Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.
Looking more precisely at the different groups (even with the resampling approach), there are no significant differences between matrilocal and patrilocal groups. At best, as the study proposes, “this is just one of the factors at play in structuring the observed genetic variation”.
(…) we found evidence that the patterns of genetic differentiation depend on the geographical scale of the study. The magnitude of between-population differentiation in the NRY compared to the mtDNA is smaller when looking at the continental scale than in NWA (Figure 6). This is in agreement with the findings of Wilkins and Marlowe (2006), who showed that the excess of between-population differentiation for the NRY in comparison to the mtDNA decreases when comparing more geographically distant populations. Heyer et al. (2012) and Wilkins and Marlowe (2006) have proposed that at a local scale the patterns of genetic diversity reflect cultural practices over a relatively small number of generations, whereas at a larger geographic scale the genetic diversity reflects old migration and/or old common ancestry patterns(Heyer et al. 2012; Wilkins and Marlowe 2006).
The BSP plots and the diversity statistics indicate that overall the Ne of males has been smaller than that of females. One tentative explanation for this difference is that it reflects larger differences in reproductive success among males than among females. Some support for this explanation comes from the shape of the phylogenies (Supplementary Figures 1 and 6), since differences in reproductive success and the cultural transmission of fertility lead to imbalance phylogenies (Blum et al. 2006; Heyer et al. 2015). We estimated a common index of tree imbalance (Colless index) and calculated whether the mtDNA and NRY trees were more unbalanced than 1000 simulated trees generated under a Yule process (Bortolussi et al. 2006) (i.e. a simple pure birth process that assumes that the birth rate of new lineages is the same along the tree). We found that the NRY tree is more unbalanced than predicted by the Yule model (p-value=0.001), whereas the mtDNA tree is not significantly different from trees generated by the Yule model (p-value=0.628). It has been suggested that highly mobile hunter-gatherer societies, such as those typical of most of human prehistory, were polygynous bands (Dupanloup et al. 2003); similarly, nomadic horticulturalist Amazonian societies exhibit strong differences in reproductive success due to the common practice of polygyny, especially among community chiefs, whose offspring also enjoy a high fertility (Neel 1970; 1980; Neel and Weiss 1975).
Furthermore, a more recent expansion can be observed in the BSP based on the NRY, but not in the mtDNA BSP (Figure 5), indicating an expansion specifically in the paternal line. The reasons behind this recent male-biased population expansion, which starts ~3.5 kya, are as yet unclear. However, similar male-biased expansions have been observed in other studies using high-resolution NRY sequences (Batini et al. 2017; Karmin et al. 2015).
The main aim of this work was to contribute to the knowledge of pre‐Hispanic genetic variation and population structure among the South‐central Andes Area by studying individuals from Quebrada de Humahuaca, North‐western (NW) Argentina.
Materials and methods
We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900–1430 AD). Compiling autosomal, mitochondrial, and Y‐chromosome data, we evaluated population structure and differentiation among eight South‐central Andean groups from the current territories of NW Argentina and Peru.
Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre‐Hispanic history: pre‐Inca and Inca. All pre‐Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y‐chromosome analyses. We mainly found a clearly different haplotype composition between clusters.
Population structure in South America has been mostly studied on current native groups, mainly showing a west‐to‐east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South‐central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio‐political changes occurred in the evermore complex pre‐Hispanic Andean societies.
The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.
NOTE. The supplementary material seems to be full of errors right now, because it lists as R1b-M269 (and further subclades) samples that have been previously expressly said were xM269, so we will have to wait to see if there are big surprises here. So, for example, samples from Mal’ta (M269), Iron Gates (M269 and L51), and Latvia Mesolithic (L51), a Deriivka sample from 5230 BC (M269), Armenia_EBA (Z2103)…Also, the sample from Yuzhnyy Oleni Ostrov is R1a-M417 now.
EDIT (1 APR 2018): The main author has confirmed on Twitter that they have used a new Y Chr caller that calls haplogroups given the data provided, and depending on the coverage tried to provide a call to the lowest branch of the tree possible, so there are obviously a lot of mistakes – not just in the subclades of R. A revision of the paper is on its way, and soon more people will be able to work with the actual samples, since they say they are releasing them.
Nevertheless, since it is subclades (and not haplogroups) the apparent source of gross errors, for the moment it seems we can say with a great degree of confidence that:
New samples of East Yamna / Poltavka are of haplogroup R1b-L23.
Afanasevo is confirmed to be dominated by R1b-M269.
With lesser confidence in precise subclades, we find that:
A sample from Hajji Firuz in Iran ca. 5650 BC, of subclade R1b-Z2103, may confirm Mesolithic R1b-M269 lineages from the Caucasus as the source of CHG ancestry to Khvalynsk/Yamna, and be thus the reason why Reich wrote about a potential PIE homeland south of the Caucasus. (EDIT 11 APR 2018) The sample shows steppe ancestry, therefore the date is most likely incorrect, and a new radiocarbon dating is due. It is still interesting – depending on the precise subclade – for its potential relationship with IE migrations into the area.
New samples of East Yamna / Poltavka are of haplogroup R1b-Z2103.
Afanasevo migrants are mainly of haplogroup R1b-Z2103.
The Darra-e Kur sample, ca. 2655, of haplogroup R1b-L151, without a clear cultural adscription, may be the expected sign of Afanasevo migrants (Pre-Proto-Tocharian speakers) expanding a Northern Indo-European (in contrast with a Southern or Graeco-Aryan) dialect, in a region closely linked with the later desert mummies in the Tarim Basin. Its early presence there would speak in favour of a migration through the Inner Asian Mountain Corridor previous to the one caused by Andronovo migrants.
Sintashta shows a mixed R1b-Z2103 / R1a-Z93 society.
Later Indo-Iranian migrations are apparently dominated by R1a-Z2123, an early subclade of R1a-Z93, also found in Srubna.
R1b is also seen later in BMAC (ca. 1487 BC), although its subclade is not given.
There is also a sample of R1a-Z283 subclade in the eastern steppe (ca. 1600 BC). What may be interesting about it is that it could mark one of the subclades not responsible for the expansion of Balto-Slavic (or responsible for it with the expansion of Srubna, for those who support an Indo-Slavonic branch related Sintashta-Potapovka).
A sample of R1b-U106 subclade is found in Loebanr_IA ca. 950 BC, which – together with the sample of Darra-e Kur – is compatible with the presence of L51 in Yamna.
NOTE. Errors in haplogroups of previously published samples make every subclade of new samples from the supplementary table questionable, but all new samples (safe for the Darra_i_Kur one) were analysed and probably reported by the Reich Lab, and at least upper subclades in each haplogroup tree seem mostly coherent with what was expected. Also, the contribution of Iranian Farmer related (a population in turn contributing to Hajji Firuz) to Khvalynsk in their sketch of the genetic history may be a sign of the association of R1b-M269 lineages with CHG ancestry, although previous data on precise R1b subclades in the region contradict this. (EDIT 11 APR 2018) The sample of Hajji Firuz is most likely much younger than the published date, hence its younger subclade may be correct. No revision or comment on this matter has been published, though.
Also, it seems that the Corded Ware culture appears now irrelevant for Late Proto-Indo-European migrations. Observe:
Our results also shed light on the question of the origins of the subset of Indo-European languages spoken in India and Europe (45). It is striking that the great majority of Indo-European speakers today living in both Europe and South Asia harbor large fractions of ancestry related to Yamnaya Steppe pastoralists (corresponding genetically to the Steppe_EMBA cluster), suggesting that “Late Proto-Indo-European”—the language ancestral to all modern Indo- European languages—was the language of the Yamnaya (46). While ancient DNA studies have documented westward movements of peoples from the Steppe that plausibly spread this ancestry to Europe (5, 31), there has not been ancient DNA evidence of the chain 488 of transmission to South Asia. Our documentation of a large-scale genetic pressure from Steppe_MLBA groups in the 2nd millennium BCE provides a prime candidate, a finding that is consistent with archaeological evidence of connections between material culture in the Kazakh middle-to-late Bronze Age Steppe and early Vedic culture in India (46).
NOTE. If they correct the haplogroups soon, I will update the information in this post. Unless there is a big surprise that merits a new one, of course.
EDIT (1 APR 2018): Multiple minor edits to the original post.
EDIT (2 APR 2018): While I and other simple-minded people were only looking to confirm our previous theories using Y-DNA haplogroups, and are content with wildly speculating over the consequences if some of those strange (probably wrong) ones were true, intelligent people are using their time for something useful, interpreting the results of the investigation as described in the paper, to offer a clearer picture of Indo-Iranian migrations for everyone:
Featured image, from the article: “A Tale of Two Subcontinents. The prehistory of South Asia and Europe are parallel in both being impacted by two successive spreads, the first from the Near East after 7000 BCE bringing agriculturalists who mixed with local hunter-gatherers, and the second from the Steppe after 3000 BCE bringing people who spoke Indo-European languages and who mixed with those they encountered during their migratory movement. Mixtures of these mixed populations then produced the rough clines of ancestry present in both South Asia and in Europe today (albeit with more variable proportions of local hunter-gatherer-related ancestry in Europe than in India), which are (imperfectly) correlated to geography. The plot shows in contour lines the time of the expansion of Near Eastern agriculture. Human movements and mixtures, which also plausibly contributed to the spread of languages, are shown with arrows.”
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.
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.
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 Europecompared 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.
Nevertheless, lacking more data, it is unclear if the disease expanded with both steppe groups.
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.
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  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 , 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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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:
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.
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).
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.
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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.