search this blog


Sunday, October 4, 2015

Yamnaya's exotic ancestry: The Kartvelian connection

I've made a discovery. The Near Eastern-related ancestors of the Yamnaya steppe pastoralists were also the ancestors of present-day Georgian Mingrelians, or their very close relatives, and in all likelihood speakers of Kartvelian, which has a long history in the Caucasus. Here's a nice map from Wikipedia and a pic of some Mingrelians. Check out the impressive headware.

TreeMix is very specific and precise about this. In my analyses, based on a couple of different methods, the Mingrelians are the only population chosen as a source for the Near Eastern-related ancestry in the Yamnaya.

Keep in mind, this is an unsupervised test and the algorithm has an infinite number of choices, because migration edges can run from any part of the tree, and yet it chooses the Mingrelians. By the way, if anyone's wondering, I did also try the Bronze Age Armenians, to no avail.

This outcome is also more or less reproducible with more complex topologies, including samples from Central Asia. In the graph below the Georgian Mingrelians form a clade with the Near Eastern-related ancestry of the Yamnaya. It'd be interesting to see if other Georgian groups, like the Svan, do even better, if that's actually possible, but they're not available at the moment.

I actually came up with basically the same result earlier this year using qpAdm (see here). But at the time I was skeptical of its usefulness because qpAdm only offers a supervised test, so picking Georgians as a reference population and getting a good statistical fit doesn't mean as much as a reproducible unsupervised migration edge.

Now, judging by their ADMIXTURE results, these Georgian Mingrelians do carry some Early European farmer-related ancestry, which is missing in the Yamnaya (see here). Therefore, it's likely that ancient samples from the west or northwest Caucasus will prove to be even better proxies for the Near Eastern-related ancestry in the Yamnaya.

The samples used to produce the above TreeMix graphs are listed here. They're sourced from the Allentoft et al., Haak et al., and Lazaridis et al. datasets. I limited the markers to ~65K transversion (high confidence) SNPs that overlap between these datasets.

Saturday, October 3, 2015

Linguistics, Archeology and Genetics (L-A-G) Conference abstracts

The Max Planck Institute is holding a conference in a few days dedicated to the latest developments in the search for the Indo-European homeland.

Linguistics, Archeology and Genetics: Integrating new evidence for the origin and spread of Indo-European languages

A draft book of presentation abstracts is available here. This one from Danish linguist Guus Kroonen looks very promising.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis and the Steppe hypothesis the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, and thus patterns with the prehistoric migration of Europe’s first farming populations. These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans.

Also, we've known for a while now that the good people at Broad MIT/Harvard have analyzed remains from Neolithic Anatolia, but it's nice to see this framed in the context of the Indo-European homeland debate.

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis et al.

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (FST=0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

Indeed, my view is that the implications of this data for the Anatolian hypothesis are fatal (see here). It might also have dire implications for the Armenian Plateau hypothesis, although for the time being this hypothesis limps on (see here).

Feel free to post and discuss your favorite abstracts in the comments below. If anyone reading is going to this thing, I'd love to hear more about the Y-haplogroups of the Anatolian farmers.

Friday, October 2, 2015

Essential reading: Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe

To help things run more smoothly in the comments, I urge everyone taking part in the debates here about the colonization of the Eurasian steppe and the Indo-European homeland question to read carefully the following three papers. They're all open access:

1) Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe Bronze Age

2) The Steppe and the Caucasus During the Bronze Age Mutual Relationships and Mutual Enrichments

3) New Radiocarbon Dates and a Review of the Chronology of Prehistoric Populations from the Minusinsk Basin, Southern Siberia, Russia

In particular, please note the latest calibrated radiocarbon-based dates of the main archaeological cultures being discussed:

- Khvalynsk, Eneolithic, 4300–3800 cal BC

- Steppe Maikop, Early Bronze Age, 3800–3000 cal BC

- Yamnaya, Early Bronze Age, 3000–2450 cal BC

- Afanasievo, Early Bronze Age, 2900-2500 cal BC

- Early Catacomb, Early Bronze Age, 2600–2350 cal BC

Of course, Yamnaya are in large part of Eastern European hunter-gatherer (EHG) origin but with roughly 50% of Near Eastern-related ancestry from an unknown population (Haak et al. 2015). Paper #2 linked to above provides tentative isotopic evidence that the latter might be the Steppe Maikop people or their descendants (see paragraph 4 on page 58).

However, the Khvalynsk population from the Samara region harbors around 25% of the same or very similar Near Eastern-related ancestry (unpublished data courtesy of David Anthony). And, as per the dates above, Khvalynsk existed before Steppe Maikop.

Thus, although the increase of the Near Eastern-related ancestry on the steppe from the Khvalynsk to the Yamnaya periods can be tentatively attributed to Maikop influence, this cannot be the initial source of this type of ancestry on the steppe.

Moreover, dates older than 3,000 cal BC for Afanasievo appear to be spurious (see paper #3 above). If so, what this means is that Afanasievo is around the same age as Yamnaya, or perhaps a little younger, and thus the generally accepted hypothesis that Afanasievo derives from Yamnaya or pre-Yamnaya looks safe.

Now, it's especially important that everyone concerned is aware of the key climatic shifts on the steppe, because climatic changes are often invoked as likely causes of major population movements within and out of the steppe. So I'm re-posting here Table 1 from paper #1 (click to enlarge).

I'll update this post as new information comes in, which will hopefully be very soon. There are signals that something big is on the way from the Reich Lab pertaining to the Indo-European homeland debate (for instance, see here).

See also...

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas

Thursday, October 1, 2015

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas

Update 05/10/2015: Yamnaya's exotic ancestry: The Kartvelian connection


The Afanasievo and Yamnaya samples published to date are remarkably homogeneous. Hopefully the bar graphs below, based on a couple of my recent ADMIXTURE runs, illustrate this well enough.

The Near Eastern-related ancestry proportions among the Yamnaya individuals do appear to rise steadily from early Yamnaya to late Yamnaya/early Catacomb. But the ancestral components remain the same, and if the increase in the Near Eastern-related admixture is real, the process is very subtle.

What this suggests to me is that groups of a southern provenance - in all likelihood Neolithic farmers seeking new land - arrived somewhere on the Pontic-Caspian steppe very early, perhaps even during the Early Neolithic, to eventually blend with local foragers. That's because the basic Yamnaya genotype had to have existed before the Yamnaya or pre-Yamnaya ancestors of the Afanasievo nomads set off on their 2000 km trek to the Minusinsk Basin in South Siberia, probably around 3,300 BC.

No doubt, the mixing didn't stop after the initial farmer/forger admixture event, and this is probably why the Near Eastern-related ancestry proportions rise gradually throughout the Yamnaya period. Indeed, considering the high mobility of Bronze Age steppe pastoralists, it's likely that long distance trade, alliances and marriages resulted in the genetic homogenization of vast stretches of Eastern Europe during their reign.

In this analysis I used samples from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

Wednesday, September 30, 2015

The 1000 Genomes paper

To be honest, I'm really looking forward to some papers based on the new Simons Genome Diversity Project dataset. Unlike the 1000 Genomes, it includes samples from a wide range of West Eurasian populations sequenced to at least 30x coverage (see here). But for now, open access at Nature:

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

The 1000 Genomes Project Consortium, A global reference for human genetic variation, Nature 526, 68–74 (01 October 2015) doi:10.1038/nature15393

Cranial affinities of Mesolithic populations from Eastern Europe and Siberia (teaser)

This looks like an excellent example of modern physical anthropology work. Unfortunately it's only an abstract. Can't wait to see the paper.

Mesolithic populations from the Eastern Europe and Siberia: cranial shape analysis with the help of geometric morphometric methodology

Ekaterina Bulygina(1), Anna Rasskasova(1), Denis Pezhemski(1)

1 - Research Institute and Museum of Anthropology, Moscow State University, Russia

Several Mesolithic and early Neolithic populations dated to 10,000 – 6,000 years BC from Russia, Romania and Ukraine have been analysed by means of quantifying their 3D cranial shape. The whole sample comprised 85 individuals, including Mesolithic and Neolithic groups from Yuzhny Oleni Ostrov (Russia); Vasilievka, Voloshkoe and Vovnigi (Ukraine); Varasti (Romania); Itkul and Ust-Isha (South Siberia) and Locomotiv (East Siberia). A comparative set of modern populations was sampled to include representatives from Europe, Africa, Eastern Asia and (native) America. Apart from the standard geometric morphometric procedures, we cluster ordinated data to establish potential relationships between groups and use permutation of individual distances to establish the significance of the group differentiation. The method of analysis is first verified with the help of the modern populations that have varied geographical provenance. We establish that no cranial data, whether the face and the neurocranium are analysed together or separately, allow us to recover geographical relationships between the modern populations in our sample. Nevertheless, clusters that have been recovered with the help of the whole cranium data correspond well with the expected generic relationships between the sampled modern groups. As a result, we choose to analyse the shape of the complete cranium, where such is available, in fossil individuals as well. Our results highlight a high level of variation within Mesolithic and within Neolithic populations of the Eastern Europe and Siberia as compared with the pooled sample of the modern humans from different geographical locations worldwide. However, a certain structure among the analysed groups can still be revealed. The results suggest that Mesolithic groups from the Dnieper region have close morphological affinities with each other, while Yushny Oleni Ostrov have a large overlap with modern humans in general and with some of the mongoloid groups in particular. Neolithic groups are, on the whole, closer to modern populations than to the Mesolithic sample. At the same time, Siberian individuals show a complex pattern of morphological relationships which may be revealing of their genetic identity. On the whole, our results invite further discussion on the origins and affinities of the Eastern European Mesolithic and Early Neolithic groups as well as call for the research into the impact that the choice of data has on the results of 3D morphological analyses. Acknowledgements: This work has been supported by the grant of the Russian Foundation for Basic Research No № НК 13-06-00045.

Source: European Society for the study of Human Evolution (ESHE) 5th Annual Meeting PESHE4 final abstracts volume.

Tuesday, September 29, 2015

Domestic cattle in Neolithic Uzbekistan

Below are a few abstracts from a recent conference on Southwest Asian archaeozoology. The full selection is available here.

Early domestic ungulates in Central Asia: archaeozoological results from Ajakagytma (Uzbekistan, Kel’teminar, 9th-7th millennia cal BP)

Jean-Denis Vigne(1), Florian Brunet(2), Karine Debue(1), M. Khudzhanazarov(3)

1. Centre National de la Recherche Scientifique – Muséum national d’Histoire naturelle; France;
2. Centre National de la Recherche Scientifique - Université Panthéon-Sorbonne; France
3. Academy of Sciences of Uzbekistan; Uzbekistan

Ajakagytma is a Neolithic lake shore site located in the central desert of Uzbekistan (Kyzyl-Kum), a region for which the archaeozoological data are rare and sometimes questionable. New excavations conducted since 2005 by the French-Uzbek mission MAFANAC evidenced several successive Kel’teminar occupations dating from the end of the 7th to the 5th millennium. They provided more than 50 000 microlithic artefacts, and smaller series of degraded pottery, stone pendants, bone industry, animal and plant remains. They also provided more than 2000 faunal remains. Most of them are badly preserved, due to the extreme fluctuations in climate (heating and cooling and wetting and drying). However, 580 specimens could be attributed to a taxon, and more than 200 of them could be identified at the level of genus or species. They provide a clear image of the wild large mammals which lived in this area and which were hunted by the Kel’teminar people: the goitered gazelle (34%), aurochs (16%), onager (11%) and the wild camel (11%). We also find 15% of Caprini but, due to the poor preservation of the material, it was impossible to tell if they were hunted wild bezoar goats or early domesticated sheep or goat. Conversely, 13% of the specimens clearly refer to very small size bovids. This is the earliest evidence of domestic cattle in Central Asia. This presentation will discuss the consequences of this observation in the scope of the origin of cattle husbandry between the Iranian Plateau and North China.

Subsistence economy at Kul Tepe (North-Western Iran) from Early Chalcolithic to the Early Bronze Age

S. Davoudi(1), Marjan Mashkour(2) and Akbara Abedi(3)

1. Department of Archaeology; Tarbiat Modares University; Tehran; Iran;
2. UMR 7209 Archaeozoology; Sorbonne Universités; Natural History Museum of Paris; Centre national de la recherché scientifique;
France; 3. Department of Archaeology; University of Tehran; Iran;

The site of Kul Tepe is located near the city of Hadishahr 10 km to the south of the Araxes River in western Azerbaijan (Iran). Excavations were carried out by A. Abedi and H. Khatib Shahidi in 2010, the cultural material including the animal bones belongs to the Early Chalcolithic, to Late Bronze Age, Iron III, and Achaemenid periods. The faunal remains are very well preserved and cover a period from Early Chalcolithic to Early Bronze Age (5000 to 2200 BC) providing a continuous record for animal exploitation at the site. The faunal study was conducted in the archaeozoology laboratory of the University of Tehran. A wide range of domestic and wild animals are present in the faunal remains. Domestic sheep, goat, and cattle are dominant as the main animal resource in all periods, with an increase of cattle proportions during the Kura-Araxes 1 period. Also a rather important number of hunted species, cervids, gazelle, wild goat, sheep and bovids are present in this collection, especially during the Late Chalcolithic and Kura-Araxes 1 (4400-3200 BC). Also equid remains were found among the bones. Horse remains are present in the Kura-Araxes 1 levels and Early Bronze Age (3600-2200 BC). The quasi absence of suid remains is outstanding here. The study of Kul Tepe faunal remains brings a set of novel data for this region and this period and provides a continuous picture of the subsistence economy from the fifth to the third millennium BC, including three important prehistoric cultural transitions. The strategic location of site at the cross roads of major routes linking the Iranian Plateau to Anatolia and the Caucasus to Northern Mesopotamia suggests relations and interactions between human communities of these areas, and makes it possible to compare the results with other contemporaneous sites.

Early animal husbandry in Azerbaijan: Implications for the origin and development of the Neolithic in the Southern Caucasus

Saiji Arai(1), Seiji Kadowaki(2), K. Ohnishi(2), Farhad Guliyev(3) and Yoshihiro Nishiaki(1)

1. The University of Tokyo; Japan
2. Nagoya University; Japan
3. Institute of Archaeology and Ethnology, Azerbaijan Academy of Sciences; Azerbaijan

Recent archaeological research in Armenia, Georgia and Azerbaijan has significantly extended our knowledge about Neolithic cultures in the Southern Caucasus region. Archaeozoological studies to reconstruct general trends of animal economy during the period have also made substantial progress.

In this paper we present new archaeozoological data on the faunal assemblages from two Pottery Neolithic sites in Azerbaijan: Göytepe and Hacı Elamxanlı Tepe. Both sites are located in the Tovuz region, west Azerbaijan. While Göytepe is one of the largest mounds in the region dated to early and mid-6th millennium BC and belongs to Shomutepe-Shulaveri culture, Hacı Elamxanlı Tepe represents a small mound settled during the beginning of 6th millennium BC. Since no earlier Neolithic site has been found, comparative study of these sites is of great importance to trace the establishments of early agricultural villages in the region. Faunal assemblages from these two sites mainly consist of domestic animals. However, significant differences are also present. Firstly, cattle is almost absent at Hacı Elamxanlı Tepe. Secondly, red deer antler objects are more common at Göytepe, reflecting the practice of a more enhanced broad-spectrum economy. This trend, together with the higher frequency of forestial mammals and the increase of stone axes at Göytepe, indicates more intensive exploitation of forest environment. Thirdly, while the culling profile for caprine is little different between these two sites, the measurement data of sheep shows an increase of female individuals at Göytepe, indicating a development of herding technique.

Finally, on the basis of these archaeozoological results as well as analysis of other archaeological data, we will discuss the possible origin and development of Neolithic economy in the Southern Caucasus. Results of a DNA analysis of domestic goats, which suggest a link with eastern Turkey during early 6th millennium BC, will also be reported.