Corded Ware—Uralic (II): Finno-Permic and the expansion of N-L392/Siberian ancestry

finno-ugric-samoyedic

This is the second of four posts on the Corded Ware—Uralic identification:

I read from time to time that “we have not sampled Uralic speakers yet”, and “we are waiting to see when Uralic-speaking peoples are sampled”. Are we, though?

Proto-language homelands are based on linguistic data, such as guesstimates for dialectal evolution, loanwords and phonetic changes for language contacts, toponymy for ancient territories, etc. depending on the available information. The trace is then followed back, using available archaeological data, from the known historic speakers and territory to the appropriate potential prehistoric cultures. Only then can genetic analyses help us clarify the precise prehistoric population movements that better fit the models.

uralic-language-family
The traditional family tree of the Uralic branches. Kallio (2014)

The linguistic homeland

We thought – using linguistic guesstimates and fitting prehistoric cultures and their expansion – that Yamna was the Late Proto-Indo-European culture, so when Yamna was sampled, we had Late Proto-Indo-Europeans sampled. Simple deduction.

We thought that north-eastern Europe was a Uralic-speaking area during the Neolithic:

  • For those supporting a western continuity (and assuming CWC was Indo-European), the language was present at least since the Comb Ware culture, potentially since the Mesolithic.
  • For those supporting a late introduction into Finland, Uralic expanded the latest with Abashevo-related movements after its incorporation of Volosovo and related hunter-gatherers.

The expansion to the east must have happened through progressive infiltrations with Seima-Turbino / Andronovo-related expansions.

uralic-time-space
Some datings for the traditional proto-stages from Uralic to Finnic. Kallio (2014).

Finding the linguistic homeland going backwards can be described today as follows:

I. Proto-Fennic homeland

Based on the number of Baltic loanwords, not attested in the more eastern Uralic branches (and reaching only partially Mordvinic), the following can be said about western Finno-Permic languages (Junttila 2014):

The Volga-Kama Basin lies still too far east to be included in a list of possible contact locations. Instead, we could look for the contact area somewhere between Estonia in the west and the surroundings of Moscow in the east, a zone with evidence of Uralic settlement in the north and Baltic on the south side.

The only linguistically well-grounded version of the Stone Age continuation theory was presented by Mikko Korhonen in 1976. Its validity, however, became heavily threatened when Koivulehto 1983a-b proved the existence of a Late Proto-Indo-European or Pre-Baltic loanword layer in Saami, Finnic, and Mordvinic. Since this layer must precede the Baltic one and it was presumably acquired in the Baltic Sea region, Koivulehto posited it on the horizon of the Battle Axe period. This forces a later dating for the Baltic–Finnic contacts.

Today the Battle Axe culture is dated at 3200 to 3000 BC, a period far too remote to correspond linguistically with Proto-Baltic (Kallio 1998a).

Since the Baltic contacts began at a very initial phase of Proto-Finnic, the language must have been relatively uniform at that time. Hence, if we consider that the layer of Baltic loanwords may have spread over the Gulf of Finland at that time, we could also insist that the whole of the Proto-Finnic language did so.

migration-theory
Prehistoric Balts as the southern neighbours of Proto-Finnic speakers. 1 = The approximated area of Proto-Uralic. 2 = The approximated area of Finnic during the Iron Age. 3 = The area of ancient Baltic hydronyms. 4 = The area of Baltic languages in about 1200 AD. 5 = The problem: When did Uralic expand westwards and when did it meet Baltic? Junntila (2012).

II. Proto-Finno-Saamic homeland

The evidence of continued Palaeo-Germanic loanwords (from Pre- to Proto-Germanic stages) is certainly the most important data to locate the Finno-Saamic homeland, and from there backwards into the true Uralic homeland. Following Kallio (2017):

(…) the loanword evidence furthermore suggests that the ancestors of Finnic and Saamic had at least phonologically remained very close to Proto-Uralic as late as the Bronze Age (ca. 1700–500 BC). In particular, certain loanwords, whose Baltic and Germanic sources point to the first millennium BC, after all go back to the Finno-Saamic proto-stage, which is phonologically almost identical to the Uralic proto-stage (see especially the table in Sammallahti 1998: 198–202). This being the case, Dahl’s wave model could perhaps have some use in Uralic linguistics, too.

The presence of Pre-Germanic loanwords points rather to the centuries around the turn of the 2nd – 1st millennium BC or earlier. Proto-Germanic words must have been borrowed before the end of Germanic influence in the eastern Baltic at the beginning of the Iron Age, which sets a clear terminus ante quem ca. 800 BC.

The arrival of Bell Beaker peoples in Scandinavia ca. 2350 BC, heralding the formation of the Dagger Period, as well as the development of Pre-Germanic in common with Finnic-like populations point to the late 3rd / early 2nd millennium BC as the first time of close interaction through the Baltic region.

III. Proto-Uralic homeland

(…) the earliest Indo-European loanwords in the Uralic languages (…) show that Proto-Uralic cannot have been spoken much earlier than Proto-Indo-European dated about 3500 BC (Koivulehto 2001: 235, 257). As the same loanword evidence naturally also shows that the Uralic and Indo-European homelands were not located far from one another, the Uralic homeland can most likely be located in the Middle and Upper Volga region, right north of the Indo-European homeland*. From the beginning of the Subneolithic period about 5900 BC onwards, this region was an important innovation centre, from where several cultural waves spread to the Finnish Gulf area, such as the Sperrings Ware wave about 4900 BC, the Combed Ware wave about 3900 BC, and the Netted Ware wave about 1900 BC (Carpelan & Parpola 2001: 78–90).

The mainstream position is nowadays trying to hold together the traditional views of Corded Ware as Indo-European, and a Uralic Fennoscandia during the Bronze Age.

The following is an example of how this “Volosovo/Forest Zone hunter-gatherer theory” of Uralic origins looks like, as a ‘mixture’ of cultures and languages that benefits from the lack of genetic data for certain regions and periods (taken from Parpola 2018):

asbestos-ware
The extent of Typical Comb Ware (TCW), Asbestos- and Organic-tempered Wares (AOW) and Volosovo and Garino-Bor cultures; areas with deposits of native copper in Karelia and copperbearing sandstone in Volga-Kama-area are marked dark gray (after Zhuravlev 1977; Krajnov 1987; Nagovitsyn 1987; Chernykh 1992; Carpelan 1999; Zhul´nikov 1999). From Nordqvist et al. (2012).

The Corded Ware (or Battle Axe) culture intruded into the Eastern Baltic and coastal Finland already around 3100 BCE. The continuity hypothesis maintains that the early Proto-Finnic speakers of the coastal regions, who had come to Finland in the 4th millennium BCE with the Comb-Pitted Ware, coexisted with the Corded Ware newcomers, gradually adopting their pastoral culture and with it a number of NW-IE loanwords, but assimilating the immigrants linguistically.

The fusion of the Corded Ware and the local Comb-Pitted Ware culture resulted into the formation of the Kiukais culture (c. 2300–1500) of southwestern Finland, which around 2300 received some cultural impulses from Estonia, manifested in the appearance of the Western Textile Ceramic (which is different from the more easterly Textile Ceramic or Netted Ware, and which is first attested in Estonia c. 2700 BCE, cf. Kriiska & Tvauri 2007: 88), and supposed to have been accompanied by an influx of loanwords coming from Proto-Baltic. At the same time, the Kiukais culture is supposed to have spread the custom of burying chiefs in stone cairns to Estonia.

The coming of the Corded Ware people and their assimilation created a cultural and supposedly also a linguistic split in Finland, which the continuity hypothesis has interpreted to mean dividing Proto-Saami-Finnic unity into its two branches. Baltic Finnic, or simply Finnic, would have emerged in the coastal regions of Finland and in the northern East Baltic, while preforms of Saami would have been spoken in the inland parts of Finland.

The Nordic Bronze Age culture, correlated above with early Proto-Germanic, exerted a strong influence upon coastal Finland and Estonia 1600–700 BCE. Due to this, the Kiukais culture was transformed into the culture of Paimio ceramics (c. 1600–700 BCE), later continued by Morby ceramics (c. 700 BCE – 200 CE). The assumption is that clear cultural continuity was accompanied by linguistic continuity. Having assimilated the language of the Germanic traders and relatively few settlers of the Bronze Age, the language of coastal Finland is assumed to have reached the stage of Proto-Finnish at the beginning of the Christian era. In Estonia, the Paimio ceramics have a close counterpart in the contemporaneous Asva ceramics.

Eastern homelands?

I will not comment on Siberian or Central Asian homeland proposals, because they are obviously not mainstream, still less today when we know that Uralic was certainly in contact with Proto-Indo-European, and then with Pre- and Proto-Indo-Iranian, as supported even by the Copenhagen group in Damgaard et al. (2018).

This is what Kallio (2017) has to say about the agendas behind such proposals:

Interestingly, the only Uralicists who generally reject the Central Russian homeland are the Russian ones who prefer the Siberian homeland instead. Some Russians even advocate that the Central Russian homeland is only due to Finnish nationalism or, as one of them put it a bit more tactfully, “the political and ideological situation in Finland in the first decades of the 20th century” (Napolskikh 1995: 4).

Still, some Finns (and especially those who also belong to the “school who wants it large and wants it early”) simultaneously advocate that exactly the same Central Russian homeland is due to Finnlandisierung (Wiik 2001: 466).

Hence, for those of you willing to learn about fringe theories not related to North-Eastern Europe, you also have then the large and early version of the Uralic homeland, with Wiik’s Palaeolithic continuity of Uralic peoples spread over all of eastern and central Europe (hence EHG and R1a included):

atlantic-finnic-theory
Palaeolithic boat peoples and Finno-Ugric. Source

These fringe Finnish theories look a lot like the Corded Ware expansion… Better not go the Russian or Finnish nationalist ways? Agreed then, let’s discuss only rational proposals based on current data.

The archaeological homeland

For a detailed account of the Corded Ware expansion with Battle Axe, Fatyanovo-Balanovo, and Abashevo groups into the area, you can read my recent post on the origin of R1a-Z645.

1. Textile ceramics

During the 2nd millennium BC, textile impressions appear in pottery as a feature across a wide region, from the Baltic area through the Volga to the Urals, in communities that evolve from late Corded Ware groups without much external influence.

While it has been held that this style represents a north-west expansion from the Volga region (with the “Netted Ware” expansion), there are actually at least two original textile styles, one (earlier) in the Gulf of Finland, common in the Kiukainen pottery, which evolves into the Textile ware culture proper, and another which seems to have an origin in the Middle Volga region to the south-east.

The Netted ware culture is the one that apparently expands into inner Finland – a region not densely occupied by Corded Ware groups until then. There are, however, no clear boundaries between groups of both styles; textile impressions can be easily copied without much interaction or population movement; and the oldest textile ornamentation appeared on the Gulf of Finland. Hence the tradition of naming all as groups of Textile ceramics.

textile-ware-cultures
Maximum distribution of Textile ceramics during the Bronze Age (ca. 2000-800 BC). Asbestos-tempered ware lies to the north (and is also continued in western Fennoscandia).

The fact that different adjacent groups from the Gulf of Finland and Forest Zone share similar patterns making it very difficult to differentiate between ‘Netted Ware’ or ‘Textile Ware’ groups points to:

  • close cultural connections that are maintained through the Gulf of Finland and the Forest Zone after the evolution of late Corded Ware groups; and
  • no gross population movements in the original Battle Axe / Fatyanovo regions, except for the expansion of Netted Ware to inner Finland, Karelia, and the east, where the scattered Battle Axe finds and worsening climatic conditions suggest most CWC settlements disappeared at the end of the 3rd millennium BC and recovered only later.

NOTE. This lack of population movement – or at least significant replacement by external, non-CWC groups – is confirmed in genetic investigation by continuity of CWC-related lineages (see below).

The technology present in Textile ceramics is in clear contrast to local traditions of sub-Neolithic Lovozero and Pasvik cultures of asbestos-tempered pottery to the north and east, which point to a different tradition of knowledge and learning network – showing partial continuity with previous asbestos ware, since these territories host the main sources of asbestos. We have to assume that these cultures of northern and eastern Fennoscandia represent Palaeo-European (eventually also Palaeo-Siberian) groups clearly differentiated from the south.

The Chirkovo culture (ca. 1800-700 BC) forms on the middle Volga – at roughly the same time as Netted Ware formed to the west – from the fusion of Abashevo and Balanovo elites on Volosovo territory, and is also related (like Abashevo) to materials of the Seima-Turbino phenomenon.

Bronze Age ethnolinguistic groups

In the Gulf of Finland, Kiukainen evolves into the Paimio ceramics (in Finland) — Asva Ware (in Estonia) culture, which lasts from ca. 1600 to ca. 700 BC, probably representing an evolving Finno-Saamic community, while the Netted Ware from inner Finland (the Sarsa and Tomitsa groups) and the groups from the Forest Zone possibly represent a Volga-Finnic community.

NOTE. Nevertheless, the boundaries between Textile ceramic groups are far from clear, and inner Finland Netted Ware groups seem to follow a history different from Netted Ware groups from the Middle and Upper Volga, hence they could possibly be identified as an evolving Pre-Saamic community.

Based on language contacts, with Early Baltic – Early Finnic contacts starting during the Iron Age (ca. 500 BC onwards), this is a potential picture of the situation at the end of this period, when Germanic influence on the coast starts to fade, and Lusatian culture influence is stronger:

aikio-finnic-saamic
The linguistic situation in Lapland and the northern Baltic Sea Area in the Early Iron Age prior to the expansion of Saami languages; the locations of the language groups are schematic. The black line indicates the distribution of Saami languages in the 19th century, and the gray line their approximate maximal distribution before the expansion of Finnic. Aikio (2012)

The whole Finno-Permic community remains thus in close contact, allowing for the complicated picture that Kallio mentions as potentially showing Dahl’s wave model for Uralic languages.

Genetic data shows a uniform picture of these communities, with exclusively CWC-derived ancestry and haplogroups. So in Mittnik et al. (2018) all Baltic samples show R1a-Z645 subclades, while the recent session on Estonian populations in ISBA 8 (see programme in PDF) clearly states that:

[Of the 24 Bronze Age samples from stone-cist graves] all 18 Bronze Age males belong to R1a.

Regarding non-Uralic substrates found in Saami, supposedly absorbed during the expansion to the north (and thus representing languages spoken in northern Fennoscandia during the Bronze Age) this is what Aikio (2012) has to say:

The Saami substrate in the Finnish dialects thus reveals that also Lakeland Saami languages had a large number of vocabulary items of obscure origin. Most likely many of these words were substrate in Lakeland Saami, too, and ultimately derive from languages spoken in the region before Saami. In some cases the loan origin of these words is obvious due to their secondary Proto-Saami vowel combinations such as *ā–ë in *kāvë ‘bend; small bay’ and *šāpšë ‘whitefish’. This substrate can be called ‘Palaeo-Lakelandic’, in contrast to the ‘Palaeo-Laplandic’ substrate that is prominent in the lexicon of Lapland Saami. As the Lakeland Saami languages became extinct and only fragments of their lexicon can be reconstructed via elements preserved in Finnish place-names and dialectal vocabulary, we are not in a position to actually study the features of this Palaeo-Lakelandic substrate. Its existence, however, appears evident from the material above.

If we wanted to speculate further, based on the data we have now, it is very likely that two opposing groups will be found in the region:

A) The central Finnish group, in this hypothesis the Palaeo-Lakelandic group, made up of the descendants of the Mesolithic pioneers of the Komsa and Suomusjärvi cultures, and thus mainly Baltic HG / Scandinavian HG ancestry and haplogroups I / R1b(xM269) (see more on Scandinavian HG).

siberian-ancestry-map
Frequency map of the so-called ‘Siberian’ component. From Tambets et al. (2018).

B) Lapland and Kola were probably also inhabited by similar Mesolithic populations, until it was eventually assimilated by expanding Siberian groups (of Siberian ancestry and N1c-L392 lineages) from the east – entering the region likely through the Kola peninsula – , forming the Palaeo-Laplandic group, which was in turn later replaced by expanding Proto-Saamic groups.

Siberian ancestry appears first in Fennoscandia at Bolshoy Oleni Ostrov ca. 1520 BC, with haplogroup N1c-L392 (2 samples, BOO002 and BOO004), and with Siberian ancestry. This is their likely movement in north-eastern Europe, from Lamnidis et al (2018):

The large Siberian component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millenium BC, and the spread of even-based arrowheads in Lapland from 1,900 BCE. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the east. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period.

saamic-lovozero-pca
PCA plot of 113 Modern Eurasian populations, with individuals from this study projected on the principal components. Uralic speakers are highlighted in light purple. Image modified from Lamnidis et al. (2018)

Obviously, these groups of asbestos-tempered ware are not connected to the Uralic expansion. From the same paper:

The fact that the Siberian genetic component is consistently shared among Uralic-speaking populations, with the exceptions of Hungarians and the non-Uralic speaking Russians, would make it tempting to equate this component with the spread of Uralic languages in the area. However, such a model may be overly simplistic. First, the presence of the Siberian component on the Kola Peninsula at ca. 4000 yBP predates most linguistic estimates of the spread of Uralic languages to the area. Second, as shown in our analyses, the admixture patterns found in historic and modern Uralic speakers are complex and in fact inconsistent with a single admixture event. Therefore, even if the Siberian genetic component partly spread alongside Uralic languages, it likely presented only an addition to populations carrying this component from earlier.

2. The Early Iron Age

The Ananino culture appears in the Vyatka-Kama area, famed for its metallurgy, with traditions similar to the North Pontic area, by this time developing Pre-Sauromatian traditions. It expanded to the north in the first half of the first millennium BC, remaining in contact with the steppes, as shown by the ‘Scythian’ nature of its material culture.

NOTE. The Ananino culture can be later followed through its zoomorphic styles into Iron Age Pjanoborskoi and Gljadenovskoi cultures, later to Ural-Siberian Middle Age cultures – Itkuska, Ust’-Poluiska, Kulaiska cultures –, which in turn can be related as prototypes of medieval Permian styles.

ananino-culture-homeland
Territory of (early and maximum) Ananino material culture. Vasilyev (2002).

At the same time as the Ananino culture begins to expand ca. 1000 BC, the Netted Ware tradition from the middle Oka expanded eastwards into the Oka-Vyatka interfluve of the middle Volga region, until then occupied by the Chirkovo culture. Eventually the Akozino or Akhmylovo group (ca. 800-300 BC) emerged from the area, showing a strong cultural influence from the Ananino culture, by that time already expanding into the Cis-Urals region.

The Akozino culture remains nevertheless linked to the western Forest Zone traditions, with long-ranging influences from as far as the Lusatian culture in Poland (in metallurgical techniques), which at this point is also closely related with cultures from Scandinavia (read more on genetics of the Tollense Valley).

malar-celts-ananino
Mälar celts and molds for casting (a) and the main distribution area (в) of Mälar-type celts of the Mälar type in the Volga-Kama region (according to Kuzminykh 1983: figure 92) and Scandinavia (according to Baudou 1960: Karte 10); Ananino celts and molds for casting (б) and the main distribution area (г) of the distribution of the celts of the Ananino type in the Volga-Kama area (according to Kuzminykh 1983: figure 9); dagger of Ananino type (д).Map from (Yushkova 2010)

Different materials from Akozino reach Fennoscandia late, at the end of the Bronze Age and beginning of the Early Iron Age, precisely when the influence of the Nordic Bronze Age culture on the Gulf of Finland was declining.

This is a period when Textile ceramic cultures in north-eastern Europe evolve into well-armed chiefdom-based groups, with each chiefdom including thousands or tens of thousands, with the main settlements being hill forts, and those in Fennoscandia starting ca. 1000-400 BC.

Mälar-type celts and Ananino-type celts appear simultaneously in Fennoscandia and the Forest Zone, with higher concentrations in south-eastern Sweden (Mälaren) and the Volga-Kama region, supporting the existence of a revived international trade network.

akozino-malar-axes-fennoscandia
Distribution of the Akozino-Mälar axes according to Sergej V. Kuz’minykh (1996: 8, Abb. 2).

The Paimio—Asva Ware culture evolves (ca. 700-200 BC) into the Morby (in Finland) — Ilmandu syle (in Estonia, Latvia, and Mälaren) culture. The old Paimio—Asva tradition continues side by side with the new one, showing a clear technical continuity with it, but with ornamentation compared to the Early Iron Age cultures of the Upper Volga area. This new south-eastern influence is seen especially in:

  • Akozino-Mälar axes (ca. 800-500 BC): introduced into the Baltic area in so great numbers – especially south-western Finland, the Åland islands, and the Mälaren area of eastern Sweden – that it is believed to be accompanied by a movement of warrior-traders of the Akozino-Akhmylovo culture, following the waterways that Vikings used more than a thousand years later. Rather than imports, they represent a copy made with local iron sources.
  • Tarand graves (ca. 500 BC – AD 400): these ‘mortuary houses’ appear in the coastal areas of northern and western Estonia and the islands, at the same time as similar graves in south-western Finland, eastern Sweden, northern Latvia and Courland. Similar burials are found in Akozino-Akhmylovo, with grave goods also from the upper and middle Volga region, while grave goods show continuity with Textile ware.

The use of asbestos increases in mainland Finnish wares with Kjelmøy Ware (ca. 700 BC – AD 300), which replaced the Lovozero Ware; and in the east in inner Finland and Karelia with the Luukonsaari and Sirnihta wares (ca. 700-500 BC – AD 200), where they replaced the previous Sarsa-Tomitsa ceramics.

The Gorodets culture appears during the Scythian period in the forest-steppe zone north and west of the Volga, shows fortified settlements, and there are documented incursions of Gorodets iron makers into the Samara valley, evidenced by deposits of their typical pottery and a bloom or iron in the region.

Iron Age ethnolinguistic groups

According to (Koryakova and Epimakhov 2007):

It is commonly accepted by archaeology, ethnography, and linguistics that the ancestors of the Permian peoples (the Udmurts, Komi-Permians, and Komi-Zyryans) left the sites of Ananyino cultural intercommunity.

NOTE. For more information on the Late Metal Ages and Early Medieval situation of Finno-Ugric languages, see e.g. South-eastern contact area of Finnic languages in the light of onomastics (Rahkonen 2013).

finno-saamic-mordvin
Yakhr-, -khra, yedr-, -dra and yer-/yar, -er(o), -or(o) names of lakes in Central and North Russia and the possible boundary of the proto-language words *jäkra/ä and *järka/ä. Rahkonen (2011)

Certain innovations shared between Proto-Fennic (identified with the Gulf of Finland) and Proto-Mordvinic (from the Gorodets culture) point to their close contact before the Proto-Fennic expansion, and thus to the identification of Gorodets as Proto-Mordvinic, hence Akozino as Volgaic (Parpola 2018):

  • the noun paradigms and the form and function of individual cases,
  • the geminate *mm (foreign to Proto-Uralic before the development of Fennic under Germanic influence) and other non-Uralic consonant clusters.
  • the change of numeral *luka ‘ten’ with *kümmen.
  • The presence of loanwords of non-Uralic origin, related to farming and trees, potentially Palaeo-European in nature (hence possibly from Siberian influence in north-eastern Europe).
ananino-textile-ware-cultures
Map of archaeological cultures in north-eastern Europe ca. 8th-3rd centuries BC. [The Mid-Volga Akozino group not depicted] Shaded area represents the Ananino cultural-historical society. Purple area show likely zones of predominant Siberian ancestry and N1c-L392 lineages. Blue areas likely zones of predominant CWC ancestry and R1a-Z645 lineages. Fading purple arrows represent likely stepped movements of haplogroup N1c-L392 for centuries (Siberian → Ananino → Akozino → Fennoscandia), found eventually in tarand graves. Blue arrows represent eventual expansions of Fennic and (partially displaced) Saamic. Modified image from Vasilyev (2002).

The introduction of a strongly hierarchical chiefdom system can quickly change the pre-existing social order and lead to a major genetic shift within generations, without a radical change in languages, as shown in Sintashta-Potapovka compared to the preceding Poltavka society (read more about Sintashta).

Fortified settlements in the region represented in part visiting warrior-traders settled through matrimonial relationships with local chiefs, eager to get access to coveted goods and become members of a distribution network that could guarantee them even military assistance. Such a system is also seen synchronously in other cultures of the region, like the Nordic Bronze Age and Lusatian cultures (Parpola 2013).

The most likely situation is that N1c subclades were incorporated from the Circum-Artic region during the Anonino (Permic) expansion to the north, later emerged during the formation of the Akozino group (Volgaic, under Anonino influence), and these subclades in turn infiltrated among the warrior traders that spread all over Fennoscandia and the eastern Baltic (mainly among Fennic, Saamic, Germanic, and Balto-Slavic peoples), during the age of hill forts, creating alliances partially based on exogamy strategies (Parpola 2013).

Over the course of these events, no language change is necessary in any of the cultures involved, since the centre of gravity is on the expanding culture incorporating new lineages:

  • first on the Middle Volga, when Ananino expands to the north, incorporatinig N1c lineages from the Circum-Artic region.
  • then with the expansion of the Akozino-Akhmylovo culture into Ananino territory, admixing with part of its population;
  • then on the Baltic region, when materials are imported from Akozino into Fennoscandia and the eastern Baltic (and vice versa), with local cultures being infiltrated by foreign (Akozino) warrior-traders and their materials;
  • and later with the different population movements that led eventually to a greater or lesser relevance of N1c in modern Finno-Permic populations.

To argue that this infiltration and later expansion of lineages changed the language in one culture in one of these events seems unlikely. To use this argument of “opposite movement of ethnic and language change” for different successive events, and only on selected regions and cultures (and not those where the greatest genetic and cultural impact is seen, like e.g. Sweden for Akozino materials) is illogical.

NOTE. Notice how I write here about “infiltration” and “lineages”, not “migration” or “populations”. To understand that, see below the next section on autosomal studies to compare Bronze Age, Iron Age, Medieval and Modern Estonians, and see how little the population of Estonia (homeland of Proto-Fennic and partially of Proto-Finno-Saamic) has changed since the Corded Ware migrations, suggesting genetic continuity and thus mostly close inter-regional and intra-regional contacts in the Forest Zone, hence a very limited impact of the absorbed N1c lineages (originally at some point incorporated from the Circum-Artic region). You can also check on the most recent assessment of R1a vs. N1c in modern Uralic populations.

Iron Age and later populations

From the session on Estonian samples on ISBA 8, by Tambets et al.:

[Of the 13 samples from the Iron Age tarand-graves] We found that the Iron Age individuals do in fact carry chrY hg N3 (…) Furthermore, based on their autosomal data, all of the studied individuals appear closer to hunter-gatherers and modern Estonians than Estonian CWC individuals do.

EDIT (16 OCT) A recent abstract with Saag as main author (Tambets second) cites 3 out of 5 sampled Iron Age individuals as having haplogroup N3.

EDIT (28 OCT): Notice also the appearance of N1a1a1a1a1a1a1-L1025 in Lithuania (ca. 300 AD), from Damgaard (Nature 2018); the N1c sample of the Krivichi Pskov Long Barrows culture (ca. 8th-10th c. AD), and N1a1a1a1a1a1a7-Y4341 among late Vikings from Sigtuna (ca. 10th-12th c. AD) in Krzewinska (2018).

estonian-pca
PCA of Estonian samples from the Bronze Age, Iron Age and Medieval times. Tambets et al. (2018, upcoming).

Looking at the plot, the genetic inflow marking the change from the Bronze Age to the Iron Age looks like an obvious expansion of nearby peoples with CWC-related ancestry, i.e. likely from the south-east, near the Middle Volga, where influence of steppe peoples is greater (hence likely Akozino) into a Proto-Fennic population already admixed (since the arrival of Corded Ware groups) with Comb Ware-like populations.

All of these groups were probably R1a-Z645 (likely R1a-Z283) since the expansion of Corded Ware peoples, with an introduction of some N1c lineages precisely during this Iron Age period. This infiltration of N1c-L392 with Akozino is obviously not directly related to Siberian cultures, given what we know about the autosomal description of Estonian samples.

Rather, N1c-L392 lineages were likely part of the incoming (Volgaic) Akozino warrior-traders, who settled among developing chiefdoms based on hill fort settlements of cultures all over the Baltic area, and began to appear thus in some of the new tarand graves associated with the Iron Age in north-eastern Europe.f

A good way to look at this is to realize that no new cluster appears compared to the data we already have from Baltic LN and BA samples from Mittnik et al. (2018), so the Estonian BA and IA clusters must be located (in a proper PCA) in the cline from Pit-Comb Ware culture through Baltic BA to Corded Ware groups:

baltic-samples
PCA and ADMIXTURE analysis reflecting three time periods in Northern European prehistory. a Principal components analysis of 1012 present-day West Eurasians (grey points, modern Baltic populations in dark grey) with 294 projected published ancient and 38 ancient North European samples introduced in this study (marked with a red outline). Population labels of modern West Eurasians are given in Supplementary Fig. 7 and a zoomed-in version of the European Late Neolithic and Bronze Age samples is provided in Supplementary Fig. 8. b Ancestral components in ancient individuals estimated by ADMIXTURE (k = 11)

This genetic continuity from Corded Ware (the most likely Proto-Uralic homeland) to the Proto-Fennic and Proto-Saamic communities in the Gulf of Finland correlates very well with the known conservatism of Finno-Saamic phonology, quite similar to Finno-Ugric, and both to Proto-Uralic (Kallio 2017): The most isolated region after the expansion of Corded Ware peoples, the Gulf of Finland, shielded against migrations for almost 1,500 years, is then the most conservative – until the arrival of Akozino influence.

NOTE. This has its parallel in the phonetic conservatism of Celtic or Italic compared to Finno-Ugric-influenced Germanic, Balto-Slavic, or Indo-Iranian.

Only later would certain regions (like Finland or Lappland) suffer Y-DNA bottlenecks and further admixture events associated with population displacements and expansions, such as the spread of Fennic peoples from their Estonian homeland (evidenced by the earlier separation of South Estonian) to the north and east:

diversification-finnic
The Finnic family tree. Kallio (2014).

The initial Proto-Fennic expansion was probably coupled with the expansion of Proto-Saami to the north, with the Kjelmøy Ware absorbing the Siberian population of Lovozero Ware, and potentially in inner Finland and Karelia with the Luukonsaari and Sirnihta wares (Carpelan and Parpola 2017).

This Proto-Saami population expansion from the mainland to the north, admixing with Lovozero-related peoples, is clearly reflected in the late Iron Age Saamic samples from Levänluhta (ca. 400-800 AD), as a shift (of 2 out of 3 samples) to Siberian-like ancestry from their original CWC_Baltic-like situation (see PCA from Lamnidis et al. 2018 above).

Also, Volgaic and Permic populations from inner Finland and the Forest Zone to the Cis-Urals and Circum-Artic regions probably incorporate Siberian ancestry and N1c-L392 lineages during these and later population movements, while the westernmost populations – Estonian, Mordvinic – remain less admixed (see PCA from Tambets et al. 2018 below).

We also have data of N1c-L392 in Nordic territory in the Middle Ages, proving its likely strong presence in the Mälaren area since the Iron Age, with the arrival of Akozino warrior traders. Similarly, it is found among Balto-Slavic groups along the eastern Baltic area. Obviously, no language change is seen in Nordic Bronze Age and Lusatian territory, and none is expected in Estonian or Finnish territory, either.

Therefore, no “N1c-L392 + Siberian ancestry” can be seen expanding Finno-Ugric dialects, but rather different infiltrations and population movements with limited effects on ancestry and Y-DNA composition, depending on the specific period and region.

estonians-hungarians-mordvinian
Selection of the PCA, with the group of Estonians, Mordovians, and Hungarians selected. See Tambets et al. (2018) for more information.

An issue never resolved

Because N1c-L392 subclades & Siberian ancestry, which appear in different proportions and with different origins among some modern Uralic peoples, do not appear in cultures supposed to host Uralic-speaking populations until the Iron Age, people keep looking into any direction to find the ‘true’ homeland of those ‘Uralic N1c peoples’? Kind of a full circular reasoning, anyone? The same is valid for R1a & steppe ancestry being followed for ‘Indo-Europeans’, or R1b-P312 & Neolithic farmer ancestry being traced for ‘Basques’, because of their distribution in modern populations.

I understand the caution of many pointing to the need to wait and see how samples after 2000 BC are like, in every single period, from the middle and upper Volga, Kama, southern Finland, and the Forest Zone between Fennoscandia and the steppe. It’s like waiting to see how people from Western Yamna and the Carpathian Basin after 3000 BC look like, to fill in what is lacking between East Yamna and Bell Beakers, and then between them and every single Late PIE dialect.

But the answer for Yamna-Bell Beaker-Poltavka peoples during the Late PIE expansion is always going to be “R1b-L23, but with R1a-Z645 nearby” (we already have a pretty good idea about that); and the answer for the Forest Zone and northern Cis- and Trans-Urals area – during the time when Uralic languages are known to have already been spoken there – is always going to be “R1a-Z645, but with haplogroup N nearby”, as is already clear from the data on the eastern Baltic region.

So, without a previously proposed model as to where those amateurs expressing concern about ‘not having enough data’ expect to find those ‘Uralic peoples’, all this waiting for the right data looks more like a waiting for N1c and Siberian ancestry to pop up somewhere in the historic Uralic-speaking area, to be able to say “There! A Uralic-speaking male!”. Not a very reasonable framework to deal with prehistoric peoples and their languages, I should think.

But, for those who want to do that, let me break the news to you already:

ananino-culture-balto-slavic
First N1c – Finno-Ugric person arrives in Estonia to teach Finno-Saamic to Balto-Slavic peoples.

And here it is, an appropriate fantasy description of the ethnolinguistic groups from the region. You are welcome:

  • During the Bronze Age, late Corded Ware groups evolve as the western Textile ware Fennic Balto-Slavic group in the Gulf of Finland; the Netted Ware Saamic Balto-Slavic group of inner Finland; the south Netted Ware / Akozino Volgaic Balto-Slavic groups of the Middle Volga; and the Anonino Permic Balto-Slavic group in the north-eastern Forest Zone; all developing still in close contact with each other, allowing for common traits to permeate dialects.
  • These Balto-Slavic groups would then incorporate west of the Urals during and after the Iron Age (ca. 800-500 BC first, and also later during their expansion to the north) limited ancestry and lineages from eastern European hunter-gatherer groups of Palaeo-European Fennic and Palaeo-Siberian Volgaic and Permic languages from the Circum-Artic region, but they adopted nevertheless the language of the newcomers in every single infiltration of N1c lineages and/or admixture with Siberian ancestry. Oh and don’t forget the Saamic peoples from central Sweden, of course, the famous N1c-L392 ‘Rurikid’ lineages expanding Saamic to the north and replacing Proto-Germanic…

The current model for those obsessed with modern Y-DNA is, therefore, that expanding Neolithic, Bronze Age and Iron Age cultures from north-eastern Europe adopted the languages of certain lineages originally from sub-Neolithic (Scandinavian and Siberian) hunter-gatherer populations of the Circum-Artic region; lineages that these cultures incorporated unevenly during their expansions. Hmmmm… Sounds like an inverse Western movie, where expanding Americans end up speaking Apache, and the eastern coast speaks Spanish until Italian migrants arrive and make everyone speak English… or something. A logic, no-nonsense approach to ethnolinguistic identification.

I kid you not, this is the kind of models we are going to see very soon. In 2018 and 2019, with ancient DNA able to confirm or reject archaeological hypotheses based on linguistic data, people will keep instead creating new pet theories to support preconceived ideas based on the Y-DNA prevalent among modern populations. That is, information available in the 2000s.

So what’s (so much published) ancient DNA useful for, exactly?

[Next post on the subject: Corded Ware—Uralic (III): Seima-Turbino and the Ugric and Samoyedic expansion]

Related

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

indo-european-uralic-migrations-corded-ware

This is the first of four posts on the Corded Ware—Uralic identification:

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

Evolution of Steppe, Neolithic, and Siberian ancestry in Eurasia (ISBA 8, 19th Sep)

jena-isba8

Some information is already available from ISBA 8 (see programme in PDF), thanks to the tweets from Alexander M. Kim.

Official abstracts are listed first (emphasis mine), then reports and images with link to Kim’s tweets. Here is the list for quick access:

Updates (17:00 CET):

Turkic and Hunnic expansions

Tracing the origin and expansion of the Turkic and Hunnic confederations, by Flegontov et al.

Turkic-speaking populations, now spread over a vast area in Asia, are highly heterogeneous genetically. The first confederation unequivocally attributed to them was established by the Göktürks in the 6th c. CE. Notwithstanding written resources from neighboring sedentary societies such as Chinese, Persian, Indian and Eastern Roman, earlier history of the Turkic speakers remains debatable, including their potential connections to the Xiongnu and Huns, which dominated the Eurasian steppe in the first half of the 1st millennium CE. To answer these questions, we co-analyzed newly generated human genome-wide data from Central Asia (the 1240K panel), spanning the period from ca. 3000 to 500 YBP, and the data published by de Barros Damgaard et al. (137 ancient human genomes from across the Eurasian steppes, Nature, 2018). Firstly, we generated a PCA projection to understand genetic affinities of ancient individuals with respect to present-day Tungusic, Mongolic, Turkic, Uralic, and Yeniseian-speaking groups. Secondly, we modeled hundreds of present-day and few ancient Turkic individuals using the qpAdm tool, testing various modern/ancient Siberian and ancient West Eurasian proxies for ancestry sources.

A majority of Turkic speakers in Central Asia, Siberia and further to the west share the same ancestry profile, being a mixture of Tungusic or Mongolic speakers and genetically West Eurasian populations of Central Asia in the early 1st millennium CE. The latter are themselves modelled as a mixture of Iron Age nomads (western Scythians or Sarmatians) and ancient Caucasians or Iranian farmers. For some Turkic groups in the Urals and the Altai regions and in the Volga basin, a different admixture model fits the data: the same West Eurasian source + Uralic- or Yeniseian-speaking Siberians. Thus, we have revealed an admixture cline between Scythians and the Iranian farmer genetic cluster, and two further clines connecting the former cline to distinct ancestry sources in Siberia. Interestingly, few Wusun-period individuals harbor substantial Uralic/Yeniseian-related Siberian ancestry, in contrast to preceding Scythians and later Turkic groups characterized by the Tungusic/Mongolic-related ancestry. It remains to be elucidated whether this genetic influx reflects contacts with the Xiongnu confederacy. We are currently assembling a collection of samples across the Eurasian steppe for a detailed genetic investigation of the Hunnic confederacies.

jeong-population-clines
Three distinct East/West Eurasian clines across the continent with some interesting linguistic correlates, as earlier reported by Jeong et al. (2018). Alexander M. Kim.
siberian-genetic-component-chronology
Very important observation with implication of population turnover is that pre-Turkic Inner Eurasian populations’ Siberian ancestry appears predominantly “Uralic-Yeniseian” in contrast to later dominance of “Tungusic-Mongolic” sort (which does sporadically occur earlier). Alexander M. Kim

New interesting information on the gradual arrival of the “Uralic-Yeniseian” (Siberian) ancestry in eastern Europe with Iranian and Turkic-speaking peoples. We already knew that Siberian ancestry shows no original relationship with Uralic-speaking peoples, so to keep finding groups who expanded this ancestry eastwards in North Eurasia should be no surprise for anyone at this point.

Central Asia and Indo-Iranian

The session The Genomic Formation of South and Central Asia, by David Reich, on the recent paper by Narasimhan et al. (2018).

bmac-reich
One important upside of dense genomic sampling at single localities – greater visibility of outliers and better constraints on particular incoming ancestries’ arrival times. Gonur Tepe as a great case study of this. Alexander M. Kim
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

British Isles

Ancient DNA and the peopling of the British Isles – pattern and process of the Neolithic transition, by Brace et al.

Over recent years, DNA projects on ancient humans have flourished and large genomic-scale datasets have been generated from across the globe. Here, the focus will be on the British Isles and applying aDNA to address the relative roles of migration, admixture and acculturation, with a specific focus on the transition from a Mesolithic hunter-gatherer society to the Neolithic and farming. Neolithic cultures first appear in Britain ca. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, in Britain, at the margins of the expansion the pattern and process of the British Neolithic transition remains unclear. To examine this we present genome-wide data from British Mesolithic and Neolithic individuals spanning the Neolithic transition. These data indicate population continuity through the British Mesolithic but discontinuity after the Neolithic transition, c.6000 BP. These results provide overwhelming support for agriculture being introduced to Britain primarily by incoming continental farmers, with surprisingly little evidence for local admixture. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

british-isles
Millennium of lag between farming establishment in NW mainland Europe & British Isles. Only 25 Mesolithic human finds from Britain. Alexander M. Kim.
british-admixture
– Evidently no resurgence of hunter-gatherer ancestry across Neolithic
– Argument for at least two geographically distinct entries of Neolithic farmers
Alexander M. Kim.

MN Atlantic / Megalithic cultures

Genomics of Middle Neolithic farmers at the fringe of Europe, by Sánchez Quinto et al.

Agriculture emerged in the Fertile Crescent around 11,000 years before present (BP) and then spread, reaching central Europe some 7,500 years ago (ya.) and eventually Scandinavia by 6,000 ya. Recent paleogenomic studies have shown that the spread of agriculture from the Fertile Crescent into Europe was due mainly to a demic process. Such event reshaped the genetic makeup of European populations since incoming farmers displaced and admixed with local hunter-gatherers. The Middle Neolithic period in Europe is characterized by such interaction, and this is a time where a resurgence of hunter-gatherer ancestry has been documented. While most research has been focused on the genetic origin and admixture dynamics with hunter-gatherers of farmers from Central Europe, the Iberian Peninsula, and Anatolia, data from farmers at the North-Western edges of Europe remains scarce. Here, we investigate genetic data from the Middle Neolithic from Ireland, Scotland, and Scandinavia and compare it to genomic data from hunter-gatherers, Early and Middle Neolithic farmers across Europe. We note affinities between the British Isles and Iberia, confirming previous reports. However, we add on to this subject by suggesting a regional origin for the Iberian farmers that putatively migrated to the British Isles. Moreover, we note some indications of particular interactions between Middle Neolithic Farmers of the British Isles and Scandinavia. Finally, our data together with that of previous publications allow us to achieve a better understanding of the interactions between farmers and hunter-gatherers at the northwestern fringe of Europe.

megalithic-europe
-Novel genomic data from 21 individuals from 6 sites.
– “Megalithic” individuals not systematically diff. from geographically proximate “non-megalithic” burials
– Mild evidence for over-representation of males in some British Isles megalithic tombs
– Megalithic tombs in W & N Neolithic Europe may have link to kindred structures
Alexander M. Kim

Central European Bronze Age

Ancient genomes from the Lech Valley, Bavaria, suggest socially stratified households in the European Bronze Age, by Mittnik et al.

Archaeogenetic research has so far focused on supra-regional and long-term genetic developments in Central Europe, especially during the third millennium BC. However, detailed high-resolution studies of population dynamics in a microregional context can provide valuable insights into the social structure of prehistoric societies and the modes of cultural transition.

Here, we present the genomic analysis of 102 individuals from the Lech valley in southern Bavaria, Germany, which offers ideal conditions for such a study. Several burial sites containing rich archaeological material were directly dated to the second half of the 3rd and first half of the 2nd millennium BCE and were associated with the Final Neolithic Bell Beaker Complex and the Early and Middle Bronze Age. Strontium isotope data show that the inhabitants followed a strictly patrilocal residential system. We demonstrate the impact of the population movement that originated in the Pontic-Caspian steppe in the 3rd millennium BCE and subsequent local developments. Utilising relatedness inference methods developed for low-coverage modern DNA we reconstruct farmstead related pedigrees and find a strong association between relatedness and grave goods suggesting that social status is passed down within families. The co-presence of biologically related and unrelated individuals in every farmstead implies a socially stratified complex household in the Central European Bronze Age.

lech-bavaria
Diminishing steppe ancestry and resurgent Neolithic ancestry over time. Alexander M. Kim

Notice how the arrival of Bell Beakers, obviously derived from Yamna settlers in Hungary, and thus clearly identified as expanding North-West Indo-Europeans all over Europe, marks a decrease in steppe ancestry compared to Corded Ware groups, in a site quite close to the most likely East BBC homeland. Copenhagen’s steppe ancestry = Indo-European going down the toilet, step by step…

UPDATES

Russian Far East populations

Gene geography of the Russian Far East populations – faces, genome-wide profiles, and Y-chromosomes, by Balanovsky et al.

Russian Far East is not only a remote area of Eurasia but also a link of the chain of Pacific coast regions, spanning from East Asia to Americas, and many prehistoric migrations are known along this chain. The Russian Far East is populated by numerous indigenous groups, speaking Tungusic, Turkic, Chukotko-Kamchatka, Eskimo-Aleut, and isolated languages. This linguistic and geographic variation opens question about the patterns of genetic variation in the region, which was significantly undersampled and received minor attention in the genetic literature to date. To fill in this gap we sampled Aleuts, Evenks, Evens, Itelmens, Kamchadals, Koryaks, Nanais, Negidals, Nivkhs, Orochi, Udegeis, Ulchi, and Yakuts. We also collected the demographic information of local populations, took physical anthropological photos, and measured the skin color. The photos resulted in the “synthetic portraits” of many studied groups, visualizing the main features of their faces.

north-eurasia

far-east-pca
Impressive North Eurasian biobank including 30,500 individual samples with broad consent, some genealogical info, phenotypic data. Alexander M. Kim

Finland AD 5th-8th c.

Sadly, no information will be shared on the session A 1400-year transect of ancient DNA reveals recent genetic changes in the Finnish population, by Salmela et al. We will have to stick to the abstract:

Objectives: Our objective was to use aDNA to study the population history of Finland. For this aim, we sampled and sequenced 35 individuals from ten archaeological sites across southern Finland, representing a time transect from 5th to 18th century.

Methods: Following genomic DNA extraction and preparation of indexed libraries, the samples were enriched for 1,2 million genomewide SNPs using in-solution capture and sequenced on an Illumina HighSeq 4000 instrument. The sequence data were then compared to other ancient populations as well as modern Finns, their geographical neighbors and worldwide populations. Authenticity testing of the data as well as population history inference were based on standard computational methods for aDNA, such as principal component analysis and F statistics.

Results: Despite the relatively limited temporal depth of our sample set, we are able to see major genetic changes in the area, from the earliest sampled individuals – who closely resemble the present-day Saami population residing markedly further north – to the more recent ancient individuals who show increased affinity to the neighboring Circum-Baltic populations. Furthermore, the transition to the present-day population seems to involve yet another perturbation of the gene pool.

So, most likely then, in my opinion – although possibly Y-DNA will not be reported – Finns were in the Classical Antiquity period mostly R1a with secondary N1c in the Circum-Baltic region (similar to modern Estonians, as I wrote recently), while Saami were probably mostly a mix of R1a-Z282 and I1 in southern Finland. That’s what the first transition after the 5th c. probably reflects, the spread of Finns (with mainly N1c lineages) to the north, while the more recent transition shows probably the introduction of North Germanic ancestry (and thus also R1b-U106, R1a-Z284, and I1 lineages) in the west.

Dairying in ancient Mongolia

The History of Dairying in ancient Mongolia, by Wilkin et al.

The use of mass spectrometry based proteomics presents a novel method for investigating human dietary intake and subsistence strategies from archaeological materials. Studies of ancient proteins extracted from dental calculus, as well as other archaeological material, have robustly identified both animal and plant-based dietary components. Here we present a recent case study using shotgun proteomics to explore the range and diversity of dairying in the ancient eastern Eurasian steppe. Contemporary and prehistoric Mongolian populations are highly mobile and the ephemerality of temporarily occupied sites, combined with the severe wind deflation common across the steppes, means detecting evidence of subsistence can be challenging. To examine the time depth and geographic range of dairy use in Mongolia, proteins were extracted from ancient dental calculus from 32 individuals spanning burial sites across the country between the Neolithic and Mongol Empire. Our results provide direct evidence of early ruminant milk consumption across multiple time periods, as well as a dramatic increase in the consumption of horse milk in the late Bronze Age. These data provide evidence that dairy foods from multiple species were a key part of subsistence strategies in prehistoric Mongolia and add to our understanding of the importance of early pastoralism across the steppe.

The confirmation of the date 3000-2700 BC for dairying in the eastern steppe further supports what was already known thanks to archaeological remains, that the pastoralist subsistence economy was brought for the first time to the Altai region by expanding late Khvalynsk/Repin – Early Yamna pastoralists that gave rise to the Afanasevo culture.

Neolithic transition in Northeast Asia

Genomic insight into the Neolithic transition peopling of Northeast Asia, by C. Ning

East Asian representing a large geographic region where around one fifth of the world populations live, has been an interesting place for population genetic studies. In contrast to Western Eurasia, East Asia has so far received little attention despite agriculture here evolved differently from elsewhere around the globe. To date, only very limited genomic studies from East Asia had been published, the genetic history of East Asia is still largely unknown. In this study, we shotgun sequenced six hunter-gatherer individuals from Houtaomuga site in Jilin, Northeast China, dated from 12000 to 2300 BP and, 3 farming individuals from Banlashan site in Liaoning, Northeast China, dated around 5300 BP. We find a high level of genetic continuity within northeast Asia Amur River Basin as far back to 12000 BP, a region where populations are speaking Tungusic languages. We also find our Compared with Houtaomuga hunter-gatherers, the Neolithic farming population harbors a larger proportion of ancestry from Houtaomuga related hunter-gathers as well as genetic ancestry from central or perhaps southern China. Our finding further suggests that the introduction of farming technology into Northeast Asia was probably introduced through demic diffusion.

A detail of the reported haplogroups of the Houtaomuga site:

houtaomuga-site-y-dna-mtdna

Y-DNA in Northeast Asia shows thus haplogroup N1b1 ~5000 BC, probably representative of the Baikal region, with a change to C2b-448del lineages before the Xiongnu period, which were later expanded by Mongols.

Modern Sardinians show elevated Neolithic farmer ancestry shared with Basques

sardinia-europe-relation

New paper (behind paywall), Genomic history of the Sardinian population, by Chiang et al. Nature Genetics (2018), previously published as a preprint at bioRxiv (2016).

#EDIT (18 Sep 2018): Link to read paper for free shared by the main author.

Interesting excerpts (emphasis mine):

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.

sardinia-pca
PCA results of merged Sardinian whole-genome sequences and the HGDP Sardinians. See below for a map of the corresponding regions.

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.

density-nuraghi-sardinia-genetics
Left: Geographical map of Sardinia. The provincial boundaries are given as black lines. The provinces are abbreviated as Cag (Cagliari), Cmp (Campidano), Car (Carbonia), Ori (Oristano), Sas (Sassari), Olb (Olbia-tempio), Nuo (Nuoro), and Ogl (Ogliastra). For sampled villages within Ogliastra, the names and abbreviations are indicated in the colored boxes. The color corresponds to the color used in the PCA plot (Fig. 2a). The Gennargentu region referred to in the main text is the mountainous area shown in brown that is centered in western Ogliastra and southeastern Nuoro.
Right: Density of Nuraghi in Sardinia, from Wikipedia.

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.

sardinian-admixture
Mixture proportions of the three-component ancestries among Sardinian populations. Using a method first presented in Haak et al. (Nature 522, 207–211, 2015), we computed unbiased estimates of mixture proportions without a parameterized model of relationships between the test populations and the outgroup populations based on f4 statistics. The three-component ancestries were represented by early Neolithic individuals from the LBK culture (LBK_EN), pre-Neolithic huntergatherers (Loschbour), and Bronze Age steppe pastoralists (Yamnaya). See Supplementary Table 5 for standard error estimates computed using a block jackknife.

Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.

Interestingly, haplogroup I2a1a1 is actually found among northern Iberians during the Neolithic and Chalcolithic, and is therefore associated with Neolithic ancestry in Iberia, too, and consequently – unless there is a big surprise hidden somewhere – with the ancestry found today among Basques.

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.

Related

Early Medieval Alemannic graveyard shows diverse cultural and genetic makeup

alemannic-niederstotzingen

Open access Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard, by O’Sullivan et al., Science (2018) 4(9):eaao1262

Interesting excerpts:

Introduction

The Alemanni were a confederation of Germanic tribes that inhabited the eastern Upper Rhine basin and surrounding region (Fig. 1) (1). Roman ethnographers mentioned the Alemanni, but historical records from the 3rd to the 6th century CE contain no regular description of these tribes (2). The upheaval that occurred during the European Migration Period (Völkerwanderung) partly explains the interchangeability of nomenclature with the contemporaneous Suebi people of the same region and periods of geographic discontinuity in the historical record (3). This diverse nomenclature reflects centuries of interactions between Romans and other Germanic groups such as the Franks, Burgundians, Thuringians, Saxons, and Bavarians. With the defeat of the Alemanni by Clovis I of the Franks in 497 CE, Alamannia became a subsumed Duchy of the Merovingian Kingdom. This event solidified the naming of the inhabitants of this region as Alemanni (3). From the 5th to the 8th century CE, integration between the Franks and the Alemanni was reflected by changed burial practices, with households (familia) buried in richly furnished graves (Adelsgrablege) (4). The splendor of these Adelsgräber served to demonstrate the kinship structure, wealth, and status of the familia and also the power of the Franks (Personenverbandstaaten, a system of power based on personal relations rather than fixed territory). Because inclusion in familia during the Merovingian period was not necessarily based on inheritance or provenance, debate continues on the symbolism of these burial rites (5).

The 7th century CE Alemannic burial site at Niederstotzingen in southern Germany, used circa 580 to 630 CE, represents the best-preserved example of such an Alemannic Adelsgrablege. (…)

alemannic-haplogroup

Strontium and oxygen isotope data from the enamel showed that most individuals are local rather than migrants (Table 1, table S2, and fig. S2), except for individuals 10 and 3B. (…)

Analysis of uniparental markers

mtDNA haplogroups were successfully assigned to all 13 individuals (Table 1). Notably, there are three groups of individuals that share, among the assigned positions, identical haplotypes: individuals 4, 9, and 12B in haplogroup X2b4; individuals 1 and 3A in haplogroup K1a; and individuals 2 and 5 in haplogroup K1a1b2a1a.

Most individuals belong to the R1b haplogroup (individuals 1, 3A, 3C, 6, 9, 12A, 12B, and 12C), which has the highest frequency (>70%) in modern western European populations (20). Five individuals (1, 3A, 9, 12B, and 12C) share the same marker (Z319) defining haplogroup R1b1a2a1a1c2b2b1a1 [=ISOGG R1b1a1a2a1a1c2b2b1a1a] (…) individuals 1, 3A, and 6 have R1b lineage and marker Z347 (R1b1a2a1a1c2b2b) [=ISOGG R1b1a1a2a1a1c2b2b], which belongs to the same male ancestral lineage as marker Z319 [i.e. all R1b-U106]. Individual 3B instead carries NRY haplogroup G2a2b1, which is rare in modern north, west, and east European populations (<5%), only reaching common abundance in the Caucasus (>70%), southern Europe, and the Near East (10 to 15%)

Genome-wide capture

alemannic-pca
PCA plot of Niederstotzingen individuals, modern west Eurasians, and selected ancient Europeans. Genome-wide ancient data were projected against modern west Eurasian populations. Colors on PCA indicate more general Eurasian geographic boundaries than countries: dark green, Caucasus; bright green, eastern Europe; yellow, Sardinia and Canary Islands; bright blue, Jewish diaspora; bright purple, western and central Europe; red, southern Europe; dark brown, west Asia; light purple, Spain; dark purple, Russia; pale green, Middle East; orange, North Africa. The transparent circles serve to highlight the genetic overlap between regions of interest.

Genomically, the individuals buried at Niederstotzingen can be split into two groups: Niederstotzingen North (1, 3A, 6, 9, 12B, and 12C), who have genomic signals that most resemble modern northern and eastern European populations, and Niederstotzingen South (3B and 3C), who most resemble modern-day Mediterraneans, albeit with recent common ancestry to other Europeans. Niederstotzingen North is composed of those buried with identifiable artifacts: Lombards (individual 6), Franks (individual 9), and Byzantines (individuals 3A and 12B), all of whom have strontium and oxygen isotope signals that support local provenance (fig. S2) (8). Just two individuals, 3B (Niederstotzingen South) and 10 (no sufficient autosomal data, with R1 Y-haplogroup), have nonlocal strontium isotope signals. The δ18O values suggest that individuals 10 and 3B may have originated from a higher-altitude region, possibly the Swiss-German Alpine foothills (8). Combined with the genome affinity of individual 3B to southern Europeans, these data provide direct evidence for incoming mobility at the site and for contact that went beyond exchange of grave goods (4). Familia had holdings across the Merovingian Kingdom and traveled long distances to maintain them; these holdings could have extended from northern Italy to the North Sea. Nobles displayed and accrued power by recruiting outside individuals into the household as part of their traveling retinue. Extravagant burial rites of these familia are symbolic evidence of the Frankish power systems based on people Personenverbandstaaten imposed from the 5th until the 8th century CE (4). The assignment of grave goods and the burial pattern do not follow any apparent pattern with respect to genetic origin or provenance, suggesting that relatedness and fellowship were held in equal regard at this burial.

Kinship

Both kinship estimates show first-degree relatedness for pairs 1/3A, 1/6, 1/9, 3A/9, and 9/12B and second-degree relatedness for 1/12B, 3A/6, 3A/12B, and 6/9. Except for 12C, all of the Niederstotzingen North individuals are detectably and closely related. The Niederstotzingen South individuals are not detectably related to each other or any other members of the cohort. (…)

We demonstrated that five of the individuals (1, 3A, 6, 9, and 12B) were kin to at least second degree (Fig. 3 and tables S15 and S16); four of these were buried with distinguishable grave goods (discussed above and in fig. S1). These data show that at Niederstotzingen, at least in death, diverse cultural affiliations could be appropriated even within the same family across just two generations. This finding is somewhat similar to the burial of the Frankish King Childeric in the 5th century CE with a combination of Frankish and Byzantine grave goods that symbolized both his provenance and military service to the Romans (4). The burial of three unrelated individuals (3B, 3C, and 12C) in multiple graves beside the rest of the cohort would imply that this Alemannic group buried their dead based on a combination of familial ties and fellowship. One explanation could be that they were adopted as children from another region to be trained as warriors, which was a common practice at the time; these children were raised with equal regard in the familia (2, 4).

alemannic-family
Reconstruction of first- and second-degree relatedness among all related individuals. Bold black lines and blue lines indicate first- and second-degree relatedness, respectively. Dark blue squares are identified males with age-at-death estimates years old (y.o.), mtDNA haplotypes, and NRY haplogroups. Red circles represent unidentified females that passed maternal haplotypes to their offspring. The light square represents one male infant that shares its maternal haplotype with individuals 12B and 9. N.D., not determined.

Conclusion

The 7th century CE burial in Niederstotzingen represents the best-preserved example of an Alemannic Adelsgrablege. The observation that burial of the remains was close to a Roman crossroads, orientated in a considered way, and associated with rich grave goods points to a noble gravesite of an Alemannic familia with external cultural influences. The high percentage of males in the burial site suggests that this site was intended for a ranked warrior group, meaning that the individuals are not representative of the population existing in 7th century CE Alemannia. The kinship estimates show that kinship structure was organized around the familia, which is defined by close association of related and unrelated individuals united for a common purpose. The apparent kinship structure is consistent with the hypothesized Personenverbandstaaten, which was a system by which Merovingian nobles enforced rule in the Duchies of Alemannia, Thuringia, Burgundy, and elsewhere. Beyond the origin of the grave goods, we show isotopic and genetic evidence for contact with communities external to the region and evidence for shared ancestry between northern and southern Europeans. This finding invites debate on the Alemannic power system that may have been highly influenced by mobility and personal relations.

Texts and images distributed under the terms of the Creative Commons Attribution-NonCommercial license.

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Viking Age town shows higher genetic diversity than Neolithic and Bronze Age

sigtuna-vikings

Open access Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town, by Krzewińska et al., Current Biology (2018).

Interesting excerpts (emphasis mine, some references deleted for clarity):

The town of Sigtuna in eastern central Sweden was one of the pioneer urban hubs in the vast and complex communicative network of the Viking world. The town that is thought to have been royally founded was planned and organized as a formal administrative center and was an important focal point for the establishment of Christianity [19]. The material culture in Sigtuna indicates that the town had intense international contacts and hosted several cemeteries with a Christian character. Some of them may have been used by kin-based groups or by people sharing the same sociocultural background. In order to explore the character and magnitude of mobility and migration in a late Viking Age town, we generated and analyzed genomic (n = 23) and strontium isotope (n = 31) data from individuals excavated in Sigtuna.

y-dna-vikings

The mitochondrial genomes were sequenced at 1.5× to 367× coverage. Most of the individuals were assigned to haplogroups commonly found in current-day Europeans, such as H, J, and U [14, 26, 27]. All of these haplotypes are present in Scandinavia today.

The Y chromosome haplogroups were assigned in seven males. The Y haplogroups include I1a, I2a, N1a, G2a, and R1b. Two identified lineages (I2a and N1a) have not been found in modern-day Sweden or Norway [28, 29]. Haplogroups I and N are associated with eastern and central Europe, as well as Finno-Ugric groups [30]. Interestingly, I2a was previously identified in a middle Neolithic Swedish hunter-gatherer dating to ca. 3,000 years BCE [31].

In Sigtuna, the genetic diversity in the late Viking Age was greater than the genetic diversity in late Neolithic and Bronze Age cultures (Unetice and Yamnaya as examples) and modern East Asians; it was on par with Roman soldiers in England but lower than in modern-day European groups (GBR and FIN; Figure 2B). Within the town, the group excavated at church 1 has somewhat greater diversity than that at cemetery 1. Interestingly, the diversity at church 1 is nearly as high as that observed in Roman soldiers in England, which is remarkable, since the latter was considered to be an exceptionally heterogeneous group in contemporary Europe [39].

pca-vikings
A PCA plot visualising all 23 individuals from Sigtuna used in ancient DNA analyses (m – males, f – females).

Different sex-related mobility patterns for Sigtuna inhabitants have been suggested based on material culture, especially ceramics. Building on design and clay analyses, some female potters in Sigtuna are thought to have grown up in Novgorod in Rus’ [40]. Moreover, historical sources mention female mobility in connection to marriage, especially among the elite from Rus’ and West Slavonic regions [41, 42]. Male mobility is also known from historical sources, often in connection to clergymen moving to the town [43].

Interestingly, we found a number of individuals from Sigtuna to be genetically similar to the modern-day human variation of eastern Europeans, and most harbor close genetic affinities to Lithuanians (Figure 2A). The strontium isotope ratios in 28 adult individuals with assigned biological sex and strontium values obtained from teeth (23 M1 and five M2) show that 70% of the females and 44% of the males from Sigtuna were non-locals (STAR Methods). The difference in migrant ratios between females and male mobility patterns was not statistically significant (Fisher’s exact test, p = 0.254 for 28 individuals and p = 0.376 for 16 individuals). Hence, no evidence of a sex-specific mobility pattern was found.

(…) As these social groups are not mirrored by our genetic or strontium data, this suggests that the inclusion in them was not based on kinship. Therefore, it appears as if socio-cultural factors, not biological bonds, governed where people were interred (i.e., the choice of cemetery).

diversity-yamna
Average pairwise genetic diversity measured in complete Sigtuna, St. Gertrud (church 1) and cemetery 1 (the Nunnan block) compared to both ancient and modern populations ranked by time period (Yamnaya, Unetice, and GBR-Roman, Roman Age individuals from Great Britain; GBR-AS, Anglo-Saxon individuals from Great Britain; GBR-IA, Iron Age individuals from Great Britain; JPT-Modern, presentday Japanese from Tokyo; FIN-Modern, present-day Finnish; GBR-Modern, present-day British; GIHModern, present-day Gujarati Indian from Houston, Texas). Error bars show ±2 SEs.

Interesting from this paper is the higher genetic (especially Y-DNA) diversity found in more recent periods (see e.g. here) compared to Neolithic and Bronze Age cultures, which is probably the reason behind some obviously wrong interpretations, e.g. regarding links between Yamna and Corded Ware populations.

The sample 84001, a “first-generation short-distance migrant” of haplogroup N1c-L392 (N1a in the new nomenclature) brings yet more proof of how:

  • Admixture changes completely within a certain number of generations. In this case, the N1c-L392 sample clusters within the genetic variation of modern Norwegians, near to the Skane Iron Age sample, and not with its eastern origin (likely many generations before).
  • This haplogroup appeared quite late in Fennoscandia but still managed to integrate and expand into different ethnolinguistic groups; in this case, this individual was probably a Viking of Nordic language, given its genetic admixture and its non-local (but neighbouring Scandinavian) strontium values.

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The father tongue and mother tongue hypotheses in Indo-European populations

New paper (behind paywall) Reconciling the father tongue and mother tongue hypotheses in Indo-European populations, by Zhang et al. National Science Review (2018) nwy083.

Interesting excerpts:

Here, we reassessed the correlation between genetic and linguistic characteristics in 34 modern IE populations (Fig. 1a), for which all four types of datasets (lexicon, phonemes, Y-chromosomal composition, and mitochondrial DNA (mtDNA) composition) are available. We assembled compositions of the Y-chromosomal and mtDNA haplogroups or paragroups from the corresponding IE populations, which reflect paternal and maternal lines, respectively (…)

Neighbour-Nets were constructed to delineate the differences between 34 IE population groups clustering at the genetic and linguistic levels (Fig. 2). The reticulations within each net reflect conflicting signals against tree-like structures and support incompatible groupings [21]. These structures are likely produced by potential horizontal transmissions between populations or languages such as admixture, and potential parallel evolution in linguistics as well [22]. The Neighbour-Net for Y-chromosomes with substantial reticulations shows complicated relationships among IE populations (Fig. 2a), indicating a substantial historical population contact and admixture among the males. In contrast, the Neighbour-Net for mtDNA in Fig. 2b clearly illustrates an East-West geographic polarization, indicating two major IE populations in matrilineages: Indo-Iranian and European. (…)

y-dna-mtdna-phoneme-lexicon
Neighbour-Nets of 34 Indo-European populations calculated from the Euclidean distance matrices using (a) Y-chromosomal haplogroups and (b) mtDNA haplogroups; Neighbour-Nets of IE languages calculated from the Hamming distance matrices using (c) lexicon and (d) phonemes. The colours in the legend correspond to the language groups.

The language learning by local women could constitute the reason for unbalanced correlation of mtDNA to lexicon and phonemes. Due to the social prestige of male immigrants, their local spouses have to adopt the language of their husbands and pass it to future generations [6, 10, 15]. This process is second language acquisition and easily develops language fossilization [31]. The language fossilization is a linguistic mechanism that a learner of a second language tends to preserve some linguistic features of the first language, and develops a form of inter-language [31]. Under this circumstance, women can easily replace the lexicon from another [21], but attempt to retain local accents influenced by their native language [32]. In other words, women change to adopt the same word usage as their husbands in daily life but still speak using their own pronunciation. In mixed-language marriages with these male immigrants, women prefer to pass down their inter-languages to offspring [10, 33]. As a result, it yields the correlation between mtDNA and phonemes we observed. Hence, we courageously proposed a hypothetical scenario in Indo-European populations that lexical system of language dominated by their father, while the phonemic system of language determined by their mother.

I am not a fan of this kind of statistical studies for Comparative Grammar, and there are many pitfalls just by looking at this paper superficially: use of modern languages and modern haplogroup distributions, improper classification of phonemes – as is usual in glottochronological studies – , etc… Which render their results ipso facto unacceptable.

But just yesterday I was discussing where the Copenhagen group and their fans were going to end up when Yamna samples turn out not to be the origin of haplogroup R1a-Z645 expansion, and Anthony’s proposal of a patron-client relationship came up. Since the Danish workgroup is always one step behind, such a reactionary view seems like a reasonable assumption for the future.

This mother tongue vs. father tongue theory is another good possibility for what we are going to see, then, when they use e.g. the exogamy of eastern Corded Ware groups with Yamna to explain the adoption of the language. Maybe that’s what Kristiansen’s invented Yamna → Corded Ware arrows mean… Anything to prove that Corded Ware peoples were Indo-European speakers.

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Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model are likely to hold and to validate specific features of the results. Each also comes with its own pitfalls and difficulties of interpretation. It is not obvious that any single approach represents a direct replacement as a data summary tool. Here we build more directly on the results of STRUCTURE/ADMIXTURE by developing a new approach, badMIXTURE, to examine which features of the data are poorly fit by the model. Rather than intending to replace more specific or sophisticated analyses, we hope to encourage their use by making the limitations of the initial analysis clearer.

The default interpretation protocol

Most researchers are cautious but literal in their interpretation of STRUCTURE and ADMIXTURE results, as caricatured in Fig. 1, as it is difficult to interpret the results at all without making several of these assumptions. Here we use simulated and real data to illustrate how following this protocol can lead to inference of false histories, and how badMIXTURE can be used to examine model fit and avoid common pitfalls.

admixture-protocol
A protocol for interpreting admixture estimates, based on the assumption that the model underlying the inference is correct. If these assumptions are not validated, there is substantial danger of over-interpretation. The “Core protocol” describes the assumptions that are made by the admixture model itself (Protocol 1, 3, 4), and inference for estimating K (Protocol 2). The “Algorithm input” protocol describes choices that can further bias results, while the “Interpretation” protocol describes assumptions that can be made in interpreting the output that are not directly supported by model inference

Discussion

STRUCTURE and ADMIXTURE are popular because they give the user a broad-brush view of variation in genetic data, while allowing the possibility of zooming down on details about specific individuals or labelled groups. Unfortunately it is rarely the case that sampled data follows a simple history comprising a differentiation phase followed by a mixture phase, as assumed in an ADMIXTURE model and highlighted by case study 1. Naïve inferences based on this model (the Protocol of Fig. 1) can be misleading if sampling strategy or the inferred value of the number of populations K is inappropriate, or if recent bottlenecks or unobserved ancient structure appear in the data. It is therefore useful when interpreting the results obtained from real data to think of STRUCTURE and ADMIXTURE as algorithms that parsimoniously explain variation between individuals rather than as parametric models of divergence and admixture.

For example, if admixture events or genetic drift affect all members of the sample equally, then there is no variation between individuals for the model to explain. Non-African humans have a few percent Neanderthal ancestry, but this is invisible to STRUCTURE or ADMIXTURE since it does not result in differences in ancestry profiles between individuals. The same reasoning helps to explain why for most data sets—even in species such as humans where mixing is commonplace—each of the K populations is inferred by STRUCTURE/ADMIXTURE to have non-admixed representatives in the sample. If every individual in a group is in fact admixed, then (with some exceptions) the model simply shifts the allele frequencies of the inferred ancestral population to reflect the fraction of admixture that is shared by all individuals.

Several methods have been developed to estimate K, but for real data, the assumption that there is a true value is always incorrect; the question rather being whether the model is a good enough approximation to be practically useful. First, there may be close relatives in the sample which violates model assumptions. Second, there might be “isolation by distance”, meaning that there are no discrete populations at all. Third, population structure may be hierarchical, with subtle subdivisions nested within diverged groups. This kind of structure can be hard for the algorithms to detect and can lead to underestimation of K. Fourth, population structure may be fluid between historical epochs, with multiple events and structures leaving signals in the data. Many users examine the results of multiple K simultaneously but this makes interpretation more complex, especially because it makes it easier for users to find support for preconceptions about the data somewhere in the results.

In practice, the best that can be expected is that the algorithms choose the smallest number of ancestral populations that can explain the most salient variation in the data. Unless the demographic history of the sample is particularly simple, the value of K inferred according to any statistically sensible criterion is likely to be smaller than the number of distinct drift events that have practically impacted the sample. The algorithm uses variation in admixture proportions between individuals to approximately mimic the effect of more than K distinct drift events without estimating ancestral populations corresponding to each one. In other words, an admixture model is almost always “wrong” (Assumption 2 of the Core protocol, Fig. 1) and should not be interpreted without examining whether this lack of fit matters for a given question.

admixture-pitfalls
Three scenarios that give indistinguishable ADMIXTURE results. a Simplified schematic of each simulation scenario. b Inferred ADMIXTURE plots at K= 11. c CHROMOPAINTER inferred painting palettes.

Because STRUCTURE/ADMIXTURE accounts for the most salient variation, results are greatly affected by sample size in common with other methods. Specifically, groups that contain fewer samples or have undergone little population-specific drift of their own are likely to be fit as mixes of multiple drifted groups, rather than assigned to their own ancestral population. Indeed, if an ancient sample is put into a data set of modern individuals, the ancient sample is typically represented as an admixture of the modern populations (e.g., ref. 28,29), which can happen even if the individual sample is older than the split date of the modern populations and thus cannot be admixed.

This paper was already available as a preprint in bioRxiv (first published in 2016) and it is incredible that it needed to wait all this time to be published. I found it weird how reviewers focused on the “tone” of the paper. I think it is great to see files from the peer review process published, but we need to know who these reviewers were, to understand their whiny remarks… A lot of geneticists out there need to develop a thick skin, or else we are going to see more and more delays based on a perceived incorrect tone towards the field, which seems a rather subjective reason to force researchers to correct a paper.

PCA of SNP data

Open access Effective principal components analysis of SNP data, by Gauch, Qian, Piepho, Zhou, & Chen, bioRxiv (2018).

Interesting excerpts:

A potential hindrance to our advice to upgrade from PCA graphs to PCA biplots is that the SNPs are often so numerous that they would obscure the Items if both were graphed together. One way to reduce clutter, which is used in several figures in this article, is to present a biplot in two side-by-side panels, one for Items and one for SNPs. Another stratagem is to focus on a manageable subset of SNPs of particular interest and show only them in a biplot in order to avoid obscuring the Items. A later section on causal exploration by current methods mentions several procedures for identifying particularly relevant SNPs.

One of several data transformations is ordinarily applied to SNP data prior to PCA computations, such as centering by SNPs. These transformations make a huge difference in the appearance of PCA graphs or biplots. A SNPs-by-Items data matrix constitutes a two-way factorial design, so analysis of variance (ANOVA) recognizes three sources of variation: SNP main effects, Item main effects, and SNP-by-Item (S×I) interaction effects. Double-Centered PCA (DC-PCA) removes both main effects in order to focus on the remaining S×I interaction effects. The resulting PCs are called interaction principal components (IPCs), and are denoted by IPC1, IPC2, and so on. By way of preview, a later section on PCA variants argues that DC-PCA is best for SNP data. Surprisingly, our literature survey did not encounter even a single analysis identified as DC-PCA.

The axes in PCA graphs or biplots are often scaled to obtain a convenient shape, but actually the axes should have the same scale for many reasons emphasized recently by Malik and Piepho [3]. However, our literature survey found a correct ratio of 1 in only 10% of the articles, a slightly faulty ratio of the larger scale over the shorter scale within 1.1 in 12%, and a substantially faulty ratio above 2 in 16% with the worst cases being ratios of 31 and 44. Especially when the scale along one PCA axis is stretched by a factor of 2 or more relative to the other axis, the relationships among various points or clusters of points are distorted and easily misinterpreted. Also, 7% of the articles failed to show the scale on one or both PCA axes, which leaves readers with an impressionistic graph that cannot be reproduced without effort. The contemporary literature on PCA of SNP data mostly violates the prohibition against stretching axes.

pca-how-to
DC-PCA biplot for oat data. The gradient in the CA-arranged matrix in Fig 13 is shown here for both lines and SNPs by the color scheme red, pink, black, light green, dark green.

The percentage of variation captured by each PC is often included in the axis labels of PCA graphs or biplots. In general this information is worth including, but there are two qualifications. First, these percentages need to be interpreted relative to the size of the data matrix because large datasets can capture a small percentage and yet still be effective. For example, for a large dataset with over 107,000 SNPs for over 6,000 persons, the first two components capture only 0.3693% and 0.117% of the variation, and yet the PCA graph shows clear structure (Fig 1A in [4]). Contrariwise, a PCA graph could capture a large percentage of the total variation, even 50% or more, but that would not guarantee that it will show evident structure in the data. Second, the interpretation of these percentages depends on exactly how the PCA analysis was conducted, as explained in a later section on PCA variants. Readers cannot meaningfully interpret the percentages of variation captured by PCA axes when authors fail to communicate which variant of PCA was used.

Conclusion

Five simple recommendations for effective PCA analysis of SNP data emerge from this investigation.

  1. Use the SNP coding 1 for the rare or minor allele and 0 for the common or major allele.
  2. Use DC-PCA; for any other PCA variant, examine its augmented ANOVA table.
  3. Report which SNP coding and PCA variant were selected, as required by contemporary standards in science for transparency and reproducibility, so that readers can interpret PCA results properly and reproduce PCA analyses reliably.
  4. Produce PCA biplots of both Items and SNPs, rather than merely PCA graphs of only Items, in order to display the joint structure of Items and SNPs and thereby to facilitate causal explanations. Be aware of the arch distortion when interpreting PCA graphs or biplots.
  5. Produce PCA biplots and graphs that have the same scale on every axis.

I read the referenced paper Biplots: Do Not Stretch Them!, by Malik and Piepho (2018), and even though it is not directly applicable to the most commonly available PCA graphs out there, it is a good reminder of the distorting effects of stretching. So for example quite recently in Krause-Kyora et al. (2018), where you can see Corded Ware and BBC samples from Central Europe clustering with samples from Yamna:

NOTE. This is related to a vertical distorsion (i.e. horizontal stretching), but possibly also to the addition of some distant outlier sample/s.

pca-cwc-yamna-bbc
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015). https://doi.org/10.7554/eLife.36666.006

The so-called ‘Yamnaya’ ancestry

Every time I read papers like these, I remember commenters who kept swearing that genetics was the ultimate science that would solve anthropological problems, where unscientific archaeology and linguistics could not. Well, it seems that, like radiocarbon analysis, these promising developing methods need still a lot of refinement to achieve something meaningful, and that they mean nothing without traditional linguistics and archaeology… But we already knew that.

Also, if this is happening in most peer-reviewed publications, made by professional geneticists, in journals of high impact factor, you can only wonder how many more errors and misinterpretations can be found in the obscure market of so many amateur geneticists out there. Because amateur geneticist is a commonly used misnomer for people who are not geneticists (since they don’t have the most basic education in genetics), and some of them are not even ‘amateurs’ (because they are selling the outputs of bioinformatic tools)… It’s like calling healers ‘amateur doctors’.

NOTE. While everyone involved in population genetics is interested in knowing the truth, and we all have our confirmation (and other kinds of) biases, for those who get paid to tell people what they want to hear, and who have sold lots of wrong interpretations already, the incentives of ‘being right’ – and thus getting involved in crooked and paranoid behaviour regarding different interpretations – are as strong as the money they can win or loose by promoting themselves and selling more ‘product’.

As a reminder of how badly these wrong interpretations of genetic results – and the influence of the so-called ‘amateurs’ – can reflect on research groups, yet another turn of the screw by the Copenhagen group, in the oral presentations at Languages and migrations in pre-historic Europe (7-12 Aug 2018), organized by the Copenhagen University. The common theme seems to be that Bell Beaker and thus R1b-L23 subclades do represent a direct expansion from Yamna now, as opposed to being derived from Corded Ware migrants, as they supported before.

NOTE. Yes, the “Yamna → Corded Ware → Únětice / Bell Beaker” migration model is still commonplace in the Copenhagen workgroup. Yes, in 2018. Guus Kroonen had already admitted they were wrong, and it was already changed in the graphic representation accompanying a recent interview to Willerslev. However, since there is still no official retraction by anyone, it seems that each member has to reject the previous model in their own way, and at their own pace. I don’t think we can expect anyone at this point to accept responsibility for their wrong statements.

So their lead archaeologist, Kristian Kristiansen, in The Indo-Europeanization of Europé (sic):

kristiansen-migrations
Kristiansen’s (2018) map of Indo-European migrations

I love the newly invented arrows of migration from Yamna to the north to distinguish among dialects attributed by them to CWC groups, and the intensive use of materials from Heyd’s publications in the presentation, which means they understand he was right – except for the fact that they are used to support a completely different theory, radically opposed to those defended in Heyd’s model

Now added to the Copenhagen’s unending proposals of language expansions, some pearls from the oral presentation:

  • Corded Ware north of the Carpathians of R1a lineages developed Germanic;
  • R1b borugh [?] Italo-Celtic;
  • the increase in steppe ancestry on north European Bell Beakers mean that they “were a continuation of the Yamnaya/Corded Ware expansion”;
  • Corded Ware groups [] stopped their expansion and took over the Bell Beaker package before migrating to England” [yep, it literally says that];
  • Italo-Celtic expanded to the UK and Iberia with Bell Beakers [I guess that included Lusitanian in Iberia, but not Messapian in Italy; or the opposite; or nothing like that, who knows];
  • 2nd millennium BC Bronze Age Atlantic trade systems expanded Proto-Celtic [yep, trade systems expanded the language]
  • 1st millennium BC expanded Gaulish with La Tène, including a “Gaulish version of Celtic to Ireland/UK” [hmmm, dat British Gaulish indeed].

You know, because, why the hell not? A logical, stable, consequential, no-nonsense approach to Indo-European migrations, as always.

Also, compare still more invented arrows of migrations, from Mikkel Nørtoft’s Introducing the Homeland Timeline Map, going against Kristiansen’s multiple arrows, and even against the own recent fantasy map series in showing Bell Beakers stem from Yamna instead of CWC (or not, you never truly know what arrows actually mean):

corded-ware-migrations
Nørtoft’s (2018) maps of Indo-European migrations.

I really, really loved that perennial arrow of migration from Volosovo, ca. 4000-800 BC (3000+ years, no less!), representing Uralic?, like that, without specifics – which is like saying, “somebody from the eastern forest zone, somehow, at some time, expanded something that was not Indo-European to Finland, and we couldn’t care less, except for the fact that they were certainly not R1a“.

This and Kristiansen’s arrows are the most comical invented migration routes of 2018; and that is saying something, given the dozens of similar maps that people publish in forums and blogs each week.

NOTE. You can read a more reasonable account of how haplogroup R1b-L51 and how R1-Z645 subclades expanded, and which dialects most likely expanded with them.

We don’t know where these scholars of the Danish workgroup stand at this moment, or if they ever had (or intended to have) a common position – beyond their persistent ideas of Yamnaya™ ancestral component = Indo-European and R1a must be Indo-European – , because each new publication changes some essential aspects without expressly stating so, and makes thus everything still messier.

It’s hard to accept that this is a series of presentations made by professional linguists, archaeologists, and geneticists, as stated by the official website, and still harder to imagine that they collaborate within the same professional workgroup, which includes experienced geneticists and academics.

I propose the following video to close future presentations introducing innovative ideas like those above, to help the audience find the appropriate mood:

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