The genetic makings of South Asia – IVC as Proto-Dravidian

south-asian-language-families

Review (behind paywall) The genetic makings of South Asia, by Metspalu, Monda, and Chaubey, Current Opinion in Genetics & Development (2018) 53:128-133.

Interesting excerpts (emphasis mine):

(…) the spread of agriculture in Europe was a result of the demic diffusion of early Anatolian farmers, it was discovered that the spread of agriculture to South Asia was mediated by a genetically completely different farmer population in the Zagros mountains in contemporary Iran (IF). The ANI-ASI cline itself was interpreted as a mixture of three components genetically related to Iranian agriculturalists, Onge and Early and Middle Bronze Age Steppe populations (Steppe_EMBA).

The first ever autosomal aDNA from South Asia comes from Northern Pakistan (Swat Valley, early Iron Age). This study presented altogether 362 aDNA samples from the broad South and Central Asia and contributes substantially to our understanding of the evolutionary past of South and Central Asia. The study redefines the three genetic strata that form the basis of the Indian Cline. The Indus Periphery (IP) component is composed of (varying proportions of): first, IF, second, Ancient Ancestral South Asians (AASI), which represents an ancient branch of human genetic variation in Asia arising from a population split contemporaneous with the splits of East Asian, Onge and Australian Aboriginal ancestors and third, West_Siberian Hunter gatherers (WS_HG).

The authors argue that IP could have formed the genetic base of the Indus Valley Civilization (IVC). Upon the collapse of the IVC IP contributes to the formation of both ASI and ANI. ASI is formed as IP admixes further with AASI. ANI in turn forms when IP admixes with the incoming Middle and Late Bronze Age Steppe (Steppe_MLBA) component, (rather than the Steppe_EMBA groups suggested earlier)

ane-whg-ehg-chg-wshg-steppe
A sketch of the peopling history of South Asia. Depicting the full complexity of available reconstructions is not attempted. Placing of population labels does not indicate precise geographic location or range of the population in question. Rather we aim to highlight the essentials of the recent advancements in the field. We divide the scenario into three time horizons: Panels (a) before 10 000 BCE (pre agriculture era.); (b) 10 000 BCE to 3000 BCE (agriculture era) and (c) 3000 BCE to prehistoric era/modern era. (iron age).

Dating of the arrival of the Austro-Asiatic speakers in South Asia-based on Y chromosome haplogroup O2a1-M95 expansion estimates yielded dates between 3000 and 2000 BCE [30]. However, admixture LD decay-based approach on genome-wide data suggests the admixture between South Asian and incoming Austro-Asiatic speakers occurred slightly later between 1800 and 0 BCE (Tätte et al. submitted). It is interesting that while the mtDNA variants of the Mundas are completely South Asian, the Y chromosome variation is dominated at >60% by haplogroup O2a which is phylogeographically nested in East Asian-specific paternal lineages.

In India, the speakers of Tibeto-Burman (TB) languages live in the Seven Sisters States in Northeast India and in the very north of the country. Genetically they show a clear East Asian origin and around 20% of subsequent admixture with South Asians within the last 1000 years.The genetic flavour of East Asia in TB is different from that in Munda speakers as the best surrogates for the East Asian admixing component are contemporary Han Chinese.

I found the simplistic migration maps especially interesting to illustrate ancient population movements. The emergence of EHG is supposed to involve a WHG:ANE cline, though, and this isn’t clear from the map. Also, there is new information on what may be at the origin of WHG and Anatolian hunter-gatherers.

From the recent Reich’s session on South Asia at ISBA 8:

ani-asi-steppe-cline
– Tale of three clines, with clear indication that “Indus Periphery” samples drawn from an already-cosmopolitan and heterogeneous world of variable ASI & Iranian ancestry. (I know how some people like to pore over these pictures – so note red dots = just dummy data for illustration.)
– Some more certainty about primary window of steppe ancestry injection into S. Asia: 2000-1500 BC
Alexander M. Kim

Featured image: map of South Asian languages from http://llmap.org.

Related

Resurge of local populations in the final Corded Ware culture period from Poland

poland-kujawy

Open access A genomic Neolithic time transect of hunter-farmer admixture in central Poland, by Fernandes et al. Scientific Reports (2018).

Interesting excerpts (emphasis mine, stylistic changes):

Most mtDNA lineages found are characteristic of the early Neolithic farmers in south-eastern and central Europe of the Starčevo-Kőrös-Criş and LBK cultures. Haplogroups N1a, T2, J, K, and V, which are found in the Neolithic BKG, TRB, GAC and Early Bronze Age samples, are part of the mitochondrial ‘Neolithic package’ (which also includes haplogroups HV, V, and W) that was introduced to Europe with farmers migrating from Anatolia at the onset of the Neolithic17,31.

A noteworthy proportion of Mesolithic haplogroup U5 is also found among the individuals of the current study. The proportion of haplogroup U5 already present in the earliest of the analysed Neolithic groups from the examined area differs from the expected pattern of diversity of mtDNA lineages based on a previous archaeological view and on the aDNA findings from the neighbouring regions which were settled by post-Linear farmers similar to BKG at that time. A large proportion of Mesolithic haplogroups in late-Danubian farmers in Kuyavia was also shown in previous studies concerning BKG samples based on mtDNA only, although these frequencies were derived on the basis of very small sample sizes.

y-dna-poland

A significant genetic influence of HG populations persisted in this region at least until the Eneolithic/Early Bronze Age period, when steppe migrants arrived to central Europe. The presence of two outliers from the middle and late phases of the BKG in Kuyavia associated with typical Neolithic burial contexts provides evidence that hunter-farmer contacts were not restricted to the final period of this culture and were marked by various episodes of interaction between two societies with distinct cultural and subsistence differences.

The identification of both mitochondrial and Y-chromosome haplogroup lineages of Mesolithic provenance (U5 and I, respectively) in the BKG support the theory that both male and female hunter-gatherers became part of these Neolithic agricultural societies, as has been reported for similar cases from the Carpathian Basin, and the Balkans. The identification of an individual with WHG affinity, dated to ca. 4300 BCE, in a Middle Neolithic context within a BKG settlement, provides direct evidence for the regional existence of HG enclaves that persisted and coexisted at least for over 1000 years, from the arrival of the LBK farmers ca. 5400 BCE until ca. 4300 BCE, in proximity with Neolithic settlements, but without admixing with their inhabitants.

poland-pca
Principal component analysis with modern populations greyed out on the background (top), ADMIXTURE results with K = 10 with samples from this study amplified (bottom).

The analysis of two Late Neolithic cultures, the GAC and CWC, shows that steppe ancestry was present only among the CWC individuals analysed, and that the single GAC individual had more WHG ancestry than previous local Neolithic individuals. (…) The CWC’s affinity to WHG, however, contrasts with results from published CWC individuals that identified steppe ancestry related to Yamnaya as the major contributor to the CWC genomes, while here we report also substantial contributions from WHG that could relate to the late persistence of pockets of WHG populations, as supported by the admixture results of N42 and the finding of the 4300-year-old N22 HG individual. These results agree with archaeological theories that suggest that the CWC interaction with incoming steppe cultures was complex and that it varied by region.

Some comments

About the analyzed CWC samples, it is remarkable that, even though they are somehow related to each other, they do not form a tight cluster. Also, their Y-DNA (I2a), and this:

When compared to previously published CWC data, our CWC group (not individuals) is genetically significantly closer to WHG than to steppe individuals (Z = −4.898), a result which is in contrast with those for CWC from Germany (Z = 2.336), Estonia (Z = 0.555), and Latvia (Z = 1.553).

ancestry-proportions-poland
Ancestry proportions based on qpAdm. Visual representation of the main results presented in Supplementary Table S5. Populations from this study marked with an asterisk. Values and populations in brackets show the nested model results marked in green in Supplementary Table S5.

Włodarczak (2017) talks about the CWC period in Poland after ca. 2600 BC as a time of emergence of an allochthnous population, marked by the rare graves of this area, showing infiltrations initially mainly from Lesser Poland, and later (after 2500 BC) from the western Baltic zone.

Since forest sub-Neolithic populations would have probably given more EHG to the typical CWC population, these samples support the resurge of ‘local’ pockets of GAC- or TRB-like groups with more WHG (and also Levant_Neolithic) ancestry.

The known presence of I2a2a1b lineages in GAC groups in Poland also supports this interpretation, and the subsistence of such pockets of pre-steppe-like populations is also seen with the same or similar lineages appearing in comparable ‘resurge’ events in Central Europe, e.g. in samples from the Únětice and Tumulus culture.

About the Bronze Age sample, we have at last official confirmation of haplogroup R1a1a (sadly no subclade*) at the very beginning of the Trzciniec period – in a region between western (Iwno) and eastern (Strzyżów) groups related to Mierzanowice – , which has to be put in relation with the samples from the final Trzciniec period in the Baltic published in Mittnik et al. (2018).

EDIT (8 OCT 2018): More specific subclades have been published, including a R1a-Z280 lineage for the Bronze Age sample (see spreadsheet).

This confirms the early resurge of R1a-Z645 (probably R1a-Z282) lineages at the core of the developing East European Bronze Age, a province of the European Bronze Age that emerged from evolving Bell Beaker groups in Poland.

bell-beakers-poland-kujawy
Arrival of Bell Beakers in Poland after ca. 2400 BC, and their origin in other BBC centres (Czebreszuk and Szmyt 2011).

I don’t have any hope that the Balto-Slavic evolution through BBC Poland → Mierzanowice/Iwno → Trzciniec → Lusatian cultures is going to be confirmed any time soon, until we have a complete trail of samples to follow all the way to historic Slavs of the Prague culture. However, I do think that the current data on central-east Europe – and the recent data we are receiving from north-east Europe and the Iranian steppes, at odds with the Indo-Slavonic alternative – supports this model.

I guess that, in the end, similar to how the Yamna vs. Corded Ware question is being solved, the real route of expansion of Proto-Balto-Slavic (supposedly spoken ca. 1500-1000 BC) is probably going to be decided by the expansion of either R1a-M458 (from the west) or R1a-Z280 lineages (from the east), because the limited precision of genetic data and analyses available today are going to show ‘modern Slavic’-like populations from the whole eastern half of Europe for the past 4,000 years…

Related

Corded Ware—Uralic (I): Differences and similarities with Yamna

indo-european-uralic-migrations-corded-ware

I was reading The Bronze Age Landscape in the Russian Steppes: The Samara Valley Project (2016), and I was really surprised to find the following excerpt by David W. Anthony:

The Samara Valley links the central steppes with the western steppes and is a north-south ecotone between the pastoral steppes to the south and the forest-steppe zone to the north [see figure below]. The economic contrast between pastoral steppe subsistence, with its associated social organizations, and forest-zone hunting and fishing economies probably explains the shifting but persistent linguistic border between forest-zone Uralic languages to the north (today largely displaced by Russian) and a sequence of steppe languages to the south, recently Turkic, before that Iranian, and before that probably an eastern dialect of Proto-Indo-European (Anthony 2007). The Samara Valley represents several kinds of borders, linguistic, cultural, and ecological, and it is centrally located in the Eurasian steppes, making it a critical place to examine the development of Eurasian steppe pastoralism.

uralic-languages-forest-zone-volga
Language map of the middle Volga-Ural region. After “Geographical Distribution of the Uralic Languages” by Finno-Ugrian Society, Helsinki, 1993.

Khokhlov (translated by Anthony) further insists on the racial and ethnic divide between both populations, Abashevo to the north, and Poltavka to the south, during the formation of the Abashevo – Sintashta-Potapovka community that gave rise to Proto-Indo-Iranians:

Among all cranial series in the Volga-Ural region, the Potapovka population represents the clearest example of race mixing and probably ethnic mixing as well. The cultural advancements seen in this period might perhaps have been the result of the mixing of heterogeneous groups. Such a craniometric observation is to some extent consistent with the view of some archaeologists that the Sintashta monuments represent a combination of various cultures (principally Abashevo and Poltavka, but with other influences) and therefore do not correspond to the basic concept of an archaeological culture (Kuzmina 2003:76). Under this option, the Potapovka-Sintashta burial rite may be considered, first, a combination of traits to guarantee the afterlife of a selected part of a heterogeneous population. Second, it reflected a kind of social “caste” rather than a single population. In our view, the decisive element in shaping the ethnic structure of the Potapovka-Sintashta monuments was their extensive mobility over a fairly large geographic area. They obtained knowledge of various cultures from the populations with whom they interacted.

steppe-lmba-sintashta-potapovka-filatovka
Late Middle Bronze Age cultures with the Proto-Indo-Iranian Sintashta-Potapovka-Filatovka group (shaded). After Anthony (2007 Figure 15.5), from Anthony (2016).

Interesting is also this excerpt about the predominant population in the Abashevo – Sintashta-Potapovka admixture (which supports what Chetan said recently, although this does not seemed backed by Y-DNA haplogroups found in the richest burials), coupled with the sign of incoming “Uraloid” peoples from the east, found in both Sintashta and eastern Abashevo:

The socially dominant anthropological component was Europeoid, possibly the descendants of Yamnaya. The association of craniofacial types with archaeological cultures in this period is difficult, primarily because of the small amount of published anthropological material of the cultures of steppe and forest belt (Balanbash, Vol’sko-Lbishche) and the eastern and southern steppes (Botai-Tersek). The crania associated with late MBA western Abashevo groups in the Don-Volga forest zone were different from eastern Abashevo in the Urals, where the expression of the Old Uraloid craniological complex was increased. Old Uraloid is found also on a single skull of Vol’sko-Lbishche culture (Tamar Utkul VII, Kurgan 4). Potentially related variants, including Mongoloid features, could be found among the Seima-Turbino tribes of the forest-steppe zone, who mixed with Sintashta and Abashevo. In the Sintashta Bulanova cemetery from the western Urals, some individuals were buried with implements of Seima-Turbino type (Khalyapin 2001; Khokhlov 2009; Khokhlov and Kitov 2009). Previously, similarities were noted between some individual skulls from Potapovka I and burials of the much older Botai culture in northern Kazakhstan (Khokhlov 2000a). Botai-Tersek is, in fact, a growing contender for the source of some “eastern” cranial features.

khvalynsk-yamna-srubna-facial-reconstruction
Facial reconstructions based on skulls from (a) Khvalynsk II Grave 24, a young adult male; (b) Poludin Grave 6, Yamnaya culture, a mature male (both by A. I. Nechvaloda); and (c) Luzanovsky cemetery, Srubnaya culture (by L. T. Yablonsky). In Khokhlov (2016).

The wave of peoples associated with “eastern” features can be seen in genetics in the Sintashta outliers from Narasimhan et al. (2018), and it probably will be eventually seen in Abashevo, too. These may be related to the Seima-Turbino international network – but most likely it is directly connected to Sintashta through the starting Andronovo and Seima-Turbino horizons, by admixing of prospective groups and small-scale back-migrations.

Corded Ware – Yamna similarities?

So, if peoples of north-eastern Europe have been assumed for a long time to be Uralic speakers, what is happening with the Corded Ware = IE obsession? Is it Gimbutas’ ghost possessing old archaeologists? Probably not.

It is about certain cultural similarities evident at first sight, which have been traditionally interpreted as a sign of cultural diffusion or migration. Not dissimilar to the many Bell Beaker models available, where each archaeologist is pushing certain differences, mixing what seemed reasonable, what still might seem reasonable, and what certainly isn’t anymore after the latest ancient DNA data.

kurgan-expansion
“European dialect” expansion of Proto-Indo-European according to Gimbutas (1963)

The initial models of Gimbutas, Kristiansen, or Anthony – which are known to many today – were enunciated in the infancy of archaeological studies in the regions, during and just after the fall of the USSR, and before many radiocarbon dates that we have today were published (with radiocarbon dating being still today in need of refinement), so it is only logical that gross mistakes were made.

We have similar gross mistakes related to the origins of Bell Beakers, and studying them was certainly easier than studying eastern data.

  • Gimbutas believed – based mainly on Kurgan-like burials – that Bell Beaker formed from a combination of Yamna settlers with the Vučedol culture, so she was not that far from the truth.
  • The expansion of Corded Ware from peoples of the North Pontic forest-steppe area, proposed by Gimbutas and later supported also by Kristiansen (1989) as the main Indo-European expansion – , is probably also right about the approximate origins of the culture. Only its ‘Indo-European’ nature is in question, given the differences with Khvalynsk and Yamna evolution.
  • Anthony only claimed that Yamna migrants settled in the Balkans and along the Danube into the Hungarian steppes. He never said that Corded Ware was a Yamna offshoot until after the first genetic papers of 2015 (read about his newest proposal). He initially claimed that only certain neighbouring Corded Ware groups “adopted” Indo-European (through cultural diffusion) because of ‘patron-client’ relationships, and was never preoccupied with the fate of Corded Ware and related cultures in the east European forest zone and Finland.

So none of them was really that far from the true picture; we might say a lot people are more way off the real picture today than the picture these three researchers helped create in the 1990s and 2000s. Genetics is just putting the last nail in the coffin of Corded Ware as a Yamna offshoot, instead of – as we believed in the 2000s – to Vučedol and Bell Beaker.

So let’s revise some of these traditional links between Corded Ware and Yamna with today’s data:

Archaeology

Even more than genetics – at least until we have an adequate regional and temporary sampling – , archaeological findings lead what we have to know about both cultures.

It is essential to remember that Corded Ware, starting ca. 3000/2900 BC in east-central Europe, has been proposed to be derived from Early Yamna, which appeared suddenly in the Pontic-Caspian steppes ca. 3300 BC (probably from the late Repin expansion), and expanded to the west ca. 3000.

Early Yamna is in turn identified as the expanding Late Proto-Indo-European community, which has been confirmed with the recent data on Afanasevo, Bell Beaker, and Sintashta-Potapovka and derived cultures.

The question at hand, therefore, is if Corded Ware can be considered an offshoot of the Late PIE community, and thus whether the CWC ethnolinguistic community – proven in genetics to be quite homogeneous – spoke a Late PIE dialect, or if – alternatively – it is derived from other neighbouring cultures of the North Pontic region.

NOTE. The interpretation of an Indo-Slavonic group represented by a previous branching off of the group is untenable with today’s data, since Indo-Slavonic – for those who support it – would itself be a branch of Graeco-Aryan, and Palaeo-Balkan languages expanded most likely with West Yamna (i.e. R1b-L23, mainly R1b-Z2103) to the south.

The convoluted alternative explanation would be that Corded Ware represents an earlier, Middle PIE branch (somehow carrying R1a??) which influences expanding Late PIE dialects; this has been recently supported by Kortlandt, although this simplistic picture also fails to explain the Uralic problem.

Kurgans: The Yamna tradition was inherited from late Repin, in turn inherited from Khvalynsk-Novodanilovka proto-Kurgans. As for the CWC tradition, it is unclear if the tumuli were built as a tradition inherited from North and West Pontic cultures (in turn inherited or copied from Khvalynsk-Novodanilovka), such as late Trypillia, late Kvityana, late Dereivka, late Sredni Stog; or if they were built because of the spread of the ‘Transformation of Europe’, set in motion by the Early Yamna expansion ca. 3300-3000 BC (as found in east-central European cultures like Coţofeni, Lizevile, Șoimuș, or the Adriatic Vučedol). My guess is that it inherits an older tradition than Yamna, with an origin in east-central Europe, because of the mound-building distribution in the North Pontic area before the Yamna expansion, but we may never really know.

pit-graves-central-europe-cwc
Distribution of Pit-Grave burials west of the Black Sea likely dating to the 2nd half of the IVth millennium BC (triangles: side-crouched burials; filled circles: supine extended burials; open circles: suspected). Frînculeasa, Preda, and Heyd (2015)

Burial rite: Yamna features (with regional differences) single burials with body on its back, flexed upright knees, poor grave goods, common orientation east-west (heads to the west) inherited from Repin, in turn inherited from Khvalynsk-Novodanilovka. CWC tradition – partially connected to Złota and surrounding east-central European territories (in turn from the Khvalynsk-Novodanilovka expansion) – features single graves, body in fetal position, strict gender differentiation – men on the right, women on the left -, looking to the south, graves with standardized assemblages (objects representing affirmation of battle, hunting, and feasting). The burial rites clearly represent different ideologies.

pit-grave-burial-schemes
Left: Pit-Grave burial types expanded with Khvalynsk-Novodanilovka. Right: Pit-Grave burial types associated with the Yamna expansion and influence. Frînculeasa, Preda, and Heyd (2015)

Corded decoration: Corded ware decoration appears in the Balkans during the 5th millennium, and represents a simple technique whereby a cord is twisted, or wrapped around a stick, and then pressed directly onto the fresh surface of a vessel leaving a characteristic decoration. It appears in many groups of the 5th and 4th millennium BC, but it was Globular Amphorae the culture which popularized the drinking vessels and their corded ornamentation. It appears thus in some regional groups of Yamna, but it becomes the standard pottery only in Corded Ware (especially with the A-horizon), which shows continuity with GAC pottery.

corded-ware-first-horizon
Origins of the first Corded Ware horizon (5th millennium BC) after the Khvalynsk-Novodanilovka expansion. Corded Ware (circles) and horse-head scepters (rectangles) and other steppe elements (triangles). Image from Bulatović (2014).

Economy: Yamna expands from Repin (and Repin from Khvalynsk-Novodanilovka) as a nomadic or semi-nomadic purely pastoralist society (with occasional gathering of wild seeds), which naturally thrives in the grasslands of the Pontic-Caspian, lower Danube and Hungarian steppes. Corded Ware shows agropastoralism (as late Eneolithic forest-steppe and steppe groups of eastern Europe, such as late Trypillian, TRB, and GAC groups), inhabits territories north of the loess line, with heavy reliance of hunter-gathering depending on the specific region.

Cattle herding: Interestingly, both west Yamna and Corded Ware show more reliance on cattle herding than other pastoralist groups, which – contrasted with the previous Eneolithic herding traditions of the Pontic-Caspian steppe, where sheep-goats predominate – make them look alike. However, the cattle-herding economy of Yamna is essential for its development from late Repin and its expansion through the steppes (over western territories practising more hunter-gathering and sheep-goat herding economy), and it does not reach equally the Volga-Ural region, whose groups keep some of the old subsistence economy (read more about the late Repin expansion). Corded Ware, on the other hand, inherits its economic strategy from east European groups like TRB, GAC, and especially late Trypillian communities, showing a predominance of cattle herding within an agropastoral community in the forest-steppe and forest zones of Volhynia, Podolia, and surrounding forest-steppe and forest regions.

yamna-scheme
Scheme of interlinked socio-economic-ideological innovations forming the Yamnaya. Frînculeasa, Preda, and Heyd (2015)

Horse riding: Horse riding and horse transport is proven in Yamna (and succeeding Bell Beaker and Sintashta), assumed for late Repin (essential for cattle herding in the seas of grasslands that are the steppes, without nearby water sources), quite likely during the Khvalynsk expansion (read more here), and potentially also for Samara, where the predominant horse symbolism of early Khvalynsk starts. Corded Ware – like the north Pontic forest-steppe and forest areas during the Eneolithic – , on the other hand, does not show a strong reliance on horse riding. The high mobility and short-term settlements characteristic of Corded Ware, that are often associated with horse riding by association with Yamna, may or may not be correct, but there is no need for horses to explain their herding economy or their mobility, and the north-eastern European areas – the one which survived after Bell Beaker expansion – did certainly not rely on horses as an essential part of their economy.

NOTE: I cannot think of more supposed similarities right now. If you have more ideas, please share in the comments and I will add them here.

Genetic similarities

EHG: This is the clearest link between both communities. We thought it was related to the expansion of ANE-related ancestry to the west into WHG territory, but now it seems that it will be rather WHG expanding into ANE territory from the Pontic-Caspian region to the east (read more on recent Caucasus Neolithic, on , and on Caucasus HG).

NOTE. Given how much each paper changes what we know about the Palaeolithic, the origin and expansion of the (always developing) known ancestral components and specific subclades (see below) is not clear at all.

CHG: This is the key link between both cultures, which will delimit their interaction in terms of time and space. CHG is intermediate between EHG and Iran N (ca. 8000 BC). The ancestry is thus linked to the Caucasus south of the steppe before the emergence of North Pontic (western) and Don-Volga-Ural (eastern) communities during the Mesolithic. The real question is: when we have more samples from the steppe and the Caucasus during the Neolithic, how many CHG groups are we going to find? Will the new specific ancestral components (say CHG1, CHG2, CHG3, etc.) found in Yamna (from Khvalynsk, in the east) and Corded Ware (probably from the North Pontic forest-steppe) be the same? My guess is, most likely not, unless they are mediated by the Khvalynsk-Novodanilovka expansion (read more on CHG in the Caucasus).

yamnaya-chg-ancestry
Formation of Yamna and CHG contribution, in Damgaard et al. (Science 2018). A 10-leaf model based on combining the models in Fig. S16 and Fig. S19 and re-estimating the model parameters.

WHG/EEF: This is the obvious major difference – known today – in the formation of both communities in the steppe, and shows the different contacts that both groups had at least since the Eneolithic, i.e. since the expansion of Repin with its renewed Y-DNA bottleneck, and probably since before the early Khvalynsk expansion (read more on Yamna-Corded Ware differences contrasting with Yamna-Afanasevo, Yamna-Bell Beaker, and Yamna-Sintashta similarities).

NOTE 1. Some similarities between groups can be seen depending on the sampled region; e.g. Baltic groups show more similarities with southern Pontic-Caspian steppe populations, probably due to exogamy.

yamna-corded-ware-diff-qpgraph
Tested qpGraph model in Tambets et al. (2018). The qpGraph model fitting the data for the tested populations. “Colour codes for the terminal nodes: pink—modern populations (‘Population X’ refers to test population) and yellow—ancient populations (aDNA samples and their pools). Nodes coloured other than pink or yellow are hypothetical intermediate populations. We putatively named nodes which we used as admixture sources using the main recipient among known populations. The colours of intermediate nodes on the qpGraph model match those on the admixture proportions panel.”

NOTE 2. We have this information on the differences in “steppe ancestry” between Yamna and Corded Ware, compared to previous studies, because now we have more samples of neighbouring, roughly contemporaneous Eneolithic groups, to analyse the real admixture processes. This kind of fine scale studies is what is going to show more and more differences between Khvalynsk-Yamna and Sredni Stog-Corded Ware as more data pours in. The evolution of both communities in archaeology and in PCA (see below) is probably witness to those differences yet to be published.

R1: Even though some people try very hard to think in terms of “R1” vs. (Caucasus) J or G or any other upper clade, this is plainly wrong. It is possible, given what we know now, that Q1a2-M242 expanded ANE ancestry to the west ca. 13000 BC, while R1b-P279 expanded WHG ancestry to the east with the expansion of post-Swiderian cultures, creating EHG as a WHG:ANE cline. The role of R1a-M459 is unknown, but it might be related to any of these migrations, or others (plural) along northern Eurasia (read more on the expansion of R1b-P279, on Palaeolithic Q1a2, and on R1a-M417).

NOTE. I am inclined to believe in a speculative Mesolithic-Early Neolithic community involving Eurasiatic movements accross North Eurasia, and Indo-Uralic movements in its western part, with the last intense early Uralic-PIE contacts represented by the forming west (Mariupol culture) and east (Don-Volga-Ural cultures, including Samara) communities developing side by side. Before their known Eneolithic expansions, no large-scale Y-DNA bottleneck is going to be seen in the Pontic-Caspian steppe, with different (especially R1a and R1b subclades) mixed among them, as shown in North Pontic Neolithic, Samara HG, and Khvalynsk samples.

PCA-trypillia-greece-neolithic-outlier-anatolian
Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. Marked and labelled are the Balkan samples referenced in this text An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them. See the original file here.

Corded Ware and ‘steppe ancestry’

If we take a look at the evolution of Corded Ware cultures, the expansion of Bell Beakers – dominated over most previous European cultures from west to east Europe – influenced the development of the whole European Bronze Age, up to Mierzanowice and Trzciniec in the east.

The only relevant unscathed CWC-derived groups, after the expansion of Sintashta-Potapovka as the Srubna-Andronovo horizon in the Eurasian steppes, were those of the north-eastern European forest zone: between Belarus to the west, Finland to the north, the Urals to the east, and the forest-steppe region to the south. That is, precisely the region supposed to represent Uralic speakers during the Bronze Age.

This inconsistency of steppe ancestry and its relation with Uralic (and Balto-Slavic) peoples was observed shortly after the publication of the first famous 2015 papers by Paul Heggarty, of the Max-Planck Institute for Evolutionary Anthropology (read more):

Haak et al. (2015) make much of the high Yamnaya ancestry scores for (only some!) Indo-European languages. What they do not mention is that those same results also include speakers of other languages among those with the highest of all scores for Yamnaya ancestry. Only these are languages of the Uralic family, not Indo-European at all; and their Yamnaya-ancestry signals are far higher than in many branches of Indo-European in (southern) Europe. Estonian ranks very high, while speakers of the very closely related Finnish are curiously not shown, and nor are the Saami. Hungarian is relevant less directly since this language arrived only c. 900 AD, but also high.

uralic-steppe-ancestry

These data imply that Uralic-speakers too would have been part of the Yamnaya > Corded Ware movement, which was thus not exclusively Indo-European in any case. And as well as the genetics, the geography, chronology and language contact evidence also all fit with a Yamnaya > Corded Ware movement including Uralic as well as Balto-Slavic.

Both papers fail to address properly the question of the Uralic languages. And this despite — or because? — the only Uralic speakers they report rank so high among modern populations with Yamnaya ancestry. Their linguistic ancestors also have a good claim to have been involved in the Corded Ware and Yamnaya cultures, and of course the other members of the Uralic family are scattered across European Russia up to the Urals.

NOTE. Although the author was trying to support the Anatolian hypothesis – proper of glottochronological studies often published from the Max Planck Institute – , the question remains equally valid: “if Proto-Indo-European expands with Corded Ware and steppe ancestry, what is happening with Uralic peoples?”

For my part, I claimed in my draft that ancestral components were not the only relevant data to take into account, and that Y-DNA haplogroups R1a and R1b (appearing separately in CWC and Yamna-Bell Beaker-Afanasevo), together with their calculated timeframes of formation – and therefore likely expansion – did not fit with the archaeological and linguistic description of the spread of Proto-Indo-European and its dialects.

In fact, it seemed that only one haplogroup (R1b-M269) was constantly and consistenly associated with the proposed routes of Late PIE dialectal expansions – like Anthony’s second (Afanasevo) and third (Lower Danube, Balkan) waves. What genetics shows fits seamlessly with Mallory’s association of the North-West Indo-European expansion with Bell Beakers (read here how archaeologists were right).

balanovksy-yamnaya-ancestry
Map of the much beloved steppe (or “Yamnaya”) ancestry in modern populations, by Balanovsky. Modified from Klejn (2017).

More precise inconsistencies were observed after the publication of Olalde et al. (2017) and Mathieson et al. (2017), by Volker Heyd in Kossinna’s smile (2017). Letting aside the many details enumerated (you can read a summary in my latest draft), this interesting excerpt is from the conclusion:

NOTE. An open access ealier draft version of the paper is offered for download by the author.

Simple solutions to complex problems are never the best choice, even when favoured by politicians and the media. Kossinna also offered a simple solution to a complex prehistoric problem, and failed therein. Prehistoric archaeology has been aware of this for a century, and has responded by becoming more differentiated and nuanced, working anthropologically, scientifically and across disciplines (cf. Müller 2013; Kristiansen 2014), and rejecting monocausal explanations. The two aDNA papers in Nature, powerful and promising as they are for our future understanding, also offer rather straightforward messages, heavily pulled by culture-history and the equation of people with culture. This admittedly is due partly to the restrictions of the medium that conveys them (and despite the often relevant additional detail given as supplementary information, which is unfortunately not always given full consideration).

While I have no doubt that both papers are essentially right, they do not reflect the complexity of the past. It is here that archaeology and archaeologists contributing to aDNA studies find their role; rather than simply handing over samples and advising on chronology, and instead of letting the geneticists determine the agenda and set the messages, we should teach them about complexity in past human actions and interactions. If accepted, this could be the beginning of a marriage made in heaven, with the blessing smile of Gustaf Kossinna, and no doubt Vere Gordon Childe, were they still alive, in a reconciliation of twentieth- and twenty-first-century approaches. For us as archaeologists, it could also be the starting point for the next level of a new archaeology.

heyd-yamnaya-expansion
Main distribution of Yamnaya kurgans in the Pontic-Caspian steppe of modern day Russia, Ukraine, and Kazakhstan, and its western branch in modern south-east European countries of Romania, Bulgaria, Serbia, and Hungary, with numbers of excavated kurgans and graves given. Picture: Volker Heyd (2018).

The question was made painfully clear with the publication of Olalde et al. (2018) & Mathieson et al. (2018), where the real route of Yamna expansion into Europe was now clearly set through the steppes into the Carpathian basin, later expanded as Bell Beakers.

This has been further confirmed in more recent papers, such as Narasimhan et al. (2018), Damgaard et al. (2018), or Wang et al. (2018), among others.

However, the discussion is still dominated by political agendas based on prevalent Y-DNA haplogroups in modern countries and ethnic groups.

Related

Expansion of haplogroup G2a in Anatolia possibly associated with the Mature Aceramic period

anatolian-hunter-gatherer-sampling

Preprint Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, by Feldman et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

Anatolian hunter-gatherers experienced climatic changes during the last glaciation and inhabited a region that connects Europe to the Near East. However, interactions between Anatolia and Southeastern Europe in the later Upper Palaeolithic/Epipalaeolithic are so far not well documented archaeologically. Interestingly, a previous genomic study showed that present-day Near-Easterners share more alleles with European hunter-gatherers younger than 14,000 BP (‘Later European HG’) than with earlier ones (‘Earlier European HG’). With ancient genomic data available, we could directly compare the Near-Eastern hunter-gatherers (AHG and Natufian) with the European ones. As is the case for present-day Near-Easterners, the Near-Eastern hunter-gatherers share more alleles with the Later European HG than with the Earlier European HG, shown by the significantly positive statistic D(Later European HG, Earlier European HG; AHG/Natufian, Mbuti). Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’), are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna and Ranchot respectively) as the next two European hunter-gatherers genetically closest to AHG. Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component.

anatolian-hunter-gatherer-pca
Ancient genomes (marked with color-filled symbols) projected onto the principal components 5 computed from present-day west Eurasians (grey circles) (fig. S4). The geographic location of each ancient group is marked in (A). Ancient individuals newly reported in this study are additionally marked with a black dot inside the symbol

We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry 5 component (α), which is prevalent in the Near East but undetectable in European hunter-gatherers. Following a published approach, we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians, consistent with previous estimates for the latter. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %, suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

near-eastern-european-hg
Basal Eurasian ancestry proportions (α) as a marker for Near-Eastern gene flow. Mixture proportions inferred by qpAdm for AHG and the Iron Gates HG are schematically represented. The lower schematic shows the expected α in Iron Gates HG under 10 assumption of unidirectional gene flow, inferred from α in the AHG source population. The observed α for Iron Gates HG is considerably smaller than expected thus, the unidirectional gene flow from the Near East to Europe is not sufficient to explain the above affinity.

While ancestry is not always relevant to distinguish certain population movements (see here), especially – as in this case – when there are few samples (thus neither geographically nor chronologically representative) and no previous model to test, it seems that ancestry and Y-DNA show a great degree of continuity in Anatolia since the Palaeolithic until the Neolithic, at least in the sampled regions. C1a2 appears in Europe since ca. 40,000 years ago (viz. Kostenki, Goyet, Vestonice, etc., and later emerges again in the Balkans after the Anatolian Neolithic expansion, probably a resurge of European groups).

The potential transition of a G2a-dominated agricultural society – that is later prevalent in Anatolian and European farmers – may have therefore happened during the Aceramic III period (ca. 8000 BC), a process of haplogroup expansion probably continuing through the early part of the Pottery Neolithic, as the society based on kinship appeared (Rosenberg and Erim-Özdoğan 2011). There is still much to know about the spread of ceramic technology and southwestern Asia domesticate complex, though.

anatolian-palaeolithic-hg

Without a proper geographical sampling, representative of previous and posterior populations, it is impossible to say. But the expansion of R1b-L754 through Anatolia to form part of the Villabruna cluster (and also the Iron Gates HG) seems perfectly possible with this data, although this paper does not help clarify the when or how. We have seen significant changes in ancestry happen within centuries with expanding populations admixing with locals. Palaeolithic sampling – like this one – shows few individuals scattered geographically over thousands of km and chronologically over thousands of years…

Related

Polygyny as a potential reason for Y-DNA bottlenecks among agropastoralists

polygyny-estimates

Open access Greater wealth inequality, less polygyny: rethinking the polygyny threshold model by Ross et al. Journal of the Royal Society Interface (2018).

Interesting excerpts, from the discussion (emphasis mine):

We use cross-cultural data and a new mutual mate choice model to propose a resolution to the polygyny paradox. Following Oh et al. [17], we extend the standard polygyny threshold model to a mutual mate choice model that accounts for both female supply to, and male demand for, polygynous matchings, in the light of the importance of, and inequality in, rival and non-rival forms of wealth. The empirical results presented in figures 5 and 6 demonstrate two phenomena that are jointly sufficient to generate a transition to more frequent monogamy among populations with a co-occurring transition to a more unequal, highly stratified, class-based social structure. In such populations, fewer men can cross the wealth threshold required to obtain a second wife, and those who do may be fabulously wealthy, but—because of diminishing marginal fitness returns to increasing number of marriages—do not acquire wives in full proportion to their capacity to support them with rival wealth. Together, these effects reduce the population-level fraction of wives in polygynous marriages.

Our model demonstrates that a low population-level frequency of polygyny will be an equilibrium outcome among fitness maximizing males and females in a society characterized by a large class of wealth-poor peasants and a small class of exceptionally wealthy elite. Our mutual mate choice model thus provides an empirically plausible resolution to the polygyny paradox and the transition to monogamy which co-occurred with the rise of highly unequal agricultural populations.

polygyny-pastoralists
(a) Mean frequency of married women who are married polygynously by production system (+2 s.e.) using the Standard Cross-Cultural Sample [30]. Rates of polygyny are measured with variable ]872, per cent of wives with co-wives. (b) Rates of monogamy and polygyny by production system are measured with variable ]861, the standard polygamy code. Data on subsistence come from variable ]858, categorized subsistence. In general, agricultural populations show reduced rates of polygyny and increased rates of monogamy relative to other subsistence systems. See electronic supplementary material for more information. (c) Gini of wealth by production system in our sample.

The reasons for this decrease in marginal fitness returns are explained as either a) a potential missing of important rival forms of wealth in the statistical model, or b) one or more of the following reasons:

  • [A] male’s time and attention are rival inputs to his own fitness (…) A single rich man will have to defend his 10 wives from nine unmarried men on average.”As the wealth ratio grows even more skewed, this situation could become increasingly difficult to manage (e.g. requiring the use of eunochs to defend harems [74]).
  • A related possibility is that a growing number of unmarried men could socially censure wealthy polygynous males, imposing costs on them that reduce male demand for and/or female supply to polygynous marriage [23,24]. (…)
  • A third possibility is that sexually transmitted infection (STI) burden [22,75] could diminish returns to polygyny, if polygyny enhances infection rates [76,77]. (…)
  • Finally, impediments to cooperation or even outright conflict among co-wives can be greater as the number of wives increases. Interference competition among co-wives could impose significant fitness costs in settings where effective child rearing benefits from cooperation [79,80].(…)
polygyny-agropastoralists
between the Gini coefficient on completed rival wealth and per cent completed female polygyny.

I have previously argued against some reasons traditionally given to explain the replacement of native male populations after migrations (i.e. polygyny, slavery, targeted male extermination, etc.), because I believe that a gradual successful expansion of patrilineal clans over some generations based on wealth alone is enough to explain the obvious Y-DNA bottlenecks that happened in many different prehistoric and historic cultures (especially among steppe pastoralists, including Indo-Europeans).

I realize that I haven’t really used any study to support my opinion, though, and data from modern and ancient pastoralists from different regions seem to contradict it, so maybe ancient DNA can show that Indo-Europeans had often children with more than one woman at the same time. I don’t remember seeing that kind of information in supplementary materials to date. From memory I can think of maybe two or three examples of agnate siblings published, but I doubt the archaeological age estimation (based on simple observation of skeletal remains) combined with radiocarbon age (usually given with broad CI) could be enough to prove a similar age of conception. Maybe a case of many siblings clearly of the same age and from many different mothers in the same burial could be a strong proof of this…

I recently read that theoretical models are actually trusted by no one except for the researchers who propose them, and experimental data are trusted by everyone except for the researchers who worked with them. I cannot agree more. However, we lack information about this question (as far as I know), so we may have to rely on indirect estimations, like the kind of models presented in the paper (or the one proposed for Post-Neolithic Y-chromosome bottlenecks).

The Late Proto-Indo-European word for bride comes from a root meaning ‘drive, lead’, hence literally ‘deportation’, so the bride was transferred from her father’s family to her husband’s house. Marriage was certainly an asymmetrical contract for its members, and the reconstructible word for ‘dowry’ further supports the weaker position of the wife in it. Also, ancient marriage could differ from a family agreement, because marriage by elopement, bride kidnapping or hostage was probably common (more or less socially regulated) for people belonging the same culture. Apart from this, I don’t know about reconstructed linguistic data pointing to polygyny, and I doubt archaeological data alone – without genetics – can help.

Related

Wang et al. (2018) Suppl. data: R1b-M269 in Baltic Neolithic?

eneolithic-forest-zone

Looking for information on Novosvobodnaya samples from Wang et al. (2018) for my latest post, I stumbled upon this from the Supplementary Data 2 (download the Excel table):

Latvia_MN1.SG (ZVEJ26)

Skeletal element: petrous
Sample: Latvia_MN_dup.I4627.SG
Date: 4251-3976 calBCE
Location: Zvejnieki
mtDNA: U4a1
Y-DNA: R1b1a1a2
Coverage: 0.15
SNPs hit on autosomes: 167445

The data on Mathieson et al. (2018) is as follows:

I4627 (ZVEJ26)

Skeletal element: petrous
Origin: ThisStudy (New data; Individual first published in JonesNatureCommunications2017)
Sample: Latvia_MN
Date:4251-3976 calBCE (5280±55 BP, Ua-3639)
Location:Zvejnieki
mtDNA: U4a1
Y-DNA: R1b1a1a(xR1b1a1a2)
Coverage: 1.77
SNPs hit on autosomes: 686273

Y-Chromosome derived SNPs: R1b1a1a:PF6475:17986687C->A; R1b1a1a:CTS3876:15239181G->C; R1b1a1a:CTS5577:16376495A->C; R1b1a1a:CTS9018:18617596C->T; R1b1a1a:FGC57:7759944G->A; R1b1a1a:L502:19020340G->C; R1b1a1a:PF6463:16183412C->A; R1b1a1a:PF6524:23452965T->C; R1b1a:A702:10038192G->A; R1b1a:FGC35:18407611C->T; R1b1a:FGC36:13822833G->T; R1b1a:L754:22889018G->A; R1b1a:L1345:21558298G->T; R1b1a:PF6249:8214827C->T; R1b1a:PF6263:21159055C->A; R1b1:CTS2134:14193384G->A; R1b1:CTS2229:14226692T->A; R1b1:L506:21995972T->A; R1b1:L822:7960019G->A; R1b1:L1349:22722580T->C; R1b:M343:2887824C->A; R1:CTS2565:14366723C->T; R1:CTS3123:14674176A->C; R1:CTS3321:14829196C->T; R1:CTS5611:16394489T->G; R1:L875:16742224A->G; R1:P238:7771131G->A; R1:P286:17716251C->T; R1:P294:7570822G->C; R:CTS207:2810583A->G; R:CTS2913:14561760A->G; R:CTS3622:15078469C->G; R:CTS7876:17722802G->A; R:CTS8311:17930099C->A; R:F33:6701239G->A; R:F63:7177189G->A; R:F82:7548900G->A; R:F154:8558505T->C; R:F370:16856357T->C; R:F459:18017528G->T; R:F652:23631629C->A; R:FGC1168:15667208G->C; R:L1225:22733758C->G; R:L1347:22818334C->T; R:M613:7133986G->C; R:M734:18066156C->T; R:P224:17285993C->T; R:P227:21409706G->C

Context of Latvia_MN1

The Middle Neolithic is known to mark the westward expansion of Comb Ware and related cultures in North-Eastern Europe.

Mathieson et al. (2017 and 2018) had this to say about the Middle Neolithic in the Baltic:

At Zvejnieki in Latvia, using 17 newly reported individuals and additional data for 5 previously reported34 individuals, we observe a transition in hunter-gatherer-related ancestry that is opposite to that seen in Ukraine. We find that Mesolithic and Early Neolithic individuals (labelled ‘Latvia_HG’) associated with the Kunda and Narva cultures have ancestry that is intermediate between WHG (approximately 70%) and EHG (approximately 30%), consistent with previous reports34–36(Supplementary Table 3). We also detect a shift in ancestry between Early Neolithic individuals and those associated with the Middle Neolithic Comb Ware complex (labelled ‘Latvia_MN’), who have more EHG-related ancestry; we estimate that the ancestry of Latvia_MN individuals comprises 65% EHG-related ancestry, but two of the four individuals appear to be 100% EHG in principal component space (Fig. 1b).

mathieson-2018-pca
From Mathieson et al. (2018). Ancient individuals projected onto principal components defined by 777 presentday west Eurasians (shown in Extended Data Fig. 1); data include selected published individuals (faded circles, labelled) and newly reported individuals (other symbols, outliers enclosed in black circles). Coloured polygons cover individuals that had cluster memberships fixed at 100% for supervised ADMIXTURE analysis.

Other samples and errors on Y-SNP calls

The truth is, this is another sample (Latvia_MN_dup.I4627.SG) from the same individual ZVEJ26.

There is another sample used for the analysis of ZVEJ26, with the same data as in Mathieson et al. (2018), i.e. better coverage, and Y-DNA R1b1a1a(xR1b1a1a2).

Most samples in the tables from Wang et al. (2018) seem to be classified correctly, as in previous papers, but for:

  • Blätterhöhle Cave sample from Lipson et al. (2017), wrongly classified (again) as R1b1a1a2a1a2a1b2 (I am surprised no R1b-autochtonous-continuity-fan rushed to proclaim something based on this);
  • Mal’ta 1 sample from Raghavan et al. (2013) as R1b1a1a2;
  • Iron Gates HG, Schela Cladovey from Gonzalez Fortes (2017) as R1b1a1a2;
  • Oase1 from Fu (2015) as N1c1a;
  • samples from Skoglund et al. (2017) from Africa also wrongly classified as R1b1a1a2 and subclades.

It seems therefore that the poor coverage / SNPs hit on autosomes is the key common factor here for these Y-SNP calls, and so it is in the Zvejnieki MN1 duplicated sample. Anyway, if all Y-SNP calls come from the same software applied to all data, and this is going to be used in future papers, this seems to be a great improvement compared to Narasimhan et al. (2018)

EDIT (25 JUN 2018): I have been reviewing some more papers apart from Mathieson et al. (2018) and Olalde et al. (2018) to compare the reported haplogroups, and there seems to be many potential errors (or updated data, difficult to say sometimes, especially when the newly reported haplogroup is just one or two subclades below the reported one in ‘old’ papers), not only those listed above.

The sample accession number in the European Nucleotide Archive (ENA) is SAMEA45565168 (Latvia_MN1/ZVEJ26) (see here), in case anyone used to this kind of analysis wishes to repeat the Y-SNP calls on both samples.

EDIT (25 JUN 2018): Added that it is another sample with lesser coverage from the same ZVEJ26 individual.

Related:

Male-biased expansions and migrations also observed in Northwestern Amazonia

Open access preprint Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia, by Arias et al., bioRxiv (2018).

Abstract (emphasis mine):

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

y-dna-mtdna-amazonia
MDS plots for mtDNA and NRY. Stress values (within parentheses) are indicated in percentages.

Looking more precisely at the different groups (even with the resampling approach), there are no significant differences between matrilocal and patrilocal groups. At best, as the study proposes, “this is just one of the factors at play in structuring the observed genetic variation”.

Interesting excerpts:

(…) we found evidence that the patterns of genetic differentiation depend on the geographical scale of the study. The magnitude of between-population differentiation in the NRY compared to the mtDNA is smaller when looking at the continental scale than in NWA (Figure 6). This is in agreement with the findings of Wilkins and Marlowe (2006), who showed that the excess of between-population differentiation for the NRY in comparison to the mtDNA decreases when comparing more geographically distant populations. Heyer et al. (2012) and Wilkins and Marlowe (2006) have proposed that at a local scale the patterns of genetic diversity reflect cultural practices over a relatively small number of generations, whereas at a larger geographic scale the genetic diversity reflects old migration and/or old common ancestry patterns(Heyer et al. 2012; Wilkins and Marlowe 2006).

y-dna-mtdna-amazon
BSPs for the mtDNA and NRY sequences from NWA. The dotted lines indicate the 95% HPD intervals. Ne was corrected for generation time according to (Fenner 2005), using 26 years for mtDNA and 31 years for NRY.

The BSP plots and the diversity statistics indicate that overall the Ne of males has been smaller than that of females. One tentative explanation for this difference is that it reflects larger differences in reproductive success among males than among females. Some support for this explanation comes from the shape of the phylogenies (Supplementary Figures 1 and 6), since differences in reproductive success and the cultural transmission of fertility lead to imbalance phylogenies (Blum et al. 2006; Heyer et al. 2015). We estimated a common index of tree imbalance (Colless index) and calculated whether the mtDNA and NRY trees were more unbalanced than 1000 simulated trees generated under a Yule process (Bortolussi et al. 2006) (i.e. a simple pure birth process that assumes that the birth rate of new lineages is the same along the tree). We found that the NRY tree is more unbalanced than predicted by the Yule model (p-value=0.001), whereas the mtDNA tree is not significantly different from trees generated by the Yule model (p-value=0.628). It has been suggested that highly mobile hunter-gatherer societies, such as those typical of most of human prehistory, were polygynous bands (Dupanloup et al. 2003); similarly, nomadic horticulturalist Amazonian societies exhibit strong differences in reproductive success due to the common practice of polygyny, especially among community chiefs, whose offspring also enjoy a high fertility (Neel 1970; 1980; Neel and Weiss 1975).

Furthermore, a more recent expansion can be observed in the BSP based on the NRY, but not in the mtDNA BSP (Figure 5), indicating an expansion specifically in the paternal line. The reasons behind this recent male-biased population expansion, which starts ~3.5 kya, are as yet unclear. However, similar male-biased expansions have been observed in other studies using high-resolution NRY sequences (Batini et al. 2017; Karmin et al. 2015).

Related:

Ancient genomes from North Africa evidence Neolithic migrations to the Maghreb

BioRxiv preprint now published (behind paywall) Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe, by Fregel et al., PNAS (2018).

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.

north-africa-genomes-pca
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. PCA analysis using the Human Origins panel (European, Middle Eastern, and North African populations) and LASER projection of aDNA samples.

Relevant excerpts:

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.

north-africa-iberia-admixture
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. (B) ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, and North African populations) for modern and ancient samples (K = 8). (D) Detail of ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, North African, and sub-Saharan African populations) for modern and ancient samples, including Taforalt.

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.

See here: