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