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Tuesday, August 4, 2015

Armenian population structure across time and space


There are some subtle but potentially important genetic substructures among the ancient and present-day Armenians in my dataset.

Note that in the Principal Component Analysis (PCA) below, based on the ADMIXTURE results listed here, the Bronze and Iron Age Armenians cluster with groups from the Caucasus. Moreover, two of the Late Bronze Age (LBA) Armenians are pulling out towards the Eurasian steppe and Central Asia, respectively. Unfortunately, we'll need more ancient samples and higher quality data to get to the bottom of this.


The ancient Armenians are from the Rise project, and marked RISE_baArm/irArm in the spreadsheet. They were published recently along with Allentoft et al., and are available on request from the authors of the paper. Most of the other samples are from the fully public Haak et al. dataset available here. The regional Armenian samples are from the Wellcome Trust Sanger ftp site.

See also...

Genetic substructures among Armenians from Armenia and Lebanon

The Near East ain't what it used to be

Sunday, August 2, 2015

European Archaeological Association (EAA) 2015 abstracts


The abstract book is available here. Lots of interesting stuff, as usual, although probably a little light on ancient genomics. If anyone happens to be in Glasgow at the right time, I'd love to hear reports from these talks...

ESTABLISHING MIGRATION LINK BETWEEN EUROPE AND INDIA IN CONTEXT OF ARYAN CULTURE

Ketan Sakhalin

SHRIMAD RAJCHANDRA PRAKRUT NIDHI

The original habitats of Indian peninsula are divided in to two catagories namely Aryans and Non Aryans. The major paradox is question of Aryans being migrated from Europe through Mediterranean and going further was accepted by many scholars including father Heras and Whitman.

The excavation of various Harappa sites has thrown more light on the living standards and culture of the ancient people. It has also shown the link and trade with various part of the world by local people. There was clear picture of various phases of development of the culture on the basis of available materials. But how it was destructed, was the question that remained unanswered. Unfortunately, the theory of Aryan invasion was put forward and it was opposed to such extent by some scholar that they have even denied the migration of Aryans too.

We have worked on this problem based on the new material available and analysing the problem from different aspects. It was true that Aryan invasion was not the reason for decline of the harappa Cities. But on the other hand it was equally true that Aryans had migrated from Europe and settled in this land. A co-existence of two different cultures with quite different look, life style, social system, religios beliefs, cultural values and rituals was studied with reference to various material sources and ethnic aspects. The visual comparison of present day practices with ancient images in support of the cultural diversity was also made in support of the migration of Aryans.

THE BRONZE AGE BATTLEFIELD IN THE TOLLENSE VALLEY, MECKLENBURG-WESTERN POMERANIA, NORTHEAST GERMANY – CONFLICT SCENARIO RESEARCH

Gundula Lidke , Detlef Jantzen , Thomas Terberger , Sebastian Lorenz

NIEDERSÄCHSISCHES LANDESAMT FÜR DENKMALPFLEGE, LANDESAMT FÜR KULTUR UND DENKMALPFLEGE, MECKLENBURG-VORPOMMERN, INSTITUT FÜR GEOGRAPHIE UND GEOLOGIE, UNIVERSITÄT GREIFSWALD

Introduction: The Tollense Valley has come into the focus of interdisciplinary research following the discoveries of human skeletal remains of up to now more than 120 individuals, mostly young males, often with traumatic lesions, as well as horse remains and various weapons as well as other metal finds, dating to about 1.300-1.250 calBC. The remarkable material is interpreted as the remains of a Bronze Age group conflict on a so far unexpected scale.

Material and Methods: Find material comes from a stretch of river more than 2.5 km long. It is detected in situ under water in riverbanks as well as on land. Besides the human remains weapon finds, partly found in close relation to the bones, play an important role. Analyses of ancient DNA as well as of various isotopes are conducted to understand the population group(s) involved. Archaeological experiments are carried out to investigate possible fighting techniques; geo-scientific analyses aim at reconstructing the palaeo-landscape.

Results: Dating results place skeletal remains and weapons in a narrow time span at about 1300-1250 calBC. Weaponry includes long range, but also close-combat weapons. Find material as well as skeletal remains point to a heterogeneous group of at least hundreds of combatants.

Conclusions: The find assemblage from the Tollense Valley indicates violent conflict in the Bronze Age on an exceptionally high level. A possible conflict scenario, involving hundreds of participants in a greater stretch of the river valley, is put forward.

GREATER POLAND IN MIDDLE AGES - SOCIETY AND DYNASTY IN THE CONTEXT OF THE ORIGIN AND ETHNICITY

Anna Burmistrzak

ADAM MICKIEWICZ UNIVERSITY IN POZNAŃ

The aim of this paper is to present you new project that is currently implemented in Greater Poland. In the Middle Ages this region of Poland was the center of all country-making events, the chroniclers wrote about Poland being built from there, also the residence of the Piast Dynasty had its place in there. The main objective of that project is to answer questions important to the Polish and European history, like the origin of the Piast Dynasty and the Piast state’s elites in 10th century - whether they were descended from local people or if they were outlanders. The project focuses on few different aspects but the main remains the same – where did they come from? In Poland it is still very controversial subject, therefore our studies performed within the project are going to be based not only on excavations and archaeological analysis but with the use of standard methods of physical anthropology and modern bioarchaeological techniques, including the analysis of the fossil DNA. We plan multidimensional and interdisciplinary (historical, archaeological, anthropological, genetic and genomic) studies of populations inhabiting the territory of the present–day Greater Poland.

Wednesday, July 29, 2015

The ancient DNA case against the Anatolian hypothesis


In the debate over the location of the Proto-Indo-European urheimat, Colin Renfrew's Anatolian hypothesis is usually mentioned as the most viable alternative to the steppe or Kurgan hypothesis. But probably not for very much longer.

Below is a Principal Component Analysis (PCA) featuring extant Indo-European and non-Indo-European groups from West Eurasia, a couple of typical early Neolithic farmers from Central Europe, a typical Western Hunter-Gatherer, also from Central Europe, and the Iceman from the Copper Age Tyrolean Alps, again typical of his time and place.*

It's just a taste of the ancient genomic data we have available from prehistoric Europe, but it has almost everything that is pertinent to the issue at hand.


You don't need to be familiar with PCA methodology to be able to read the plot. Basically, it shows that the present-day European population structure is the result of two main events:

- the arrival of early farmers from Anatolia during the Neolithic transition, which eventually caused the extinction of people like the Western Hunter-Gatherer, who is the most obvious outlier on the plot

- the expansion of Kurgan groups such as the Yamnaya, which led to the formation of the Corded Ware horizon across much of Europe and shifted the genetic structure of almost all Europeans to the east, away from the Neolithic and Copper Age samples.

These were massive population turnovers, and, as a rule, massive population turnovers are accompanied by language change. So it's highly unlikely that any Europeans today are speaking languages derived from those of the Western Hunter-Gatherers or early Neolithic farmers of Central Europe (ie. according to Renfrew the ancestors of Celts, Germanics and other Indo-Europeans). Moreover, consider this:

- most present-day Indo-European speaking Europeans form an elongated cluster between the Neolithic farmers and the Corded Ware sample, pointing to the steppe-derived Corded Ware Culture as the proximate agent of the Indo-European expansion in much of Europe

- the only present-day Europeans who closely resemble Neolithic farmers are some Sardinians (the small Romance cluster just above the two Neolithic samples), but Sardinians spoke Paleo-Sardinian or Nuragic languages until they adopted Indo-European speech, in the form of Latin, from the Romans.

Also, this isn't shown on the plot, but the dominant Y-chromosome haplogroup of early Neolithic farmers is G-P15, which is a low frequency marker in Europe today. The two most common Y-chromosome haplogroups among present-day Europeans are R-M198 and R-M269, which are also typical of Corded Ware and Yamnaya males, respectively, and probably originally from the steppe.

So is there any way to rework the Anatolian hypothesis so that it can be salvaged? I doubt it. Even making the steppe a homeland for all of the main Indo-European branches apart from Anatolian and Armenian probably won't help.

It is true that the Yamnaya nomads carried Near Eastern-related ancestry which may represent Proto-Indo-European admixture from outside of the steppe. But there's no evidence that it came from Anatolia.

In fact, if Neolithic Anatolians were basically identical to early Neolithic European farmers, which seems to be the case (see here), then it's unlikely that it did, because the latter carried a peculiar genome-wide signal that is missing in Yamnaya genomes (orange cluster in the ADMIXTURE bar graph below).** Heck, even the early Corded Ware genomes from Germany barely show any of it.

I won't go into the linguistics arguments here why the Anatolian hypothesis is implausible. But it might be worth checking out a new book on the topic by linguists Asya Pereltsvaig and Martin W. Lewis: The Indo-European Controversy: Facts and Fallacies in Historical Linguistics. I haven't read it yet, so I welcome the opinions here of those who have. I did, however, read a lot of the online articles on which the book is based. As far as I know most of them are still available here and here.


*Another version of the same PCA, with the samples labeled individually, is available here. All possible combinations of dimensions 1 to 4 are shown here. The samples are listed here. All of the samples are from Haak et al. and Allentoft et al. The PCA was run using ~56K high confidence SNPs listed here.

The Corded Ware sample is a composite of Corded Ware sequences from Germany, Scandinavia, Estonia and Poland. The Yamnaya sample is a composite of Yamnaya sequences from the Rostov and Samara regions of Russia.

I chose to use these composites instead of individual sequences because I didn't want to run any samples with genotype rates of less than 98%.

** For a more detailed ADMIXTURE analysis comparing early Neolithic farmers to Yamnaya refer to Haak et al. Supplementary Information 6. Note the minimal sharing of components at the higher K between the early Neolithic farmers and Yamnaya, especially at K=16, which has the lowest median cross-validation (CV) error. This is in agreement with the PCA above.

See also...

Population genomics of Early Bronze Age Europe in three simple graphs

Sunday, July 26, 2015

Global PCA of selected Late Neolithic/Bronze Age Eurasians


I was curious what the Bronze Age steppe and Corded Ware genomes from the Rise dataset would look like on Principal Component Analysis (PCA) plots alongside populations from across the globe. Ten genomes had enough high confidence (transversion) markers to be analyzed accurately in such a way. I also ran an Iron Age Swedish sample, just to see how it differed from the older genomes.

Click on the links to go to my drive to download the plots. If you're having trouble finding the ancient samples, type their IDs into the PDF search field and hit enter.

RISE509_Afanasievo
RISE509_Afanasievo
RISE509_Afanasievo

RISE511_Afanasievo
RISE511_Afanasievo
RISE511_Afanasievo

RISE500_Andronovo
RISE500_Andronovo
RISE500_Andronovo

RISE505_Andronovo
RISE505_Andronovo
RISE505_Andronovo

RISE00_Corded_Ware
RISE00_Corded_Ware
RISE00_Corded_Ware

RISE94_Corded_Ware
RISE94_Corded_Ware
RISE94_Corded_Ware

RISE493_Karasuk
RISE493_Karasuk
RISE493_Karasuk

RISE496_Karasuk
RISE496_Karasuk
RISE496_Karasuk

RISE548_Yamnaya
RISE548_Yamnaya
RISE548_Yamnaya

RISE552_Yamnaya
RISE552_Yamnaya
RISE552_Yamnaya

RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia

I can't see any major surprises. But I do find it remarkable how very European the Andronovo individuals appear on these plots. Keep in mind that they're ~3,000-year-old samples from the Altai region of Russia. Their ancestors probably emigrated there from the Trans-Urals steppe sometime during the Middle Bronze Age.

The Andronovo Culture was succeeded in the Altai region during the Late Bronze Age by the Karasuk Culture, which was probably a new composite of local and perhaps foreign groups. Interestingly, the Karasuk samples featured above are obviously of mixed European/East Asian origin.

Note also that the Afanasievo and Yammnaya individuals fall outside the range of present-day European variation in many of the dimensions, basically as if they were pulling towards the Karitiana Indians of the Amazon. No doubt, this is their excess ANE talking.

By the way, I recently ran some of the same samples in PCA limited to West Eurasian populations. You can see the results here.

Wednesday, July 22, 2015

High-res R1b tree featuring 16 ancient sequences


Here's a useful R1b phylogenetic tree that was posted recently at the R1b-M269 (P312- U106-) DNA Project site.


If these results are correct (and judging by the quality of work at the aforementioned R1b project, I'm pretty sure they are), it would appear that the Samara hunter-gatherer, marked I0124, was not directly ancestral or even all that closely related to any of the Yamnaya/Pit-Grave samples from the North Caspian region (each one also marked with an I~ ID).

On the other hand, the North Caspian Yamnaya sequences are very similar to the rest of the Yamnaya sequences, which come from just north of the Caucasus (marked RISE~). Indeed, all of these Yamnaya samples are almost identical in terms of genome-wide genetic structure (see here).

What this suggests is that the Yamnaya nomads emigrated to the North Caspian from somewhere near the Caucasus, or they were the descendents of such migrants. And if we assume that their ancestral homeland abutted the territory of the Maikop Culture, as shown on this map from Dolukhanov 2014 (look for 9 - early Pit-graves), it becomes easy to understand why they carried such significant maternal and genome-wide genetic Caucasus-related admixture (usually estimated at around 50%).

However, if you're one of those online Near Eastern patriots who like to imagine the Yamnaya as your own, please don't jump for joy just yet. The Yamnaya nomads still look very much like a people native to the western steppe, and this is probably also where their R1b comes from.