Luxmanda: a 3,000 years-old proto-Horner in Tanzania

I knew, more intuitively than rationally, that the Horner (Ethiopian, Somali, Eritrean) type of Afro-Eurasian admixture was very old but no idea it was so much. I knew that West Eurasian Upper Paleolithic had an impact on Africa (LSA) but I did not know it went so deep South nor that it had left such a massive legacy as ancient DNA reveals.

Pontus Skoglund et al. Reconstructing Prehistoric African Population Structure. Cell 2017 (open access). DOI:10.1016/j.cell.2017.08.049

The data analysis speaks volumes by itself:

Figure 1 - Overview of Ancient Genomes and African Population Structure

Figure S2 - Ancient Individuals and African Population Structure

Figure 2 - Ancestral Components in Eastern and Southern Africa

We show bar plots with the proportions inferred for the best model for each target population. We used a model that inferred the ancestry of each target population as 1-source, 2-source, or 3-source mixture of a set of potential source populations.

So much that I don't really know what else to say. Of course this is just a sample of what there is in the paper, read it. I'm sure there will be plenty of comments even if the study was published months ago.

Regarding haploid DNA, I don't see anything outstanding but, as I know there is generally quite a bit of interest, these are screenshots of the ancient lineages found (full data in the supp. materials of the study):

Ancient Y-DNA (screenshot)

Ancient mtDNA (screenshot)

Related: No Iberian in Iberomaurusian.

Correction: I first titled this "a 30,000 years-old...". That was a major error on my part and I apologize for any confusion it may have caused. Thanks to Capra Internetensis for spotting it.

No Iberian in Iberomaurusian

After almost a century of controversy on the matter, it seems that archaeogenetics solved the riddle. Not in the sense I thought it would but it did anyhow.

Marieke van de Loosdrecht et al., Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 2018 (pay per view). DOI:10.1126/science.aar8380 -- See also supplementary materials (free but hard to find). 

Ancient DNA samples from Taforalt (Iberomaurusian or Oranian culture, Upper Paleolithic of North Africa) show no trace of Paleoeuropean ancestry (WHG), however they show strong affinity to West Asians of Palestinian type, showing also some significant amount of African Aboriginal ancestry, probably closer to East African Hadza and Sandawe and ancient Mota than to West African types. The result is something roughly similar to Afars but not quite the same in any case. 

Fig. S8 - Taforalt individuals on the top PCs of present-day African, Near Eastern and South European populations.

Fig. S11 - ADMIXTURE results for a few informative K values.

So the conclusion must thus be that the Eurasian influence in North African Upper Paleolithic (call it Iberomaurusian, Oranian or my personal unorthodox preference: Taforaltian) arrived from West Asia with whichever intermediate stage in Egypt and Cyrenaica, where that influence is quite apparently much older in the archaeological record. This seems contradictory to the chronology of Taforaltian, with Western sites producing older radiocarbon dates but the genetic data seems overwhelming. 

I must say I wish they would have contrasted with older (and available) Paleoeuropean samples than WHG (Epipaleolithic) but I guess that some WHG influence would have shown up if there was some older European influx because the various Paleoeuropean layers are not disconnected. But it is still something someone should test, just in case. 

Haploid DNA

The Taforalt sample was rich in mtDNA U6a, with also one instance of M1b:

All six male samples carried Y-DNA E1b1b, with most of them being well defined as E1b1b1a1-M78 (see table S16 for details).


Related: Luxmanda: a 3,000 years-old proto-Horner in Tanzania.

Ironworks the Iron Age style: the true thing done again by Burkinabe elders for the sake of historical document

This is a truly fascinating film, made by the people of Burkina Faso documenting their own, now vanishing tradition of iron smelting and forging, done again for the sake of historical documentation by the elders who used to do it decades ago (and some youngsters helping too) reproducing all the steps: from charcoal making and iron ore mining and selection, to the construction of the furnaces, the smelting of ore and finally tool-making itself. I cannot recommend it more wholeheartedly:

Chad's Eurasian genetic input similar to that in Ethiopia

Quickies

Marc Haber et al. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. AJHG 2016. Open access → LINK [doi:10.1016/j.ajhg.2016.10.012]

Summary

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

Worth a read no doubt but careful, careful, careful with their chronological guesstimates. Their starting point is the assumption (once and again demonstrated all kinds of WRONG) of:

Eurasians and Africans diverged around 60,000–80,000 ya and subsequently had different patterns of population-size changes: in particular, compared with Africans, the Eurasian population experienced a sharp decrease in size ∼60,000 ya.

So add around 65-70% (x1.7) to all dates, else you are bound to fall in the pit of molecular-clock-o-logical self-complacent pseudoscience. So where it reads c. 6-7 Ka for the first migration (R1b-related), it should be 10,000 years ago (which is the actual dating of Afroasiatic expansion by most accounts, with origin not exactly in "Eurasia" but rather in or near Sudan, where those Eurasian lineages, R1b and J1, had since long before most likely), and when they say 3 Ka ago, it's probably 5000 years ago, within the context of Neolithic inflows possibly: 3000 years ago was already well into Ancient Egypt and peoples just did not cross it without proper paperwork anymore, actually 3000 years ago is the Bronze Age collapse and Egypt, Lower Egypt specifically, fell to Africans, to Libyans and other Berbers known as Meshwesh (Amazigh, probably from modern Tunisia) to be precise.

Dr. Haber: time to update your clock, it just doesn't work, and you are confusing people to no avail.

Genetic structure in South-Eastern Africa

Quickies

Another quite interesting paper on Khoesan and Southern African genetics:

Caitlin Uren et al., Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries. Genetics 2016. Freely accessible → LINK [doi:10.1534/genetics.116.187369]

Abstract

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

 

Figure 2

Five spatially distinct ancestries indicate deep population structure in southern Africa. Using global ancestry proportions inferred from ADMIXTURE k = 10, we plot the mean ancestry for each population in southern Africa. The five most common ancestries in southern Africa, from the Affymetrix HumanOrigins data set, are shown separately in A–E. The x- and y-axes for each map correspond to latitude and longitude, respectively. Black dots represent the sampling location of populations in southern Africa. The third dimension in each map (depth of color) represents the mean ancestry proportion for each group for a given k ancestry, calculated from ADMIXTURE using unrelated individuals, and indicated in the color keys as 0–100% for five specific k ancestries. Surface plots of the ancestry proportions were interpolated across the African continent.

See also:

• Relevant article at Science Daily
• Khoesan and Coloured autosomal DNA in context
• Khoesan genetics helping to understand the evolutionary history of Humankind as a whole
• SW African Bantu matrilineages
• Khoe-San matrilineages and prehistory
• Khoisan autosomal genetics

Gobero (Green Sahara key site) documentary

This site of Gobero (Niger) was news in the archaeology and anthropology circles a few years ago and today I stumbled on this quite nice video documentary on it that I believe will be of interest for many readers:

African admixture events

Quickies

This paper is probably of interest to many but I don't have the insight to make a proper analysis. Just to mention that I feel deeply uncomfortable with the use of the "Sub-Saharan" term, which has so many wrong ideas attached to it, particularly the word "sub" (under, below) that it really irks me. Why not Trans-Saharan or Ultra-Saharan?, very Roman and not the least Eurocentric but definitely not just all kinds of wrong, as "Sub" is. Why not Tropical and Southern Africa?

Sub-Saharan is not just implicitly Eurocentric and almost certainly racist (sub-what?! subordinated?, sub-human maybe?) but, most importantly, it is geometrically and geographically very wrong. The South is not "under" the North: they are all on the same spheroid surface or equivalent cuasi-plane. Even a primary school student knows that!

Anyhow, this is what they have to say in minimalistic terms:

George BJ Busby et al., Admixture into and within sub-Saharan Africa. eLife 2016. Open access → LINK [doi: eLife 2016;5:e15266]

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Figure 4. Inference of admixture in sub-Saharan African using GLOBETROTTER. (A) For each group we show the ancestry region identity of the best matching source for the first and, if applicable, second events. Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted by golden and red colours, respectively. Second events can be either multiway, in which case there is a single date estimate, or two-date in which case 2ND EVENT refers to the earlier event. The point estimate of the admixture date is shown as a black point, with 95% CI shown with lines. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. The coefficients of this regression sum to 1 and are coloured by ancestry region. 1ST EVENT SOURCES and 2ND EVENT SOURCES show the ancestry breakdown of the admixture sources inferred by GLOBETROTTER, coloured by ancestry region as in the key top right. (B) and (C) Comparisons of dates inferred by MALDER and GLOBETROTTER. Because the two methods sometimes inferred different numbers of events, in (B) we show the comparison based on the inferred number of events in the MALDER analysis, and in (C) for the number of events inferred by GLOBETROTTER. Point symbols refer to populations and are as in Figure 1 and source data can be found in Figure 4—source data 1

Genetic structure of pearl millet, an African cereal

Quickies

Zhenbin Hu et al., Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. BMC genomics 2015. Open access → LINK [doi:10.1186/s12864-015-2255-0]

Abstract

Background

Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.

Results

We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.

Conclusions

We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.

Fig. 4

The genetic relatedness of pearl millet accessions. a F-statistic (F _ST ) between populations with different origins. The circles indicate the countries of origin, and the values represent the F _ST between accessions from the two countries. The thickness of the lines is proportional to the value of F _ST . b Genetic relatedness among 500 accessions assessed with the neighbor joining method. Global accessions are colored by countries of origin, and Senegalese landraces are colored by regions of origin

See also: Review of Tropical Neolithic flows (a most important agricultural development in the African and Asian Tropics).

How different is Howieson Port Middle Paleolithic tech from its neighbors and successors?

Quickies

That's what a recently published paper discusses. Oh, by the way, context for the casual reader: Howieson Port and related industries are among the oldest ones in South Africa, yet they are very advanced for their time, suggesting that our species was innovating in ways that our (now essentially extinct) cousins were not doing. See also: this entry on African Middle Paleolithic.

Paloma de la Peña, Refining Our Understanding of Howiesons Poort Lithic Technology: The Evidence from Grey Rocky Layer in Sibudu Cave (KwaZulu-Natal, South Africa). Open access → LINK [doi:10.1371/journal.pone.0143451]

Abstract

The detailed technological analysis of the youngest Howiesons Poort occupation in Sibudu Cave, layer Grey Rocky, has shown the importance of blade production (with different knapping methods involved), but also of flaking methods in coarse grained rock types. Moreover, new strategies of bifacial production and microlithism were important. Grey Rocky lithic technology shows a really versatile example of reduction strategies that were highly influenced by the characteristics of the rock types. This lithic assemblage is another example of the technological variability linked to the Howiesons Poort technocomplex. The reasons for this variability are still difficult to elucidate. Discrepancies between sites might be for different reasons: diachronic variations, functional variations, organizational variations or maybe different regional variations within what has been recognized traditionally and typologically as Howiesons Poort. The technological comparison of the Grey Rocky assemblage with assemblages from other Howiesons Poort sites demonstrates that there are common technological trends during the late Pleistocene, but they still need to be properly circumscribed chronologically. On the one hand, Howiesons Poort characteristics such as the bifacial production in quartz are reminiscent of production in some Still Bay or pre-Still Bay industries and the flake production or the prismatic blade production described here could be a point in common with pre-Still Bay and post-Howiesons Poort industries. On the other hand, the detailed analysis of the Grey Rocky lithics reinforces the particular character of this Howiesons Poort technocomplex, yet it also shows clear technological links with other Middle Stone Age assemblages.

Most Africans do not have significant Eurasian admixture

This is major news: the authors of the study on the ancient East African genome of Mota have recanted their conclusions. In a correction note echoed by Nature they say:

Erratum'to'Gallego'Llorente'et'al.'2015'

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few SubUSaharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

This makes much better sense admittedly. I strongly appreciate the willingness of Gallego, Jones et al. for publicly amending their wrong as quickly as possible. It's said that erring is human but correcting is only for the wise.

Good documentaries on human Prehistory

I just watched the documentary "First Peoples - Asia" (by NOVA) and found it quite good, discussing many of the issues that I and the readers of this blog have been following and discussing the last years on the settling of Asia (and geographical dependencies): the Zhirendong jaw, the Nubian points of Arabia, the archaic admixture events... 

The only issue is that for some odd reason (copyright masking?) interviewed people voices often have a too high pitch.

I hope the other four documentaries of the series are similarly good. I haven't watched them yet but the full playlist is embedded below beginning with the Asian colonization movie. For many readers it won't be that interesting personally (they already know all or most of it, maybe even better than what the movie explains) but it is still a promising tool to share your hobby with family and friends, so watch it in good company. 

Enjoy!

Update (Jan 9):

I've watched already four of them (Africa, Asia, Australia and Europe) and the European one is no doubt the worst: a superficial Neanderthal hybridization neo-myth spearheaded by John Hawks. Also the only map or description of the route followed by modern humans to Europe is absolute nonsense: directly from Africa via Palestine, when in fact it's extremely clear that at least most of the lineages went all the way to SE Asia and back before ever entering Europe. What happened to the spear in the rib of Zawi Chemi Shanidar man? What happened to the very fast replacement in the early Aurignacian, coincident with the Campanian Ignimbrite eruption? What about dogs? Not a word! Just whitewashing of the probably quite violent Sapiens-Neanderthal interaction. You can skip that one, really, it's pretty much nonsense.

Some hyper-hybridationism permeates all the documentaries but the others seem much better: the Asia one is quite good, the Africa one is not bad either (although could be much better if they paid more attention to archaeology, also Africa deserves 50% of the documentary space probably), the Australia one is OK but it simply ignores Papua and Wallacea altogether, what is a bit perplexing to say the least. The Europe one is just horrible: it has some facts but half of it its John Hawks' preaching his particular ideology about people being oh-so-nice that they probably used spears as toothpicks, Paabo making a lot of extra work for the cleaning crew (spectacular admittedly but should be in a separate Neanderthal docu, not in one dedicated to H. sapiens) and some real archaeology scattered around (but definitely not enough at all).

First African ancient nuclear DNA

Major update (Feb 12 2016): the authors have publicly corrected their conclusions: the alleged Eurasian admixture in Yoruba and Mbuti does not exist. See HERE for further details.

Mota cave

Whatever we may think of the conclusions (see below), this study is a most important breakthrough because it shows that ancient DNA can be obtained from remains preserved in hostile (hot) conditions, removing the technical barriers for research in these areas, which make up most of the inhabited world. The method, which relies in the vault-like conditions of the inner petrous earbone, was demonstrated earlier this year by Pinhasi et al. (open access) and is in itself a technical revolution in ancient DNA research.

M. Gallego Llorente, E.R. Jones et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 2015. Pay per view → LINK [doi:10.1126/science.aad2879]

Supplementary materials are free (as usual) and most information seems to be there anyhow.

Abstract

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Massive and late European Neolithic-like migration into Africa, even into the Bushmen, Pygmy and Hadza hunter-gatherers?! Well, that's the thesis and the authors seem to have some reasons to believe it. However I am a bit skeptic to say the least. 

The logic behind Llorente & Jones' conclusions is that, when replacing the "non-admixed African" baseline from the usual reference populations such as the Yoruba (a major SW Nigerian population) and Mbuti (Eastern Pygmies from the Ituri jungle of NE Congo) to this newly sequenced paleo-Ethiopian genome from Mota cave, all Africans appear more similar to West Eurasians, particularly to the reference ancient farmer "Stuttgart" (LBK) or his closest modern relatives: Sardinians. 

However this is untrue for some of the populations from the same region as Mota: most Ethiopian populations actually show a slight but significant decrease in their putative Eurasian ancestry (table S5). This is very intriguing, as is the main thesis of the study, and I have the impression that at least part of that appearance of European-like admixture may be explained by ancient internal African structure rather than true immigration. This possibility is not addressed in the study, so we will have to wait for counter-studies, be them professional or amateur. It would not be the first case where a pioneer study "finds" things that become less clear as new research is done, I am thinking of course on stuff like the problematic "ANE" component of Lazaridis 2014 or the extreme "Indoeuropean admixture" conclusions of Haak & Lazaridis 2015, which are much milder and clinal in other comparable studies.

So let's keep calm and wait for more data or improved analyses.

Fig. S6. The proportion of West Eurasian ancestry in modern eastern African populations. λYoruba,Druze (using Yoruba as the non-admixed reference and Druze as the source), estimated for individuals belonging to a number of Ethiopian populations.

Affinities

Mota seems to be most akin to modern Ari people of SW Ethiopia, who speak an Omotic language. He is also rather similar to the Sandawe of Southern Tanzania, who speak a distinct click language. These similitudes underline the importance that "tribal" nations have, among other reasons, for deciphering the ancient African demographic landscape.  

Fig. S5. PCA showing the relationship between Mota and contemporary Ethiopian populations. Components were loaded on contemporary Ethiopian populations using ~480k SNPs, with Mota projected on these dimensions.

His mtDNA haplogroup is L3x2a (table S3), described by Behar 2008 in Ethiopia and the Arabian peninsula (but most likely original from The Horn) and his Y-DNA one is E1b1 (table S4), a major African haplogroup, most likely original from the same Upper Nile region, with some offshoots in West Eurasia.

He did not carry any known allele for lactase persistance (table S13) but he was homozygous for three alleles that seem to confer altitude adaptation (resistance to hypoxia, table S14). 

He had brown eyes and dark or black hair, skin color determination was inconclusive (the matter is still ill-understood) but he did not carry any European alleles associated with lighter pigmentation, so most likely he was black (or, with more chromatic descriptive precision, brown).

Neanderthal admixture testing

This seems to be the detail that most strongly supports the thesis of the study: Mota is even less akin to Neanderthals than modern Africans. From article S11:

The two African genomes, Yoruba and Mbuti, also have slightly positive D values, indicating that they are slightly more similar to Neanderthal than Mota is. This result is likely driven by the West Eurasian component found in modern Africans.

However when we look at the raw data (table S9), we can see that, while the Yoruba Neanderthal admixture estimate is slightly larger than the error margin, the Mbuti one is markedly smaller, so we can still consider the latter to be effectively zero or at the very least negligible. 

This is potentially contradictory with the alleged 6-7% West Eurasian admixture that the study claims for Mbuti (table S5), which would be almost the same as that of Yorubas (7-8%), so I think that there is something not properly pondered and that, while Yorubas may have some (very minor?) West Eurasian admixture, the case for the Mbuti is very much suspect of false positive caused by confounding factors, such as ill understood ancient African diversity. 

Most strange is the case of Khoisan populations. While two of them (Nama and Khomani) do seem to have clear Eurasian admixture, as they stick up well above the average, several others (Xun, Juhoansi or GuiGhanaKgal) are very low when using Yoruba as reference and the tiny bit can be attributed to the pull effect caused by the mere fact that Yoruba and Khoisan are very different populations, which diverged (at least in the essentials) even before the Out-of-Africa migration took place. I strongly suspect that this confounding factor is also at play when comparing with Mota and even more strongly so, because Mota quite obviously lacks the later intra-African partial homogenization tendency caused by migrations such as the Nilotic or Bantu ones. 

Fig. S7. Maps showing the proportion of West Eurasian ancestry in African populations. The proportion of West Eurasian ancestry calculated using either (A), Druze. λMota,Druze, or (B), LBK, λMota,LBK, as a source, and Mota as the non-admixed African reference in both cases.

Early European farmers or...?

Sure, among the tested populations, Sardinians are the best apparent matches for the source of the alleged Eurasian admixture in Africa (tables S6 and S7). But next in line are Belorussians and Lithuanians, what is a bit perplexing, because in the European analyses these are two completely opposite poles along the PC1. Basques and Russians however are surprisingly bad matches, with French, Italian, Spaniards, etc. being in between. 

Among ancient populations, Stuttgart (LBK) appears as a good match when using a Yoruba reference but not so good when using a Mbuti one. Inversely, Lochsbour (Epi-Magdalenian) looks a very bad match when using Yoruba but a bit better when using Mbuti. As Mbuti seem still to be a more clear outgroup than Yoruba, I think that table S7 holds preference over S6. 

Hence I'd rather discard that the source of the apparent Eurasian admixture is LBK-like. However Sardinians (or a similar ancient population) are a better candidate. But what about Belorussians and Lithuanians, whose scores are also very high? Perplexing.

So basically I have all kind of doubts and I look forward to further research that may clarify them.

Vasco-Nubian?

This is something I've been chewing on for more than a year now and yet never got myself to blog about (although I have mentioned in private or in comments here and there). Impelled by the minor but quite apparent NE African influence, genetic and cultural, on the Neolithic peoples of the Levant, whose offshoots eventually landed in Greece triggering the European Neolithic, I decided in the Spring of 2014 to explore, via mass-lexical comparison, if Basque language (and by extension the wider Vasconic family, which I believe now to be that of mainline European Neolithic) might have any relation with Nubian languages. I did not expect to find anything but noise but to my surprise the number of apparent cognates is quite significant. 

My primary analysis was this one but now I have combined it with a comparison with Proto-Indoeuropean (PIE), which is also very probably related to the roots of Vasconic: LINK (open office spreadsheet). 

The synthesis is as follows:

Of course the "cognates" are only apparent cognates at this stage of the research and the evaluation is necessarily subjective. But judge yourselves. 

If we discard the "weak" apparent cognates, the vocabulary correlation between Basque and Nubian and between Basque and PIE is pretty similar. But, in my understanding, both are well above the noise threshold, an example of which could be the PIE-Nubian apparent cognates, which are many many less. 

I must say anyhow that the oblique apparent cognates, that is when one word sounds much not like its strict synonym but a related one (for example words meaning hot and fire), look all very solid and most intriguing. 

Also, when attributing probabilities to origins of Basque words, Nubian appears to be at the origin of almost double the words (26%) that can be attributed to PIE (15%). Of course, for lack of data or because they actually have other origins, the unknown origins apply to the majority of words (56%), double than the Nubian origin ones.

However Nubian here is constituted of three different languages (Dilling, Nobiin and Midob), while PIE is just a single theoretical construct. This last must be done this way because many modern and historical IE languages, notably in Europe, have other Vasconic substrate influences, which must be studied separately from general PIE-Vasconic shared vocabulary. This kind of late Vasconic influence is very much unlikely in the case of Nubian instead. In any case I don't know of any a proto-Nubian Swadesh list readily available. 

Finally I must mention that because the PDF format is horrible for copy-pasting, I chose to re-transcribe the Nubian words according to my best approximation using a normal keyboard (not always the same characters that the original list uses).

Strongest Basque-Nubian apparent simple cognates

• Basque - Nubian languages (English)
  
• azal - àzì, àzzì-di (bark)
• haragi - árízh (meat)
• odol - ógór, èggér (blood)
• buru - úr (head)
• oin - ó:y (foot)
• esku - ish-i, ès-sì (hand)
• hil* - di-ìl (to die)
• euri - are, ara, áwwí, áré, árí, áró (rain)
• harri - kugor, kakar (stone) [notice also the pre-IE root *kharr- speculated to be at the origin of Karst, etc.] 
• lur - gùr (soil, ground)
• haize - irsh-i, éss-í (wind)

There are some others that are shared with Indo-European and with similar subjective "weight", not listing them here to keep things clear. There are also other apparent cognates that are arguably less clear like bat - be (one) that I'm also skipping here but you can find in the spreadsheet.

*Hil (meaning both to die and to kill in Basque, which can't be confused because they conjugate differently) seems ancestral to English ill and kill (this one via a Germanic precursor).

The intriguing oblique cognates

Notice that these words do not mean the same, yet their meanings seem strikingly related.

• Nubian (English) - Basque (English)
• hor, koy, kà:r (tree) - harri (stone) [notice that zuhaitz (tree) can be interpreted etymologically as zur-haitz = wood-rock, so the relation is not that weird]
• ok-i, og (breast) - ogi (bread)
• a-l (heart) - ahal (can (verb), potential, power)
• azh, àz-ír, àzza (to bite) - (h)ortz (tooth), aitz (rock, peak) [some argue that originally "to cut", present in many cutting tool names: aizkor = axe, aitzur = hoe, aizto = knife, etc.*]
• shu, zhúù (to walk) - joan (to go) [often pronounced jun or shun]
• é:zhi (water) - heze (wet) [also archaic particle *iz-, meaning "water" by all accounts: itxaso = sea, izurde = dolphin, izotz = ice, and common in Vasconic river toponymy]
• zhuge (to burn) - su (fire) 
• zhùg, sù, sú:w (hot) - su (fire)
• úr-i, úrúm (black) - urdin (blue) [archaic also green, grey]

*This one is an obvious and very prevalent Vasconic substrate infiltrator in Western IE languages: axe, adze, azada (hoe in Spanish), etc.

How can this be possible?

It is of course a mere working hypothesis and ultimately you judge but I find it hard to disdain. However there is no apparent connection, notably no significant genetic connection, between Basques and Nubians. So how can we explain this?

I have it reasonably clear myself, so I made a map to explain it:

Basque is after all just the last survivor of a once much larger family (Vasconic), a family that most likely corresponds to the languages spoken by the early European farmers (mainline Neolithic of Aegean roots). As that expansion was largely done in about a mere thousand years, I estimate that when both branches met near the Rhine, the two peoples could still understand each other, even if with some difficulty. Only the Southern/Western branch(-es) survived long enough to leave historical evidence, so it is hard to guess how the Northern branch evolved anyhow.

The Nubian linguistic connection is anyhow not the only thing that requires the Levant or Palestinian Neolithic step, also Y-DNA E1b-M78 (mostly V13 in Europe, attested in some early farmers and still very important among Greeks and Albanians particularly) and probably the so-called "Basal Eurasian" component that Lazaridis detected among early European farmers and that could well be the signature of African genetics from the Nile.

Linguistically, also the very notorious presence of Semitic (an Afroasiatic branch) in West Asia is surely another legacy of the same African influences in the Mesolithic Levant. Before this research, I thought it was the only one but now I strongly suspect that at some point Nubian (Nilo-Saharan) languages were also present in the region. Maybe one (Nubian evolving towards Vasconic) corresponded to Natufian proper and the other (proto-Semitic) to Harifian, the semi-desert pastoralist facies of the same wider culture. Can't say for sure.

The chain was once long but now only some of the most distant links remain unbroken. It is difficult to imagine that they were ever connected at all...

To do...

A lot remains to be done, of course:

• These mass lexical comparisons only apply to a few families in the region and the rest should also be tested for. My energies are limited and so are my qualifications as "linguist", so I encourage others, hopefully more energetic and knowledgeable, to expand.
• Grammatical features cannot be analyzed by this methodology. Again my means are limited. 
• Anthropological research would be an interesting complement. So far the only shared cultural trait I could spot would be the use of bells attached to ankles for dancing but there could be others. 
• ...

Sudan and South Sudan autosomal genetics

Quantity over quality series.

Begoña Dobon et al., The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Nature - Scientific Reports 2015. Open access → LINK [doi:10.1038/srep09996]

Abstract

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

Figure 3: ADMIXTURE results for the 14 populations.

Pondering the Middle Paleolithic of South Africa

Quantity over quality series.

Sylvain Soriano et al. The Still Bay and Howiesons Poort at Sibudu and Blombos: Understanding Middle Stone Age Technologies. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0131127]

Abstract

The classification of archaeological assemblages in the Middle Stone Age of South Africa in terms of diversity and temporal continuity has significant implications with respect to recent cultural evolutionary models which propose either gradual accumulation or discontinuous, episodic processes for the emergence and diffusion of cultural traits. We present the results of a systematic technological and typological analysis of the Still Bay assemblages from Sibudu and Blombos. A similar approach is used in the analysis of the Howiesons Poort (HP) assemblages from Sibudu seen in comparison with broadly contemporaneous assemblages from Rose Cottage and Klasies River Cave 1A. Using our own and published data from other sites we report on the diversity between stone artifact assemblages and discuss to what extent they can be grouped into homogeneous lithic sets. The gradual evolution of debitage techniques within the Howiesons Poort sequence with a progressive abandonment of the HP technological style argues against the saltational model for its disappearance while the technological differences between the Sibudu and Blombos Still Bay artifacts considerably weaken an interpretation of similarities between the assemblages and their grouping into the same cultural unit. Limited sampling of a fragmented record may explain why simple models of cultural evolution do not seem to apply to a complex reality.

Ancient inter-continental admixture in the Horn of Africa

A new and quite interesting study finds strong support for Upper Paleolithic (~ LSA) Eurasian inflows into the Horn of Africa and confirms that most of the populations of that region are in essence an ancient mix of West Eurasian and African ancestries.

Jason A. Hodgson et al., Early Back-to-Africa Migration into the Horn of Africa. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004393]

Abstract

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

The study makes three different formal admixture tests (f3, Adler and D-stat), as well as a Rolloff simulation, in order to confirm these findings. This part is quite technical and therefore I am not going to discuss it further. Feel free to explore the extensive supplemental materials. 

I will instead stop on what I know better, which is ADMIXTURE and FST distances, which are more visually amenable and ultimately tell the same story. 

Figure 2. Population structure of Horn of Africa populations in a broad context.
ADMIXTURE analysis reveals both well-established and novel ancestry components in HOA populations. We used a cross-validation procedure to estimate the best value for the parameter for the number of assigned ancestral populations (K) and found that values from 9 to 14 had the lowest and similar cross-validation errors (Figure S2). (A) The differences in inferred ancestry from K = 9–14 are most pronounced in the HOA for K = 10–12, where two ancestry components that are largely restricted to the HOA appear (the dark purple and dark green components). (B) Surface interpolation of the geographic distribution of eight inferred ancestry components that are relatively unchanging and common to the ADMIXTURE results from K = 10–12. (C) Individual ancestry estimation for HOA populations (with language groups indicated) and surface plots of the changing distributions of the Nilo-Saharan (light blue) and Arabian (brown) ancestry components for K = 10–12. At K = 11, a new HOA-specific ancestry component that we call Ethiopic appears (dark purple) and at K = 12 a second new ancestry component that we call Ethio-Somali (dark green) appears with its highest frequencies in the HOA.

Above we have the original presentation of ADMIXTURE results for K=10-12. It must be said that the cross validation score is lowest (optimal) for K=12 but that this value is only slightly smaller than those for K=9-14, which make a plateau (fig. S2). 

Therefore their use of K=10 and K=11 is justified, particularly because it is also interesting to turn off the old amalgamation reflected in the Ethiopic (Ari, Woloytta) and Ethio-Somali (Cushitic, Ethiopian Semitic) components, and that is done by using K=10 instead of the optimal K=12.

This issue is best perceived in the FST distances table (within text S1), which I include here with some convenient annotations:

The red-orange colored frames (as well as the red notes on the components) in the table above were added by me to better illustrate the meaning of these FST values:

• The red frames capture two groups of components with very low differences (<50): West Asia-Europe and West-East Africa.
• The dark orange frames indicate other two groups with quite low distances (<70): South-Central Asian and the West Eurasian core.
• The lighter orange frames indicate large clusters of middling distances (<125) of continental nature: Eurasian and African. 
• Intercontinental FST scores are systematically larger, for example European-West African is 176, while European East African ("Nilo-Saharan") is 172, only slightly smaller. 

K=12

It is quite apparent that there are three components that overflow these continental boundaries:

• The so-called Mahgrebi (North African) has some extra affinity with the Ethiopic (Omotic) component, and vice versa. These two components fall otherwise within my approximative continental boxes but they still show lower scores for all the other components of the other "box". This is consistent with their nature as Afro-Eurasian admixed components, each with its own proportions.
• The Ethio-Somali (Cushitic?) component is actually more intermediate than the previous ones: although its strongest affiliation is towards Eurasia and particularly with the North African and Arabian components, it also shows strong affinity with the core African components (East and West African, i.e. Nilo-Saharan and Niger-Congo). This is consistent with the other evidence in this study that reveals it as an ancient Afro-Asian mix.

I must mention here that some of the labels used by the authors are not at all the ones I would have chosen and this is particularly true re. the Nilo-Saharan (light blue) component, which peaks among the Sandawe (Aboriginal East Africans from Southern Tanzania, speaking a click language), the Anuak (Nilo-Saharan Ethiopians) and the Gumuz (other Ethiopians of quite dubious Nilo-Saharan linguistic affiliation). Hence I prefer to call it East African or East African 1. 

The authors conclude with the following remarks (emphasis mine):

We find that most of the non-African ancestry in the HOA can be assigned to a distinct non-African origin Ethio-Somali ancestry component, which is found at its highest frequencies in Cushitic and Semitic speaking HOA populations (Table 2, Figure 2). In addition to verifying that most HOA populations have substantial non-African ancestry, which is not controversial [11]–[14], [16], we argue that the non-African origin Ethio-Somali ancestry in the HOA is most likely pre-agricultural. In combination with the genomic evidence for a pre-agricultural back-to-Africa migration into North Africa [43], [61] and inference of pre-agricultural migrations in and out-of-Africa from mitochondrial and Y chromosome data [13], [32]–[37], [47], [99]–[102], these results contribute to a growing body of evidence for migrations of human populations in and out of Africa throughout prehistory [5]–[7] and suggests that human hunter-gatherer populations were much more dynamic than commonly assumed.

We close with a provisional linguistic hypothesis. The proto-Afro-Asiatic speakers are thought to have lived either in the area of the Levant or in east/northeast Africa [8], [107], [108]. Proponents of the Levantine origin of Afro-Asiatic tie the dispersal and differentiation of this language group to the development of agriculture in the Levant beginning around 12 ka [8], [109], [110]. In the African-origins model, the original diversification of the Afro-Asiatic languages is pre-agricultural, with the source population living in the central Nile valley, the African Red Sea hills, or the HOA [108], [111]. In this model, later diversification and expansion within particular Afro-Asiatic language groups may be associated with agricultural expansions and transmissions, but the deep diversification of the group is pre-agricultural. We hypothesize that a population with substantial Ethio-Somali ancestry could be the proto-Afro-Asiatic speakers. A later migration of a subset of this population back to the Levant before 6 ka would account for a Levantine origin of the Semitic languages [18] and the relatively even distribution of around 7% Ethio-Somali ancestry in all sampled Levantine populations (Table S6). Later migration from Arabia into the HOA beginning around 3 ka would explain the origin of the Ethiosemitic languages at this time [18], the presence of greater Arabian and Eurasian ancestry in the Semitic speaking populations of the HOA (Table 2, S6), and ROLLOFF/ALDER estimates of admixture in HOA populations between 1–5 ka (Table 1).

K=12 detail for a fraction of the Horn of Africa and distribution of the four main components

A genetic legacy of North Africa: mtDNA U6 under the microscope

An excellent new study on mtDNA haplogroup U6 has been published this week:

Bernard Sechel et al., The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents. BMC Evolutionary Biology 2014. Open access → LINK [doi:10.1186/1471-2148-14-109]

Abstract (provisional)

Background

Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.

Results

Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.

Conclusions

The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

Figure 1 Surface maps, based on HVI frequencies (in o/oo), for total U6 (U6), total U6a
(Tot U6a), U6a without 16189 (U6a), U6a with 16189 (U6a-189), U6b'd, U6c, U6b and U6d.

U6 can be considered a somewhat strange haplogroup. While it is derived from U (and hence from R and N), which has an Asian origin, it seems to have expanded from NW Africa, more specifically from the Northern mountainous areas of the Moroccan state, a country known as Rif or in the native Tamazigh language Arif (of which Rif is an Arabized version), not the usual place one tends to imagine as the origin of any human expansion wave. 

Actually there is at least one important cultural expansion from that area: the Oranian or Iberomaurusian culture of the Mid-to-Late Upper Paleolithic. To some extent at least the expansion of this lineage is probably associated to this ancient culture. 

Whatever the case, U6 is not a common haplogroup: its highest peak in frequency is in the Canary Islands (16%), followed by North-West Africa (5-9%). Then come Portugal and its insular colonies, as well as Cape Verde and Ethiopia (~3%) and then there is some scatter in Spain, West Africa, NE Africa and peninsular Arabia (~1%), as well as in some other parts of Europe, Africa and West Asia (<1%). 

On the other hand it is one of the four basal branches of the major West Eurasian haplogroup U (U5 and U2'3'4'7'8'9 are more common, while U1 is even rarer and less studied), so understanding U6 seems important to better understand its parent lineage. 

Therefore this new study with its great wealth of detail and care is much welcome.

Chronological estimates and expansion patterns of U6

It may surprise you that I am even in tentative agreement with the chronological estimates for U6 and its subclades, listed in tables 2 and 3. But it is for a good reason: they make sense (assuming a reasonable CI). And the fact that they seem to make sense is probably because the authors took great care to calibrate the ages for this lineage, using as main (but not only) reference a Canadian derived lineage that seems to be a colonial founder effect. 

Anyhow all these dates should be considered as center-points of a variably wider range of possibilities, the so-called confidence interval (CI) or error margin (em). If we do that, as we should, we get the "power" to stretch the figures forth and back as need be to some extent without losing consistency, and that alone should be enough to get the estimates fit better with the material evidence (archaeology mostly). 

The authors actually mention some of those CIs in a lengthy section dedicated to explore the possible patterns of U6 spread in Africa and elsewhere.

Interestingly they suggest that the first radiation of U6 took place from NW Africa in largely eastwards direction, belonging almost necessarily to the Iberomaurusian (Oranian) culture:

This first African expansion of U6a in the Maghreb was suggested in a previous analysis [6]. This radiation inside Africa occurred in Morocco around 26 kya (Table 2) and, ruling out the earlier Aterian, we suggested the Iberomaurusian as the most probable archaeological and anthropological correlate of this spread in the Maghreb [6]. Others have pointed to the Dabban industry in North Africa and its supposed source in the Levant, the Ahmarian, as the archaeological footprints of U6 coming back to Africa [7,9]. However, we disagree for several reasons: firstly, they most probably evolved in situ from previous cultures, not being intrusive in their respective areas [42-44]; second, their chronologies are out of phase with U6 and third, Dabban is a local industry in Cyrenaica not showing the whole coastal expansion of U6. In addition, recent archaeological evidence, based on securely dated layers, also points to the Maghreb as the place with the oldest implantation of the Iberomaurusian culture [45], which is coincidental with the U6 radiation from this region proposed in this and previous studies [6].

Some millennia later, U62 appears to expand in Ethiopia, while, as mentioned, U6a1 does the same in Europe (mostly Western Iberia) and other sister lineages do the same in NW Africa itself.

A second wave of radiation corresponds to the early Holocene:

Basic clusters like U6b, U6c and U6d also emerged within a window between 13 to 10 kya (Table 2). U6b lineages spread from the Maghreb, through the Sahel, to West Africa and the Canary Islands (U6b1a), and are also present from the Sudan to Arabia, but not detected in Ethiopia. In contrast, U6c and U6d are more localized in the Maghreb. Further spreads of secondary U6a branches are also apparent, going southwards to Sahel countries and  reaching West Africa (U6a5a). Autochthonous clusters in sub-Saharan Africa first appeared at around 7 kya (U6a5b), coinciding with a period of gradual desiccation that would have obliged pastoralists to abandon many desert areas [52]. Consequently, no more U6 lineages in the Sahel are detected, while later expansions continued in West Africa (U6a3f, U6a3c, and U6b3) and the Maghreb with an additional spread to the Mediterranean shores of Europe involving U6b2, U6a3e, U6a1b and U6a3b1.

For easier understanding of the U6 phylogeny and its sometimes hard to interpret migration patterns, I made up the following graph, based on the supplemental material of this study:

U6 phylogeny, color coded by regions:

• North Africa
• Europe
• Tropical Africa
• West Asia
• intermediate colors: equal weight between two regions, black: undecided
• italic type: unnamed lineages

I must say that, I have some doubts about the exact origins of several subhaplogroups, notably:

• U6a is so diverse in some branches that it is difficult to identify it as unmistakably of NW African origin. NW Africa still gets the greatest weight (3/7) but not a clear majority.
• In U6b Tropical African lineages weight 4.5/10, while NW African ones weight only 3/10. It is a good candidate for expansion from the "Wet Sahara" indeed.
• In U6c1 European and NW African lineages weight exactly the same, although I guess that it may be reasonable to imagine Andalusian U6c1c as derived from North Africa.

However overall U6, as well as its derived lineages U6b'd and U6c clearly originated in NW Africa, so I understand that, when unclear, NW Africa gets the benefit of doubt for the derived origins.