Stone Age plague accompanying migrants from the steppe, probably Yamna, Balkan EBA, and Bell Beaker, not Corded Ware

copper-age-late-bell-beaker

In the latest revisions of the Indo-European demic diffusion model, using the results from the article Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, by Rasmussen et al., Cell (2015), I stated (more or less indirectly) that the high east-west mobility of the Corded Ware migrants across related cultures might have been responsible for the spread of this disease, which seems to have been originally expanded from Central Eurasia.

New results appeared recently in the article The Stone Age Plague and Its Persistence in Eurasia, by Valtueña et al., Current Biology (2017), which may contradict that interpretation.

corded-ware-map
Diachronic map of Copper Age migrations ca. 3100-2600 BC – Corded Ware

Abstract:

Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6th century AD, which persisted until the 8th century [ 1 ]; the renowned Black Death of the 14th century [ 2, 3 ], with recurrent outbreaks until the 18th century [ 4 ]; and the most recent 19th century pandemic, in which Y. pestis spread worldwide [ 5 ] and became endemic in several regions [ 6 ]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [ 7 ]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [ 8, 9 ]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.

plague_phylogeny_eurasia
Maximum-Likelihood Tree and Percent Coverage Plot of Virulence Factors of Yersinia pestis. (A) Maximum-likelihood tree of all Yersinia pestis genomes, including 1,265 SNP positions with complete deletion. Nodes with support R95% are marked with an asterisk. The colors represent different branches in the Y. pestis phylogeny: branch 0 (black), branch 1 (red), branch 2 (green), branch 3 (blue), branch 4 (orange), and LNBA Y. pestis branch (purple). Y. pseudotuberculosis-specific SNPs were excluded from the tree for clarity of representation. In the light-colored boxes, discussed losses and gains of genomic regions and genes are indicated. Related

It seems that, notwithstanding the simplistic (white) arrows of steppe ancestry expansion shown in their map (see below), the actual expansion of Yersinia pestis might have in fact accompanied Yamna migrants from the Pontic-Caspian steppe into Early Bronze Age cultures from the Balkans, including Bell Beaker migrants, as the phylogenetic analysis and dates suggest – and as the potential arrows of the plague expansion in the map (in green) show.

Late Corded Ware migrants would have only later expanded the disease to eastern Europe, as shown in the second map, most likely because of their close contact with Bell Beaker migrants (but remaining culturally distinct from them), and indeed because of the mobility accross related Corded Ware cultures up to the Urals.

The cultural-historical community in the Late Neolithic between steppe peoples that would evolve into Uralic-speaking Sredni Stog/Corded Ware migrants in the western steppe, and Late Indo-European-speaking Yamna/SE EBA/Bell Beaker migrants originally from the eastern steppe, would allow for the spread of the disease first among steppe groups, and then from both distinct late groups into their respective expanded regions.

The phylogenetic tree of Y. pestis available right now (see above), however, seems to suggest a stronger initial link to Yamna migrants, i.e. an origin in the North Caspian steppe, and an expansion with Yamna into the north Pontic area, into the Caucasus, and with the Afansevo culture, spreading later with Balkan EBA cultures and the expansion of Bell Beaker peoples.

Instead of warring nature, close ties, and mobility of Corded Ware peoples (reasons I used to justify the rapid spread of the disease among CWC groups), I guess it was rather the higher population density of SE Europe compared to the regions north of the loess belt, as well as the greater admixture of Yamna migrants with native SE European populations, the factors which might have helped expand the disease.

plague-expansion-europe
Map of Proposed Yersinia pestis Circulation throughout Eurasia (A) Entrance of Y. pestis into Europe from Central Eurasia with the expansion of Yamnaya pastoralists around 4,800 years ago. (B) Circulation of Y. pestis to Southern Siberia from Europe. Only complete genomes are shown.

Nevertheless, lacking more data, it is unclear if the disease expanded with both steppe groups.

Related:

Globular Amphora not linked to Pontic steppe migrants – more data against Kristiansen’s Kurgan model of Indo-European expansion

eneolithic-steppe-cultures

New open access article, Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages, by Tassi et al. (2017).

Abstract:

It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.

globular-amphora-pca-admixture
(a) Principal component analysis on genomic diversity in ancient and modern individuals. (b) K = 3,4 ADMIXTURE analysis based only on ancient variation. (a) Principal component analysis of 777 modern West Eurasian samples with 199 ancient samples. Only transversions considered in the PCA (to avoid confounding effects of post-mortem damage). We represented modern individuals as grey dots, and used coloured and labelled symbols to represent the ancient individuals. (b) Admixture plots at K = 3 and K = 4 of the analysis conducted only considering the ancient individuals. The full plot is shown in electronic supplementary material, figure S7. The ancient populations are sorted by a temporal scale from Pleistocene to Iron Age. The GAC samples of this study are displayed in the box on the right.

Excerpt, from the discussion:

In its classical formulation, the Kurgan hypothesis, i.e. a late Neolithic spread of proto-Indo-European languages from the Pontic steppes, regards the GAC people as largely descended from Late Neolithic ancestors from the East, most likely representing the Yamna culture; these populations then continued their Westward movement, giving rise to the later Corded Ware and Bell Beaker cultures. Gimbutas [23] suggested that the spread of Indo-European languages involved conflict, with eastern populations spreading their languages and customs to previously established European groups, which implies some degree of demographic change in the areas affected by the process. The genomic variation observed in GAC individuals from Kierzkowo, Poland, does not seem to agree with this view. Indeed, at the nuclear level, the GAC people show minor genetic affinities with the other populations related with the Kurgan Hypothesis, including the Yamna. On the contrary, they are similar to Early-Middle Neolithic populations, even geographically distant ones, from Iberia or Sweden. As already found for other Late Neolithic populations [18], in the GAC people’s genome there is a component related to those of much earlier hunting-gathering communities, probably a sign of admixture with them. At the nuclear level, there is a recognizable genealogical continuity from Yamna to Corded Ware. However, the view that the GAC people represented an intermediate phase in this large-scale migration finds no support in bi-dimensional representations of genome diversity (PCA and MDS), ADMIXTURE graphs, or in the set of estimated f3-statistics.

globular-amphora-hunter-gatherer-farmer-yamnaya
Scheme summarizing the five alternative models compared via ABC random forest. We generated by coalescent simulation mtDNA sequences under five models, differing as to the number of migration events considered. The coloured lines represent the ancient samples included in the analysis, namely Unetice (yellow line), Bell Beaker (purple line), Corded Ware (green line) and Globular Amphorae (red line) from Central Europe, Yamnaya (light blue line) and Srubnaya (brown line) from Eastern Europe. The arrows refer to the three waves of migration tested. Model NOMIG was the simplest one, in which the six populations did not have any genetic exchanges; models MIG1, MIG2 and MIG1, 2 differed from NOMIG in that they included the migration events number 1, 2 (from Eastern to Central Europe, respectively before and after the onset of the GAC), or both. Model MIG2, 3 represents a modification of MIG2 model also including a back migration from Central to Eastern Europe after the development of the Corded Ware culture.

Together with Globular Amphora culture samples from Mathieson et al. (2017), this suggests that Kristiansen’s Indo-European Corded Ware Theory is wrong, even in its latest revised models of 2017.

gimbutas-kurgan-indo-european
The background shading indicates the tree migratory waves proposed by Marija Gimbutas, and personally
checked by her in 1995. The symbols refer to the ancient populations considered in the ABC analysis

On the other hand, the article’s genetic finds have some interesting connections in terms of mtDNA phylogeography, but without a proper archaeological model it is difficult to explain them.

mtdna-yamnaya-gac-corded-ware-bell-beaker
Haplogroup frequencies were obtained for Early Neolithic (EN), Middle Neolithic (MN), Chalcolithic (CA), and Late Neolithic (LN). The color assigned to each haplogroup is represented on the lower right part of each plot. Haplogroup frequencies were plotted geographically using QGIS v2.14.

Text and images from the article under Creative Commons Attribution 4.0 license.

Discovered first via Bernard Sécher’s blog.

See also:

The renewed ‘Kurgan model’ of Kristian Kristiansen and the Danish school: “The Indo-European Corded Ware Theory”

Allentoft Corded Ware

A popular science article on Indo-European migrations has appeared at Science News, entitled How Asian nomadic herders built new Bronze Age cultures, signed by Bruce Bower. While the article is well-balanced and introduces new readers to the current status quo of the controversy on Indo-European migrations – including the opposing theories led by Kristiansen/Anthony vs. Heyd – , it reverberates yet again the conclusions of the 2015 Nature articles on the subject, especially with its featured image.

I have argued many times why the recent ‘Yamnaya -> Corded Ware -> Bell Beaker’ migration model is wrong, mainly within my essay Indo-European demic diffusion model, but also in articles of this blog, most recently in the post Correlation does not mean causation: the damage of the ‘Yamnaya ancestral component’, and the ‘Future America’ hypothesis). It is known that Nature is a bit of a ‘tabloid’ in the publishing industry, and these 2015 articles offered simplistic conclusions based on a wrong assessment of archaeological and linguistic data, in search for groundbreaking conclusions.

An excerpt from Bower’s article:

Corded Ware culture emerged as a hybrid way of life that included crop cultivation, breeding of farm animals and some hunting and gathering, Kristiansen argues. Communal living structures and group graves of earlier European farmers were replaced by smaller structures suitable for families and single graves covered by earthen mounds. Yamnaya families had lived out of their wagons even before trekking to Europe. A shared emphasis on family life and burying the dead individually indicates that members of the Yamnaya and Corded Ware cultures kept possessions among close relatives, in Kristiansen’s view.

“The Yamnaya and the Corded Ware culture were unified by a new idea of transmitting property between related individuals and families,” Kristiansen says.

Yamnaya migrants must have spoken a fledgling version of Indo-European languages that later spread across Europe and parts of Asia, Kristiansen’s group contends. Anthony, a longtime Kristiansen collaborator, agrees. Reconstructed vocabularies for people of the Corded Ware culture include words related to wagons, wheels and horse breeding that could have come only from the Yamnaya, Anthony says.

I have already talked about Kristiansen’s continuation of Gimbutas’ outdated ideas: we are seeing a renewed effort by some Scandinavian (mainly Danish) scholars to boost (and somehow capitalise) the revitalised concept of the “Kurgan people”, although now the fundamental issue has been more clearly shifted to the language spoken by Corded Ware migrants.

As far as I can tell, this renewed interest began two years ago, with the simultaneous publication of genetic studies by Haak et al. (2015), and Allentoft et al. (2015), and the misuse of the cursed concept of ‘Yamnaya ancestry‘ to derive far-fetched conclusions.

On the other hand, genetic research is not solely responsible for this: David Anthony – who was apparently consulted by Haak et al. (2015) for their paper, where he appears as co-author – has kept a low (or lower) profile, and only recently has he merely suggested potential links between Corded Ware and Bell Beaker cultures in Lesser Poland, that might explain what (some geneticists have told him) appeared as a potential Yamna -> Corded Ware -> Bell Beaker migration in the first ancient samples studied.

Anthony’s migration model remains otherwise strongly based on Archaeology, offering a careful interpretation of potential contacts and migrations in the Pontic-Caspian steppe, and only marginally offers some views on Linguistics (based on Ringe’s controversial ‘glottochronological model’ of 2006), to the extent that he is compelled to explain the potential adoption of Indo-European by Corded Ware culture (CWC) peoples as multiple cultural diffusion events, since no migration is observed from the steppe to CWC territories.

I think he is thus showing a great deal of restraint, not jumping on the bandwagon of this recent trend based on scarce genetic finds – and therefore losing also the opportunity to publish articles in journals of high impact factor….

This newly created Danish school, on the other hand, seems to be swimming with the tide. Kristiansen, known for his controversial ‘universal’ interpretations of European Prehistory – which are nevertheless more readable and interesting than most specialised literature on Archaeology, at least for us non-archaeologists – , has apparently seized the opportunity to give a strong impulse to his theories.

Not that there is nothing wrong with that, of course, but sometimes it might seem that a lot of papers (or even researchers) support something, when in fact there are only a few of them, working closely together

I see therefore three main “branches” of this support (two of them, Genetics and Linguistics, only recently giving some limited air to this dying hypothesis), with a closely related group of people involved in this model, and they are lending continuous support to each other, by repeating the same theory – and repeating the same misleading map images (like the one shown in the article) – , so that the circular reasoning they represent is concealed behind seemingly independent works.

The theory and its development

The main theory is officially rooted then in Kristiansen’s hypothesis, whose first article on the subject seems to be Prehistoric Migrations – the Case of the Single Grave and Corded Ware Cultures (1989), supporting the Kurgan model applied to the Corded Ware migrations. It was probably a kind of a breakthrough in Archaeology, bringing migration to mainstream Archaeology again (followed closely by Anthony), and he deserves merit for this.

After this proposal, there are mostly just his publications supporting this model. Nevertheless, Kristiansen’s model, I gather, did not involve the sudden Yamnaya -> Corded Ware migrations discussed in recent genetic articles, but long-lasting contacts between peoples and cultures from the North Pontic steppe, Trypillian, and Globular Amphora, that formed a new mixed one, the Corded Ware people and culture. Also, in Gimbutas’ original model of migration (1963), waves of Kurgan migrants are also described into Vučedol and Bell Beaker, which have been apparently forgotten in recent models*.
* The most recent model by Anthony describes such migrations into Early Bronze Age Balkan cultures – as do most archaeological publications today – , but he is unable to recognize migration waves from Yamna into the Corded Ware culture, and because of that describes mere potential routes (or modes) of cultural diffusion including language change.

kristiansen-corded-ware-kurgan
Proposal for the origin and spread of the Corded Ware/ Battle Axe cultural complex: 1) Distribution of CWC groups; 2) Yamna culture; 3) presumed area of origin; 4) presumed main directions of the primary distribution. Also numbered are other individual CW cultures. From Kristiansen (1989).

Then – skipping the years of simplistic phylogeography based on modern haplogroup distribution – we have to jump directly to Allentoft (of the Natural History Museum of Denmark) and cols. and their article on population genomics of Bronze Age Eurasia (2015), with which Kristiansen collaborated, and which offers the first direct association of Corded Ware as the vector of expansion of Indo-European peoples and languages from Yamna. An interesting take on the Yamna -> Corded Ware -> Bell Beaker question is represented by their very ‘kurgan-like’ Corded Ware-centric map:

allentoft-yamna-corded-ware
Detail of Fig. 1 from Allentoft et al. (2015): “Distribution of Early Bronze Age cultures Yamnaya, Corded Ware, and Afanasievo with arrows showing the Yamnaya expansions”.

And suddenly, we are now seeing more works that support the central thesis of the group – that Corded Ware must have brought Indo-European languages to Europe:

Recent publications by K-G Sjögren – from the same department as Kristiansen, at the University of Gothenburg – seem to imply that there was a direct connection Corded Ware -> Bell Beaker in central Europe.

Guus Kroonen‘s recent hypothesis of a potential (Proto-Semitic-like) Germanic substrate (2012) has been added recently to the cause, in supporting with Iversen (also from the University of Copenhaguen) a link with the Battle Axe/Funnelbeaker culture interaction. However, in the archaeological-linguistic model it seems that Germanic must predominate over the rest of Indo-European languages in terms of age, representing the first wave of Indo-Europeanization in Europe (wat?!), whereas Balto-Slavic is much younger and unrelated…? But didn’t they share the same substrate (as did partially Greek) in Kroonen (2012)? I think Kroonen’s hypothesis might be better explained through an earlier contact in the North Pontic steppe

kroonen-iversen
Modified from Kristiansen et al. (2017). “Schematic representation of how different Indo-European branches have absorbed words (circles) from a lost Neolithic language or language group (dark fill) in the reconstructed European linguistic setting of the third millennium BC, possibly involving one or more hunter gatherer languages (light fill) (after Kroonen & Iversen 2017)”.

Wrap-up

This recently created Danish pressure group is not something bad per se. I don’t agree with their hypothesis (or rather evolving hypotheses, since they change with new genetic results and linguistic proposals, as is shown in Kristiansen et al. 2017), but I understand that the group continues a recent tradition:

Publications are always great to advance in knowledge, and if they bring some deal of publicity, and more publications (with the always craved impact factor), and maybe more investment in the departments (with more local jobs and prestige)… why not?

However, this model of workgroup research system is reminiscent of the Anatolian homeland group loosely created around Renfrew; the Palaeolithic Continuity workgroup around Cavalli-Sforza; or (more recently) the Celtic from the West group around Cunliffe and Koch. The difference between Kristiansen’s workgroup and supporters of all those other models, in my opinion, is that (at least for the moment) their collaboration is not obvious to many.

Therefore, to be fair with any outsider, I think this group should clearly state their end model: I propose the general term “Indo-European Corded Ware Theory” (IECWT) workgroup, because ‘Danish’ is too narrow, and ‘Scandinavian’ too broad to represent the whole group. But any name will do.

My opinion on the IECWT

As you can see, no single strong proof exists in support of the IECWT:

  • Not for a solid model of PIE expansion from Corded Ware, not even within the IECWT group, where there is no support (to date) for a Balto-Slavic expansion associated with the Corded Ware culture… Or any other dialect, for that matter;
  • Not for a Corded Ware -> Bell Beaker connection – that is, before the publication of Allentoft et al. (2015) and articles reverberating their conclusions;
  • Not for a unified Pre-Germanic community before the Dagger Period, and still less linked with the expansion of the Corded Ware culture from the steppe – that connection is found only in Anthony (2007), where he links it with a cultural diffusion into Usatovo, which seems too late for a linguistic expansion with Corded Ware peoples, with the current genetic data.

The wrong interpretation of scarce initial ancient samples has been another feeble stone put over the ruins of Gimbutas’ theory. While her simple theory of Kurgan invaders was certainly a breakthrough in her time – when speaking about migrating Indo-European peoples was taboo -, it has since been overcome by more detailed archaeological and linguistic accounts of what happened in east and central Europe during the Chalcolithic and Bronze Age.

However, a lot of people are willing to consume post-truth genetic-based citebait like crazy, in a time when Twitter, Facebook, blogs, etc. seem to shape the general knowledge, while dozens of new, carefully prepared papers on Archaeology and Linguistics related to Indo-European peoples get published weekly and don’t attract any attention, just because they do not support these simplistic claims, or precisely because they fully reject them.

An older connection of Germanic to Scandinavia – and thus an ancestral Indo-European cultural diffusion from north to south – seems to better fit the traditional idea of an autochthonous Germanic homeland in Scandinavia, instead of a bunch of southern Bell Beaker invaders bringing the language that could only later develop as a common Nordic language during the Bronze Age, in a genetically-diverse community…

One is left to wonder whether the support of Corded Ware + haplogroup R1a representing Pre-Germanic is also in line with the most natural human Kossinnian trends, whereby the older your paternal line and your ancestral language are connected to your historical territory, the better. The lack of researchers from Norway – where R1b subclades brought by Bell Beakers peak – in the workgroup is revealing.

Just as we are seeing strong popular pressure e.g. to support the Out of India Theory by Hindu nationalists, or some Slavic people supporting to recreate a ‘Northern IE group’ with a Germano-Balto-Slavic Corded Ware culture – and a renewed interest in skin, hair and eye colour by amateur geneticists – , it is only natural to expect similar autochtonous-first trends in certain regions of the Germanic-speaking community.

NOTE: I feel a bit like an anti-IECWT hooligan here, and once again fulfilling Godwin’s Law. Judging by previous reactions in this blog to criticism of the Out of India Theory, and to criticism of R1a as the vector of expansion of Indo-European languages, this post is likely to cause some people to feel bad.

It is not intended to be against these researchers individually, though. All of them have certainly contributed in great ways to their fields, indeed more than I have to any field: Kristiansen is well-known for his careful, global interpretations of European prehistory (and has been supporting his model for quite a long time). I do like Kroonen’s ideas of a Pre-Germanic substratum. And people involved in the group do so probably because they collaborate closely with each other, and because of the huge pressure to publish in journals of high impact factor, so to mix their disparate research within a common model seems only natural.

But their collaboration is boosting certain wrong ideas, and is giving way to certain misconceptions in Linguistics, and also sadly renewed past ethnocentric views of language in Northern Europe – that will be luckily demonstrated, again, wrong. After all, publications (like ideas in general) are subjected to criticism, as mine are. Researchers who publish know their work is subjected to criticism, and not only before publication, but also – and probably more so – after it. That a paper can be incorrect, biased, or even completely absurd, does not mean the person who wrote it is a fool. That’s the difference between criticising ideas and insulting. If criticism offends you, you shouldn’t be publishing. Period.

Related:

Featured image: From Allentoft et al. (2015)“>Allentoft et al. (2015). See here for full caption.

Indo-European demic diffusion model, 3rd edition

pca-yamna-corded-ware

I have just uploaded the working draft of the third version of the Indo-European demic diffusion model. Unlike the previous two versions, which were published as essays (fully developed papers), this new version adds more information on human admixture, and probably needs important corrections before a definitive edition can be published.

The third version is available right now on ResearchGate and Academia.edu. I will post the PDF at Academia Prisca, as soon as possible:

pca-map-yamna-corded-ware-bell-beaker
Map overlaid by PCA including Yamna, Corded Ware, Bell Beaker, and other samples

Feel free to comment on the paper here, or (preferably) in our forum.

A working version (needing some corrections) divided by sections, illustrated with up-to-date, high resolution maps, can be found (as always) at the official collaborative Wiki website indo-european.info.

Islands across the Indonesian archipelago show complex patterns of admixture

austronesian-dna

An open access article Complex patterns of admixture across the Indonesian archipelago, by Hudjashov et al. (2017), has appeared in Molecular Biology and Evolution, and clarifies further the Austronesian (AN) expansion.

Abstract:

Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly under-characterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with maritime travelers from South Asia and strong demographic events in isolated local groups.

Among its results (emphasis is mine):

Most eastern Indonesian populations show traces of admixture that appear to reflect an expansion of AN speakers (Figure 4B, S3). There is a striking similarity between inferred events – each admixed population includes both a Philippine non-Kankanaey and western Indonesian-like source likely representing Holocene movements of Asian farming groups, as well as a Papuan-like source representing local indigenous ancestry. One reason for the lack of clear Taiwanese sources may be because the aboriginal populations of Taiwan were heavily affected by post-AN movements from mainland East Asia, most recently sinicization by Han Chinese, and thus no longer depict the ancestral AN gene pool (Mörseburg, et al. 2016). However, this notable pattern could equally be explained by the dominance of language and culture transfers during early phases of the Neolithic expansion from Taiwan into the Philippines, followed by people with predominantly Philippine ancestry driving later demic diffusion into the Indonesian archipelago. Interestingly, Mörseburg, et al. (2016), by using a different sample set and genotype-based analytical toolkit, indicated that the Kankanaey ethnic group from the Philippines is likely the closest living proxy of the source population that gave rise to the AN expansion. We did not detect this population among sources of admixture in eastern Indonesia, and therefore suggest that the place of individual Philippine groups in the AN expansion needs to be further addressed by better sampling in the Philippine archipelago.

Sumba and Flores, the two westernmost islands to the east of Wallace’s line, display a high proportion of Java and Bali surrogates in their AN admixing source. This suggests that the AN movement into eastern Indonesia, especially for Sumba and Flores, had earlier experienced some degree of genetic contact with western Indonesian groups. In contrast, the sources of AN admixture in Lembata, Alor, Pantar and Timor are dominated by Sulawesi (Figure 4B, S3, Table S3, S5). This generally agrees with expectations from the geography of the region, whereby AN groups exiting the southern Philippines were likely funneled into at least two streams, including a western path through Borneo and a central path through Sulawesi (Blust 2014).

Point estimates of genetic admixture times in eastern Indonesia lie within a narrow timeframe ranging between ca 185 BCE to 360 CE or 75 to 56 generations ago (95% CI 510 BCE – 475 CE or 87–52 generations) (Figure 4B, Table S3). These inferred dates are younger than some previous estimates (120–200 generations ago) (Xu, et al. 2012; Sanderson, et al. 2015; Sedghifar, et al. 2015). A major analysis of admixture in Indonesia estimated the date of AN contact in the eastern part of archipelago to be around 500 to 600 CE (ca 50 generations, CI estimates between 58–42 generations ago) (Lipson, et al. 2014), surprisingly young given the archaeological evidence. However, the study pooled a very small sample of genetically heterogeneous eastern Indonesian islands including, for example, Flores and Alor. As we show here (Figure 2, 4, 5, S3, Table S3, S5, S6), while the wave of AN speakers left a common genetic trace across the whole of eastern Indonesia, the details and dates of this contact vary considerably not only between islands (e.g., Flores and Alor), but also within individual islands (e.g., Flores Rampasasa vs. Flores Bama). The genetic dates, which were obtained here by denser geographical sampling of 8 eastern islands, a much larger number of individuals (28 per island on average) and a greater number of SNPs, are up to 30 generations older, predating the Common Era in many cases.

It therefore took migrants at least half a millennium to proceed from islands around Wallace’s line to the easternmost sampled part of eastern Indonesia. Nevertheless, observed dates for AN contact in eastern Indonesia are still approximately a millennium younger than the earliest Neolithic archaeological evidence in the region, and two explanations seem most likely here. First, the AN migration may have involved several waves of people leaving Taiwan, spanning multiple generations, which would bias date estimates later than the first arrival of the Neolithic archeological assemblage (Sedghifar, et al. 2015). Second, there may have been a substantial time gap between the spread of culture and technological traditions, and the beginning of extensive genetic contact between incoming farming groups and native inhabitants in Indonesia (Lansing, et al. 2011). The lack of considerable admixture with Papuan groups was recently noted in ancient Lapita individuals from Remote Oceania, whose genomes are mostly Asian and carry little to no Papuan ancestry, suggesting limited contact as they moved through Melanesia to previously uninhabited islands in the Pacific (Skoglund, et al. 2016). A lag in admixture between local and incoming Neolithic groups has also been observed in Europe, where hunter-gatherer and farming populations initially co-existed for nearly a thousand years without substantial genetic interaction (Malmström, et al. 2015).

austronesian-admixture Ancestral genomic components in regional populations. For every K, the modal solution with the highest number of ADMIXTURE runs is shown; individual ancestry proportions were averaged across all runs from the same mode and the number of runs (out of 50) assigned to the presented solution is shown in parentheses. Average cross validation statistics were calculated across all runs from the same mode (insert). The minimum cross-validation score is observed at K=9. Note major ancestry components in Indonesia and ISEA – Papuan (light purple), mainland Asian (light yellow) and AN (light blue) – as well as major differences in the distribution of these three ancestries between eastern and western Indonesia. Populations from the Philippines and Flores are abbreviated as ‘Ph.’ and ‘Fl.’, respectively.

Featured images are taken from the article.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Related posts:

Indo-European demic diffusion model, 2nd edition, revised and updated

It has been three months since I published the first paper on the Indo-European demic diffusion model.

In the meantime, important pre-print papers with samples of Bell Beaker and South-Eastern European cultures compel me to add new data in support of the model. I have taken this opportunity to revise the whole text in a new paper, Indo-European demic diffusion model, 2nd edition, and also some of the maps of Indo-European migrations, which are now hosted in this blog.

I have made changes to some of the old blogs I had, like this one, and I have merged two of them (from carlosquiles.com and indo-european.info) in this domain, indo-european.eu, to begin blogging about anthropological questions regarding Proto-Indo-Europeans and their language.

This blog was used years ago as my personal dialectic training site in English, mostly filled with controversial topics, and while I hope to keep some form of discussion, I want to turn it into a more pragmatic blog for news and reports on Indo-European studies.

Indo-European.info will be used as a collaborative Wiki website for this model to include supplementary information from published papers – such as results of individual and group’s admixture analyses, archaeological information of individual samples, and also mtDNA. To collaborate, users will have to request an account first (it will be a closed community), and those with important contributions will be added as authors of the following editions of the paper.