The Phase 3 sequence data from 20 populations, comprising five populations for each of the four main geographical regions of Europe, East Asia, South Asia and Africa, were downloaded from the 1000 Genomes Project website (www.1000genomes.org/data, ), including whole mitochondrial genome data for 1999 individuals. We decided not to analyse populations from the Americas due to the region’s complex history of admixture [13,14].
The European populations were as follows: Finnish sampled in Finland (FIN); European Caucasians resident in Utah, USA (CEU); British in England and Scotland (GBR); an Iberian population from Spain (IBS) and Toscani from Italy (TSI). Representing East Asia were the Han Chinese in Beijing (CHB); Southern Han Chinese (CHS); Dai Chinese from Xishuangbanna, China (CDX); Kinh population from Ho Chi Minh City, Vietnam (KHV) and Japanese from Tokyo (JPT). The South Asian populations were Punjabi Indians from Lahore, Pakistan (PJL); Gujarati Indians in Houston, USA (GIH) as well as Indian Telugu sampled in the UK (ITU); Bengali from Bangladesh (BEB) and Sri Lankan Tamil from the UK (STU). (…)
We analysed our mtDNA data with the extended Bayesian skyline plot (EBSP) method, a Bayesian, non-parametric technique for inferring past population size fluctuations from genetic data. Building on the previous Bayesian skyline plot (BSP) approach, EBSP uses a piecewise-linear model and Markov chain Monte Carlo (MCMC) methods to reconstruct a populations’ demographic history  and is implemented in the software package BEAST v. 2.3.2 . Alignments for each of the 20 populations were loaded separately into the Bayesian Evolutionary Analysis Utility tool (BEAUti v. 2.3.2) in NEXUS format.
Regional demographic histories
The five European profiles are presented in figure 2. The four southerly populations all show profiles with a stable size up to approximately 14 ka followed by a sudden, rapid increase that becomes progressively less steep towards the present. There is also a north-south trend, with confidence intervals becoming broader towards the north, particularly for the oldest time-points. The Finnish population profile appears rather different, but this is to be expected both because it is so far north and because previous studies have identified Finns as a strong genetic outlier in Europe [19–22].
The five profiles for South Asia are shown in figure 3. All populations reveal a period of rapid growth approximately 45–40 ka which then slows. Near the present the two southerly populations, GIH and STU both show evidence of a decline. However, this may be due to these samples being drawn from populations no longer living on the subcontinent, with the downward trend capturing a bottleneck associated with moving to Europe/America, perhaps accentuated by the tendency for immigrant populations to group by region, religion and race .
Our analysis of divergence times suggests the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations ~140–250 generations ago, corresponding to ~4,300–7,000 years ago assuming a generation time of 30 years and a mutation rate of 1.25 × 10−8 per basepair per generation. (…) in terms of relative values, the divergence time between Northern and Southern Europeans is much more recent than either is to Sardinia, signaling the relative isolation of Sardinia from mainland Europe.
We documented fine-scale variation in the ancient population ancestry proportions across the island. The most remote and interior areas of Sardinia—the Gennargentu massif covering the central and eastern regions, including the present-day province of Ogliastra— are thought to have been the least exposed to contact with outside populations. We found that pre-Neolithic hunter-gatherer and Neolithic farmer ancestries are enriched in this region of isolation. Under the premise that Ogliastra has been more buffered from recent immigration to the island, one interpretation of the result is that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. Such admixture could have occurred principally on the island or on the mainland before the hypothesized Neolithic era influx to the island. Under the alternative premise that Ogliastra is simply a highly isolated region that has differentiated within Sardinia due to genetic drift, the result would be interpreted as genetic drift leading to a structured pattern of pre-Neolithic ancestry across the island, in an overall background of high Neolithic ancestry.
We found Sardinians show a signal of shared ancestry with the Basque in terms of the outgroup f3 shared-drift statistics. This is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like, non-Indo-European words among Sardinian placenames. More recently, the Basque have been shown to be enriched for Neolithic farmer ancestry and Indo-European languages have been associated with steppe population expansions in the post-Neolithic Bronze Age. These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European Neolithic ancestry. To be cautious, while it seems unlikely, we cannot exclude that the genetic similarity between the Basque and Sardinians is due to an unsampled pre-Neolithic population that has affinities with the Neolithic representatives analyzed here.
While we can confirm that Sardinians principally have Neolithic ancestry on the autosomes, the high frequency of two Y-chromosome haplogroups (I2a1a1 at ~39% and R1b1a2 at ~18%) that are not typically affiliated with Neolithic ancestry is one challenge to this model. Whether these haplogroups rose in frequency due to extensive genetic drift and/or reflect sex-biased demographic processes has been an open question. Our analysis of X chromosome versus autosome diversity suggests a smaller effective size for males, which can arise due to multiple processes, including polygyny, patrilineal inheritance rules, or transmission of reproductive success. We also find that the genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, suggesting that male lineages may more rapidly trace back to the mainland. Considering that the R1b1a2 haplogroup may be associated with post-Neolithic steppe ancestry expansions in Europe, and the recent timeframe when the R1b1a2 lineages expanded in Sardinia, the patterns raise the possibility of recent male-biased steppe ancestry migration to Sardinia, as has been reported among mainland Europeans at large (though see Lazaridis and Reich and Goldberg et al.). Such a recent influx is difficult to square with the overall divergence of Sardinian populations observed here.
Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.
NOTE. In fact, the increase in Neolithic ancestry found in south-west Ireland with expanding Bell Beakers (likely Proto-Beakers), coupled with the finding of I2a subclades in Megalithic cultures of western Europe, would support this replacement after the Cardial and Epi-Cardial expansions, which were initially associated with G2a lineages.
I am not convinced about a survival of Palaeo-Sardo after the Bell Beaker expansion, though, since there is no clear-cut cultural divide (and posterior continuity) of pre-Beaker archaeological cultures after the arrival of Bell Beakers in the island that could be identified with the survival of Neolithic languages.
We may have to wait for ancient DNA to show a potential expansion of Neolithic ancestry from the west, maybe associated with the emergence of the Nuragic civilization (potentially linked with contemporaneous Megalithic cultures in Corsica and in the Balearic Islands, and thus with an Iberian rather than a Basque stock), although this is quite speculative at this moment in linguistic, archaeological, and genetic terms.
Nevertheless, it seems that the association of a Basque-Iberian language with the Neolithic expansion from Anatolia (see Villar’s latest book on the subject) is somehow strengthened by this paper. However, it is unclear when, how, and where expanding G2a subclades were replaced by native I2 lineages.
Several Iberian scholars have referred to stab-and-drag designs in both Bell-Beaker and Bronze Age ceramics (Maluquer de Motes 1956, 180, 196; Fernández-Posse 1982, 137), although these have not always been correctly appraised. In the 1980s it was finally realized that the sherds retrieved at the Boquique Cave should be dated to the Middle-Late Neolithic (4400-3300 BC), and that the same technique was also widely used in the Late Bronze Age (Fernández-Posse 1982, 147-149). Thus, nowadays it is possible to track this technique in inland Iberia at different moments throughout later prehistory (Alday and Moral 2011, 67). The earliest stab-and-drag motifs (Figure 2.2, 1) are, in fact, older than was initially thought (Fernández-Posse 1982); they actually date to the Early Neolithic (5500-4400 BC), contemporary to the Mediterranean Cardial impressed wares (Alday 2009, 135-137). There are also a few sporadic examples of stab-and-drag motifs among Bell-Beaker pottery (2600-2000 BC), such as the Ciempozuelos-style bowl from Las Carolinas (Madrid) (Figure 2.2, 2a) featuring so-called ‘symbolic’ schematic stags drawn by using this technique (Blasco and Baena 1996, 431, Lám. II; Garrido Pena 2000, 108). It is also possible to recognize this technique in a large Beaker from Molino Sanchón II (Zamora) (Abarquero et al. 2012, 206, fig. 190; Guerra-Doce et al. 2011, 812) (Figure 2.2, 2b) and there are other possible cases (e.g. Montero and Rodríguez 2008, 166, Lám. IX). Finally, the widespread use of this technique occurred in the Late Bronze Age (Figure 2.2, 3a & 3b) from c.1450 BC (e.g. Rodríguez Marcos 2007, 362-364; Abarquero 2005).
Analogies between Bell-Beaker and Bronze Age wares
Several Bell-Beaker styles can be discerned in the Iberian Meseta (e.g. Harrison 1977, 55-67; Garrido Pena 2000; 2014). In this subsection attention will be drawn primarily to the most frequent of these variants, the Ciempozuelos style, although more localised similarities can be recognised between the Beaker impressed-comb style and some early Cogotas I pottery. The Ciempozuelos ware (Delibes 1977; Harrison 1977, 19-20; Blasco 1994; Garrido Pena 2000, 116-126; Rodríguez Marcos 2007, 252-256) was widespread throughout the Meseta between 2600-2000 BC, in the same region subsequently occupied by Cogotas I communities (1800-1150 BC) (Fernández-Posse 1998; Abarquero 2005) (Figure 2.1). There is a wide array of resemblances between both pottery assemblages, a point that has been highlighted since the 1920s (e.g. Almagro Basch 1939, 143-144; Maluquer de Motes 1956, 196; Harrison 1977, 20; Jimeno 1984, 117-118).
The key ornamental traits that define the Ciempozuelos style are also reproduced among Cogotas I ware and are the following:
a) Widespread deployment among the early Cogotas I pottery of the more ubiquitous incised motifs in the Ciempozuelos style: herringbones, spikes and reticulates (Garrido Pena 2000, 119-120, fig. 48, themes 6 and 9; Rodríguez Marcos 2012, 155). During the Middle Bronze Age other less frequent themes are also similar to Bell-Beaker decorations, such as incised triangles filled with lines. Late Bronze Age wares feature the so-called ‘pseudo-Kerbschnitt’ (Rodríguez Marcos 2007, 369) which has striking precedents among Ciempozuelos ware (Harrison 1977, 20; Garrido Pena 2000, 120, fig. 48, theme 12) (Figure 2.3, 1a & 1b).
b) The extensive use of internal rim decoration, almost always deploying chevron motifs. This is ‘a Ciempozuelos leitmotiv’ (Harrison 1977, 20) in the Northern Meseta, where between 30% – 50% of all rims exhibit such a feature (Delibes 1977; Garrido Pena 2000, 163). The decoration of internal rims is even more widespread among Cogotas I vessels (Jimeno 1984; Rodríguez Marcos 2012, 158) (Figure 2.3, 1a).
c) White paste rubbed into the geometric decorations (Delibes 1977; Harrison 1977, 20; Jimeno 1984). Maluquer de Motes (1956, 186) in fact regarded excised and stab-and-drag techniques not as decorations per se, but as a way of anchoring encrusted inlays. He also reported that the bulk of rims in Cogotas I vessels exhibit white accretions (Maluquer de Motes 1956, 192) (Figure 2.3).
In addition, several authors agree on the likeness between the Bell-Beaker impressed-comb style and certain Cogotas I local pottery variants corresponding to its earliest phase (1800-1450 BC) (Garrido Pena 2000, 113-116). This is particularly striking for one micro-style from the western Meseta region, whose ceramics feature numerous impressed-comb motives (e.g. Fabián 2012; Rodríguez Marcos 2012, 158).
The relevance of emulated pottery decorations
 (…) there are grounds for proffering the view that the key creative mechanism responsible for the resemblances between apparently unrelated pottery assemblages was the emulation of standalone and very apparent decorative traits. It may constitute a good case for horizontal cultural transmission predicated upon iconic resemblances between easily imitated formal traits (Knappett 2010). Instead of spontaneous and autonomous innovations, it is far more compelling to regard these decorative features as interlinked and punctuated ‘way stations along the trails of living beings, moving through a world’ (Ingold and Hallam 2007, 8). No creative act can be regarded as really isolated. Instead it ought to be understood as focusing on the nodes in particular fields of associations (Lohnmann 2010, 216).
 Pottery ornamentation in the Cogotas I tradition combined and reinterpreted both local atavistic (e.g. Abarquero 2005, 24-26; Rodríguez Marcos 2007, 357-367) and widespread pan-European ornaments (e.g. Blasco 2001, 225, 2003, 67-68; Abarquero 2012, 98-101). From a semiotic perspective such things transcended large spatio-temporal distances; they were closely associated by iconical shared links in a relational or cognitive space, whereby these entities were co-presented and indirectly recalled and perceived despite being distant (Knappett 2010, 85-86). The locally-rooted biases of these creative quotations can be glimpsed from rare sequences of ceramic productions spanning several generations of potters. For instance, at Majaladares (Borja, Zaragoza) strong analogies arise between Ciempozuelos wares featuring unique decorations in this site and Cogotas I wares from the superimposed layers, exhibiting remarkably similar themes (Harrison 2007, 65-82). Likewise, it is noteworthy that the earliest triangular excisions in Cogotas I wares occurred in the eastern Meseta, where imported Duffaits vessels featuring comparable motifs were circulating from several centuries before.(…)
 There is scope for advocating that these pottery decorations cannot be envisaged as a form of irrelevant or mundane aesthetic garnish for the sake of art. Bronze Age potters drew upon a highly meaningful array of esoteric sources and, in so doing, the vessels might have echoed designs betokening genealogical, mythical or parallel worlds, in a kind of dialectical negotiation between self and other (Taussig 1993). The very involvement of ancestors and spiritual forces in making and embellishing a pot is supported by ethnographic evidence (e.g. Crown 2007, 679; Lohnmann 2010, 222) and this also seems plausible in the case of Cogotas I ceramics. These real or imagined beings might be regarded as inspiring sources of creations, whose role is often to legitimize and guarantee the accuracy of the involved knowledge (Lohnmann 2010, 222). In the same vein, the smearing of colored inlays on certain pots ought to be properly understood beyond an aesthetic action of embellishment, as our own rationale prompts us to assume. (…)
 Furthermore, this pottery tradition needs to be understood as an effective means of socialization and a key resource in the forging of identities. Decorating certain intricate Cogotas I vessels (Figure 2.2, 3b; Figure 2.4, 3) very likely involved an ostentatious difficulty (Robb and Michelaki 2012, 168; Abarquero 2005, 438) and the proficiency displayed in such tasks may have accrued even moral connotations (Hendon 2010, 146-147). Learning to perform some of the pottery decoration discussed here certainly required complex training processes involving both expert potters and mentored apprentices (Crown 2007; Hosfield 2009, 46). Thus, the stab-and-drag technique demanded time-consuming learning as well as careful and thorough execution (Alday 2009, 11-19). Likewise the selection and processing of particular raw materials – mainly bones – to attain the white inlays involved direct observation and hands-on training (Odriozola et al. 2012, 150). (…)
 Finally, the role of the Cogotas I pottery decoration was also deeply rooted in the sphere of social interactions through particular communal practices of exhibition and consumption. The celebration of commensality rituals is very often predicated as a key social practice among these communities (e.g. Harrison 1995, 74; Abarquero 2005, 56; Blanco-González 2014, 453). Potters embodied and replicated non-discursive shared tenets on a routine basis, but by means of these social gatherings and the deployment of such festive services ‘their visual materialisation made them part of the habitus of everybody’ (Chapman and Gaydarska 2007, 182). Bronze Age groups in the Meseta have recently been characterized as scarcely integrated, short-lasting and unstable social units, lacking long-term cultural rules and institutions, restricted to one generation lifespan at the most (Blanco-González 2015). (…)
If we take into account that the earliest Iberian Bell Beakers were I2a, R1b-V88, and G2a, just like previous Chalcolithic and Neolithic Iberians, it cannot get clearer how and when the first Indo-European waves reached Iberia, and thus that the Harrison and Heyd (2007) model of East Bell Beaker expansion was right. Not a single reputable geneticist contests the origin of R1b-L23 subclades in Iberia anymore (see e.g. Heyd, or Lazaridis).
While the Spanish archaeological school will be slow to adapt to genetic finds – since there are many scholars who have supported for years other ways of expansion of the different Bell Beaker motifs, and follow mostly the “pots not people” descriptive Archaeology – , many works like these can be just as well reinterpreted in light of what we already know happened in terms of population movements during this period, and this alone gives a whole new interesting perspective to archaeological finds.
On the previous, non-Indo-European stage of the Iberian Paeninsula, there is also a new paper (behind paywall), showing reasons for inter-regional differences, and thus supporting homogeneity before the arrival of Bell Beakers:
The Chalcolithic period is traditionally defined by the emergence of copper elements and associated to the beginning of defensive-style architecture (Esquivel and Navas 2007). This last characteristic only seems to appear clearly in the southeast of the Iberian Peninsula, with the denominated Millares Culture (e.g. García Sanjuán 2013; Valera et al. 2014). In the rest of the Iberian Peninsula, the Neolithic-Chalcolithic transition is scarcely defined. In fact, it is possible that this transition does not even strictly exist and rather results from the evolution of villages present in the most advanced phases of the Neolithic (e.g. Blasco et al. 2007). This continuity is also perceptible in most of the sepulchral caves over time, where radiocarbon dates show a continued use from the 4th to the 3rd millennium cal B.C. (Fernández-Crespo 2016; Utrilla et al. 2015; Villalba-Mouco et al. 2017). Moreover, it is possible to find some copper materials normally associated with burial contexts as prestigious grave goods (Blasco and Ríos 2010), but not as evidence of a massive replacement of commonly used tools such as flint blades, bone industry, polished stones or pottery without singular characteristics from a unique period (Pérez-Romero et al. 2017). (…)
The human isotope values from both sites portray a quite homogeneous overall diet among humans. This homogeneous pattern of diet based on C3 terrestrial resources seems to be general along the entire Iberian Peninsula during the Late Neolithic and Chalcolithic (e.g. Alt et al. 2016; Díaz-Zorita 2014; Fernández-Crespo et al. 2016; Fontanals-Coll et al. 2015; García-Borja et al. 2013; López-Costas et al. 2015; McClure et al. 2011; Sarasketa-Gartzia et al. 2017; Villalba- Mouco et al. 2017; Salazar-García 2011; Salazar-García et al. 2013b; Salazar-García 2014; Waterman et al. 2016). The reason of this homogeneity could be the consolidated economy based on agriculture and livestock, together with a higher mobility among the different communities and the increase of trade networks, not only in prestigious objects (Schuhmacher and Banerjee 2012) but also in food products. Isotopic analyses in fauna remains could give us more clues about animal trade, as happens in other chronologies (Salazar- García et al. 2017).
In any case, and even if the dietary interpretation does not vary, it is noteworthy to mention that there are significant differences between δ13C human values from Cova de la Guineu and δ13C human values from Cueva de Abauntz (Mann-Whitney test, p = 1.05× 10−12) (Fig. 6). This observed δ13C differences among humans is also present among herbivores (Mann-Whitney test, p = 0.0004), which define the baseline of each ecosystem. This suggests that the observed human difference between sites should not be attributed to diet, but most possibly to the existence of enough environmental differences to be recorded in the collagen δ13C values along the food web. Plants are very sensitive to different environmental factors (altitude, temperature, luminosity or water availability) and their physiological adaptation to its factors can generate a variation in their isotopic values as happens with C3 and C4 adaptations (O’Leary 1981; Ambrose 1991). This spectrum of values has been used to assess several aspects about past environmental conditions when studying the δ13C and δ15N isotopic values of a species with a fixed diet over time (e.g. Stevens et al. 2008; González-Guarda et al. 2017). Moreover, this gradual δ13C and δ15N variation among different environments is very helpful to discriminate altitudinal movements in herbivores with a high precision method based on serial dentine analysis (Tornero et al. 2016b). In our case, results reflect the influence of environment from at least two areas in Iberia (the Western Prepyrenees and the Northeastern coast of Iberia). These differences demand caution when interpreting human diets from different sites that are not contemporary and/or not in a same area, as it is possible that the environmental influence is responsible for changes otherwise attributed to different subsistence patterns and social structures (Fernández-Crespo and Schulting 2017), as has been demonstrated in neighbouring territories (Herrscher and Bras-Goude 2010; Goude and Fontugne 2016).
NOTE. I think one of the important changes in this version compared to the preprint is the addition of the recent Iberomaurusian samples.
Abstract (emphasis mine):
The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.
FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ∼15,000-y old and ∼7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa.
Genetic analyses have revealed that the population history of modern North Africans is quite complex (11). Based on our aDNA analysis, we identify an Early Neolithic Moroccan component that is (i) restricted to North Africa in present-day populations (11); (ii) the sole ancestry in IAM samples; and (iii) similar to the one observed in Later Stone Age samples from Morocco (17). We conclude that this component, distantly related to that of Epipaleolithic communities from the Levant, represents the autochthonous Maghrebi ancestry associated with Berber populations. Our data suggests that human populations were isolated in the Maghreb since Upper Paleolithic times. Our hypothesis is in agreement with archaeological research pointing to the first stage of the Neolithic expansion in Morocco as the result of a local population that adopted some technological innovations, such as pottery production or farming, from neighboring areas.
By 3,000 BCE, a continuity in the Neolithic spread brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Other archaeological remains, such as African elephant ivory and ostrich eggs found in Iberian sites, confirm the existence of contacts and exchange networks through both sides of the Gibraltar strait at this time. Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/ Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves. Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today.
Also, from the main author’s Twitter account:
I just realized that the paragraph with information on data availability is missing! Sequence data in the European Nucleotide Archive (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology Information (Accession Numbers MF991431-MF991448).
I find it hard to believe that this genetic continuity from Upper Palaeolithic to Late Neolithic could be representative of an autochthonous development of Afroasiatic. An important population movement – likely more than one – must be found in ancient DNA influencing North-Central and North-East Africa, probably during the time of the Green Sahara corridor.
Blevins (to appear) presents a new reconstruction of Proto-Basque, the mother of Basque and Aquitanian, based on standard methods in historical linguistics: the comparative method and the method of internal reconstruction. Where all previous reconstructions of Proto-Basque assume a contrast between two sibilants, *s, a voiceless apical sibilant, and *z a voiceless laminal sibilant (Martinet 1955; Michelena 1977; Lakarra 1995; Trask 1997), this proposal is unique in positing only a single sibilant *s. Under this account, all instances of Common Basque /z/ are derived from *s. More specifically, in syllable coda, *Rs > *Rz (R a sonorant) while in the syllable onset, *sT > *zT (T an oral stop). The true split of *s into /s/ vs. /z/ occurs when clusters like *Rz or *zT are further simplified to /z/.
In this talk, internal evidence for a single sibilant, *s, in Proto-Basque is presented, and sound changes underlying the sibilant split are examined within the context of Evolutionary Phonology (Blevins 2004, 2006, 2015, 2017). Similar sound changes are identified in other languages with similar cluster types (e.g. Kümmel 2007:232), and the phonetic basis of the sibilant split is informed by recent studies of sibilant retraction (e.g. Stevens and Harrington 2016; Stuart-Smith et al. 2018).
I was never convinced, not just about a genetic connection, but about the very possibility of discovering it if there was any, mainly because such a link would be quite old, and Basque is known to have been greatly influenced by surrounding IE prestige languages for millennia until it was first attested in the 16th century. Internal reconstruction can only avail a gross reconstruction of few aspects up to a certain point in time, probably not very far beyond the Pre-Roman period, and that only thanks to the available Aquitanian inscriptions.
This haplogroup is also found in Sardinia, which may be connected to the expansion of V88 subclades (which I have speculatively proposed could be linked to Afro-Asiatic) into Africa through Italy and the Green Sahara; although it could also be linked to a speculative Vasconic-Iberian – Palaeo-Sardo group.
Without knowing the exact Pre-Proto-Indo-European stage at which Blevins would place the Basque separation, it is difficult to know how it could fit within any macro-language proposal – and thus potential ancestral population expansion.
Seeing how many Basque nationalists (obviously obsessed with racial purity) are still rooting for an autochthonous Palaeolithic origin of R1b lineages (especially P312) linked with the Basque language and dat huge Vasconic Western Europe; and now, after Olalde & Mathieson 2018, how some are also suggesting a Neolithic link of R1b with the Neolithic expansion and Sardinians, for lack of further modern genetic differences with other Western Europeans… I wonder how a lot of people inclined to believe this nonsense today, and mentally linking Vasconic with haplogroup R1b, will be paradoxically necessarily tied precisely to this kind of macro-family proposals in the future.
Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.
Some people like to say that Y-DNA haplogroup analysis, or phylogeography in general, is of no use anymore (especially modern phylogeography), and they are content to see how ‘steppe admixture’ was (or even is) distributed in Europe to draw conclusions about ancient languages and their expansion. With each new paper, we are seeing the advantages of analysing ancient and modern haplogroups in ascertaining population movements.
Quite recently there was a suggestion based on steppe admixture that Basque-speaking Iberians resisted the invasion from the steppe. Observing the results of this article (dates of expansion and demographic data) we see a clear expansion of Y-DNA haplogroups precisely by the time of Bell Beaker expansion from the east. Y-DNA haplogroups of ancient samples from Portugal point exactly to the same conclusion.
The recent article on Mycenaean and Minoan genetics also showed that, when it comes to Europe, most of the demographic patterns we see in admixture are reminiscent of the previous situation, only rarely can we see a clear change in admixture (which would mean an important, sudden replacement of the previous population).
The following are excerpts from the article (emphasis is mine):
Dates and expansions
The average STR variance of DF27 and each subhaplogroup is presented in Suppl. Table 2. As expected, internal diversity was higher in the deeper, older branches of the phylogeny. If the same diversity was divided by population, the most salient finding is that native Basques (Table 2) have a lower diversity than other populations, which contrasts with the fact that DF27 is notably more frequent in Basques than elsewhere in Iberia (Suppl. Table 1). Diversity can also be measured as pairwise differences distributions (Fig. 5). The distribution of mean pairwise differences within Z195 sits practically on top of that of DF27; L176.2 and Z220 have similar distributions, as M167 and Z278 have as well; finally, M153 shows the lowest pairwise distribution values. This pattern is likely to reflect the respective ages of the haplogroups, which we have estimated by a modified, weighted version of the ρ statistic (see Methods).
Z195 seems to have appeared almost simultaneously within DF27, since its estimated age is actually older (4570 ± 140 ya). Of the two branches stemming from Z195, L176.2 seems to be slightly younger than Z220 (2960 ± 230 ya vs. 3320 ± 200 ya), although the confidence intervals slightly overlap. M167 is clearly younger, at 2600 ± 250 ya, a similar age to that of Z278 (2740 ± 270 ya). Finally, M153 is estimated to have appeared just 1930 ± 470 ya.
Haplogroup ages can also be estimated within each population, although they should be interpreted with caution (see Discussion). For the whole of DF27, (Table 3), the highest estimate was in Aragon (4530 ± 700 ya), and the lowest in France (3430 ± 520 ya); it was 3930 ± 310 ya in Basques. Z195 was apparently oldest in Catalonia (4580 ± 240 ya), and with France (3450 ± 269 ya) and the Basques (3260 ± 198 ya) having lower estimates. On the contrary, in the Z220 branch, the oldest estimates appear in North-Central Spain (3720 ± 313 ya for Z220, 3420 ± 349 ya for Z278). The Basques always produce lower estimates, even for M153, which is almost absent elsewhere.
The median value for Tstart has been estimated at 103 generations (Table 4), with a 95% highest probability density (HPD) range of 50–287 generations; effective population size increased from 131 (95% HPD: 100–370) to 72,811 (95% HPD: 52,522–95,334). Considering patrilineal generation times of 30–35 years, our results indicate that R1b-DF27 started its expansion ~3,000–3,500 ya, shortly after its TMRCA.
As a reference, we applied the same analysis to the whole of R1b-S116, as well as to other common haplogroups such as G2a, I2, and J2a. Interestingly, all four haplogroups showed clear evidence of an expansion (p > 0.99 in all cases), all of them starting at the same time, ~50 generations ago (Table 4), and with similar estimated initial and final populations. Thus, these four haplogroups point to a common population expansion, even though I2 (TMRCA, weighted ρ, 7,800 ya) and J2a (TMRCA, 5,500 ya) are older than R1b-DF27. It is worth noting that the expansion of these haplogroups happened after the TMRCA of R1b-DF27.
Sum up and discussion
We have characterized the geographical distribution and phylogenetic structure of haplogroup R1b-DF27 in W. Europe, particularly in Iberia, where it reaches its highest frequencies (40–70%). The age of this haplogroup appears clear: with independent samples (our samples vs. the 1000 genome project dataset) and independent methods (variation in 15 STRs vs. whole Y-chromosome sequences), the age of R1b-DF27 is firmly grounded around 4000–4500 ya, which coincides with the population upheaval in W. Europe at the transition between the Neolithic and the Bronze Age. Before this period, R1b-M269 was rare in the ancient DNA record, and during it the current frequencies were rapidly reached. It is also one of the haplogroups (along with its daughter clades, R1b-U106 and R1b-S116) with a sequence structure that shows signs of a population explosion or burst. STR diversity in our dataset is much more compatible with population growth than with stationarity, as shown by the ABC results, but, contrary to other haplogroups such as the whole of R1b-S116, G2a, I2 or J2a, the start of this growth is closer to the TMRCA of the haplogroup. Although the median time for the start of the expansion is older in R1b-DF27 than in other haplogroups, and could suggest the action of a different demographic process, all HPD intervals broadly overlap, and thus, a common demographic history may have affected the whole of the Y chromosome diversity in Iberia. The HPD intervals encompass a broad timeframe, and could reflect the post-Neolithic population expansions from the Bronze Age to the Roman Empire.
While when R1b-DF27 appeared seems clear, where it originated may be more difficult to pinpoint. If we extrapolated directly from haplogroup frequencies, then R1b-DF27 would have originated in the Basque Country; however, for R1b-DF27 and most of its subhaplogroups, internal diversity measures and age estimates are lower in Basques than in any other population. Then, the high frequencies of R1b-DF27 among Basques could be better explained by drift rather than by a local origin (except for the case of M153; see below), which could also have decreased the internal diversity of R1b-DF27 among Basques. An origin of R1b-DF27 outside the Iberian Peninsula could also be contemplated, and could mirror the external origin of R1b-M269, even if it reaches there its highest frequencies. However, the search for an external origin would be limited to France and Great Britain; R1b-DF27 seems to be rare or absent elsewhere: Y-STR data are available only for France, and point to a lower diversity and more recent ages than in Iberia (Table 3). Unlike in Basques, drift in a traditionally closed population seems an unlikely explanation for this pattern, and therefore, it does not seem probable that R1b-DF27 originated in France. Then, a local origin in Iberia seems the most plausible hypothesis. Within Iberia, Aragon shows the highest diversity and age estimates for R1b-DF27, Z195, and the L176.2 branch, although, given the small sample size, any conclusion should be taken cautiously. On the contrary, Z220 and Z278 are estimated to be older in North Central Spain (N Castile, Cantabria and Asturias). Finally, M153 is almost restricted to the Basque Country: it is rarely present at frequencies >1% elsewhere in Spain (although see the cases of Alacant, Andalusia and Madrid, Suppl. Table 1), and it was found at higher frequencies (10–17%) in several Basque regions; a local origin seems plausible, but, given the scarcity of M153 chromosomes outside of the Basque Country, the diversity and age values cannot be compared.
Within its range, R1b-DF27 shows same geographical differentiation: Western Iberia (particularly, Asturias and Portugal), with low frequencies of R1b-Z195 derived chromosomes and relatively high values of R1b-DF27* (xZ195); North Central Spain is characterized by relatively high frequencies of the Z220 branch compared to the L176.2 branch; the latter is more abundant in Eastern Iberia. Taken together, these observations seem to match the East-West patterning that has occurred at least twice in the history of Iberia: i) in pre-Roman times, with Celtic-speaking peoples occupying the center and west of the Iberian Peninsula, while the non-Indoeuropean eponymous Iberians settled the Mediterranean coast and hinterland; and ii) in the Middle Ages, when Christian kingdoms in the North expanded gradually southwards and occupied territories held by Muslim fiefs.
I wouldn’t trust the absence of R1b-DF27 outside France as a proof that its origin must be in Western Europe – especially since we have ancient DNA, and that assertion might prove quite wrong – but aside from that the article seems solid in its analysis of modern populations.
Iberia is unusual in harbouring a surviving pre-Indo-European language, Euskera, and inscription evidence at the dawn of history suggests that pre-Indo-European speech prevailed over a majority of its eastern territory with Celtic-related language emerging in the west. Our results showing that predominantly Anatolian-derived ancestry in the Neolithic extended to the Atlantic edge strengthen the suggestion that Euskara is unlikely to be a Mesolithic remnant. Also our observed definite, but limited, Bronze Age influx resonates with the incomplete Indo-European linguistic conversion on the peninsula, although there are subsequent genetic changes in Iberia and defining a horizon for language shift is not yet possible. This contrasts with northern Europe which both lacks evidence for earlier language strata and experienced a more profound Bronze Age migration.
Judging from the article, more precise summaries of potential consequences would have been “Proto-Basque and Proto-Iberian peoples derived from Neolithic farmers, not Mesolithic or Palaeolithic hunter-gatherers”, or “incomplete Indo-European linguistic conversion of the Iberian Peninsula” – both aspects, by the way, are already known. That would have been quite unromantic, though.
So I thought, what the hell, let’s go with the tide. Using the published dataset, I have also helped reconstruct the original phenotype of Bronze Age Iberians, and this is how our Iberian ancestors probably looked like:
As always, trying to equate steppe or Yamna admixture with invasion or language is plainly wrong. Doing it with few samples, and with the wrong assumptions of what “steppe admixture” means, well…
Proto-Basque and Proto-Iberian no doubt survived the Indo-European Bell Beaker migrations, but if Y-DNA lineages were replaced already by the Bronze Age in southern Portugal, there is little reason to support an increased “resistance” of Iberians to Bell Beaker invaders compared to other marginal regions of Europe (relative to the core Yamna expansion in eastern and central Europe).
As you know, Aquitanian (the likely ancestor of Basque) and Iberian were just two of the many non-Indo-European languages spoken in Europe at the dawn of historical records, so to speak about Iberia as radically different than Italy, Greece, Northern Britain, Scandinavia, or Eastern Europe, is reminiscent of the racism (or, more exactly, xenophobia) that is hidden behind romantic views certain people have of their genetic ancestry.
Some groups formed by a majority of R1b-DF27 lineages, now prevalent in Iberia, spoke probably Iberian languages during the Iron Age in north and eastern Iberia, before their acculturation during the expansion of Celtic-speaking peoples, and later during the expansion of Rome, when most of them eventually spoke Latin. In Mediaeval times, these lineages probably expanded Romance languages southward during the Reconquista.
Before speaking Iberian languages, R1b-DF27 lineages (or older R1b-P312) were probably Indo-European speakers who expanded with the Bell Beaker culture from the lower Danube – in turn created by the interaction of Yamna with Proto-Bell Beaker cultures, and adopted probably the native Proto-Basque and Proto-Iberian languages (or possibly the ancestor of both) near the Pyrenees, either by acculturation, or because some elite invaders expanded successfully (their Y-DNA haplogroup) over the general population, for generations.
Maybe some kind of genetic bottleneck happened, that expanded previously not widespread lineages, as with N1c subclades in Finland.
There is nothing wrong with hypothetic models of ancient genetic prehistory: there are still too many potential scenarios for the expansion of haplogroup R1b-DF27 in Iberia. But, please, stop supporting romantic pictures of ethnolinguistic continuity for modern populations. It’s embarrassing.
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