Villabruna cluster in Late Epigravettian Sicily supports South Italian corridor for R1b-V88

epipalaeolithic-whg-expansion

New preprint Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily), by Catalano et al. bioRxiv (2019).

Interesting excerpts (emphasis mine):

Grotta d’Oriente is a small coastal cave located on the island of Favignana, the largest (~20 km2) of a group of small islands forming the Egadi Archipelago, ~5 km from the NW coast of Sicily.

The Oriente C funeral pit opens in the lower portion of layer 7, specifically sublayer 7D. Two radiocarbon dates on charcoal from the sublayers 7D (12149±65 uncal. BP) and 7E, 12132±80 uncal. BP are consistent with the associated Late Epigravettian lithic assemblages (Lo Vetro and Martini, 2012; Martini et al., 2012b) and refer the burial to a period between about 14200-13800 cal. BP, when Favignana was connected to the main island (Agnesi et al., 1993; Antonioli et al., 2002; Mannino et al. 2014).

sicily-grotta-oriente
A-B) Geographic location of Grotta d’Oriente.

The anatomical features of Oriente C are close to those of Late Upper Palaeolithic populations of the Mediterranean and show strong affinity with other Palaeolithic individuals of Sicily. As suggested by Henke (1989) and Fabbri (1995) the hunter-gatherer populations were morphologically rather uniform.

Genetic analysis

We confirmed the originally reported mitochondrial haplogroup assignment of U2’3’4’7’8’9. This haplogroup is present in both pre- and post-LGM populations, but is rare by the Mesolithic, when U5 dominates (Posth et al.2016).

Lipson et al. (2018) (their supplementary Figure S5.1) and Villalba-Mouco et al. (2019) (their Figure 2A) showed that European Late Palaeolithic and Mesolithic hunter-gatherers fall along two main axes of genetic variation. Multidimensional scaling (MDS) of f3-statistics shows that these axes form a “V” shape (Fig. 3). (…)

Focusing further on Oriente C, we find that it shares most drift with individuals from Northern Italy, Switzerland and Luxembourg, and less with individuals from Iberia, Scandinavia, and East and Southeast Europe (Fig. 4A-B). Shared drift decreases significantly with distance (Fig. 4C) and with time (Fig. 4D) although in a linear model of drift with distance and time as a covariate, only distance (p=1.3×10-6) and not time (p=0.11) is significant. Consistent with the overall E-W cline in hunter-gatherer ancestry, genetic distance to Oriente C increases more rapidly with longitude than latitude, although this may also be affected by geographic features. For example, Oriente C shares significantly more drift with the 8,000 year-old 1,400 km distant individual from Loschbour in Luxembourg (Lazaridis et al.,2014), than with the 9,000 year old individual from Vela Spila in Croatia (Mathieson et al.,2018) only 700 km away as shown by the D-statistic (Patterson et al.,2012) D (Mbuti, Oriente C, Vela Spila, Villabruna); Z=3.42. Oriente C’s heterozygosity was slightly lower than Villabruna (14% lower at 1240k transversion sites), but this difference is not significant (bootstrap P=0.12).

oriente-c-villabruna-f3-statistics
Multidimensional scaling of outgroup f3-statistics for Late 531 Upper Palaeolithic and Mesolithic hunter-gatherers.

Discussion and Conclusion

The robust record of radiocarbon dates proves that they reached Sicily not before 15-14 ka cal. BP, several millennia after the LGM peak. In our opinion, in fact, the hypothesis about an early colonization of Sicily by Aurignacians (Laplace, 1964; Chilardi et al., 1996) must be rejected, on the basis of a recent reinterpretation of the techno-typological features of the lithic industries from Riparo di Fontana Nuova (Martini et al., 2007; Lo Vetro and Martini, 2012; on this topic see also Di Maida et al., 2019).

These analyses have implications for understanding the origin and diffusion of the hunter-gatherers that inhabited Europe during the Late Upper Palaeolithic and Mesolithic. Our findings indicate that Oriente C shows a strong genetic relationship with Western European Late Upper Palaeolithic and Mesolithic hunter-gatherers, suggesting that the “Western hunter-gatherers” was a homogeneous population widely distributed in the Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the LGM.

shared-drift-whg-villabruna-oriente-c
The same statistic as in A plotted with geographic position

The South Italian corridor

Once again, a hypothesis based on phylogeography – apart from scarce archaeological and palaeolinguistic data (“Semitic”-like topo-hydronymy and substrates in Europe) – seems to be confirmed step by step. Since the finding of the Villabruna individual of hg. R1b-L754 (likely R1b-V88, like south-eastern European lineages expanded with WHG ancestry), it was quite likely to find out that southern Europe was the origin of the expansion of R1b-V88 into Africa.

The most likely explanation for the presence of “archaic” R1b-V88 subclades among modern Sardinians was, therefore, that they represented a remnant from a Late Upper Palaeolithic/Early Mesolithic population that had not been replaced in subsequent migrations, and thus that the migration of these lineages into Northern Africa and the Green Sahara happened during a period when Italy was connected by a shallower Mediterranean (and more land connections) to Northern Africa.

late-epigravettian
Likely Late Epigravettian/Mesolithic expansion of R1b-V88 into Northern Africa. See full map.

Nevertheless, the arguments for a quite recent expansion of R1b-V88 through the Mediterranean and into Africa keep being repeated, probably based on ancestry from the few ancient (and many modern) populations that have been investigated to date, a simplistic approach prone to important errors that overarch whole migration models.

For example, in the recent paper by Marcus et al. (2019) the presence of these lineages among ancient Sardinians (from the late 4th millennium BC on) is interpreted as an expansion of R1b-V88 with the Cardial Neolithic based on their ancestry, disregarding the millennia-long gap between these samples and the presence of this haplogroup in Palaeolithic/Mesolithic Northern Iberia and Northern Italy, and the comparatively much earlier splits in the phylogenetic tree and dispersal among African populations.

Afroasiatic and Nostratic

I was asked recently if I really believed that we could reconstruct Proto-Nostratic and connect it with any ancestral population. My answer is simple: until the Chalcolithic – when the whole picture of Indo-Europeans, Uralians, Egyptians or Semites becomes quite clear – we have just very few (linguistic, archaeological, genetic) dots which we would like to connect, and we do so the best we can. The earlier the population and proto-language, the more difficult this task becomes.

NOTE. 1) I tentatively connected hg. R with Nostratic in a previous text – when it appeared that R1a expanded from around Lake Baikal, hence Eurasiatic; R1b from the south with AME-WHG ancestry, hence Afroasiatic; and R2 with Dravidian.

2) After that, I though it was more likely to be connected to AME ancestry and the Middle East, because of the apparent expansion of WHG from south-eastern Europe, and the potential association of Afroasiatic and (Elamo-?)Dravidian to Middle Eastern populations.

3) However, after finding more and more R1b samples expanding through northern Eurasia, spreading through the (then wider) steppe regions; and R1a essentially surviving among other groups in eastern Europe for thousands of years without being associated to significant migrations (like, say, hg. C after the Palaeolithic), it didn’t seem like this division was accurate, hence my most recent version.

But, in essence, it’s all about connecting the dots, and we have very few of them…

eurasiatic-phylum-ultraconserved-words
Phylogenetic tree from Pagel et al. (2013), partially in agreement with Kortlandt’s view on Eurasiatic. “Consensus phylogenetic tree of Eurasiatic superfamily (A) superimposed on Eurasia and (B) rooted tree with estimated dates of origin of families and of superfamily. (A) Unrooted consensus tree with branch lengths (solid lines) shown to scale and illustrating the correspondence between the tree and the contemporary north-south and east-west geographical positions of these language families. Abbreviations: P (proto) followed by initials of language family: PD, proto-Dravidian; PK, proto-Kartvelian; PU, proto-Uralic; PIE, proto–Indo-European; PA, proto-Altaic; PCK, proto–Chukchi-Kamchatkan; PIY, proto–Inuit-Yupik. The dotted line to PIY extends the inferred branch length into the area in which Inuit-Yupik languages are currently spoken: it is not a measure of divergence. The cross-hatched line to PK indicates that branch has been shortened (compare with B). The branch to proto-Dravidian ends in an area that Dravidian populations are thought to have occupied before the arrival of Indo-Europeans (see main text). (B) Consensus tree rooted using proto-Dravidian as the outgroup. The age at the root is 14.45 ± 1.75 kya (95% CI = 11.72–18.38 kya) or a slightly older 15.61 ± 2.29 kya (95% CI = 11.72–20.40 kya) if the tree is rooted with proto-Kartvelian. The age assumes midpoint rooting along the branch leading to proto-Dravidian (rooting closer to PD would produce an older root, and vice versa), and takes into account uncertainty around proto–Indo-European date of 8,700 ± 544 (SD) y following ref. 35 and the PCK date of 692 ± 67 (SD) y ago.”

In linguistics, I trust traditional linguists who tend to trust other more experimental linguists (like Hyllested or Kortlandt) who consider that – in their experience – an Indo-Uralic and a Eurasiatic phylum can be reconstructed. Similarly, linguists like Kortlandt are apparently (partially) supportive of attempts like that of Allan Bomhard with Nostratic – although almost everyone is critic of the Muscovite school‘s attachment to the Brugmannian reconstruction, stuck in pre-laryngeal Proto-Indo-Anatolian and similar archaisms.

I mostly use Nostratic as a way to give a simplistic ethnolinguistic label to the genetically related prehistoric peoples whose languages we will probably never know. I think it’s becoming clear that the strongest connection right now with the expansion of potential Eurasiatic dialects is offered by ANE-related populations (hence Y-chromosome bottlenecks under hg. R, Q, probably also N), however complicated the reconstruction of that hypothetic community (and its dialectalization) may be.

Therefore, the multiple expansions of lineages more or less closely associated to ANE-related peoples – like R1b-V88 in the case of Afrasian, or R2 in the case of Dravidians – are the easiest to link to the traditionally described Nostratic dialects and their highly hypothetic relationship.

green-sahara-neolithic
Reconstruction of North African vegetation during past green Sahara periods. Estimated and reconstructed MAP for the Holocene GSP (6–10 kyr BP) projected onto a cross-section along the eastern Sahara (left panel) and map view of reconstructed MAP, vegetation and physiographic elements [7,8,11,45] (right panel). Image from Larrasoaña et al. (2013).

What should be clear to anyone is that the attempt of many modern Afroasiatic speakers to connect their language to their own (or their own community’s main) haplogroups, frequently E and/or J, is flawed for many reasons; it was simplistic in the 2000s, but it is absurd after the advent of ancient DNA investigation and more recent investigation on SNP mutation rates. R1b-V88 should have been on the table of discussions about the expansion of Afroasiatic communities through the Green Sahara long ago, whether one supports a Nostratic phylum or not.

The fact that the role of R1b bottlenecks and expansions in the spread of Afroasiatic is usually not even discussed despite their likely connection with the most recent population expansions through the Green Sahara fitting a reasonable time frame for Proto-Afroasiatic reconstruction, a reasonable geographical homeland, and a compatible dialectal division – unlike many other proposed (E or J) subclades – reveals (once again) a lot about the reasons behind amateur interest in genetics.

Just like seeing the fixation in (and immobility of) recent writings about the role of I1, I2, or (more recently) R1a in the Proto-Indo-European expansion, R1b with Vasconic, or N1c with Proto-Uralic.

NOTE. That evident interest notwithstanding, it is undeniable that we have a much better understanding of the expansions of R1b subclades than other haplogroups, probably due in great part to the easier recovery of ancient DNA from Eurasia (and Europe in particular), for many different – sociopolitical, geographical, technological – reasons. It is quite possible that a more thorough temporal transect of ancient DNA from the Middle East and Africa might radically change our understanding of population movements, especially those related to the Afroasiatic expansion. I am referring in this post to interpretations based on the data we currently have, despite that potential R1b-based bias.

Related

Fulani from Cameroon show ancestry similar to Afroasiatic speakers from East Africa

sahel-region-fulani

Open access African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, by Fan et al. Genome Biology (2019) 20:82.

Interesting excerpts (emphasis mine):

Introduction

To extend our knowledge of patterns of genomic diversity in Africa, we generated high coverage (> 30×) genome sequencing data from 43 geographically diverse Africans originating from 22 ethnic groups, representing a broad array of ethnic, linguistic, cultural, and geographic diversity (Additional file 1: Table S1). These include a number of populations of anthropological interest that have never previously been characterized for high-coverage genome sequence diversity such as Afroasiatic-speaking El Molo fishermen and Nilo-Saharan-speaking Ogiek hunter-gatherers (Kenya); Afroasiatic-speaking Aari, Agaw, and Amhara agro-pastoralists (Ethiopia); Niger-Congo-speaking Fulani pastoralists (Cameroon); Nilo-Saharan-speaking Kaba (Central African Republic, CAR); and Laka and Bulala (Chad) among others. We integrated this data with 49 whole genome sequences generated as part of the Simons Genome Diversity Project (SGDP) [14] (…)

afroasiatic-samples
Locations of samples included in this study. Each dot is an individual and the color indicates the language classification

Results and discussion

We found that the CRHG populations from central Africa, including the Mbuti from the Demographic Republic of Congo (DRC), Biaka from the CAR, and Baka, Bakola, and Bedzan from Cameroon, also form a basal lineage in the phylogeny. The other two hunter-gatherer populations, Hadza and Sandawe, living in Tanzania, group with populations from eastern Africa (Fig. 2). The two Nilo-Saharan-speaking populations, the Mursi from southern Ethiopia and the Dinka from southern Sudan, group into a single cluster, which is consistent with archeological data indicating that the migration of Nilo-Saharan populations to eastern Africa originated from a source population in southern Sudan in the last 3000 years [4, 23, 24, 25].

phylogenetic-relationship-africans
Phylogenetic relationship of 44 African and 32 west Eurasian populations determined by a neighbor joining analysis assuming no admixture. Here, the dots of each node represent bootstrap values and the color of each branch indicates language usage of each population. Human_AA human ancestral alleles

The Fulani people are traditionally nomadic pastoralists living across a broad geographic range spanning Sudan, the Sahel, Central, and Western Africa. The Fulani in our study, sampled from Cameroon, clustered with the Afroasiatic-speaking populations in East Africa in the phylogenetic analysis, indicating a potential language replacement from Afroasiatic to Niger-Congo in this population (Fig. 2). Prior studies suggest a complex history of the Fulani; analyses of Y chromosome variation suggest a shared ancestry with Nilo-Saharan and Afroasiatic populations [24], whereas mtDNA indicates a West African origin [26]. An analysis based on autosomal markers found traces of West Eurasian-related ancestry in this population [4], which suggests a North African or East African origin (as North and East Africans also have such ancestry likely related to expansions of farmers and herders from the Near East) and is consistent with the presence at moderate frequency of the −13,910T variant associated with lactose tolerance in European populations [15, 16].

Phylogenetic reconstruction of the relationship of African individuals under a model allowing for migration using TREEMIX [27] largely recapitulates the NJ phylogeny with the exception of the Fulani who cluster near neighboring Niger-Congo-speaking populations with whom they have admixed (Additional file 2: Figure S1). Interestingly, TREEMIX analysis indicates evidence for gene flow between the Hadza and the ancestors of the Ju|‘hoan and Khomani San, supporting genetic, linguistic, and archeological evidence that Khoesan-speaking populations may have originated in Eastern Africa [28, 29, 30].

afroasiatic-niger-congo-admixture
ADMIXTURE analysis of 92 African and 62 West Eurasian individuals. Each bar is an individual and colors represent the proportion of inferred ancestry from K ancestral populations. The bottom bar shows the language classification of each individual. With the increasing of K, the populations are largely grouped by their current language usage

About the Fulani, this is what the referenced study of Y‐chromosome variation among 15 Sudanese populations by Hassan et al. (2008), had to say:

  • Haplogroups A-M13 and B-M60 are present at high frequencies in Nilo-Saharan groups except Nubians, with low frequencies in Afro-Asiatic groups although notable frequencies of B-M60 were found in Hausa (15.6%) and Copts (15.2%).
  • Haplogroup E (four different haplotypes) accounts for the majority (34.4%) of the chromosome and is widespread in the Sudan. E-M78 represents 74.5% of haplogroup E, the highest frequencies observed in Masalit and Fur populations. E-M33 (5.2%) is largely confined to Fulani and Hausa, whereas E-M2 is restricted to Hausa. E-M215 was found to occur more in Nilo-Saharan rather than Afro-Asiatic speaking groups.
  • In contrast, haplogroups F-M89, I-M170, J-12f2, and JM172 were found to be more frequent in the Afro-Asiatic speaking groups. J-12f2 and J-M172 represents 94% and 6%, respectively, of haplogroup J with high frequencies among Nubians, Copts, and Arabs.
  • Haplogroup K-M9 is restricted to Hausa and Gaalien with low frequencies and is absent in Nilo-Saharan and Niger-Congo.
  • Haplogroup R-M173 appears to be the most frequent haplogroup in Fulani, and haplogroup R-P25 has the highest frequency in Hausa and Copts and is present at lower frequencies in north, east, and western Sudan.
  • Haplogroups A-M51, A-M23, D-M174, H-M52, L-M11, OM175, and P-M74 were completely absent from the populations analyzed.
fulfulde-fulani-language
Image modified from “Fulfulde Language Family Report” Author: Annette Harrison; Cartographer: Irene Tucker; SIL International 2003.

This is what David Reich will talk about in the seminar Insights into language expansions from ancient DNA:

In this talk, I will describe how the new science of genome-wide ancient DNA can provide insights into past spreads of language and culture. I will discuss five examples: (1) the spread of Indo-European languages to Europe and South Asia in association with Steppe pastoralist ancestry, (2) the spread of Austronesian languages to the open Pacific islands in association with Taiwanese aboriginal-associated ancestry, (3) the spread of Austroasiatic languages through southeast Asia in association with the characteristic ancestry type that is also represented in western Indonesia suggesting that these languages were once widespread there, (4) the spread of Afroasiastic languages through in East Africa as part of the Pastoral Neolithic farming expansion, and (5) the spread of Na-Dene languages in North America in association with Proto-Paleoeskimo ancestry. I will highlight the ways that ancient DNA can meaningfully contribute to our understanding of language expansions—increasing the plausibility of some scenarios while decreasing the plausibility of others—while emphasizing that with genetic data by itself we can never definitively determine what languages ancient people spoke.

EDIT (3 MAY 2019): Apparently, there was not much to take from the talk:

neolithic-pastoralist-africa
Pastoralist Neolithic in Africa, through a pale-green Sahelo-Sudanian steppe corridor. See full map.

This seminar (and maybe some new paper on the Neolithic expansion in Africa) could shed light on population movements that may be related to the spread of Afroasiatic dialects. Until now, it seems that Bantu peoples have been more interesting for linguistics and archaeology, and South and East Africans for anthropology.

Archaeology in Africa appears to be in its infancy, as is population genomics. From the latest publication by Carina Schlebusch, Population migration and adaptation during the African Holocene: A genetic perspective, a chapter from Modern Human Origins and Dispersal (2019):

The process behind the introduction and development of farming in Africa is still unclear. It is not known how many independent invention events there were in the continent and to which extent the various first instances of farming in northern Africa are linked. Based on the archeological record, it was proposed that at least three regions in Africa may have developed agriculture independently: the Sahara/Sahel (around 7 ka), the Ethiopian highlands (7-4 ka), and western Africa (5-3 ka). In addition to these developments, the Nile River Valley is thought to have adopted agriculture (around 7.2 ka), from the Neolithic Revolution in the Middle East (Chapter 12 – Jobling et al. 2014; Chapter 35, 37 – Mitchell and Lane 2013). From these diverse centers of origin, farmers or farming practices spread to the rest of Africa, with domesticate animals reaching the southern tip of Africa ~2 ka and crop farming ~1,8 ka (Mitchell 2002; Huffman 2007)

african-popularion-movements
Schematic representation of possible migration routes related to the expansion of herders and crop farmers during Holocene times. Arrow color indicate source populations; Brown-Eurasian, Green-western African, Blue-eastern African.

Similar to the case in Europe and the 1990s-2000s wrong haplogroup history based on the modern distribution of R1b, R1a, N, or I2, it is possible that neither of the most often mentioned haplogroups linked to the Afroasiatic expansion, E and J, were responsible for its early spread within Africa, despite their widespread distribution in certain modern Afroasiatic-speaking areas. The fact that such assessments include implausible glottochronological dates spanning up to 20,000 years for the parent language, combined with regional language continuities despite archaeological changes, makes them even more suspicious.

Similar to the case with Indo-Europeans and the “steppe ancestry” concept of the 2010s, it may be that the often-looked-for West Eurasian ancestry among Africans is the effect of recent migrations, unrelated to the Afroasiatic expansion. The results of this paper could be offering another sign of how this ancestry may have expanded only quite recently westwards from East Africa through the Sahel, after the Semitic expansion to the south:

1. From approximately 1000 BC, accompanying Nilo-Saharan peoples.

2. From approximately AD 1500, with the different population movements related to the nomadic Fulani:

sahel-nomadic-sedentary
Image from Sahel in West African History – Oxford Research Encyclopedia of African History.
  • Arguably, since the Fulani caste system wasn’t as elaborate in northern Nigeria, eastern Niger, and Cameroon, these specific groups would be a good example of the admixture with eastern populations, based on the (proportionally) huge amount of slaves they dealt with.
  • Similarly, it could be argued that the castes-based social stratification in most other territories (including Sudan) would have helped them keep a genetic make-up similar to their region of origin in terms of ancient lineages, hence similar to Chadic populations from west to east.

Reich’s assertion of the association of the language expansion with the spread of Pastoral Neolithic is still too vague, but – based on previous publications of ancient DNA in Africa and the Levant – I don’t have high hopes for a revolutionary paper in the near future. Without many samples and proper temporal transects, we are stuck with speculations based on modern distributions and scarce historical data.

fula-people-distribution
A distribution map of Fula people. Dark green: a major ethnic group; Medium: significant; Light: minor. Modified from image by Sarah Welch at Wikipedia.

About the potential genetic make-up of Cameroon before the arrival of the Neolithic, from the recent SAA 84th Annual Meeting (Abstracts in PDF):

Lipson, Mark (Harvard Medical School), Mary Prendergast (Harvard University), Isabelle Ribot (Université de Montréal), Carles Lalueza-Fox (Institute of Evolutionary Biology CSIC-UPF) and David Reich (Harvard Medical School)

[253] Ancient Human DNA from Shum Laka (Cameroon) in the Context of African Population History We generated genome-wide DNA data from four people buried at the site of Shum Laka in Cameroon between 8000–3000 years ago. One individual carried the deeply divergent Y chromosome haplogroup A00 found at low frequencies among some present-day Niger-Congo speakers, but the genome-wide ancestry profiles for all four individuals are very different from the majority of West Africans today and instead are more similar to West-Central African hunter-gatherers. Thus, despite the geographic proximity of Shum Laka to the hypothesized birthplace of Bantu languages and the temporal range of our samples bookending the initial Bantu expansion, these individuals are not representative of a Bantu source population. We present a phylogenetic model including Shum Laka that features three major radiations within Africa: one phase early in the history of modern humans, one close to the time of the migration giving rise to non-Africans, and one in the past several thousand years. Present-day West Africans and some East Africans, in addition to Central and Southern African hunter-gatherers, retain ancestry from the first phase, which is therefore still represented throughout the majority of human diversity in Africa today.

Related

Ancient Sardinia hints at Mesolithic spread of R1b-V88, and Western EEF-related expansion of Vasconic

nuragic-sardinia-neolithic

New preprint Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective, by Marcus et al. bioRxiv (2019)

Interesting excerpts (emphasis mine, edited for clarity):

On the high frequency of R1b-V88

Our genome-wide data allowed us to assign Y haplogroups for 25 ancient Sardinian individuals. More than half of them consist of R1b-V88 (n=10) or I2-M223 (n=7).

Francalacci et al. (2013) identi fied three major Sardinia-specifi c founder clades based on present-day variation within the haplogroups I2-M26, G2-L91 and R1b-V88, and here we found each of those broader haplogroups in at least one ancient Sardinian individual. Two major present-day Sardinian haplogroups, R1b-M269 and E-M215, are absent.

Compared to other Neolithic and present-day European populations, the number of identi fied R1b-V88 carriers is relatively high.

(…)ancient Sardinian mtDNA haplotypes belong almost exclusively to macro-haplogroups HV (n = 16), JT (n = 17) and U (n = 9), a composition broadly similar to other European Neolithic populations.

r1b-v88-europe
Geographic and temporal distribution of R1b-V88 Y-haplotypes in ancient European samples. We plot the geographic position of all ancient samples inferred to carry R1b-V88 equivalent markers. Dates are given as years BCE (means of calibrated 2s radio-carbon dates). Multiple V88 individuals with similar geographic positions are vertically stacked. We additionally color-code the status of the R1b-V88 subclade R1b-V2197, which is found in most present-day African R1b-V88 carriers.

On the origin of a Vasconic-like Paleosardo with the Western EEF

(…) the Neolithic (and also later) ancient Sardinian individuals sit between early Neolithic Iberian and later Copper Age Iberian populations, roughly on an axis that differentiates WHG and EEF populations and embedded in a cluster that additionally includes Neolithic British individuals. This result is also evident in terms of absolute genetic differentiation, with low pairwise FST ~ 0.005 +- 0.002 between Neolithic Sardinian individuals and Neolithic western mainland European populations. Pairwise outgroup-f3 analysis shows a very similar pattern, with the highest values of f3 (i.e. most shared drift) being with Neolithic and Copper Age Iberia, gradually dropping off for temporally and geographically distant populations.

In explicit admixture models (using qpAdm, see Methods) the southern French Neolithic individuals (France-N) are the most consistent with being a single source for Neolithic Sardinia (p ~ 0:074 to reject the model of one population being the direct source of the other); followed by other populations associated with the western Mediterranean Neolithic Cardial Ware expansion.

sardinians-ancient-eef
Principal Components Analysis based on the Human Origins dataset. A: Projection of ancient individuals’ genotypes onto principal component axes de fined by modern Western Eurasians (gray labels).

Pervasive Western Hunter-Gatherer ancestry in Iberian/French/Sardinian population

Similar to western European Neolithic and central European Late Neolithic populations, ancient Sardinian individuals are shifted towards WHG individuals in the top two PCs relative to early Neolithic Anatolians Admixture analysis using qpAdm infers that ancient Sardinian individuals harbour HG ancestry (~ 17%) that is higher than early Neolithic mainland populations (including Iberia, ~ 8%), but lower than Copper Age Iberians (~ 25%) and about the same as Southern French Middle-Neolithic individuals (~ 21%).

sardinia-modern-ancient-nuragic-pca
Principal Components Analysis based on the Human Origins dataset. B: Zoom into the region most relevant for Sardinian individuals.

Continuity from Sardinia Neolithic through the Nuragic

We found several lines of evidence supporting genetic continuity from the Sardinian Neolithic into the Bronze Age and Nuragic times. Importantly, we observed low genetic differentiation between ancient Sardinian individuals from various time periods.

A qpAdm analysis, which is based on simultaneously testing f-statistics with a number of outgroups and adjusts for correlations, cannot reject a model of Neolithic Sardinian individuals being a direct predecessor of Nuragic Sardinian individuals (…) Our qpAdm analysis further shows that the WHG ancestry proportion, in a model of admixture with Neolithic Anatolia, remains stable at ~17% throughout three ancient time-periods.

sardinians-modern-ancient-pca-admixture
Present-day genetic structure in Sardinia reanalyzed with aDNA. A: Scatter plot of the rst two principal components trained on 1577 present-day individuals with grand-parental ancestry from Sardinia. Each individual is labeled with a location if at least 3 of the 4 grandparents were born in the same geographical location (\small” three letter abbreviations); otherwise with \x” or if grand-parental ancestry is missing with \?”. We calculated median PC values for each Sardinian province (large abbreviations). We also projected each ancient Sardinian individual on to the top two PCs (gray points). B/C: We plot f-statistics that test for admixture of modern Sardinian individuals (grouped into provinces) when using Nuragic Sardinian individuals as one source population. Uncertainty ranges depict one standard error (calculated from block bootstrap). Karitiana are used in the f-statistic calculation as a proxy for ANE/Steppe ancestry (Patterson et al., 2012).

Steppe influx in Modern Sardinians

While contemporary Sardinian individuals show the highest affinity towards EEF-associated populations among all of the modern populations, they also display membership with other clusters (Fig. 5). In contrast to ancient Sardinian individuals, present-day Sardinian individuals carry a modest “Steppe-like” ancestry component (but generally less than continental present-day European populations), and an appreciable broadly “eastern Mediterranean” ancestry component (also inferred at a high fraction in other present-day Mediterranean populations, such as Sicily and Greece).

Related

Sahara’s rather pale-green and discontinuous Sahelo-Sudanian steppe corridor, and the R1b – Afroasiatic connection

palaeolakes-world

Interesting new paper (behind paywall) Megalakes in the Sahara? A Review, by Quade et al. (2018).

Abstract (emphasis mine):

The Sahara was wetter and greener during multiple interglacial periods of the Quaternary, when some have suggested it featured very large (mega) lakes, ranging in surface area from 30,000 to 350,000 km2. In this paper, we review the physical and biological evidence for these large lakes, especially during the African Humid Period (AHP) 11–5 ka. Megalake systems from around the world provide a checklist of diagnostic features, such as multiple well-defined shoreline benches, wave-rounded beach gravels where coarse material is present, landscape smoothing by lacustrine sediment, large-scale deltaic deposits, and in places, tufas encrusting shorelines. Our survey reveals no clear evidence of these features in the Sahara, except in the Chad basin. Hydrologic modeling of the proposed megalakes requires mean annual rainfall ≥1.2 m/yr and a northward displacement of tropical rainfall belts by ≥1000 km. Such a profound displacement is not supported by other paleo-climate proxies and comprehensive climate models, challenging the existence of megalakes in the Sahara. Rather than megalakes, isolated wetlands and small lakes are more consistent with the Sahelo-Sudanian paleoenvironment that prevailed in the Sahara during the AHP. A pale-green and discontinuously wet Sahara is the likelier context for human migrations out of Africa during the late Quaternary.

The whole review is an interesting read, but here are some relevant excerpts:

Various researchers have suggested that megalakes coevally covered portions of the Sahara during the AHP and previous periods, such as paleolakes Chad, Darfur, Fezzan, Ahnet-Mouydir, and Chotts (Fig. 2, Table 2). These proposed paleolakes range in size by an order of magnitude in surface area from the Caspian Sea–scale paleo-Lake Chad at 350,000 km2 to Lake Chotts at 30,000 km2. At their maximum, megalakes would have covered ~ 10% of the central and western Sahara, similar to the coverage by megalakes Victoria, Malawi, and Tanganyika in the equatorial tropics of the African Rift today. This observation alone should raise questions of the existence of megalakes in the Sahara, and especially if they developed coevally. Megalakes, because of their significant depth and area, generate large waves that become powerful modifiers of the land surface and leave conspicuous and extensive traces in the geologic record.

megalakes-sahara
ETOPO1 digital elevation model (1 arc-minute; Amante and Eakins, 2009) of proposed megalakes in the Sahara Desert during the late Quaternary. Colors denote Köppen-Geiger climate zones: blue, Aw, Af, Am (tropical); light tan, Bwk, BSh, BSk, Csa, Csb, Cwb, Cfa, Cfb (temperate); red-brown, Bwh (arid, hot desert and steppe climate). Lake area at proposed megalake high stands and present Lake Victoria are in blue, and contributing catchment areas are shown as thin solid black lines. The main tributaries of Lake Chad are denoted by blue lines (from west to east: the Komadougou-Yobe, Logone, and Chari Rivers; source: Global Runoff Data Center, Koblenz, Germany). Rainfall isohyets (50, 200, 800, 1200, and 1600) are marked in dashed gray-scale lines. Physical parameters of each basin are shown in white boxes: Abt, total basin area; AW, lake area; Vw, lake volume; and aW= AW/Abt. Black dots mark the location of the paleohydrological records from Lezine et al. (2011), also compiled in Supplementary Table S5.

Lakes, megalakes, and wetlands

Active ground-water discharge systems abound in the Sahara today, although they were much more widespread in the AHP. They range from isolated springs and wet ground in many oases scattered across the Sahara (e.g., Haynes et al., 1989) to wetlands and small lakes (Kröpelin et al., 2008). Ground water feeding these systems is dominated by fossil AHP-age and older water (e.g., Edmunds and Wright 1979; Sonntag et al., 1980), although recently recharged water (<50 yr) has been locally identified in Saharan ground water (e.g., Sultan et al., 2000; Maduapuchi et al., 2006).

Megalake Chad

In our view, Lake Chad is the only former megalake in the Sahara firmly documented by sedimentologic and geomorphic evidence. Mega-Lake Chad is thought to have covered ~ 345,000 km2, stretching for nearly 8° (10–18°N) of latitude (Ghienne et al., 2002) (Fig. 2). The presence of paleo- Lake Chad was at one point challenged, but several—and in our view very robust—lines of evidence have been presented to support its development during the AHP. These include: (1) clear paleo-shorelines at various elevations, visible on the ground (Abafoni et al., 2014) and in radar and satellite images (Schuster et al., 2005; Drake and Bristow, 2006; Bouchette et al., 2010); (2) sand spits and shoreline berms (Thiemeyer, 2000; Abafoni et al., 2014); and (3) evaporites and aquatic fauna such as fresh-water mollusks and diatoms in basin deposits (e.g., Servant, 1973; Servant and Servant, 1983). Age determinations for all but the Holocene history of mega- Lake Chad are sparse, but there is evidence for Mio-Pliocene lake (s) (Lebatard et al., 2010) and major expansion of paleo- Lake Chad during the AHP (LeBlanc et al., 2006; Schuster et al., 2005; Abafoni et al., 2014; summarized in Armitage et al., 2015) up to the basin overflow level at ~ 329m asl.

Insights from hydrologic mass balance of megalakes

sahara-annaul-rainfall
Graph of mean annual rainfall (mm/yr) versus aw (area lake/area basin, AW/AL); their modeled relationship using our Sahelo-Sudanian hydrologic model for the different lake basins are shown as solid colored lines. Superimposed on this (dashed lines) are the aw values for individual megalake basins and the mean annual rainfall required to sustain them. Mean annual paleo-rainfall estimates of 200– 400 mm/yr during the AHP from fossil pollen and mollusk evidence is shown as a tan box. The intersection of this box with the solid colored lines describes the resulting aw for Saharan paleolakes on the y-axis. The low predicted values for aw suggest that very large lakes would not form under Sahelo-Sudanian conditions where sustained by purely local rainfall and runoff. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Using these conservative conditions (i.e., erring in the direction that will support megalake formation), our hydrologic models for the two biggest central Saharan megalakes (Darfur and Fezzan) require minimum annual average rainfall amounts of ~ 1.1 m/yr to balance moisture losses from their respective basins (Supplementary Table S1). Lake Chad required a similar amount (~1 m/yr; Supplementary Table S1) during the AHP according to our calculations, but this is plausible, because even today the southern third of the Chad basin receives ≥1.2 m/yr (Fig. 2) and experiences a climate similar to Lake Victoria. A modest 5° shift in the rainfall belt would bring this moist zone northward to cover a much larger portion of the Chad basin, which spans N13° ±7°. Estimated rainfall rates for Darfur and Fezzan are slightly less than the average of ~ 1.3 m/yr for the Lake Victoria basin, because of the lower aw values, that is, smaller areas of Saharan megalakes compared with their respective drainage basins (Fig. 15).

Estimates of paleo-rainfall during the AHP

Here major contradictions develop between the model outcomes and paleo-vegetation evidence, because our Sahelo-Sudanian hydrologic model predicts wetter conditions and therefore more tropical vegetation assemblages than found around Lake Victoria today. In fact, none of the very wet rainfall scenarios required by all our model runs can be reconciled with the relatively dry conditions implied by the fossil plant and animal evidence. In short, megalakes cannot be produced in Sahelo-Sudanian conditions past or present; to form, they require a tropical or subtropical setting, and major displacements of the African monsoon or extra-desert moisture sources.

sahara-palaeoclimate
Change in mean annual precipitation over northern Africa between mid-Holocene (6 ka) and pre-industrial conditions in PMIP3 models (affiliations are provided in Supplementary Table S4). Lakes Victoria and Chad outlined in blue. (a) Ensemble mean change in mean annual precipitation and positions of the African summer (July–September) ensemble mean ITCZ during mid-Holocene (solid red line) and pre-industrial conditions (solid blue line). (b) Zonal average of change in mean annual precipitation over land (20°W–30°E) for the ensemble mean (thick black) and individual models are listed on right). The range of minimal estimated change in mean annual precipitation required to sustain steppe is shown in shaded green (Jolly et al., 1998).

Conclusions

If not megalakes, what size lakes, marshes, discharging springs, and flowing rivers in the Sahara were sustainable in Sahelo-Sudanian climatic conditions? For lakes and perennial rivers to be created and sustained, net rainfall in the basin has to exceed loss to evapotranspiration, evaporation, and infiltration, yielding runoff that then supplies a local lake or river. Our hydrologic models (see Supplementary Material) and empirical observations (Gash et al., 1991; Monteith, 1991) for the Sahel suggest that this limit is in the 200–300 mm/yr range, meaning that most of the Sahara during the AHP was probably too dry to support very large lakes or perennial rivers by means of local runoff. This does not preclude creation of local wetlands supplied by ground-water recharge focused from a very large recharge area or forced to the surface by hydrologic barriers such as faults, nor megalakes like Chad supplied by moisture from the subtropics and tropics outside the Sahel. But it does raise a key question concerning the size of paleolakes, if not megalakes, in the Sahara during the AHP. Our analysis suggests that Sahelo-Sudanian climate could perhaps support a paleolake approximately ≤5000 km2 in area in the Darfur basin and ≤10,000–20,000 km2 in the Fezzan basin. These are more than an order of magnitude smaller than the megalakes envisioned for these basins, but they are still sizable, and if enclosed in a single body of water, should have been large enough to generate clear shorelines (Enzel et al., 2015, 2017). On the other hand, if surface water was dispersed across a series of shallow and extensive but partly disconnected wetlands, as also implied by previous research (e.g., Pachur and Hoelzmann, 1991), then shorelines may not have developed.

One of the underdeveloped ideas of my Indo-European demic diffusion model was that R1b-V88 had migrated through South Italy to Northern Africa, and from it using the Sahara Green Corridor to the south, from where the “upside-down” view of Bender (2007) could have occurred, i.e. Afroasiatic expanding westwards within the Green Sahara, precisely at this time, and from a homeland near the Megalake Chad region (see here).

Whether or not R1b-V88 brought the ‘original’ lineage that expanded Afroasiatic languages may be contended, but after D’Atanasio et al. (2018) it seems that only two lineages, E-M2 and R1b-V88, fit the ‘star-like’ structure suggesting an appropriate haplogroup expansion and necessary regional distribution that could explain the spread of Afroasiatic languages within a reasonable time frame.

palaeolithic
Palaeolithic migrations

This review shows that the hypothesized Green Sahara corridor full of megalakes that some proposed had fully connected Africa from west to east was actually a strip of Sahelo-Sudanian steppe spread to the north of its current distribution, including the Chad megalake, East Africa and Arabia, apart from other discontinuous local wetlands further to the north in Africa. This greenish belt would have probably allowed for the initial spread of early Afroasiatic proto-languages only through the southern part of the current Sahara Desert. This and the R1b-V88 haplogroup distribution in Central and North Africa (with a prevalence among Chadic speakers probably due to later bottlenecks), and the Near East, leaves still fewer possibilities for an expansion of Afroasiatic from anywhere else.

If my proposal turns out to be correct, this Afroasiatic-like language would be the one suggested by some in the vocabulary of Old European and North European local groups (viz. Kroonen for the Agricultural Substrate Hypothesis), and not Anatolian farmer ancestry or haplogroup G2, which would have been rather confined to Southern Europe, mainly south of the Loess line, where incoming Middle East farmers encountered the main difficulties spreading agriculture and herding, and where they eventually admixed with local hunter-gatherers.

NOTE. If related to attested languages before the Roman expansion, Tyrsenian would be a good candidate for a descendant of the language of Anatolian farmers, given the more recent expansion of Anatolian ancestry to the Tuscan region (even if already influenced by Iran farmer ancestry), which reinforces its direct connection to the Aegean.

The fiercest opposition to this R1b-V88 – Afroasiatic connection may come from:

  • Traditional Hamito-Semitic scholars, who try to look for any parent language almost invariably in or around the Near East – the typical “here it was first attested, ergo here must be the origin, too”-assumption (coupled with the cradle of civilization memes) akin to the original reasons behind Anatolian or Out-of-India hypotheses; and of course
  • autochthonous continuity theories based on modern subclades, of (mainly Semitic) peoples of haplogroup E or J, who will root for either one or the other as the Afroasiatic source no matter what. As we have seen with the R1a – Indo-European hypothesis (see here for its history), this is never the right way to look at prehistoric migrations, though.

I proposed that it was R1a-M417 the lineage marking an expansion of Indo-Uralic from the east near Lake Baikal, then obviously connected to Yukaghir and Altaic languages marked by R1a-M17, and that haplogroup R could then be the source of a hypothetic Nostratic expansion (where R2 could mark the Dravidian expansion), with upper clades being maybe responsible for Borean.

nostratic-tree
Simple Nostratic tree by Bomhard (2008)

However, recent studies have shown early expansions of R1b-297 to East Europe (Mathieson et al. 2017 & 2018), and of R1b-M73 to East Eurasia probably up to Siberia, and possibly reaching the Pacific (Jeong et al. 2018). Also, the Steppe Eneolithic and Caucasus Eneolithic clusters seen in Wang et al. (2018) would be able to explain the WHG – EHG – ANE ancestry cline seen in Mesolithic and Neolithic Eurasia without a need for westward migrations.

Dravidian is now after Narasimhan et al. (2018) and Damgaard et al. (Science 2018) more and more likely to be linked to the expansion of the Indus Valley civilization and haplogroup J, in turn strongly linked to Iranian farmer ancestry, thus giving support to an Elamo-Dravidian group stemming from Iran Neolithic.

NOTE. This Dravidian-IVC and Iran connection has been supported for years by knowledgeable bloggers and commenters alike, see e.g. one of Razib Khan’s posts on the subject. This rather early support for what is obvious today is probably behind the reactionary views by some nationalist Hindus, who probably saw in this a potential reason for a strengthened Indo-Aryan/Dravidian divide adding to the religious patchwork that is modern India.

I am not in a good position to judge Nostratic, and I don’t think Glottochronology, Swadesh lists, or any statistical methods applied to a bunch of words are of any use, here or anywhere. The work of pioneers like Illich-Svitych or Starostin, on the other hand, seem to me solid attempts to obtain a faithful reconstruction, if rather outdated today.

NOTE. I am still struggling to learn more about Uralic and Indo-Uralic; not because it is more difficult than Indo-European, but because – in comparison to PIE comparative grammar – material about them is scarce, and the few available sources are sometimes contradictory. My knowledge of Afroasiatic is limited to Semitic (Arabic and Akkadian), and the field is not much more developed here than for Uralic…

y-haplogroup-r1b-p343
Spread of Y-haplogroup R1b(xM269) in Eurasia, according to Jeong et al. (2018).

If one wanted to support a Nostratic proto-language, though, and not being able to take into account genome-wide autosomal admixture, the only haplogroup right now which can connect the expansion of all its branches is R1b-M343:

  • R1b-L278 expanded from Asia to Europe through the Iranian Plateau, since early subclades are found in Iran and the Caucasus region, thus supporting the separation of Elamo-Dravidian and Kartvelian branches;
  • From the Danube or another European region ‘near’ the Villabruna 1 sample (of haplogroup R1b-L754):
    • R1b-V88 expanding everywhere in Europe, and especially the branch expanding to the south into Africa, may be linked to the initial Afroasiatic expansion through the Pale-Green Sahara corridor (and even a hypothetic expansion with E-M2 subclades and/or from the Middle East would also leave open the influence of V88 and previous R1b subclades from the Middle East in the emergence of the language);
    • R1b-297 subclades expanding to the east may be linked to Eurasiatic, giving rise to both Indo-Uralic (M269) and Macro- or Micro-Altaic (M73) expansions.

This is shameless, simplistic speculation, of course, but not more than the Nostratic hypothesis, and it has the main advantage of offering ‘small and late’ language expansions relative to other proposals spanning thousands (or even tens of thousands) of years more of language separation. On the other hand, that would leave Borean out of the question, unless the initial expansion of R1b subclades happened from a community close to lake Baikal (and Mal’ta) that was also at the origin of the other supposedly related Borean branches, whether linked to haplogroup R or to any other…

NOTE. If Afroasiatic and Indo-Uralic (or Eurasiatic) are not genetically related, my previous simplistic model, R1b-Afroasiatic vs. R1a-Eurasiatic, may still be supported, with R1a-M17 potentially marking the latest meaningful westward population expansion from which EHG ancestry might have developed (see here). Without detailed works on Nostratic comparative grammar and dialectalization, and especially without a lot more Palaeolithic and Mesolithic samples, all this will remain highly speculative, like proposals of the 2000s about Y-DNA-haplogroup – language relationships.

Related:

Tales of Human Migration, Admixture, and Selection in Africa

african-migrations

Comprehensive review (behind paywall) Tales of Human Migration, Admixture, and Selection in Africa, by Carina M. Schlebusch & Mattias Jakobsson, Annual Review of Genomics and Human Genetics (2018), Vol. 9.

Abstract (emphasis mine):

In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter–gatherers, as the world’s deepest population divergences occur among these groups, and that the deepest population divergence dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. With today’s sequencing technologies, we can obtain full genome sequences from diverse sets of extant and prehistoric Africans. The coming years will contribute exciting new insights toward deciphering human evolutionary history in Africa.

Regarding potential Afroasiatic origins and expansions:

It is currently believed that farming practices in northeastern and eastern Africa developed independently in the Sahara/Sahel (around 7,000 BP) and the Ethiopian highlands (7,000–4,000 BP), while farming in the Nile River Valley developed as a consequence of the Neolithic Revolution in the Middle East (84). Northeastern and eastern African farmers today speak languages from the Afro-Asiatic and Nilo-Saharan linguistic groups, which is also reflected in their genetic affinities (Figure 3, K=6). In the northern parts of East Africa (South Sudan, Somalia, and Ethiopia), Nilo-Saharan and Afro-Asiatic speakers with farming lifeways have completely replaced hunter–gatherers. It is still largely unclear how farming and herding practices influenced the northeastern African prefarming population structure and whether the spread of farming is better explained by demic or cultural diffusion in this part of the world. Genetic studies of contemporary populations and aDNA have started to provide some insights into population continuity and incoming gene flow in this region of Africa.

african-demographic-history
Demographic model of African history and estimated divergences. (a) Population split times, hierarchy, and population sizes (summarized from 123). Horizontal width represents population size; horizontal colored lines represent migrations, with down-pointing triangles indicating admixture into another group. (b) Population structure analysis at 5 assumed ancestries (K=5) for 93 African and 6 non-African populations. Non-Africans (brown), East Africans (blue), West Africans ( green), central African hunter–gatherers (light blue), and Khoe-San (red ) populations are sorted according to their broad historical distributions.

For example, studies have shown that a back-migration from Eurasia into Africa affected most of northeastern and eastern Africa (36, 46, 53, 89, 132) (Figure 1b). A genetic baseline of eastern African ancestral genetic variation unaffected by recent Eurasian admixture and farming migrations within the last 4,500 years has been suggested in the form of the genome sequence of a 4,500-year-old individual from Mota, Ethiopia (36). Based on comparisons with the ancient Mota genome, we know that certain populations from northeastern Africa show deep continuity in their local area with very limited gene flow resulting from recent population movements. For example, the Nilotic herder populations from South Sudan (e.g., Dinka, Nuer, and Shilluk) appear to have remained relatively isolated over time and received little to no gene flow from Eurasians, West African Bantu-speaking farmers, and other surrounding groups (53) (Figures 2 and 3). By contrast, the Nubian and Arab populations to their north show gene flow with Eurasians, which has been connected to the Arab expansion (53). The Nubian, Arab, and Beja populations of northeastern Africa roughly display equal admixture fractions from a local northeastern African gene pool (similar to the Nilotic component) and an incoming Eurasian migrant component (53) (Figure 3). The Eurasian component has been linked to the Middle East and the Arab migration, but only the Arab groups shifted to the Semitic languages; the Nubians and Beja groups kept their original languages. The Eurasian gene flow appears to have spread from north to south along the Nile and Blue Nile in a succession of admixture events (53).

Skoglund and Mathieson’s preprint has also been published in the same volume, without meaningful changes.

Related:

A history of male migration in and out of the Green Sahara

Open access research highlight A history of male migration in and out of the Green Sahara, by Yali Xue, Genome Biology (2018) 19:30, on the recent paper by D’Atanasio et al.

Insights from the Green Saharan Y-chromosomal findings (emphasis mine):

It is widely accepted that sub-Saharan Y chromosomes are dominated by E-M2 lineages carried by Bantu-speaking farmers as they expanded from West Africa starting < 5 kya, reaching South Africa within recent centuries [4]. The E-M2-Bantu lineages lie phylogenetically within the E-M2-Green Sahara lineage and show at least three explosive lineage expansions beginning 4.9–5.3 kya [5] (Fig. 1a). These events of E-M2-Bantu expansion are slightly later than the R-V88 expansion, and highlight the range of male demographic changes in the mid-Holocene. North of the Sahara, in addition to the four trans-Saharan haplogroups, haplogroup E-M81 (which diverged from E-M78 ~ 13 kya) became very common in present-day populations as a result of another massive expansion ~ 2 kya [6] (Fig. 1a).

african-sahara-y-dna
Simplified Y-chromosomal phylogeny and inferred past or observed present-day distribution of relevant Y-chromosomal lineages. a Calibrated phylogenetic tree of Y-chromosomal lineages discussed in the text. Green shading represents the period when the present-day Sahara Desert was green and fertile. Lineages represented by filled pentagons have undergone very rapid expansions. b [featured image] The Green Sahara period 5–12 kya. Green shading indicates that the present-day Sahara Desert was green and fertile. The colors within the large oval represent the four Y-chromosomal haplogroups deduced to be present in the region at this time; specific locations are not implied. The arrows indicate the inferred origins of these haplogroups to the north or south, but specific origins and routes are not implied. c The present-day distributions of the four Green Saharan Y-chromosomal haplogroups. Yellow shading indicates the Sahara Desert. Each circle represents a sampled population, with the presence or absence of the four Green Saharan haplogroups shown by the colored sectors; other haplogroups may also be present in these populations, but are not shown. The small arrows indicate the inferred northwards and southwards movements of these haplogroups when the Sahara became uninhabitable.

Although Y chromosomes exist within populations and so share and reflect the general history of those populations, they can sometimes show some departures from other parts of the genome that result from differences in male and female behaviors. D’Atanasio et al. [1] highlight one such contrast in their study. Present-day North African populations show substantial sub-Saharan autosomal and mtDNA genetic components ascribed to the Roman and Arab slave trades 1–2 kya [7], but carry few sub-Saharan Y lineages from this source, probably reflecting the smaller numbers of male slaves and their reduced reproductive opportunities when compared to those of female slaves. The sub-Saharan Y chromosomes in these North African populations thus originate predominantly from the earlier Green Sahara period.

In this part of Africa, the indigenous languages that are spoken belong to three of the four African linguistic families (Afro-Asiatic, Nilo-Saharan and Niger-Congo). Interestingly, these languages show non-random associations with Y lineages. For example, Chadic languages within the Afro-Asiatic family are associated with haplogroup R-V88, whereas Nilo-Saharan languages are associated with specific sublineages within A3-M13 and E-M78, further illustrating the complex human history of the region.

The main question after D’Atanasio et al. (2018) is thus:

(…) what are the reasons for the very rapid R-V88 expansion 5–6 kya [1] and E-M81 expansion ~ 2 kya [6], and how do these expansions fit within general worldwide patterns of male-specific expansions, which in other cases have been linked to cultural and technological changes [5]?

I think that the only known haplogroup expansion that might fit today the spread and dialectalization of Afroasiatic, a proto-language probably contemporaneous or slighly older than Middle Proto-Indo-European, is that of R1b-V88 lineages. However, without ancient DNA samples to corroborate this, we cannot be sure.

See also:

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

taforalt-samples

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations, by van de Loosdrecht et al. Science (2018).

Abstract

North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.

Excerpts:

We analyzed the genetic affinities of the Taforalt individ-uals by performing principal component analysis (PCA) and model-based clustering of worldwide data (Fig. 2). When pro-jected onto the top PCs of African and West Eurasian popu-lations, the Taforalt individuals form a distinct cluster in an intermediate position between present-day North Africans (e.g., Amazighes (Berbers), Mozabite and Saharawi) and East Africans (e.g., Afar, Oromo and Somali) (Fig. 2A). Consist-ently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (18). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleolithic Natufians and Pre-Pottery Neolithic Levantines (“Levant_N”) (16). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maximized in early Holocene Levantines, East African hunter-gatherer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2B). In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2B).

Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool.

Mitochondrial consensus sequences of the Taforalt indi-viduals belong to the U6a (n = 6) and M1b (n = 1) haplogroups (15), which are mostly confined to present-day populations in North and East Africa (7). U6 and M1 have been proposed as markers for autochthonous Maghreb ancestry, which might have been originally introduced into this region by a back-to-Africa migration from West Asia (6, 7). The occurrence of both haplogroups in the Taforalt individuals proves their pre-Holocene presence in the Maghreb.
(…) the diversification of haplogroup U6a and M1 found for Taforalt is dated to ~24,000 yBP (fig. S23), which is close in time to the earliest known appearance of the Iberomaurusian in Northwest Africa (25,845-25,270 cal. yBP at Tamar Hat (26)).

taforalt-admixture
A summary of the genetic profile of the Taforalt individuals. (A) The top two PCs calculated from present-day African, Near Eastern and South European individuals from 72 populations. The Taforalt individuals are projected thereon (red-colored circles). Selected present-day populations are marked by colored symbols. Labels for other populations (marked by small grey circles) are provided in fig. S8. (B) ADMIXTURE results of chosen African and Middle Eastern populations (K = 10). Ancient individuals are labeled in red color. Major ancestry components in Taforalt are maximized in early Holocene Levantines (green), West Africans (purple) and East African Hadza (brown). The ancestry component prevalent in pre-Neolithic Europeans (beige) is absent in Taforalt.

The relationships of the Iberomaurusian culture with the preceding MSA, including the local backed bladelet technologies in Northeast Africa, and the Epigravettian in southern Europe have been questioned (13). The genetic profile of Taforalt suggests substantial Natufian-related and sub-Saharan African-related ancestries (63.5% and 36.5%, respec-tively), but not additional ancestry from Epigravettian or other Upper Paleolithic European populations. Therefore, we provide genomic evidence for a Late Pleistocene connection between North Africa and the Near East, predating the Neolithic transition by at least four millennia, while rejecting a potential Epigravettian gene flow from southern Europe into northern Africa within the resolution of our data.

It seems that the Taforalt gene pool (ca. 13000-12000 BC) cannot be explained by a connection with Upper Palaeolithic Europeans, but a more archaic admixture, so the authors cannot prove a migration through the Strait of Gibraltar or Sicily.

Nevertheless, these results apparently suggest:

  • That there is no contact before ca. 12000 BC through the Strait of Gibraltar; therefore the Sicilian route I support for the migration of R1b-V88 lineages is still the most likely one.
  • That the North African connection with Natufians is quite old – for which we already had modern Y-DNA investigation – , and therefore unlikely to be related to the Afroasiatic expansion.

I am glad I had some more time this week to read at least some interesting parts of the published papers, because the information to process is becoming insanely huge…

Related:

R1b-V88 migration through Southern Italy into Green Sahara corridor, and the Afroasiatic connection

palaeolithic

Open access article The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages, by D’Atanasio, Trombetta, Bonito, et al., Genome Biology (2018) 19:20.

Abstract:

Background
Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

Results
In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase.

Conclusions
Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

y-dna-r1b-v88-e-m78
Maximum parsimony Y chromosome tree and dating of the four trans-Saharan haplogroups. a Phylogenetic relations among the 150 samples analysed here. Each haplogroup is labelled in a different colour. The four Y sequences from ancient samples are marked by the dagger symbol. b Phylogenetic tree of the four trans-Saharan haplogroups, aligned to the timeline (at the bottom). At the tip of each lineage, the ethno-geographic affiliation of the corresponding sample is represented by a circle, coloured according to the legend (bottom left). The last Green Sahara period is highlighted by a green belt in the background

Also, interesting excerpts:

The fertile environment established in the Green Sahara probably promoted demographic expansions and rapid dispersals of the human groups, as suggested by the great homogeneity in the material culture of the early Holocene Saharan populations [62]. Our data for all the four trans-Saharan haplogroups are consistent with this scenario, since we found several multifurcated topologies, which can be considered as phylogenetic footprints of demographic expansions. The multifurcated structure of the E-M2 is suggestive of a first demographic expansion, which occurred about 10.5 kya, at the beginning of the last Green Sahara (Fig. 2; Additional file 2: Figure S4). After this initial expansion, we found that most of the trans-Saharan lineages within A3-M13, E-M2 and R-V88 radiated in a narrow time interval at 8–7 kya, suggestive of population expansions that may have occurred in the same time (Fig. 2; Additional file 2: Figures S3, S4 and S6). Interestingly, during roughly the same period, the Saharan populations adopted pastoralism, probably as an adaptive strategy against a short arid period [1, 62, 63]. So, the exploitation of pastoralism resources and the reestablishment of wetter conditions could have triggered the simultaneous population expansions observed here. R-V88 also shows signals of a further and more recent (~ 5.5 kya) Saharan demographic expansion which involved the R-V1589 internal clade. We observed similar demographic patterns in all the other haplogroups in about the same period and in different geographic areas (A3-M13/V3, E-M2/V3862 and E-M78/V32 in the Horn of Africa, E-M2/M191 in the central Sahel/central Africa), in line with the hypothesis that the start of the desertification may have caused massive economic, demographic and social changes [1].

Finally, the onset of the arid conditions at the end of the last African humid period was more abrupt in the eastern Sahara compared to the central Sahara, where an extensive hydrogeological network buffered the climatic changes, which were not complete before ~ 4 kya [6, 62, 64]. Consistent with these local climatic differences, we observed slight differences among the four trans-Saharan haplogroups. Indeed, we found that the contact between northern and sub-Saharan Africa went on until ~ 4.5 kya in the central Sahara, where we mainly found the internal lineages of E-M2 and R-V88 (Additional file 2: Figures S4 and S6). In the eastern Sahara, we found a sharper and more ancient (> 5 kya) differentiation between the people from northern Africa (and, more generally, from the Mediterranean area) and the groups from the eastern sub-Saharan regions (mainly from the Horn of Africa), as testified by the distribution and the coalescence ages of the A3-M13 and E-M78 lineages (Additional file 2: Figures S3 and S5).

green-sahara-r1b-v88-em-78
Time estimates and frequency maps of the four trans-Saharan haplogroups and major sub-clades. a Time estimates of the four trans-Saharan clades and their main internal lineages. To the left of the timeline, the time windows of the main climatic/historical African events are reported in different colours (legend in the upper left). b Frequency maps of the main trans-Saharan clades and sub-clades. For each map, the relative frequencies (percentages) are reported to the right

R-V88 has been observed at high frequencies in the central Sahel (northern Cameroon, northern Nigeria, Chad and Niger) and it has also been reported at low frequencies in northwestern Africa [37]. Outside the African continent, two rare R-V88 sub-lineages (R-M18 and R-V35) have been observed in Near East and southern Europe (particularly in Sardinia)[30, 37, 38, 39]. Because of its ethno-geographic distribution in the central Sahel, R-V88 has been linked to the spread of the Chadic branch of the Afroasiatic linguistic family [37, 40].

(…) the R-V88 lineages date back to 7.85 kya and its main internal branch (branch 233) forms a “star-like” topology (“Star-like” index = 0.55), suggestive of a demographic expansion. More specifically, 18 out of the 21 sequenced chromosomes belong to branch 233, which includes eight sister clades, five of which are represented by a single subject. The coalescence age of this sub-branch dates back to 5.73 kya, during the last Green Sahara period. Interestingly, the subjects included in the “star-like” structure come from northern Africa or central Sahel, tracing a trans-Saharan axis. It is worth noting that even the three lineages outside the main multifurcation (branches 230, 231 and 232) are sister lineages without any nested sub-structure. The peculiar topology of the R-V88 sequenced samples suggests that the diffusion of this haplogroup was quite rapid and possibly triggered by the Saharan favourable climate (Fig. 2b).

One of the theories I proposed in the Indo-European demic diffusion model since the first edition – based mainly on phylogeography – is that R1b-V88 lineages had probably crossed the Mediterranean through southern Italy into a Green Sahara region, and distributed from there throuh important green corridors, humid areas between megalakes. Even though this new study – like the rest of them – is based solely on modern samples, and as such is quite prone to error in assessing ancient distributions – as we have seen in Europe -, it seems that a southern Italian route (probably through Sicily) for R1b-V88 and a late expansion through Green Sahara is more and more likely.

If we accept that the migration of R1b-V88 lineages is the last great expansion through a Green Sahara, then this expansion is a potential candidate for the initial Afroasiatic expansion – whereas older haplogroup expansions would represent languages different than Afroasiatic, and more recent haplogroup expansions would represent subsequent expansions of Afroasiatic dialects, like Semitic, Hamitic, Cushitic, or Chadic – as I explained in an older post.

In absolutely shameless speculative terms, then – as is today common in Genetic studies, by the way, so let’s all have some fun here – instead of some sort of R1b/Eurasiatic continuity in Europe, as some autochthonous continuists would like, this could mean that there would be an old Afroasiatic – R1b connection. That would imply:

NOTE. Regarding the contribution of CHG ancestry in the Pontic-Caspian steppe cultures, it is usually explained as caused by exogamy, or by absorption of a previous population (as in the Indo-Iranian case), although a contribution of communities of mainly J subclades to the formation of Neolithic steppe cultures cannot be ruled out. As for some autochthonous continuists’ belief in some sort of mythical mixed steppe people with mixed haplogroups and mixed language, well…

nostratic-tree
Simple Nostratic tree by Bomhard (2008)

The Pre-Indo-European linguistic situation, before the formation of Neolithic steppe cultures, seems like pure speculation, because a) language macro-families (with the exception of Afroasiatic) are highly speculative, b) sound anthropological models are lacking for them, and c) migrations inferred from haplogroup distributions of modern populations are often incorrect:

  • Haplogroup R could then be argued to be the source of Nostratic, and earlier subclades the source of Starostin’s Borean, given the distribution of its subclades in Asia and the timing of their migrations.
  • But of course one could also argue that, given the comparatively late population expansions that Genomics is showing, supporting Western European linguistic schools – where Russian Nostraticists tend to date languages further back in timeR1b (and not R) expansion could be the marker of Nostratic languages, due to its most likely southern path (and their old subclades found in Iran and the Caucasus), which would be more in line with the wet dreams of Europeans proposing R1b autochthonous continuity theories. I like this option far less because of that, but it cannot be ruled out.

If you have read this blog before, you know I profoundly dislike lexicostatistical and glottochronological methods, and I don’t like mass comparisons either. Whereas these methods pretend to apply mathematics to big (raw) data where there is almost no knowledge of what one is doing, comparative grammar applies complex reasoning where there is a lot of partially processed data.

But, it is always fun to ask “what if they were right?” and follow from there…

See also: