The importance of fine-scale studies for integrating palaeogenomics and archaeology

eurasian-genomes-published

Short review (behind paywall) The importance of fine-scale studies for integrating paleogenomics and archaeology, by Krishna R. Veeramah, Current Opinion in Genetics & Development (2018) 53:83-89.

Abstract (emphasis mine):

There has been an undercurrent of intellectual tension between geneticists studying human population history and archaeologists for almost 40 years. The rapid development of paleogenomics, with geneticists working on the very material discovered by archaeologists, appears to have recently heightened this tension. The relationship between these two fields thus far has largely been of a multidisciplinary nature, with archaeologists providing the raw materials for sequencing, as well as a scaffold of hypotheses based on interpretation of archaeological cultures from which the geneticists can ground their inferences from the genomic data. Much of this work has taken place in the context of western Eurasia, which is acting as testing ground for the interaction between the disciplines. Perhaps the major finding has not been any particular historical episode, but rather the apparent pervasiveness of migration events, some apparently of substantial scale, over the past ∼5000 years, challenging the prevailing view of archaeology that largely dismissed migration as a driving force of cultural change in the 1960s. However, while the genetic evidence for ‘migration’ is generally statistically sound, the description of these events as structured behaviours is lacking, which, coupled with often over simplistic archaeological definitions, prevents the use of this information by archaeologists for studying the social processes they are interested in. In order to integrate paleogenomics and archaeology in a truly interdisciplinary manner, it will be necessary to focus less on grand narratives over space and time, and instead integrate genomic data with other form of archaeological information at the level of individual communities to understand the internal social dynamics, which can then be connected amongst communities to model migration at a regional level. A smattering of recent studies have begun to follow this approach, resulting in inferences that are not only helping ask questions that are currently relevant to archaeologists, but also potentially opening up new avenues of research.

Interesting excerpts (emphasis mine, reference numbers removed for clarity):

There are two major, somewhat intertwined, problems that currently exist.

First, archaeologists are not critiquing whether the migrations identified by paleogenomics using sophisticated population genetic machinery are actually occurring. Instead, the technical criticism arrives in terms of how these migrations are being ascribed to specific cultures. In many paleogenomic papers, there is a tendency (and often an analytical and technical need) to associate samples with particular archaeological cultures, for which all samples are then treated as possessing some kind homogenous and pervasive social identity that is bound in space and time. The major critiques of this thus far have been directed to those studies examining Corded-Ware and Bell-Beaker-related individuals and their potential relationship to the Yamnaya [Vander Linden (2016), Heyd (2017), Furholt (2017)], but are applicable to many other ‘migration’ scenarios described in the recent literature. This is compounded by the use of sometimes small numbers of samples to represent certain cultures from a particular geographic area as representatives of the entire culture at a supra-regional level. Yet often these archaeological cultures such as Corded-Ware and Bell-Beaker themselves show considerable variability in space and time, and even within cemeteries, which is not factored into the genetic analysis.

From a population geneticists point of view, this kind of simplification is somewhat understandable and will often likely have very little impact on the final analysis, given that the primary goal is usually to use ancient samples to better understand modern genetic variation. Though there may be a specific historical interest in some of these past events, I would argue that the aim for most population geneticists at a higher level is to try and fit modern patterns of genetic variation using the simplest models possible that take into account past demographic events (for example fitting f-statistics using the ADMIXTUREGRAPH approach), as this is how we are trained. Although sharing an archaeological culture may not mean that a set of individuals are part of the same homogeneous social group in reality, this approach may be a good enough heuristic to find broad genetic connections compared to another group represented by a different culture, which can then ultimately help understand and model modern human population structure. However, for an archaeologists interested in the ancient individuals themselves and their social identity, this lumping is unsatisfactory, where sophisticated narratives of the individual migrants and their ancient communities are the intended goal.

eurasian-genomes
From the paper. Barplot showing cumulative number of ancient Eurasian genomes published on a yearly basis up to 8th July 2018. Includes samples undergoing both whole genome shotgun and SNP capture sequencing.

The second related problem is that ‘migration’ in the sense used currently in the paleogenomics literature lacks sufficient detail to be of much use for an archaeologists attempting to disentangle the complex social dynamics within and between communities. To truly understand the role of migration as a social process and its contribution towards cultural changes, it is necessary to describe it as a structured behaviour, rather than treating it as an explanatory ‘black box’. Are the migrations occurring as a result of short range waves-of-advance movements, or as long-distance movements via leapfrogging models or stream migrations along established routes dependent on key kinship networks. Are there return migrants, and are some subset of individuals more predisposed to migration driving the signals? Although such models were implemented in past studies (even with classical markers [1]) and are part of the population genetics literature, they are lacking in the current paleogenomics literature when discussing migration. The finding that there is an increase of 12.3% of ancestry type X in population A compared to the preceding population B that is suggestive of a migration, is not particularly useful for examining these kind of models. It is also unclear to what degree standard population genetic parameters estimated from genomic data such as effective population size, Ne, and gene flow are relevant to models studied in archaeology, given they reflect (somewhat undefined) long-term population sizes and average rates of movements over time, rather than reflecting any kind of reality of census size and mobility in the ancient communities the archaeologists are actually attempting to study.

The text goes on to talk about ways of studying fine-grained social dynamics of local cultures, such as:

define levels of genetic relatedness, but also in terms of material culture, age, sex, stress and activity indicators, stable isotopes for diet reconstruction (nitrogen, d13C and d15N, carbon, 13C/12C) and strontium and oxygen isotopes for mobility (87Sr/86Sr, d18O). Where possible, sites should be examined over multiple generations. In addition it will be incredibly useful to characterize the impact of disease in these communities, which is also proving to be a highly fruitful realm for paleogenomics.

I would say that the main problem is not the obvious limitations of palaeogenomics in terms of identifying prehistoric ethnolinguistic communities and their evolution, which is why it is just another tool to complement archaeology and linguistics. The main problem is the narrow understanding that some people have of the inherent limitations of palaeogenomics – especially when it interests them – , when publicizing simplistic conclusions based on these tools and their results. And I am not referring only to amateurs.

Related

The future of the Reich Lab’s studies and interpretations of Late Indo-European migrations

yamna-corded-ware-bell-beaker-reich

Short report on advances in Genomics, and on the Reich Lab:

Some interesting details:

  • The Lab is impressive. I would never dream of having something like this at our university. I am really jealous of that working environment.
  • They are currently working on population transformations in Italy; I hope we can have at last Italic and Etruscan samples.
  • It is always worth it to repeat that we are all the source of multiple admixture events, many of them quite recent; and I liked the Star Wars simile.
  • Also, some names hinting at potential new samples?? Zajo-I, Chanchan, Gurulde?, Володарка (Ukraine – medieval?), Autodrom, Облевка, Кресты, Кудуксай (Ural region, palaeo-metal?), Золкут, etc.
reich-lab-samples
Ancient DNA sample bag?

On the bad aspect, they keep repeating the same “steppe ancestry” meme (in the featured image above, or the one below). I know this is the news report (i.e. science communication), not exactly the Reich Lab, but these maps didn’t appear out of the blue.

steppe-admixture-reich
Steppe ancestry distribution in Europe, according to PBS.

Interesting for future interpretations is the whiteboard behind David Reich’s back (apparently they like to keep relevant information on whiteboards…):

reich-indo-european-tree
Whiteboard behind David Reich’s back (at his office?).

It seems that while the Copenhagen group will still be bound (see here) by the Gimbutas/Kristiansen starting point, the Reich Lab will remain bound by Anthony’s selection of Ringe’s (2002) glottochronological model, and they will try to make genomic data fit in with it.

In fact, the whiteboard doesn’t even include Ringe’s link of Germanic with Italo-Celtic, which could maybe hint at Anthony’s recent change of heart? (i.e. Yamna Hungary -> Corded Ware). That would mean still less Linguistics (if glottochronology can be called that), and more Archaeology…

anthony-ringe-migration-model
Image from Anthony & Ringe (2015). “The Proto-Indo-European homeland, with migrations outward at about 4200 BCE (1), 3300 BCE (2), and 3000 BCE (3a and 3b). A tree diagram (inset) shows the pre-Germanic split as unresolved. Modified from Anthony (2013).”

I don’t know why university labs need to do this: To select the linguistic model preferred by a single archaeologist, which happens to be the lead archaeologist of the group, and then try to make genetic data agree again and again with that model. I guess it is a strategic question, and has to do with granting continued contacts with archaeological sites, and access to samples from them?

I understand none of them will try to learn ancient languages, too much work probably. But, wouldn’t it have been more scientifish, at least, to depart from, say, three or four reasonable potential linguistic models (that is, from Indo-Europeanists), and from there discuss the best potential fits for the current genomic data in each paper?

This is, for example, how the Heyd (archaeologist) + German/Spanish Indo-Europeanist schools would look like:

yamnaya-heyd-dunkel
Yamnaya expansion coupled with Meid’s (1975) description of three stages of Proto-Indo-European development (as interpreted by Adrados 1998) and depiction of Heyd’s proposal of Yamna expansion.

Wouldn’t you say it could have fitted the statistical and Y-DNA data seamlessly, in contrast to Gimbutas/Trager (i.e. Kristiansen today), or to Anthony/Ringe?

NOTE. I would say the mainstream German school follows Meid’s (1975) three-stage theory coupled with Dunkel’s (e.g. 1997) nomenclature. The Spanish school follows Adrados, who has repeated ad nauseam that he was the first to mention the three-stage theory in conferences and papers previous to and coincident with Meid’s proposal (see his latest JIES article, a paper available in Scribd). In any case, Spanish and German scholars have been working hand in hand in accepting and developing a general linguistic model similar to the one above.

Archaeological theories like those of Heyd or Mallory for Yamna and Bell Beaker (in contrast to Kristiansen or Anthony), and Prescott and Walderhaug for Bell Beaker and Germanic (contrasting with Kristiansen and Iversen) are compatible with this German/Spanish model.

The French school is non-existent on the homeland matter, Italian scholars seem to be behind even in the description of Anatolian as archaic (probably related to the general wish to have Latin as derived from Vergil’s Troy), Russian scholars are still working with Nostratic and Mesolithic expansions, and Leiden, as the leading IE publisher worldwide today, is full of very different ‘divos’, each with his own pet theory (some obviously agreeing with the German/Spanish model; and especially interesting is that some of them are strong supporters of an Indo-Uralic proto-language).

The English-speaking world, on the other hand, has seen the most varied models being either proposed or translated into its language, with the most popular ones being those publicized by archaeologists (Winfred P. Lehmann being one of the noteworthy exceptions), which may explain why for some people (archaeologists or geneticists) linguistics seems more like a game. It is to be assumed that these same people haven’t taken a look at the dozens of genetic papers published to date – and hundreds of archaeological papers using a bit of linguistics to support their models – , and how wrong they have all been in their interpretations, or else they would realize that genomics does (sadly) not really look like a serious discipline at all right now among most linguists, and among many archaeologists either…

Thus, instead of comparing the main theories on Proto-Indo-European (i.e. linguistics->archaeology->genetics), which would have offered the most stable framework to assess potential prehistoric ethnolinguistic identifications, they keep using a single, simplistic language tree liked by an archaeologist, and trying to fit genetic data to it, while also adapting archaeology to genetics, i.e. genetics->archaeology->linguistics; which, as you can imagine, is not going to convince any linguist.

Especially disappointing is that the world’s leading genetic lab still relies on a marginal proposal based on glottochronology, the homeopathy of linguistics… At least in that regard everyone should know better by now.

Also, they keep interacting with the wrong audience: instead of trying to engage linguists into the real homeland and dialectal quest, to keep Genomics a serious discipline among academics, they tend to discuss with politically- or racially-motivated people, which is probably also in line with strategic decisions.

In the example below, we see the main author of their recent paper on Indo-Iranian migrations seeking once again interaction, this time through “news” promoted by Hindu nationalist bigots, so that – even if that makes them look more neutral in the eyes of those who may allow access to Indian samples – , in the end, we see in genomics a fictitious revival of the “AIT vs. OIT debate” dead long ago in linguistics and archaeology (anywhere but in India).

Pretty disappointing to see these trends; so much effort and time invested in futile discussions and infinitely reworked doomed glottochronological or 19th-century models, when it is the fine-scale population structure of expanding Yamna peoples what we should be discussing now, and thus Late PIE dialectalisation with offshoots Afanasevo, East Bell Beaker, Balkan Bronze Age, and Sintashta/Potapovka; as well as Corded Ware evolution in Uralic-speaking territory.

EDIT (7 JUN 2018): Some parts of the text have been corrected or slightly modified.

Related:

The uneasy relationship between Archaeology and Ancient Genomics

Allentoft Corded Ware

News feature Divided by DNA: The uneasy relationship between archaeology and ancient genomics, Two fields in the midst of a technological revolution are struggling to reconcile their views of the past, by Ewen Callaway, Nature (2018) 555:573-576.

Interesting excerpts (emphasis mine):

In duelling 2015 Nature papers6,7the teams arrived at broadly similar conclusions: an influx of herders from the grassland steppes of present-day Russia and Ukraine — linked to Yamnaya cultural artefacts and practices such as pit burial mounds — had replaced much of the gene pool of central and Western Europe around 4,500–5,000 years ago. This was coincident with the disappearance of Neolithic pottery, burial styles and other cultural expressions and the emergence of Corded Ware cultural artefacts, which are distributed throughout northern and central Europe. “These results were a shock to the archaeological community,” Kristiansen says.

(…)

Still, not everyone was satisfied. In an essay8 titled ‘Kossinna’s Smile’, archaeologist Volker Heyd at the University of Bristol, UK, disagreed, not with the conclusion that people moved west from the steppe, but with how their genetic signatures were conflated with complex cultural expressions. Corded Ware and Yamnaya burials are more different than they are similar, and there is evidence of cultural exchange, at least, between the Russian steppe and regions west that predate Yamnaya culture, he says. None of these facts negates the conclusions of the genetics papers, but they underscore the insufficiency of the articles in addressing the questions that archaeologists are interested in, he argued. “While I have no doubt they are basically right, it is the complexity of the past that is not reflected,” Heyd wrote, before issuing a call to arms. “Instead of letting geneticists determine the agenda and set the message, we should teach them about complexity in past human actions.”

Many archaeologists are also trying to understand and engage with the inconvenient findings from genetics. (…)
[Carlin:] “I would characterize a lot of these papers as ‘map and describe’. They’re looking at the movement of genetic signatures, but in terms of how or why that’s happening, those things aren’t being explored,” says Carlin, who is no longer disturbed by the disconnect. “I am increasingly reconciling myself to the view that archaeology and ancient DNA are telling different stories.” The changes in cultural and social practices that he studies might coincide with the population shifts that Reich and his team are uncovering, but they don’t necessarily have to. And such biological insights will never fully explain the human experiences captured in the archaeological record.

Reich agrees that his field is in a “map-making phase”, and that genetics is only sketching out the rough contours of the past. Sweeping conclusions, such as those put forth in the 2015 steppe migration papers, will give way to regionally focused studies with more subtlety.

This is already starting to happen. Although the Bell Beaker study found a profound shift in the genetic make-up of Britain, it rejected the notion that the cultural phenomenon was associated with a single population. In Iberia, individuals buried with Bell Beaker goods were closely related to earlier local populations and shared little ancestry with Beaker-associated individuals from northern Europe (who were related to steppe groups such as the Yamnaya). The pots did the moving, not the people.

This final paragraph apparently sums up a view that Reich has of this field, since he repeats it:

Reich concedes that his field hasn’t always handled the past with the nuance or accuracy that archaeologists and historians would like. But he hopes they will eventually be swayed by the insights his field can bring. “We’re barbarians coming late to the study of the human past,” Reich says. “But it’s dangerous to ignore barbarians.”

I would say that the true barbarians didn’t have a habit or possibility to learn from the higher civilizations they attacked or invaded. Geneticists, on the other hand, only have to do what they expect archaeologists to do: study.

EDIT (30 MAR 2018): A new interesting editorial of Nature, On the use and abuse of ancient DNA.

See also:

Something is very wrong with models based on the so-called ‘Yamnaya admixture’ – and archaeologists are catching up (II)

A new article by Leo S. Klejn tries to improve the Northern Mesolithic Proto-Indo-European homeland model of the Russian school of thought: The Steppe hypothesis of Indo-European origins remains to be proven, Acta Archaeologica, 88:1, 193–204.

Abstract:

Recent genetic studies have claimed to reveal a massive migration of the bearers of the Yamnaya culture (Pit-grave culture) to the Central and Northern Europe. This migration has supposedly lead to the formation of the Corded Ware cultures and thereby to the dispersal of Indo-European languages in Europe. The article is a summary presentation of available archaeological, linguistic, genetic and cultural data that demonstrates many discrepancies in the suggested scenario for the transformations caused by the Yamnaya “invasion” some 5000 years ago.

Excerpts:

Both teams [Reich/Anthony, and Willerslev/Kristiansen] interpreted this resemblance in the same way: as evidence of mass migration of the Yamnaya culture from the steppes into the Central and Northern Europe, resulting in the formation of the Corded Ware cultures, and these are universally recognised as Indo-European. Since earlier in this part of Europe existed a different pool of genomes, geneticists presumed that the Yamnaya migration alone had brought the Indo-European languages into Europe. It is difficult to say to what extent the pre-convictions of the involved archaeologists influenced these conclusions, or whether the results of the genetic studies attracted archaeologists with such beliefs.

Mismatch of cultural manifestations

First, we might question the idea of the Yamnaya culture as a unity rather than a loose conglomerate of cultures. Merpert (1974) divided it into nine local groups but did not recognise them as separate cultures. However, in 1975 I suggested that Nerushay (Budzhak) monuments should be recognised as a distinct culture (Klejn 1975), although still as a part of the same broader steppe community.

This was accepted by other specialists (Ivanova 2012; 2013; 2014). Generally, in the western branch of this community, a mixture of the eastern rites of interment with local, Balkan ceramics can be observed. It should be noted that hitherto all genetic samples were taken from eastern material (in the vicinity of Samara in the Volga basin and Kalmykia), while the central thesis concerns the intrusion of the western branch of this community (Budzhak culture) into Europe.

yamnaya-corded-ware.connection
The spread of cultural-historical communities of the Yamnaya culture and the location of the Budzhak culture. GAC – Globular Amphora culture; CWC – Corded Ware culture. After Ivanova 2013.

Simultaneity of cultures

The Yamnaya culture (Chernykh & Orlovskaya 2004a; Heyd 2011; Frȋnculeasa et al. 2015) appears not to be the predecessor of the Corded Ware cultures but is contemporary with them. The Corded Ware cultures appeared also around the turn between the fourth and third millennium BC (Stöckli 2001; Furholt 2003). Their derivation from the Yamnaya seems, therefore, to be less probable. This is evidenced by the fact that the corded beakers or amphorae found in the Budzhak culture are not the prototypes of the corded beakers or amphorae found in more northern territories, but seem instead to be an outcome of contemporaneous contacts (Ivanova 2014; Klejn 2017c).

Discrepancies across the haplogroups

Even more remarkable is the variation in the distribution of types of Y chromosome. In the Yamnaya population, R1b is not just a single occurrence (there are about seven known occurrences) while in the Corded Ware population a different clade of R1b is found and R1a is predominant (several instances). Thus the postulate of unbroken succession finds no support!

yamna-into-corded-ware
Distribution of artefacts and customs of the Yamnaya culture in the area of the Corded Ware cultures. After Bátora 2006.

Paradoxical gradient

In the tables presented in the article by Reichs’ team (Haak et al. 2015) the genetic pool connecting the Yamnaya culture with the Corded Ware people is shown to be more intense in Northern Europe (Norway and Sweden) and decreases gradually from the North to the South (Fig. 6). It is weakest around the Danube, in Hungary, i. e. areas neighbouring the western branch of the Yamnaya culture! This is the reverse image to what the proposed hypothesis by the geneticists would lead us to expect. It is true that this gradient is traced back from the contemporary materials, but it was already present during the Bronze Age (Klejn 2015a).

The author also uses questionable interpretations from selected articles to advance his (as of today) untenable positions regarding a Mesolithic origin of the reconstructible Proto-Indo-European language.

1. Glottochronology, for a PIE origin:

If based on the data of glottochronology (taking into account all disputes) the period of initial dispersal is to be dated to the 7th-5th millennium BC.

2. Doubts on the origin of R1b-L51 subclades expressed in Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia, by Balanovsky et al. (2017), Human Genetics 136, 4. 437-450:

The currently available dataset does not contradict the hypothesis that R-GG400 marks a link between the East European steppe dwellers and West Asians, though the route and even direction of this migration is disputable. It does, however, demonstrate that present-day West European R1b chromosomes do not originate from the Yamnaya populations analyzed in (Haak et al. 2015; Mathieson et al. 2015) and raises the question of their origin. A Bronze Age origin is more likely than a Neolithic one (Balaresque et al. 2010), but further ancient DNA studies may be necessary to identify this source.

Just yesterday I read the post The retraction paradox: Once you retract, you implicitly have to defend all the many things you haven’t yet retracted, by Andrew Gelman. While – in my opinion – the post does not live up to its title, it poses an interesting question, as to how ad logicam (fallacy fallacy) is often used today in research: One author proposes something that is later demonstrated to be wrong, so everything they wrote or write can be said ipso facto to be wrong…especially if they accept that it was wrong.

This is usual with amateur geneticists (those who don’t publish, and are therefore not subjected to criticism): if anyone is wrong (whether in Archaeology or Genetics), then they are wrong in everything else. It seems to me that Klejn’s theses against recent genetic results rest on the same assumption: The Yamna -> Corded Ware migration model is wrong, ergo the Yamna homeland model is wrong.

I guess this same fallacy is what a lot of angered geneticists (whether professional or amateurs) are going to use to dismiss Klejn’s criticism, trying to focus on what he clearly does not grasp – about genomic data of Yamna peoples and their expansion – to disregard his doubts on genetic interpretations entirely.

I have warned many times about how simplistic interpretations of genetic data would cause a general mistrust in the field, and that archaeologists won’t take the discipline seriously, no matter how many articles get published in famous research tabloids like Nature or Science…

Those who dismiss this warning lightly seem to forget the fate of other recent “scientific breakthroughs” which were initially so promising that Humanities appeared to matter no more, like glottochronology for Linguistics and, to some extent, that of radiocarbon analysis for Archaeology.
EDIT: see here a recent example of discusion on discrepancies between archaeological and 14C-based chronologies, whereby ‘scientific data’ obviously needs archaeological context for a meaningful interpretation

Featured image: The direction of the supposed migration of the bearers of the Yamnaya culture into the area of the Corded Ware cultures. After Haak et al. 2015.

NOTE: I obviously don’t agree with Klejn’s main model: he criticises the Proto-Indo-European steppe homeland, and more specifically the expansion of Yamna peoples with R1b-L23 subclades, which I support. But, probably because of his “pre-convictions” (as he puts it when describing proponents of the steppe hypotheses) about the Proto-Indo-European homeland in Northern Europe during the Mesolithic, he was one of the first renown archaeologists to criticise the obvious inconsistencies in the genetic model of migrations based exclusively on the “Yamnaya ancestral component” concept, and to provoke the necessary reaction from (until then) overconfident geneticists, and he deserves credit for that.

In my opinion, the Russian school’s “Northern European Mesolithic” homeland model – as I have said before – could be based on the appearance of EHG ancestry, or maybe on the expansion of haplogroup R1b with post-Swiderian cultures, but the timeframe proposed is too early for any reconstructible parent proto-language, even for Indo-Uralic.

Related:

Modern Hungarian mtDNA more similar to ancient Europeans than to Hungarian conquerors

middle-ages-europe

New preprint at BioRxiv, MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians, by Maroti et al. (2018).

hungarian-shared-mtDNA
The estimated age distribution of the shared mt Hgs between Hungarians (Hun), the best hypothetical admix (mixFreq) and the populations contributing to this admix: Belgian/Dutch (BeN), Danish (Dan), Basque (Bsq), Croatian/Serbian (CrS), Baltic Late Bronze Age culture (BalBA), Bell Beaker culture (BellB), Slovakian (Slo). The numbers in parentheses indicate the contributions to the best hypothetical admix.

Abstract (emphasis mine)

By making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FST calculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXth Hungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.

hungarian-hierarchic-cluster
Unrooted hierarchic cluster of modern and archaic populations based on the SHD matrix.

It is interesting to keep receiving data as to how language does not correlate well with Genomics, whether admixture or haplogroups, even though it is already known to happen in regions such as Anatolia, the Baltic, South-Eastern or Northern Europe.

Thorough anthropological models of migration or cultural diffusion are necessary for a proper interpretation of genetic data. There is no shortcut to that.

hungarian-mtdna
Co-occurrence of Hungarian Bronze Age mt Hgs Distribution of mt Hgs found in Hungarian Bronze Age archaic samples in the analyzed populations. The fixation dates are based on Behar et al [6].

Images made available under a CC-BY-NC-ND 4.0 International license.
See also:

Science and Archaeology (Humanities): collaboration or confrontation?

Allentoft Corded Ware

Another discussion on the role of Science for Archaeology, in The Two Cultures and a World Apart: Archaeology and Science at a New Crossroads, by Tim Flohr Sørensen, Norwegian Archaeological Review, vol. 50, 2 (2017):

Within the past decade or so, archaeology has increasingly utilised and contributed to major advances in scientific methods when exploring the past. This progress is frequently celebrated as a quantum leap in the possibilities for understanding the archaeological record, opening up hitherto inaccessible dimensions of the past. This article represents a critique of the current consumption of science in archaeology, arguing that the discipline’s grounding in the humanities is at stake, and that the notion of ‘interdisciplinarity’ is becoming distorted with the increasing fetishisation of ‘data’, ‘facts’ and quantitative methods. It is argued that if archaeology is to break free of its self-induced inferiority to and dependence on science, it must revitalise its methodology for asking questions pertinent to the humanities.

Commentators in the discussion include:

The answer of Sørensen to them is on Archaeological Paradigms: Pendulum or Wrecking Ball?. Excerpts:

Thus, I argue that what we are witnessing with ‘the third science revolution’ (Kristiansen 2014) is precisely the proliferation of an already very authoritative science ideal in archaeology. And I worry that this dominance will limit research possibilities and potentials rather than encouraging plurality and radical experimentation with different forms of knowing.
(…)
I do believe in the coexistence of disparate academic principles and that collaboration is very often necessary, but I am also of the conviction that some degree of epistemological friction keeps both fields of research progressing. Nurturing distinctions, in other words, is no less useful than aiming for assimilation. What I am arguing for is thus a more respectful friction than the one characterising the processual/post-processual collisions, hoping for an academic environment where differences between research ideals are humbly accepted and cultivated precisely for their disparate strengths.
(…)
So, what I am arguing for is a more kaleidoscopic academic landscape, where different positions do not always have to assume a defensive or compromising stance, especially in confrontation with paradigms that are prospering politically. This also implies that science is not simply in the service of archaeology, as Lidén argues, but that we need to consider how archaeology may benefit science more generally by continuing to debate epistemological grounds, methodology and our modes of inquiry. And so, my fellow archaeologists: ask not what science can do for us, but what we can do for science.
(…)
In my original article, I addressed the widespread tendency in archaeology to disseminate research findings with sometimes too much conviction, where ambiguous results (and limited statistical data) are adopted with little concern for the inherent uncertainties. It is precisely this valorisation and authority of scientific observations that I claim to lead to an implicit devaluation of studies based in the humanities. The problem is – as stated numerous times in my original article – not science, but the consumption of scientific observations in archaeology, where the subtleties and not least ambiguities of scientific results are filtered out, leaving space almost exclusively for scientifically ‘proven’ facts and unequivocal results. This mode of consumption stands in direct contrast to the epistemological observation in the sciences, dictating that ‘“proof” and “certainty” are actually in short supply in the world of science’ (Freudenburg et al. 2008, p. 5). Hence, the risk is that archaeology somewhat uncritically adopts scientific observations that are in fact ‘empirically underdetermined – based largely on evidence that is in the category of the “maybe,” being inherently ambiguous rather than being absolutely clear-cut’ (Freudenburg et al. 2008, p. 6).

As I said recently on the article Massive Migrations…, by Martin Furholt, we are living a historical debate on essential questions for the future of all these disciplines.

And, as always, there is no shortcut to reading the texts. Unlike in Science, you cannot write a table with a summary of findings…

Discovered (again) via a comment on this blog by Joshua Jonathan.

Featured image from Allentoft et al. “They conclude that the Corded Ware culture of central Europe had ancestry from the Yamnaya. Allentoft et al. also show that the Afanasievo culture to the east is related to the Yamnaya, and that the Sintashta and Andronovo cultures had ancestry from the Corded Ware. Arrows indicate migrations — those from the Corded Ware reflect the evidence that people of this archaeological culture (or their relatives) were responsible for the spreading of Indo-European languages. All coloured boundaries are approximate.”

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We are all special, which also means that none of us is

Europe_around_800_Charlemagne

Adam Rutherford writes You’re Descended from Royalty and So Is Everybody Else – Anybody you can name from ancient history is in your family tree, which I discovered via John Hawks’ new post The surprising connectedness of human genealogies over centuries.

Excerpt:

One way to think of it is to accept that everyone of European descent should have billions of ancestors at a time in the 10th century, but there weren’t billions of people around then, so try to cram them into the number of people that actually were. The math that falls out of that apparent impasse is that all of the billions of lines of ancestry have coalesced into not just a small number of people, but effectively literally everyone who was alive at that time. So, by inference, if Charlemagne was alive in the ninth century, which we know he was, and he left descendants who are alive today, which we also know is true, then he is the ancestor of everyone of European descent alive in Europe today.

Since most of this blog’s posts support academic disciplines looking for answers to the Indo-European question, and gives constantly reasons against modern genetic (and phylogenetic) identification, I think it is worth at least a quick read for anyone interested in the field.

I recently referred to the interesting series of posts by Graham Coop on this matter.

Featured image: Europe around 800 – the map is public domain from from the Historical Atlas (New York, 1911)

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Genetic vs. genealogical ancestors and actual geographical constraints

genetic_pie_2

Interesting post from Graham Coop, Where did your genetic ancestors come from?

An excerpt:

A thousand years back I’m descended from nearly everyone everywhere in Europe. I’m related to these individuals via millions of lines of descent back through my vast family tree. Yet the majority of the lines back through my pedigree trace to people living in the UK and Western Europe. Many lines trace back to more distant locations, but these are relatively few in number compared to those tracing back to closer to home. Ancestors along each of these lines are (roughly) equally likely to contribute to my genome. Therefore, most of my roughly 2600 genetic ancestors from 1000 years ago, who contributed the majority of my genome to me, will be random people living in the UK and western Europe at that time (who happened to leave descendants).

Looking back a few thousand years more, I’m a descendant of nearly everyone who ever lived almost everywhere in the world (at least those who left descendants, and many did). Yet most of the just over ~6000 individuals from that time who contributed the majority of my genome to me will mostly be found all over Western Eurasia. There’s nothing much special about these individuals who happen to be my genetic ancestors a few thousand years back. They’re likely not royalty. My genetic ancestors are just a random subset of all of my genealogical ancestors, they just happen to be my genetic ancestors due to the vagaries of meiosis and recombination.

As always, a humbling example, e.g. for those looking at haplogroups in the distant past to make modern ethnolinguistic identifications.

Genetics in combination with genealogy poses a question akin to the Ship of Theseus paradox.

Featured image (from the article): Simulation of how much of your autosomal genome is present in each genealogical ancestor as we go back up the generations. Image explained in detail in the article How many genetic ancestors do I have?

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