequencing data sets.
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Results
Genetic origins of southern African individuals
In order to examine the genetic ancestries of the six individuals, we applied ADMIXTURE11 and EIGENSOFT12 to the genotyping data set of 419,969 nuclear single-nucleotide polymorphism (SNP) genotypes from 1,448 worldwide individuals along with genotypes extracted from the 14 genome sequences for the same SNP loci (Supplementary Table 1). Figure 1 shows the results for selected populations, emphasizing our six individuals. Entire results are shown in Supplementary Figs 1–3. On the basis of the ADMIXTURE result, Khoisan populations include two different ancestries, northern Khoisan and southern Khoisan, with evidence of past gene flow within the Khoisan and/or between the Khoisan and non-Khoisan, except for the Ju/’hoansi population (Fig. 1a). Individuals NB1 and NB8 belong to the Ju/’hoansi (Fig. 1c) and appear to have only northern Khoisan ancestry (Fig. 1b). We also applied a different method13, which uses linkage disequilibrium decay, to detect admixture between the Ju/’hoansi and other populations and show the result in Supplementary Fig. 7.

Figure 1: Genetic relationships of six southern African individuals and worldwide populations.
figure1
(a) Population structure in human populations was inferred by ADMIXTURE11 using 417,593 SNPs from 490 individuals. (b) The ADMIXTURE plot for the 14 complete-genome data sets is shown separately. (c) Genetic relationships of our six southern African individuals and various African populations were estimated by the PCA analysis12 on the basis of the 417,593 SNPs from southern African and Yoruba populations. NB1 and NB8 are closely clustered with the Ju/’hoansi group, which was sampled from the northern Kalahari region in Namibia. The Ju/’hoansi samples are furthest from the Yoruba populations. MD8, from the northwestern Kalahari region, clusters with the !Xun, which belong to the same language group. KB1 and KB2, from the Tuu-speakers of the southern Kalahari, are close to the !Xun and /Gui and //Gana who lived in the central Kalahari region, but are not clearly related to them. Hence, we do not have any population data that is closely related to these two samples. ABT, a southern African Bantu, clusters with the southeastern Bantu samples.

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Inference of local ancestries along the genome using three-independent methods confirmed the exclusive Khoisan ancestry in the NB1 and NB8 genomes (Fig. 2, Supplementary Figs 4–7 and Supplementary Table 2). For the other Khoisan genomes—KB1, KB2 and MD8—the three methods and ADMIXTURE consistently assign 0.6–2.4% of each genome to western African ancestry (Supplementary Fig. 6 and Supplementary Table 2). ABT includes both western African and southern Khoisan ancestries, similar to the southeastern Bantu-speaking population (Fig. 1a). These results suggest a recent history of gene flow between the Khoisan and non-Khoisan populations, consistent with several other studies3,5,14,15,16, as well as, our previous report10 (Supplementary Fig. 8). However, we show here that two of the Ju/’hoansi genomes, NB1 and NB8, have no signature of admixture from non-Khoisan ancestries. Therefore their genome information allows us to access early population history of modern humans.

Figure 2: The local ancestry estimation for individual genomes.
figure2
Along the genome, local ancestries are inferred by PCAdmix40 for NB8 (a), ABT (b) and NA18507 (c) and are illustrated on the genome map. Blue, red, yellow colors indicate the Khoisan (combined northern and southern Khoisan), western African and European ancestries, respectively. Light purple color represents undetermined ancestry that is not significant enough to estimate the ancestry. The western African haplotypes shown in the NB8 genome are not detected by the other two different methods (Supplementary Fig. 6 and Supplementary Table 2).

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Population-history inference
The Pairwise Sequentially Markovian Coalescent (PSMC) model17 was applied to the 14 whole-genome sequences in order to reconstruct the history of changes in effective population size (Ne) over time. We used a typically reported mutation rate, 2.5e−08 per site per generation (generation time=25 years) (ref. 18), to scale Ne and time (see details in Methods). The patterns of change in Ne are consistent among the four populations (Khoisan, Yoruba, European and Asian) prior to ~0.2 myr ago, declining in all cases from 2 to 0.5 myr ago and recovering by 0.2 myr ago (Fig. 3a). All four populations appear to have experienced bottlenecks in the period ~30–120 kyr ago (Fig. 3a), but the declines in Ne varied widely among them (Fig. 3b–e). The Khoisan Ne, the average of the two Ju/’hoansi genomes (NB1 and NB8), has been the largest since ~120 kyr ago and declined to 74% of their original peak Ne observed at about ~100–150 kyr ago, while the average Ne of the three Yoruba genomes declined to 31% of their original peak, followed by a slight recovery to 43%. The average Ne of each of two European and two Asian genomes declined even more, to only 9 and 8% of their original peak, respectively (Fig. 3a).

Figure 3: The changes in the effective population size on the basis of the 14 individual genomes.
figure3
(a) The average Ne of each of four populations (see Methods). The pink shadow indicates the period where the changes in Ne varied most among the four populations. (b) Ne changes of five Khoisan genomes, (c) Ne changes of three Yoruba and one Bantu genome, (d) Ne changes of two European genomes, and (e) Ne changes of three Asian genomes. Four genomes sequenced to a relatively low coverage were corrected using the FNR option provided by the PSMC package. Estimates both with and without corrections are shown.

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We performed simulations to assess the robustness of these PSMC results under various demographic models. Genome sequences were generated by simulations under a simplified model of the population size changes inferred by PSMC from the Khoisan and Yoruba genomes. PSMC was applied to the simulated sequences, and we confirmed that the PSMC inference reconstructs the given model (Supplementary Fig. 9). Several reports have found evidence of recent admixtures between the Khoisan and non-Khoisan populations15, a population structure within the Khoisan5,15 and the Bantu population expansion within Africa1. Since the PSMC only estimates changes of effective population size and does not account for population structure, we used these simulations to examine effects of recent demographic events on the PSMC estimates. The PSMC estimates from the sequences simulated under the models including recent demographic events are not significantly different from the estimate from the sequence simulated under the model without those events (Supplementary Fig. 9). These simulations demonstrate that the large Khoisan Ne and Yoruba population decline that we estimated from the Ju/’hoansi and Yoruba genomes are not a result of the recent demographic events.

In addition, we could infer the divergence time of populations from the PSMC analysis, using male X chromosomes17. The earliest human population split has been known to be between the ancestral Khoisan and the ancestors of the other human populations and was estimated to take place ~110–150 kyr ago (refs 16, 19). Our PSMC analysis and a Bayesian inference19 support similar estimates, ~120–150 kyr ago (Supplementary Fig. 10) and ~95–130 kyr ago (Supplementary Fig. 11), respectively.

On the basis of these results, we can reconstruct early history of modern-human populations. After the earliest split, between the ancestral Khoisan and non-Khoisan populations ~100–150 kyr ago, the ancestral Khoisan population maintained their high genetic diversity, while the effective population size of the non-Khoisan continued to decline for 30~120 kyr ago and lost more than half of its diversity. The ‘Out of Africa’ migration ~40–60 kyr ago (ref. 20) accounts for the observed population split between African and non-African populations, and the subsequent smaller effective population size of non-Africans compared with non-Khoisan Africans.

Climatic changes in Africa
We focused on environmental changes during the time period of the dramatic decline in effective population size observed in our analysis of the Yoruba genomes, compared with the Khoisan. Climate changes may have impacted populations in west-central Africa, contemporaneous with environmental conditions that did not change or even improved for populations in southern Africa. Paleoclimate records and numerical models point to three modes of African precipitation variability (each with distinct causes, temporal and spatial scales) that fit such a pattern (Fig. 4).

Figure 4: The climate changes in the African continent.
figure4
Modes of African rainfall variability characterized by opposite changes in precipitation along the north–south axis. With the exception of the light green area over southwestern Africa, colors and patterns refer to modelled results. Symbols refer to proxy records. Local conditions during particular periods are given by dates in front of some legend entries. Stadials have millennial time scale and were recorded several times around ~100 kyr ago. The names of our six southern African and Yoruba (YRI) individuals refer to their sampling location. References for this figure are indicated in Supplementary Table 3. The original map was retrieved from d-maps.com and edited by authors.

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First, there is ample proxy evidence that much of Africa tends to be drier under glacial conditions21,22. Climate models show this to be due to mostly colder north Atlantic waters, stronger northern-hemisphere trade winds and weaker summer monsoons22. The exception, registered in many climate archives, are the wetter conditions found over southwest Africa during the glacial ~25–115 kyr, believed to be brought about by an increase in winter storm activity in the region23. Analysis of oceanic sediment show a significant increase in moisture over southwest Africa between ~100–120 kyr ago, the initial stages of the last glacial24.

Second, precession of the Earth’s axis of rotation generates a ~23 kyr cycle in summer insolation. Models and proxy-data show that this affects monsoon intensity leading to changes in African rainfalls that are out of phase between the hemispheres25. Oceanic and lacustrine archives indicate that the period between ~87–94 kyr ago was marked by increased precipitation in southern Africa accompanied by drier conditions over the central, western and eastern portions of the continent, and that these changes correlate to variations in summer insolation caused by precession26,27.

Third, stadials—millennial time scale events characterized by cooling in the northern-hemisphere high latitudes—have also been related in both models and proxies to rainfall increases in southern Africa accompanied by drying over central and western areas28,29. A particularly wet period recorded in the southern tip of the continent at ~91 kyr ago has been associated with this mode of precipitation variability29.

Discussion
On the basis of the parallel found between climate changes with the divergent-population history within Africa, we propose the following hypothesis regarding early human history. Modern humans may have originated anywhere in Africa and spread across the continent, with continuous gene flow among the populations. From ~100–150 kyr ago, the human species was geographically structured within Africa and eventually differentiated genetically owing to limited gene flow. At or after the time of the population differentiation, a drier climate began to affect the western and central, but not the southern regions of the African continent. This potentially contributed to a relatively severe decline in the western African populations (ancestors of the current Bantu-speaking populations) while the size of southern African populations, ancestors of the current Khoisan, was maintained or declined to a much lesser degree. Non-Africans, the majority of modern humans alive on the planet today, represent a subpopulation split from the ancestral non-Khoisan African population3,8,15, and their genetic diversity further dramatically decreased during their migration from Africa to Eurasia (Supplementary Fig. 12).

As described in the Methods, a neutral mutation rate of 2.5e−08 was used to scale the time axis in our PSMC analysis. However, recent studies have reported a lower mutation rate30,31,32 than the one we used. If we use the lower mutation rate, the population-history differentiation starts about 100 kyr earlier, ~200–250 kyr ago (Supplementary Fig. 13). Our hypothesis regarding early human history still holds with this lower mutation rate, as this would put the population-history divergence at or after the time close to the initial stages of the next-to-last glacial ~200 kyr ago (Fig. 4) (refs 22, 24), when an important determinant of precipitation would be changing in a way similar to what happened ~100 kyr ago.

Our hypothesis may explain the distinctive demographic histories among human populations and suggest that the Khoisan hunter-gatherers and their ancestors have been the largest population in terms of genetic diversity throughout modern-human history. This is in stark contrast to the current census size of the Khoisan hunter-gatherers, which is today drastically smaller compared with that of the Bantu-speaking populations. Further research into the population structure of the Ju/’hoansi and related Khoisan groups with larger sample size, therefore, will be essential for a comprehensive understanding of the deep divergence and population history of modern humans.

Methods
Southern African DNA sampling
A study permit was obtained from the Ministry of Health and Social Services (MoHSS), Namibia. Ethics approval to conduct whole-genome sequencing and analysis was obtained from the Institutional Review Board (IRB) or Human Research Ethics Committee (HREC) from three institutions, namely the Pennsylvania State University (IRB #28460 and IRB #28890), the University of New South Wales, Australia (HREC #08089 and HREC #08244) and the University of Limpopo, South Africa (Limpopo Provincial Government #011/2008).

Consents of the participants were obtained verbally (and documented via videotape) or in writing. The consent text was provided in English, Afrikaans or via an interpreter in the native language of each participant (Juu- and Tuu-language). Participants agreed that the data generated will be made freely available to the scientific community.

We consented three males and two females from two indigenous hunter-gatherer groups in the Northern and Southern Kalahari Desert. Each was among the eldest members of their respective communities. Inclusion in the study was also on the basis of their narrated-family history, as well as the remoteness of their geographical location, impeding ease of contact with other groups.

The indigenous Kalahari hunter-gatherers included in this study live in scattered family groups in the vast semi-desert regions of Namibia, an 823,145-km2 country on the southwest coast of Africa with ~2 million inhabitants (ref. 10 and references therein). Today Namibia is home to ~38,000 Khoisan people. In detail, KB1 and KB2 are members of a Tuu-speaking group of the southern Kalahari. NB1 and NB8 are Ju/’hoansi of the northern Kalahari region, separated by ~600 km aerial distance. MD8, belongs to the !Xun (!Kung)-speaking group relocated by the government from the Etosha plains region in the northwestern Kalahari. ABT is a direct descendant from the two major-linguistic groups in southern Africa, namely the Nguni-speakers (~60% of the people of South Africa) via his paternal Xhosa ancestry and from the Sotho-Tswana-speakers (~33% of the people of South Africa) via his maternal Motswana ancestry.

Genome sequencing and read alignments
The samples NB1, NB8, KB1, KB2, MD8 and ABT were sequenced to a depth of 27–55-fold using the Illumina HiSeq sequencing platform. The details regarding samplings, DNA extraction and sequencing are the same as described in Schuster et al.10 The genome sequences for the eight other human samples were downloaded from the NCBI Short Read Archive (SRA). These sequences were aligned to the human reference sequence (GRCh37/hg19) using the BWA (version 0.5.9) aligner (ref. 33). All default parameters were used with the exception of ‘–q 15’, which was used to soft-trim the low quality bases at the 3′ ends of the reads. The reads were then realigned using the GATK IndelRealigner (ref. 34), and the potential PCR duplicates were flagged using the MarkDuplicates tool from the Picard suite (Picard, http://picard.sourceforge.net). Sequence-read data for the six southern African genomes that were sequenced as part of this study have been deposited in the Sequence Read Archive under accession PRJNA263627.

SNP and consensus calls
The diploid consensus sequence for the autosomes was obtained using the ‘mpileup’ command. The option ‘–C 50’ was used to reduce the mapping quality of the reads with multiple mismatches. Locations were marked as missing data in the following cases: (a) The coverage at the location was less than three reads or greater than twice the average coverage of the genome; (b) The RMS mapping quality of the reads at the location was less than 10. The consensus for the X chromosome was derived similarly, but the pseudo-autosomal regions (chrX:60001-2699520 and chrX:154931044-155260560) were filtered as missing data. The heterozygous calls in the male X chromosomes were also discarded as errors.

We used SAMtools version 0.1.18 (ref. 33) to identify the locations of the SNPs, using the option ‘–C 50’ to reduce the mapping quality of the reads with multiple mismatches. SNP locations in the nuclear genome were filtered to maintain SNPs for which coverage in the sample was less than that expected using the Lander–Waterman equation35. We filtered out variant locations where the RMS mapping quality was less than 10, or if the SNP quality was less than 30.

Genotyping data sets
We obtained three genotyping SNP data sets from the following sources: genotyping data from HapMap36, HGDP (CEPH, http://www.cephb.fr/en/hgdp), and Schlebusch et al.5 (Supplementary Table 1). We identified the SNPs common to the three data sets. We merged those with the SNPs from our 14 whole-genome data sets. The resulting data set was then filtered to throw away flipped SNPs (SNPs on the non-reference strand) or possible flipped SNPs: the AT-GC SNPs, the triple-allelic SNPs within the merged data sets, as well as the SNPs that were homozygotes within each data set. This left us with 419,969 SNPs.

For this study, we selected only unrelated individuals. Five pairs of individuals, three Ju/’hoansi and two Southwestern Bantu, were identified as highly related, according to the Identical By Descent (IBD) analysis, which was run using PLINK37. The following five individuals were removed from the data sets based on the greatest fraction of missing data: KSP113, KSP116, KSP117, KSP196, and KSP205. Moreover, for analyses in which we identified populations, we removed the genetic-outlier individuals with respect to their populations. To detect outlier individuals, we performed PCA on the merged genotyping data set. We identified two individuals for removal as outliers in their population: HGDP00980 and KSP109. Therefore, we used 419,969 SNPs from 1,462 individuals for our population genetic analyses in this study (Supplementary Table 1). This SNP data set is available on ‘Bushman’ data library on Galaxy38.

Population structure and admixture estimations
We applied the ADMIXTURE program11 to the merged SNP data set to identify ancient population structure and ancestries of the 14 complete-genome samples. To reduce the effects of biased SNPs on clustering groups in the program, we used only 417,593 SNPs having a minor-allele frequency greater than 0.01 in the entire population of the 1,462 individuals. First, we used the entire data set of 1,462 individuals for the analysis with the number of ancestries K=4–14 (Supplementary Fig. 1). The higher K distinguished many isolated ethnic groups in Asia. Thus we ran the program using selected 490 individuals which are composed of African, European and Asian populations (Fig. 1).

Independently, we performed PCA analysis of the SNP genotyping data set, using EIGENSOFT12. We applied the analysis to the entire data set of 1,462 individuals (Supplementary Fig. 2) and then to only African and European populations including Central Asians (n=967) to examine the gene flow between African and European ancestries (Supplementary Fig. 3). To identify origins of our six southern African individuals precisely, we performed the PCA analysis for only African populations (n=274; Fig. 1c). In this analysis, the ≠Khomani and Nama populations were not included because of their recent gene flow from non-Khoisan ancestries, in order to better examine genetic clusters of individuals.

In order to identify admixtures in each of the six southern African individuals’ genome, we applied three methods: HAPMIX39, PCAdmix40 and dpmix41. To prepare the data sets for the run of PCAdmix, we needed to determine phased genotypes. The phased genotype data set of the same HapMap panel ( http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/) and the data set by Schulebusch et al.5 For the unphased data sets, we inferred a haplotype phase using BEAGLE42. PCAdmix requires three ancestor populations in order to infer the ancestry of each haplotype. Based upon the ADMIXTURE results, the samples that contained a high proportion (>0.8) of the corresponding ancestry were selected as the ancestral population, because the genetic components of the ancestral populations would likely affect the inference by PCAdmix. We used the Khoisan (n=67), Yoruba (n=85) and European (n=82) populations as putative ancestral populations for inference of ancestry of our Khoisan individuals. For the inference of ABT, we used a southeastern Bantu population with ABT as a test population. For the inference of non-African genomes, we assumed Yoruba, European and Asian (n=81) ancestral populations. We fixed the window size of the haplotype to 40 SNPs and used default for other parameters in the PCAdmix analysis. The estimated local ancestry of our six southern African samples and each from Yoruba, European and Asian samples were illustrated in Supplementary Fig. 4.

Since HAPMIX assumes only two ancestral populations, we ran the program for two sets of ancestral populations (Khoisan/Yoruba and Khoisan/European) independently. Two parameters of lambda and theta were given: the time of admixture and the admixed proportion, respectively. For both runs, we fixed lambda=5, and theta as 0.01 for admixtures from the Yoruba population and 0.001 for admixtures from the European population, according to the results of the ADMIXTURE analysis, which showed no significant admixtures from European ancestry. Before we determined the parameters, we tested several sets of parameters, and the results were pretty robust. The two sets of outputs (Khoisan/Yoruba and Khoisan/European) were unified into a single result set. When inconsistent estimates occurred between the two outputs, such as KHO/KHO versus KHO/YRI, the admixed type (KHO/YRI) was chosen, so that the unified result was biased toward detecting admixtures. When two different admixtures were inferred for one genotype, for example, KHO/YRI versus KHO/EUR, it was classified into the ‘undetermined’ category.

The third method of inferring admixtures was applied, by using the dpmix program41 on Galaxy38. We used the ‘Admixture’ tool in the ‘Genome diversity’ session. The only parameter we needed to determine was ‘genotype switch penalty’: we fixed the parameter of 10, which determined a reasonable length of admixture blocks, after testing genome switch penalties in the 2–20 range. The dpmix program allowed us to assume three ancestral populations, and we used the same three ancestral populations defined for the PCAdmix analysis.

We compared results between those three methods and collected the SNPs for which all three methods supported a consistent ancestry. The SNPs showed inconsistent ancestry among methods were assigned into the ‘undetermined’ category. The consistent results were illustrated in Supplementary Fig. 5, and a comparison between methods was shown in Supplementary Fig. 6 and Supplementary Table 2.

Effective population size inference
We ran the PSMC program17 on each of our 14 whole-genome sequencing data sets in order to infer effective population size. For the run, we used the consensus called using SAMtools as described before. The parameters and options used with PSMC were the same as the ones used in a previous study17. We measured the variance of the estimate by bootstrapping, using the option provided in the PSMC package. We repeated the run 100 times for each of the individuals (Supplementary Fig. 14).

There were a couple of issues relative to the understanding of the PSMC estimates. Since PSMC uses the heterozygote density for its inference, sequencing quality affects the PSMC estimates significantly. Sequence coverage of the 14 genome data sets varied between 19–86-fold (Table 1). Considering the associations of sequencing coverage and number of heterozygous sites (Supplementary Fig. 15), the ABT genome was sequenced to a high enough coverage (27-fold) to identify the heterozygotes. In addition, we designed an experiment to examine the impact of sequencing coverage on the PSMC estimates. We generated eight genome data sets having 10–80-fold sequencing coverage from one Yoruba genome (NA18507), which, at 86-fold, has the highest sequencing coverage, among our data sets (Table 1). Using the eight data sets, we ran PSMC independently. The pattern of changes in the PSMC estimates was very similar among those genome data sets: however the degree of change was shifted toward being more recent and smaller in size as the sequencing coverage was lowered (Supplementary Fig. 16). From this experiment, we found that a sequencing coverage cutoff of 30-fold average is sufficient for robust PSMC outputs. Therefore, half of our complete-genome sequencing data sets are suitably qualified for PSMC analysis (Table 1).

Only four genome data sets used in this study were not sequenced to a higher coverage than the ABT genome: NA12891, NA19238, NA19239 and AK1. The PSMC estimates of these four genomes were corrected, using the ‘false negative rate (FNR)’ option provided by the PSMC package. We used the KB1 genome data set to test the effectiveness of this option. We generated the KB1 genome sequence, having 15-fold sequencing coverage, and ran PSMC (KB1.15X). We used the FNR option to correct the estimates, which were shown to be KB1.15X (FNR=0.1) and KB1.15X (FNR=0.2), respectively in Supplementary Fig. 17. The original KB1 estimate was pretty similar to KB1.15X (FNR=0.2). We ended up using the FNR option for the four genomes NA12891, NA19238, NA19239 and AK1 to adjust the effect of low sequencing coverage on the PSMC estimates (Fig. 3).

The second issue was that scaling the estimates depends upon the mutation rate. Estimates of both effective population size (Ne) and time depend upon the mutation rate assumed in the PSMC analysis. Classically, the mutation rate has been known to be 2.5e−08 per site per generation18, while recent studies reported a lower rate of 1.2e−08 per site per generation30,31,32. In this study, we used 2.5e−08 per site per generation as a mutation rate, because the mutation rate estimated by a Bayesian inference (G-PhoCS; Supplementary Fig. 11) was around 2.5e−08, on the basis of our genome data set. The effect of the mutation rate is described in Supplementary Fig. 12.

In addition, the PSMC estimates for the very recent time period, such as 20–42 kyr ago to present, may not produce accurate estimations, according to the author17 and our bootstrap test (Supplementary Fig. 14). Therefore, we don’t discuss PSMC estimates in relation to recent history ~20 kyr ago, in this study.

Coalescence simulations
In order to confirm a robustness of the PSMC inference (Fig. 3), we performed coalescence simulations. Under several demographic models, nucleotide sequences were generated, using the ms program43. Commands used in this analysis and details are shown in Supplementary Fig. 9. The PSMC program was applied to the simulated sequences to confirm to reconstruct the effective population-size over time as given model and effects of recent demographic events on the PSMC estimations of past effective population size.

The estimation of population divergence time
We used PSMC analysis to infer the divergence time between populations17,44. If PSMC analysis is applied, a hybridized diploid of two haploid sequences from each population, then the time point where the inferred population size increased corresponds to the divergence time. To apply this approach, we constructed each pseudo-diploid X chromosome by combining two male X chromosomes. Supplementary Fig. 10 shows the results of PSMC analysis for pairwise pseudo-diploid X chromosomes. For example, the pairs of the European genome (JW) and each of the Khoisan, Yoruba and Asian populations are shown in Supplementary Fig. 10a. The Khoisan and European pair (JW-NB1) demonstrated a clear increase in their population size compared with the European pair (JW-NA12891) from 150–313 kyr ago, which could be the divergence time of the Khoisan and non-Khoisan populations. All other pairs stayed low in population size relative to the Khoisan and European pair, until 270–570 kyr ago. This result clearly shows the earliest population splits between the Khoisan and non-Khoisan populations, even though the time estimation is approximate.

We also applied G-PhoCS19 to our genome data set to estimate divergence time. We assumed the simplest model, illustrated in Supplementary Fig. 11, to estimate the divergence time of the Khoisan and non-Khoisan population. Both the NB1 and NB8 genomes were used as the Khoisan genome and were applied independently. The NA18507 genome was used as the western African genome. In total, randomly selected 20,000 loci of 1–2 kb-length were used as input data for the G-PhoCS run to reduce computational requirements. To prepare the input data, we followed the filtering procedure described in Gronau et al.19 In order to confirm a robustness of outputs, various sets of parameters (models, priors) were applied to the G-PhoCS run independently. We carried on 100,000 iterations for the burn-in period and an additional 200,000 iterations for the sample collection. The acceptance rates for all parameters ranged 20–70%. The analysis for the samples was performed using Tracer v1.5 (ref. 45). The estimates from the run were pretty robust and are shown in the table in Supplementary Fig. 11. The estimated mutation rate was around 1.0e−9 per site per generation, the same as 2.5e−8 per site per generation, if generation time is assumed to be 25 years. The estimates of divergence time were calibrated by the human and chimpanzee divergence time, 5.6–7.6 myr ago46. The mutation rate was calculated by an estimate of τdiv=6.5e−03, and the human-chimpanzee divergence time (Tdiv) as μ=τdiv/Tdiv.

Additional information
Accession codes: Whole-genome sequencing data generated in this study have been deposited in GenBank/EMBL/DDBJ sequence-read archive (SRA) under the accession code PRJNA263627.

How to cite this article: Kim, H. L. et al. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Nat. Commun. 5:5692 doi: 10.1038/ncomms6692 (2014).

Accession codes
Accessions
GenBank/EMBL/DDBJ
PRJNA263627

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Acknowledgements
We thank Vanessa M. Hayes for her contributions to sampling and logistics during field trips in 2008 and 2009 in Namibia. We thank Margaret Anthony (Penn State University) for assistance in editing our manuscript and Oscar Bedoya-Reina (Penn State University) for his help with analyses of SNP data set. A.M. was partially supported by Unesp’s international visiting scholar program.

Author information
Affiliations
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, 16802, Pennsylvania, USA
Hie Lim Kim, Aakrosh Ratan, Webb Miller & Stephan C. Schuster
Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
Hie Lim Kim & Stephan C. Schuster
Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, 22908, Virginia, USA
Aakrosh Ratan
Departments of Anthropology and Biology, Pennsylvania State University, 513 Carpenter Building, University Park, 16802, Pennsylvania, USA
George H. Perry
Department of Geography, Ohio State University, 154 North Oval Mall, Columbus, 43210, Ohio, USA
Alvaro Montenegro
Campus do Litoral Paulista, Unesp—Univ Estadual Paulista, São Vicente, 11330-900, Brazil
Alvaro Montenegro

Contributions
S.C.S. collected samples and generated data and designed the study; H.L.K. and G.H.P. were involved in study design; A.R. and W.M. performed bioinformatics analyses; A.M. analyzed paleoclimate records and literatures; H.L.K. performed population genetic analyses and drafted the manuscript; All authors participated to write the paper.

Corresponding authors
Correspondence to Hie Lim Kim or Stephan C. Schuster.

Ethics declarations
Competing interests
The authors declare no competing financial interests.

Supplementary Information
Supplementary Figures 1-17, Supplementary Tables 1-3, Supplementary Methods and Supplementary References (PDF 3635 kb)

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Saturday, December 14, 2019

(BLACK OPINION SA) UK election: need for new struggle after Corbyn’s defeat

COMMENT - BFLF's excellent take on the destruction of real labour by the New Labour, Conservatives and Murdoch press.

(BLACK OPINION SA) UK election: need for new struggle after Corbyn’s defeat
By admin Posted in Featured International News Politics Posted on December 14, 2019
Photo credit: Leon Neal/Getty Images
By BO Staff Writer

The following article by Moira Leahy and Josh Lees was previously published in the redflag.org.au website.

Every left-wing person watching the British general election results come in will do so with a heavy heart. The new Tory government is set to be headed by the absolute worst elements of the Etonian ruling class – a vicious, racist, anti-working-class regime with the vile Trump-loving Johnson at its head.

Many will draw conclusions similar to those drawn by the ALP and the media here after “Smoko” Morrison’s victory – that left-wing politics cannot appeal to working-class people, that working-class people are increasingly right-wing and racist and that only a Tory/Liberal-lite party can win.

This narrative will be championed loudly by the Labour right who have done their absolute best to undermine Jeremy Corbyn in their efforts to maintain Labour as a neoliberal party absolutely committed to their role as capitalism’s plan B party. They will argue that this result confirms that the sensible centre is the only way forward in politics.

Yet the story of this election is not a wholesale shift to the right in British society – but a dramatic decline in Labour’s vote. Those people who come to bury Corbyn are in large part to blame for this. Alongside their allies in the media, the Lib Dems and the establishment, the majority of the parliamentary Labour party have spent the last 4 years attacking both Corbyn himself and the more left wing policies he has championed. The attacks have been vicious and unrelenting, with Corbyn dishonestly portrayed as an antisemitic, authoritarian, Communist cult leader. At every turn they have undermined the growing left wing sentiment that put Corbyn into the leadership in the first place and saw him achieve the second best post-World War Two swing to Labour in the 2017 election.

They have been as responsible for making this a Brexit election as Johnson – with the aim of using it to crush Corbyn. They will be much happier with this result than they would have been with a Corbyn victory which cemented his position.

They posture as progressive pan-Europeans, but the small-l liberal opinion-makers of the BBC, the Guardian, the Liberal Democrats, and the centre-right of the Labour party have waged a savage campaign to slander and destroy Corbyn – and in so doing, they’ve ensured a heavy majority for Johnson’s reactionary pro-Brexit government. That shows their real priorities. For all their huffing and puffing about Europe, their main priority was stopping Corbyn from having any chance to implement a left-wing economic policy. They have used the most despicable slanders in the service of this cause, notably totally cynical accusations of anti-Semitism against anyone associated with even the mildest support for the Palestinian national movement. The impact of this ideological war will weigh heavily on the broad left in years to come. It was an ultimately successful counter-attack to the ascension of Corbyn to the Labour leadership.

In the past year they have mobilised huge numbers on the streets in the cause of Remain, have succeeded in winning Labour to support a second referendum, and contributed to the polarisation of British politics around this issue – as opposed to the class questions of inequality, austerity, education and the NHS which saw a strong result for Corbyn in 2017. Their strategy has succeeded – not in stopping Brexit, but in ensuring Labour lost votes at both ends.

Working class communities in the Labour heartlands have borne the brunt of neoliberalism since the early 1980s. Both Tory and Labour governments have carried out policies that have further entrenched the vast inequalities in British society that have seen a cycle of unemployment, poverty and neglect. For many of these people, voting for Brexit was a reflection of their anger and bitterness at politicians and the establishment. Labour in their areas represent that establishment – as the local councils, the Mayors and MPs. It was this disillusionment that outrageously created the space for Farage’s Brexit party to portray itself as the voice of the voiceless – a rhetoric reinforced by Labour’s support for a second referendum. The ultimate defection of Labour voters to Johnson’s Conservative Party in those areas, when Labour has been running on its most pro-worker platform in many years, represents a dramatic weakening of class consciousness amongst those long-suffering workers in the years since the Brexit vote. But in this election, many of them just didn’t bother to vote at all.

Corbyn’s early surge pointed to the potential for a different expression of that anger at neoliberalism. Hundreds of thousands of young people especially were drawn to Corbyn’s vision of socialism but that hope was consistently channelled into electoralism instead of mass action and struggle.

It is more accurate to describe British society as polarised than on a right wing trajectory. Corbyn received a positive swing in some constituencies like Liverpool and Manchester. The British Social Attitudes survey in 2019 showed, for example, that 86% of people believe the NHS faces a “major” or “severe” funding problem, up 14 points since 2014. 61% “would be prepared to accept” tax rises to increase NHS spending, up 21 points from 2014.

But aside from one demonstration two years ago Labour failed to mobilise its over ½ million new members into any increase in mass protests or strikes.

Neither did Corbyn put up a serious fight against the continual onslaught within his own ranks – capitulating at different times on the Trident nuclear weapon program, free movement of people, and the deselection as candidates of the Blairite MPs hell-bent on his destruction.

Without an increase of struggle and mobilisation, even popular and radical policies could not overcome the disillusionment sewn by decades of Labour betrayals from the Iraq war and privatisation to the response to the global financial crisis and austerity. This cynicism towards politicians, even more left ones like Corbyn, is in fact based in a certain reality about the world.

Even if Corbyn had won, his parliamentary approach would not have been able to overcome the right wing resistance of the bosses, the media and his own MPs to be able to implement even his moderate social democratic agenda. The woeful experience of reformist governments in Greece and Latin America demonstrates this.

The world is now witnessing an upsurge in struggle from below, from Lebanon to Iraq to Chile to France and beyond. The same anger that puts millions on the streets of Paris, Santiago and Hong Kong exists in London, Glasgow and Manchester.

Corbyn’s Labour received overwhelming support among young people, even in the Leave-voting areas of the north of England and southern Wales, alongside the Remainer stronghold of London. Those young people who tried to vote to defend the NHS, renationalise privatised industry, and reject Johnson’s reactionary politics can play an important role in building resistance to the attacks to come.

But that will be squandered if it is spent in more years of electoral work seeking power on the terrain that most favours the ruling class – building electoral majorities through official politics. That seemingly easy option has undermined the desire to resist austerity and neoliberalism in country after country. Waiting 5 years is not an option. And parliament is not where our power really lies anyway. We need the politics of struggle from below, and revolutionary, not parliamentary socialism.

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Monday, December 02, 2019

(LUSAKATIMES) Fred M’membe public discussion on Jobs

COMMENT - Fred M'Membe of the Socialist Party, owner of The Mast (formerly The Post), on the effect of technology and innovation on the destruction of jobs. The alternative is Universal Basic Income and ownership. Jobs may be going, however work will always be there, whatever form it takes.

(LUSAKATIMES) Fred M’membe public discussion on Jobs

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Monday, November 18, 2019

JTRIG - Targeting Zimbabwe Through Psyops

COMMENT - This document highlights the fact that international institutions have targeted Zimbabwe for psychological operations, which should be no surprise to anyone, however this is confirmation. - MrK

TOP SECRET

(JTRIG) Behavioural Science Support for JTRIG’s (Joint Threat Research and Intelligence Group’s) Effects and Online

HUMINT Operations
Mandeep K. Dhami, PhD
Human Systems Group, Information Management Department, Dstl
10 March 2011

Two of the Global team’s current aims are regime change in Zimbabwe by discrediting the present regime

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Tuesday, October 15, 2019

(PATRIOT ZW) Magombeyi’s fake ‘abduction’ …Vanguard fingered

COMMENT - The MDC cannot betray it's origins in the rhodesian security services and their penchant for psychological operations and false flag violence and abductions. Rhodesians like Coltart, Cross, Bennet and Kaye were all over it, and not because they loved democracy any time in their lives. In the early 2000s they committed violence through their Democratic Resistance Committees or DRCs, today they're called Vanguard. - MrK


(PATRIOT ZW) Magombeyi’s fake ‘abduction’ …Vanguard fingered
By admin -October 7, 20190476
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Patriot Reporter

FRESH details have emerged over the so-called ‘abduction’ of Dr Peter Magombeyi.

The 25-year-old Dr Magombeyi, who is also acting president of Zimbabwe Hospital Doctors’ Association (ZHDA), was allegedly ‘abducted’ at his home in Budiriro on September 14 2019.

And five days later, Dr Magombeyi surfaced in Nyabira, a few kilometres from the American Embassy.

A source who has close links to the MDC Alliance revealed that in those five days, Dr Magombeyi was housed at Number 64 Palmer Road in Milton Park.

The property is a lodge, Saita Safaris, and reportedly owned by MDC Alliance vice-president Tendai Biti.

“Dr Magombeyi was at 64 Palmer Road in Milton Park, nzvimbo iyoyo ilodge asi irikushandiswa sesafe house, chero Jacob Mafume naObey Sithole vanotogara ipapo (the place is a lodge which has been turned into a safe house for MDC activists including Jacob Mafume and Obey Sithole,” said the source who preferred to remain anonymous for fear of victimisation.

According to the source, Dr Magombeyi was taken by Vanguard leader Shakespear Mukoyi and one Bunjira.

When The Patriot visited the lodge, the gate was locked.

There was a sign: ‘Gate locked please ring bell’ and ‘Please do not hoot, press intercom’.

But there was no intercom or bell to ring.

The news crew had to knock for 10 minutes before someone attended to the gate.

Striking about the place is the huge precast wall and electric gate.

Inside and out, there is no signage of the name of the lodge.

Only the brown uniforms of housekeepers had a badge bearing the name of the lodge: Saita Lodges.

The news crew caught a glimpse of an EcoCash payment method with the number 0785 832 700. However the housekeepers said they no longer received ecocash payments as their EcoCash line had been blocked.

The EcoCash number is registered to one Winnie Manungo.

Vanguard behind the abductions?

Leaked MDC standing committee minutes revealed that MDC Alliance is reportedly militarily training its youth.

MDC standing committee is the party’s highest decision making body.

The meeting was held on September 18 2018 from 10hr to 13:45hr.

The party’s treasurer-general, David Coltart, was recorded at the meeting calling on the party to make their youths ‘more militant’.

And it is our understanding that there is a team of MDC Alliance youths scheduled to receive military training in Mozambique nex week.

There are reports that the MDC Alliance recently bought 47 unlicensed guns; FA and pistol type.

The MDC Vanguard has a history of violence.

Sometime in 2002, the MDC formed what they called the Democratic Resistance Committee (DRC), a group that was being trained militarily to cause mayhem on innocent people in the name of ‘regime change’.

White farmers then shared spaces on their farms to train these youths and this training was being allegedly led by the late Roy Bennett (late ex-MP).

The DRC morphed into the Vanguard.

Anyone who underestimated the nature of the militancy of the MDC did so at his/her own peril.

And Vangaurd is led by Mukoyi, the same person who is said to have ‘abducted’ Dr Magombeyi.

Who is Shakespear Mukoyi?

Mukoyi is an MDC Alliance member and leader of the MDC Alliance’s militia known as the Vanguard.

For long, MDC Alliance would deny the existence of Vanguard until last year in May when Mukoyi let the cat out of the bag.

The youth militia is known for ‘carrying an AK 47 and threatening to kill his rivals with it’. Running to the 2018 primary elections in the MDC Alliance, Mukoyi threatened to ‘kill Hwende’ if he (Mukoyi) was not elected House of Assembly Member for Kuwadzana East.

Charlton Hwende was running for the same seat.

Hwende took to facebook to raise alarm after being threatened with death by Mukoyi.

“I received disturbing news that my opponent was moving around with a gun threatening to shoot me. I am mentioning it here so that if anything happens to me people will know what happened to me,” he wrote.

Mukoyi claimed the constituency had apparently been given to him by the party’s presidential candidate, Nelson Chamisa, as a ‘token of appreciation’ after

λ From Page 2

he helped him ascend to the party’s presidency.

He helped Chamisa by carrying out acts of violence on Thokozani Khupe.

In 2017, in Bulawayo, members of the Vanguard were implicated in violence at that party’s offices where Khupe and her supporters were holding a meeting.

In February 2018, at the late Morgan Tsvangirai’s burial in Buhera, members of the group allegedly tried to set, on fire, a hut where Khupe and other MDC-T leaders had sought refuge.

The following month, the group was fingered, again, in acts of violence at that party’s offices in Bulawayo.

And, indeed, Mukoyi succeeded in pushing Chamisa to power through violence.

It is reported the gun-wielding Mukoyi slept in a hall where primaries were supposed to be held and threatened to ‘kill someone’ if he was not elected MP.

He is said to have declared that he had already won and no voting would take place, forcing the cancellation of the primary elections.

Mukoyi reportedly vowed he would not allow Chamisa to ‘dump him now after all he has done for him’.

Mukoyi is widely believed to have been Chamisa’s henchman and enforcer ever since the latter took over the reins at the opposition party.

And Hwende also confirmed on his facebook page that the primaries had been disrupted by the Vanguard; posting: “I would like to let you know that our primary election in Kuwadzana east was stopped by the so called vanguard youths led by their leader who was my opponent in the election…I hope the party will look into this matter as my safety is now a matter of concern.”

Ironically, the MDC-Alliance leadership, including Hwende, have all along been claiming the Vanguard is not a violent grouping despite repeated attacks on former MDC-T deputy president, Thokozani Khupe.

On April 9 2017, Mukoyi was arrested and charged for allegedly assaulting a police officer, Emmanuel Jeketera, with clenched fists and booted feet in Glen Norah but was later acquitted at the Mbare Magistrates’ Courts.

Mukoyi was arrested during a church service to pray for peace at the Nazarene Church in Glen Norah.

Prosecutors alleged Jeketera suffered a swollen lower lip and lacerations of the lower lip as a result of the assault.

He has a pending case of carrying an AK-47 during the January disturbances this year.

A litany of violence

At the Chatham House, MDC was built on the philosophy of violence as one of the key strategies for effecting regime change.

In 2000, Tsvangirai was quoted on BBC programme of September 30 saying:
“If you (President Mugabe) do not want to go peacefully, we will remove you violently.”

In 2005, Paul Temba Nyathi of the other MDC made this assessment: “Tsvangirai’s followers seem to be saying to themselves that they can win elections by beating people and by using the crudest methods of intimidation.”

And on July 3 2005, a meeting was held in Bulawayo between the Bulawayo Agenda (BA) and its sponsors the Konrad Adeneur Foundation of Germany (KAD).
It is at that meeting KAD told the BA that they would no longer fund organs which ‘concentrated on talk shows’.

However, they would readily fund ‘brave’ organisations that engage in demonstrations to remove the Government from power.

KAD made it clear that money would be availed only to programmes of confrontation.

In pursuant to the funder’s request, in 2007, the Zimbabwe Republic Police (ZRP) raided Harvest House, the MDC headquarters.

They recovered 2 000 sharp and piercing objects used in making incendiary bombs, two shortwave radios, 43 Zimbabwe passports with South Africa visa application forms, eight loud hailers, 104 spray guns, propaganda videos and cassettes.

This was just the beginning as the ZRP were to be swamped with reports of political violence, some turning into murder cases.

For example, the killing of Police Inspector Petros Mutedzi in Glen View 3, Harare, in May 2011.

In March 2007 alone, the MDC youths were credited with committing some of the most violent crimes listed below as can be confirmed by police records:

λ March 12: Petrol bombing of Zimbabwe Republic Police, Unit N Police Camp in Chitungwiza.

λ March 13: Petrol bombing of ZANU PF branch chairman’s house in Unit L, Chitungwiza.

λ March 13: A Zimbabwe National Army member and flea market vendors were assaulted by MDC youths.

λ March 13: Petrol bombing of Nehanda Police Post in Mkoba, Gweru.

λ March 14: Four MDC youths petrol-bombed a police officer’s house at Marimba Park Police Station, seriously injuring three female officers.

λ March 18: Petrol bombing of House Number 11 Zanu Yotonga Street, in Zengeza, Chitungwiza, on wrong intelligence that it belonged to a ZANU PF councillor of the area.

λ March 19: A crossborder Toyota Coaster (AAZ 3976) ferrying shoppers from Botswana was stoned and burned at Kuwadzana roundabout along Bulawayo Road, the list is endless.

λ March 23: Petrol bombing of Chisamba Police Station in Sakubva, Mutare.

λ March 23: House Number 2002 Gwinyai Street, St Mary’s, was petrol bombed. The house belonged to a ZANU PF district treasurer.

λ March 24: Muchada Supermarket and Pfukwa Night Club in Warren Park D were petrol bombed. The owner is a well-known ZANU PF member.

λ March 27: Petrol bombing of ZANU PF’s Joshua Nkomo offices in Mbare, Harare, by five MDC youths destroying all the furniture in the process.

λ March 29: House number 6847 Western Triangle, Highfields, was bombed believing it belonged to a ZNA member when it did not.

λ March 30: Petrol bombing of Gumbas Wholesalers on Leopold Takawira Street.

λ March 30: A Mazda B2500 pick-up (647-515V) belonging to a ZANU-PF supporter was petrol bombed at Current Shopping Centre in Budiriro 5.

λ April 3: ZINASU petrol bombed UZ Complexes One and Four dining halls, shattering all windows. The roof collapsed following the attack.

The above cases are an indication that violence is in the MDC’s DNA.

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(PATRIOT ZW) Plot to destabilise Zim

COMMENT: More subversion and sabotage from the MDC - MrK.

(PATRIOT ZW) Plot to destabilise Zim
By Golden Guvamatanga -October 11, 20190236
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THE MDC Alliance, in collaboration with the US Government, has embarked on a fresh two-pronged plan to destabilise the country and bring it to the UN agenda with a view of sending a supposed ‘peacekeeping mission’ to Harare, this publication can reveal.

Information at hand shows that the plan involves launching sporadic but violent attacks in the country’s high density suburbs to galvanise the masses to rise against Government.

Going under the banner ‘Free Zimbabwe Campaign’, the plan also involves a sit-in at the country’s strategic offices, including Munhumutapa Building which houses President Emmerson Mnangagwa’s offices.

The sit-in project is drawn from Venezuelan opposition leader and American-sponsored Juan Guaido’s failed plan to unseat President Nicolas Maduro using the same strategy.

Insiders within the MDC Alliance told this publication that funding for the ‘Free Zimbabwe Campaign’ has been secured, with a senior party official working in cahoots with a former youth leader to set the project in motion.

The senior MDC Alliance official, famed for selling the illicit brew commonly referred to as ‘Bronco’, is said to be the holder of the purse for key party programmes and has an account in Namibia, a country he frequently visits.

But it is in Zimbabwe where real action, according to the US’ wishes, is supposed to be.

The US Government, on the other hand, is working round the clock to tarnish President Mnangagwa’s re-engagement efforts on the international scene through presenting Zimbabwe as a pariah state that has little regard for human rights.

The Government of Zimbabwe has been on an aggressive re-engagement drive that has seen SADC coming on board on Harare’s side against Western-sponsored economic sanctions.


The US, however, denies it has imposed sanctions on Zimbabwe, instead preferring to call them ‘restrictive’ or targeted measures.


Those denials have, since December 21 2001, armed the MDC Alliance with ammunition to accuse Government of failing to develop the economy and calling on its members to violently confront the authorities.

And the MDC has been consistent on the violence front, with a record that stretches as far back as 2002.

The violent confrontation plan was laid bare by MDC Alliance leader Nelson Chamisa during his party’s 20th anniversary on September 20 2019 at Rufaro Stadium.

On September 18 2019, the party’s standing committee held a meeting at Harvest House where it was agreed that the opposition party’s youths had to be more ‘militant’ in their demonstrations.


The MDC Alliance’s violent streak was also displayed during the January 14-16 2019 violent demonstrations where there was rampant looting of shops and burning of cars and property by the party’s marauding youths.

Speaking at Rufaro Stadium, Chamisa stated that his party would be taking the Government ‘head on’, a statement that drew wild cheers from his visibly intoxicated youths.


“What we are saying is, wait and see. We will not have our demonstrations banned,” he said.

“All progressive forces must converge; so we want teachers, students, workers, churches and political parties to come together and have a ‘free Zimbabwe campaign’.

Zimbabwe is facing critical power, fuel and water shortages, and a sharp rise in the cost of living, which is not matched by disposable income.

If we call for a demo, will you come?

We want to plan in such a way that we will not go home.

We want to do a sustainable demo until we achieve what we want. December is too far.”

The threats follow the courts’ decision to ban the MDC Alliance demonstrations on August 16 2019.

This was after security services detected that the opposition was planning to destroy property and burn service stations.

US Ambassador to Zimbabwe Brian Nichols was implicated as the brains behind the August 16 2019 failed demonstration.

The following is an August 18 2019 report by The Sunday Mail which exposed Nichols role in the failed demonstration:

“Sources said Ambassador Nichols, his deputy Thomas Hastings and regional security officer Patrick Bellinger, including Mrs Nichols and Mrs Hastings, met MDC deputy chairperson Job Sikhala on Thursday — the eve of the planned demonstrations – at the latter’s home in St Mary’s, Chitungwiza.

Mr Nichols left after 30 minutes.

In their engagement with Sikhala, the American diplomats urged the MDC to go ahead with the demonstrations until their demands were met. They assured him (Sikhala) that the US was watching the developments and would impose punitive measures should Government arrest or assault the protestors,’ said the sources.”

But the US has yet to give up on punishing Zimbabwe.

On October 1 2019, the US eEbassy in Harare proudly admitted to having curtailed the sale of Zimbabwe diamonds on the international market.

Curiously, the US cited ‘forced labour’ as the reason for the withholding of the diamonds.

Said the Embassy:

“US Customs and Border Protection issued a Withhold Release Order for artisanal rough cut diamonds from Zimbabwe’s Marange diamonds fields on October 1 2019 due to evidence of forced labour, US law prohibits importation of goods made with forced labour.”

While the US saw sense, with hindsight, the damage had already been done and in future it might be difficult to sell those (diamonds) for very obvious reasons.

Parallels and overlaps

There are striking similiraties between Chamisa and the late MDC leader Morgan Tsvangirai’s Free Zimbabwe Campaign and Save Zimbabwe Campaign respectively.

Both are drawn from the same template.

On March 17 2006, Tsvangirai’s MDC was beginning its two- day convention in Harare which would adopt a programme of further destabilising Zimbabwe.
Called ‘democratic resistance’ (DRC), the programme aimed to sabotage the country and throw it into anarchy.

From March 2006, right up to March 2007, Tsvangirai and his faction of the MDC embarked on a whirlwind tour of Zimbabwe’s cities, all the time making it clear this was a build- up to the mass action.

An indicator of the rising Western belief in the inevitable success of his (Chamisa) new strategy was a major prognosis published by Harvard’s African Policy Journal which projected the unseating of President Mugabe and ZANU PF as foregone, urging the West to urgently prepare for a post-Mugabe era.

Revealingly titled, ‘After Mugabe: Applying post-conflict recovery lessons to Zimbabwe’, the article, authored by two neo-liberal warrior policy advisors to the Bush administration, Todd Moss and Stewart Patrick, predicted, ‘a major transition anytime’, with ‘change (coming) without much warning’.

It warned the US Government and other donors against being ‘caught flat-footed’ by this change, urging them to ‘start planning now for possible responses to a transition in Zimbabwe’.

Describing Zimbabwe as a ‘post-conflict situation’, the paper intimated that such preliminary preparations would be ‘catalytic’ to the transition itself.
To date, Zimbabwe is still being described as a ‘post-conflict situation’ while the MDC Alliance continues on its violent path.

America’s ever intrusive hand

A few years ago, Washington also bankrolled the disgraced Archbishop Pius Ncube’s repeated travels around the world, which had no financial implications to the local Catholic Church or the Vatican.

This was before they went public with their programme of destabilising Zimbabwe.

In its State Department report, Supporting Human Rights and Democracy: The US Record 2006, released in Washington DC on April 5 2007, the US proudly admitted to subverting President Mugabe’s Government and to supporting the opposition (MDC).

It added:

“To further strengthen pro-democracy elements, the US Government continues to support the efforts of the political opposition, the media, and civil society to create and defend democratic space and to support persons who criticise the Government (of President Mugabe).”

The report itemised the following US subversion strategies:

Direct funding to the opposition MDC.
Direct funding to MDC- affiliated international and national NGOs.
Direct funding to human rights groups affiliated to the opposition.
Direct support to the labour union, ZCTU, from which the MDC emerged.
Direct funding to committees of Parliament.
Direct funding to various forums critical of the Government of Zimbabwe.
Hostile extra-territorial broadcasts targeting Zimbabwe through VOA’s Studio 7.
At the presentation of the study in Johannesburg (South Africa) in May 2006, Tony Hawkins, a former University of Zimbabwe Economics lecturer and advisory figure to most scenario-building models on Zimbabwe, underlined both his expectations and frustrations:

“In political democracies, prolonged economic decline almost sparks political change, through the ballot box or more radical confrontation on the streets,” Hawkins said then.

American funding was also visible in the now infamous ‘Christian Alliance’ of 2007.

The Christian Alliance hosted both factions of the MDC, the NCA, ZCTU, Crisis in Zimbabwe Coalition, Women/Men of Zimbabwe Arise (WOZA/MOZA), Zimbabwe National Students Union (ZINASU), Zimbabwe Lawyers for Human Rights, Zimbabwe Doctors for Human Rights, Media Alliance and political NGOs.

The US also sponsored the creation and funding of community newspapers in urban townships, especially in Harare, Kwekwe, Gweru, Masvingo and Bulawayo, where opposition action was expected.

For rural areas, it sought to rely on its illegal broadcasts through its VOA Studio 7 station which came in to complement similar broadcasts from The Netherlands (Voice of the People) and from the UK (SW Radio).

The US Embassy funding of Church institutions and figures included that of the Christian Alliance headed by Bishop Kadenge and Archbishop Pius Ncube’s South African-based Solidarity Peace Trust.

While all these strategies have failed to work, Zimbabweans must always be armed with the knowledge that the West is after Zimbabwe’s resources.

That is why they want regime change.



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Saturday, October 05, 2019

Methodological Problems With The Nature Study Of Ancient Egypt - SOY Keita Let's Them Have It

COMMENT - This is a response to a study published in Nature titled Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods, which claims that the Ancient Egyptians were genetically the same as the people of North Africa/Middle East. There are many problems with these interpretations, and professor S.O.Y Keita lays them bare one by one. - MrK

Ancient Egyptian Genomes from northern Egypt: Further discussion

Jean-Philippe Gourdine1,4, S.O.Y Keita2,4, Jean-Luc Gourdine3 and Alain Anselin4*1
Oregon Health & Science University, 2Smithsonian Institution, 3National Institute of Agricultural Research, France(Guadeloupe), 4Ankhou/Cahiers Caribéens d'Égyptologie (Guadeloupe, Martinique),*corresponding author: alain.anselin@gmail.com

Schuenemann et al.1 seemingly suggest, based largely on the results of an ancient DNA study of later period remains from northern Egypt, that the ‘ancient Egyptians’ (AE) as an entity camefrom Asia (the Near East, NE), and that modern Egyptians “received additional sub-Saharan African (SSA) admixtures in recent times” after the latest period of the pharaonic era due to the “trans-Saharan slave trade and Islamic expansion.” In spite of the implied generalization about ‘origins’ the authors do offer the caveat that their findings may have been different if samples had been used from southern Egypt, and this is a significant admission. Their conclusions deserve further discussion from multiple perspectives which cannot be fully developed due to space limitations.


There are alternative interpretations of the results but which were not presented as is traditionally done, with the exception of the admission that results from southern Egyptians may have been different.

The alternative interpretations involve three major considerations:

1) sampling and methodology,
2) historiography and
3) definitions as they relate to populations,origins and evolution.


1) Sampling and methodological strategyThe samples can be questioned as to their representativeness of Egypt in terms of size, spatio-temporal and socio-cultural aspects.

●All of the samples are from the northern half of Egypt, from one nome which is 2.4% (1/42) of AE nomes. Ancient Egyptian culture originated southern Upper Egypt2.

●The socio-cultural dynamics are not fully considered: the information on the origin andsocial status is incomplete, or unknowable in fact. The mummies are clearly assumed tobe representative of the local population based on an incomplete archaeological report, in1
spite of the historical information provided about northern Egypt’s interaction with theNear East since the Predynastic, and the known settlements of Greeks, and others, innorthern Egypt in later periods.

●The timeline is not representative of AE history ~ 3,000 years is missing (e.g.Predynastic, Early Dynastic, Old Kingdom, Middle Kingdom

2) The samples cannot be convincingly said to represent true breeding populations or thosethat truly integrate historical information.

●The authors use Bayesian reconstruction of population size changes through time with BEAST, for which there is generally a discrepancy between the marginal prior and theoriginal prior distribution. The available information on the comparison between original and marginal priors, and on prior and posterior distributions, does not take into account possible population substructure.

Sex-biased sampling (mtDNA) cannot recover population demography of the whole country unless the sample size is large enough and representative in terms of chronology, regional variation, “ethnicities” (including the foreign presence), class and geography. It suffers from many biases that can affect the assessment of the effective population size: population size changes, mutation bias, and natural selection.

●The whole genome sample size is too small (n=3) to accurately permit a discussion of allEgyptian population history from north to south.2) Historiography and misinterpretation

●The authors do not consider explanations based on historical narrative, although theypresent historical information. NE input in AE could also be explained by old mercantile2 relationships with Lower Egypt (e.g. Maadi-Buto complex ~4,000 BC3), EgyptianizedAsiatic rulers and migrants (e.g. Hyksos ~1,650 BC), NE prisoners of war (e.g. from Thutmose III’s military campaign in NE ~ 1,490 BC), from diplomatic marriages2 (e.g.Amenhotep III and Mitanni princess, Gilukhipa~ 1,380 BC), etc.

The authors completely dismiss the results of PCR methods used on AE remains. As a Habicht et al.4 states, PCR based methods were used successfully on mummified Egyptian cats and crocodiles without creating extensive debate. Results that are likely reliable are from studies that analyzed short tandem repeats (STRs) from Amarna royal mummies5 (1,300 BC), and of Ramesses III (1,200 BC)6; Ramesses III had the Y chromosome haplogroup E1b1a, an old African lineage7. Our analysis of STRs from Amarna and Ramesside royal mummies with pop Affiliator18 based on the same published data 5,6 indicates a 41.7% to 93.9% probability of SSA affinities (see Table 1); most of the individuals had a greater probability of affiliation with “SSA” which is notthe only way to be “African” a point worth repeating.

●There are some philosophical issues as well for which space does not permit a full discussion. Conceptually what genetic markers are considered to be “African” or “Asian” needs discussion--and of what “defines” Africa as well. For example, the E1b1b1 (M35/78) lineage found in one Abusir el-Meleq sample is found not only in northern Africa, but is also well represented in eastern Africa7 and perhaps was taken to Europe across the Mediterranean before the Holocene (Trombetta, personal communication). E lineages are found in high frequency (>70%) among living Egyptians in Adaima9. The authors define all mitochondrial M1 haplogroups as “Asian” which is problematic. Gene history is not population history: ultimate “origins” and later sources to a specific region/3 population are conceptually different. Gene history is not also ethnic or linguistic history. M1 has been postulated to have emerged in Africa10, and there is no convincing evidence supporting an M1 ancestor in Asia: many M1 daughter haplogroups (M1a) are clearly African in origin and history10. The M1a1, M1a2a, M1a1i, M1a1e variants found in the Abusir el-Meleq samples1 predate Islam and are abundant in SSA groups10, particularly in East Africa. Furthermore, SSA groups indicated to have contributed to modern Egypt donot match the Muslim trade routes that have been well documented11 as SSA groups from the great lakes and southern African regions were largely absent in the internal trading routes that went north to Egypt. It is important to note that “SSA” influence may not bedue to a slave trade, an overdone explanation; the green Sahara is to be considered as Egypt is actually in the eastern Sahara. SSA affinities of modern Egyptians from AbusirEl-Meleq might be attributed to ancient early settlers as there is a notable frequency of the “Bushmen canine”- deemed a SSA trait in Predynastic samples dating to 4,000 BC9from Adaima, Upper Egypt. Haplogroup L0f, usually associated with southern Africans,is present in living Egyptians in Adaima9 and could represent the product of an ancient“ghost population” from the Green Sahara that contributed widely. Distributions and admixtures in the African past may not match current “SSA” groups12.

3) On the Definition of African

Schuenemann et al.1 seem to implicitly suggest that only SSA equals Africa and that there are no interconnections between the various regions of Africa not rooted in theslave trade, a favorite trope. It has to be noted too that that in the Islamic armies that entered Egypt that there were a notable number of eastern Africans. It is not clear why there is an emphasis on ‘sub-Saharan’ when no Saharan or supra-Saharan population4 samples--empirical or modelled are considered; furthermore, there is no one way to be“sub-Saharan.” In this study northern tropical Africans, such as lower and upper Nubians and adjacent southern Egyptians and Saharans were not included as comparison groups,as noted by the authors themselves.

4) Conclusion

The paleolithic past has to be distinguished from the biocultural emergence in the Holocene of any society, including Europe. Egypt long before the pyramids was culturally and linguistically African as evidenced by numerous studies3,13,14 based on standard research which accept Egypt’s place in the Nile corridor as having local origins. The symbolism found in the Badarian or Naqadan graves, etc. nor the pyramids werebrought from Asia (Near East). The Egyptian Neolithic cannot be shown as an entity to have come from Asia, although some domesticates were borrowed on local terms into asystem of indigenous foraging in the Fayum2. Historical linguistics shows ancientEgyptian to be Afroasiatic with borrowings from other African language phyla15.

Archaeological data would seem to indicate an early integration of the eastern delta, in northern Egypt, by early Upper Egyptian rulers since Iry Hor from Abydos (~3,250 BC),who already wrote royal inscriptions in Egyptian2 in a script and symbolic system that used African flora and fauna3,13. This region of Egypt, and northern Egypt had long had social intercourse with the Near East. The ancient Egyptians in “origin” were not settler colonists akin to the European colonists in Africa. Schuenemann et al.1 study is best seen as a contribution to understanding a local population history in northern Egypt as opposed to a population history of all Egypt from its inception. 5

Table 1: Geographical region affinities of Amarna and Ramesside mummies based onpopAffiliator 18 analysis of 8 pairs of STR 8/13 pairs of STR from Combined DNA Index System were used by Hawass et al.5,6,nevertheless, data suggest main sub-Saharan affinities of pharaonic mummies from the 18th and20th dynasty (circa 1,300 BC), far in the past before Islamic slave trade. Disclaimer:Thegeographical regions affinities were defined according to popAffiliator8, we acknowledge theremight be problems with any type of classification.(* data from Hawass et al.5,6 available herehttp://bit.ly/Pop-Affi-STR-Mummies )ContributionsJ-P.G and S.O.Y Keita performed the PopAffialiator analysis, drew tables, wrote and reviewed the maingenetic, statistical, anthropological and Egyptology portions of the article. J-L. G wrote and review thestatistical portion. A.A wrote and reviewed Egyptological/linguistics portion. Competing interestsThe authors declare no competing financial interestsAbout the authors:Jean-Philippe Gourdine, Ph.D is a metabolomics and glycomics data analyst at Oregon Health & Science University and member of editorial board of the Ankhou/Cahiers Caribéens d'Égyptologie. Email: jpgourdine@gmail.comSOY Keita, MD, D.Phil is a research affiliate of the department of anthropology, Smithsonian Institution and member of editorial board of the Ankhou Cahiers Caribéens d'Égyptologie.Email: soykeita@yahoo.comJean-Luc Gourdine, Ph.D, is a researcher in quantitative genetics at the National Institute of Agricultural Research, France (Guadeloupe)Email: jean-luc.gourdine@inra.fr6

Alain Anselin, Ph.D is the editor of the peer reviewed Egyptological journals Cahiers Caribéens d'Égyptologie & electronic papyrus i-Medjat (http://www.culturediff.org/english/ccde.htm), and director of the research group Ankhou

Email: alain.anselin@gmail.comReferences1.Schuenemann, V. J. et al.Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat. Commun.8, 15694 (2017).2.Agut-Labordère, D. & García, J. C. M. L’Égypte des pharaons: de Narmer à Dioclétien :3150 av. J.C.- 284 apr. J.-C. (Belin, 2016).3.Teeter, E. Before the Pyramids: The Origins of Egyptian Civilization. (Oriental Institute ofthe University of Chicago, 2011).https://oi-idb-static.uchicago.edu/multimedia/88/oimp33.pdf4.Habicht, M. E., Bouwman, A. S. & Rühli, F. J. Identifications of ancient Egyptian royalmummies from the 18th Dynasty reconsidered. Am. J. Phys. Anthropol.159, S216–31(2016).5.Hawass, Z. et al. Ancestry and pathology in King Tutankhamun’s family. JAMA303, 638–647 (2010).6.Hawass, Z. et al. Revisiting the harem conspiracy and death of Ramesses III:anthropological, forensic, radiological, and genetic study. BMJ345, e8268 (2012).7.Rowold, D. et al. At the southeast fringe of the Bantu expansion: genetic diversity andphylogenetic relationships to other sub-Saharan tribes. Meta Gene2, 670–685 (2014).8.Pereira, L. et al. PopAffiliator: online calculator for individual affiliation to a majorpopulation group based on 17 autosomal short tandem repeat genotype profile. Int. J. LegalMed.125, 629–636 (2011).9.Crubézy, E. Le peuplement de la vallée du Nil. Archéo-Nil20, 25–42 (2010).7

10.Pennarun, E. et al.Divorcing the Late Upper Palaeolithic demographic histories of mtDNAhaplogroups M1 and U6 in Africa. BMC Evol. Biol.12, 234 (2012).11.Lovejoy, P. E. Transformations in Slavery: A History of Slavery in Africa. (CambridgeUniversity Press, 2011).12.Busby, G. B. et al. Admixture into and within sub-Saharan Africa. Elife5, (2016).13.Anselin, A. Some Notes about an Early African Pool of Cultures from which Emerged theEgyptian Civilisation. in Egypt in its African Context. Proceedings of the Conference held atThe Manchester Museum, University of Manchester (ed. Exell, K.) 43–53 (Oxford, BARInternational, 2009).14.Wengrow, D., Dee, M., Foster, S., Stevenson, A. & Ramsey, C. B. Cultural convergence inthe Neolithic of the Nile Valley: a prehistoric perspective on Egypt’s place in Africa.Antiquity88, 95–111 (2014).15.Takács, G. Sibilant and velar consonants of South Cushitic and their regular correspondencesin Egyptian and other Afro-Asiatic branches. in Afroasiatica Tergestina. Papers from the 9thItalian Meeting of Afro-Asiatic (Hamito-Semitic) Linguistics, Trieste 393–426 (1998).8

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