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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.

Monday, September 28, 2015

Origins and uniparental genetic structure of European Roma

The EJHG has a new paper on the Y-DNA and mtDNA of European Roma. The main text is behind a paywall, but the images and supplementary info are freely available here and here, respectively. Interesting quote:

In agreement with our results, no traces of [Roma-specific] haplogroups H-M52, H-M82, or I-P259 were found in an extensive data set of 3136 non-Roma Europeans typed at similar resolution (472 Germans, 96 Danish, 340 Belgians, 90 Dutch, 370 Czechs, 520 Polish, 221 individuals from the United Kingdom, and 1027 Italians, from the Genographic project database, unpublished data), supporting our power to define founder lineages using our data set. With the exception of Hungary, for the reasons mentioned above, the presence of founder lineages in host populations confirms limited male gene flow from Roma to host. In contrast, male gene flow from hosts to Roma is much more frequent, although variable, ranging between 17% in Romania and up to 46% in Hungary.

Martínez-Cruz et al., Origins, admixture and founder lineages in European Roma, European Journal of Human Genetics advance online publication, 16 September 2015; doi:10.1038/ejhg.2015.201

Genomics of the last true wild horse

Open access at Current Biology:

Summary: Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [ 1 ]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [ 2–4 ]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878–1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Der Sarkissian et al., Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse, Current Biology, Published Online: September 24, 2015, DOI:

Thursday, September 24, 2015

Support for linguistic macrofamilies from weighted sequence alignment

Open access at PNAS:

Abstract: Computational phylogenetics is in the process of revolutionizing historical linguistics. Recent applications have shed new light on controversial issues, such as the location and time depth of language families and the dynamics of their spread. So far, these approaches have been limited to single-language families because they rely on a large body of expert cognacy judgments or grammatical classifications, which is currently unavailable for most language families. The present study pursues a different approach. Starting from raw phonetic transcription of core vocabulary items from very diverse languages, it applies weighted string alignment to track both phonetic and lexical change. Applied to a collection of ∼1,000 Eurasian languages and dialects, this method, combined with phylogenetic inference, leads to a classification in excellent agreement with established findings of historical linguistics. Furthermore, it provides strong statistical support for several putative macrofamilies contested in current historical linguistics. In particular, there is a solid signal for the Nostratic/Eurasiatic macrofamily.

Gerhard Jäger, Support for linguistic macrofamilies from weighted sequence alignment, PNAS, Published online before print September 24, 2015, doi: 10.1073/pnas.1500331112

Thursday, September 17, 2015

Uralic genes

Below is a graph based on a couple of sets of D-statistics. Note that out of the five Uralic-speaking groups, only Hungarians remain under the upward-sloping red line, clustering among Indo-European-speakers. On the other hand, the Indo-European-speaking Russians from Kargopol cluster with Uralics. However, Russia is a complex affair in this context, because much of the north and east of European Russia was Uralic-speaking until very recently. The relevant D-stats are available here.

Wednesday, September 16, 2015

Analysis of Copper Age Iberian ATP2

There's been a lot of talk online lately about possible Yamnaya-related admixture in Copper Age genome ATP3 from Sierra de Atapuerca, northern Spain, from the recent Gunther et al. paper. This sample does show an eastern shift relative to the HGDP Sardinians and Neolithic farmers in Principal Component Analyses (PCA), which is usually a solid indication of admixture from the Eurasian steppe. For instance, see Spain_CA here. However, the sequence is so limited that this might just be a mistake.

ATP2 is the youngest Copper Age sample from Gunther et al., and at 4.08x coverage, also by far the highest quality genome in the paper. Thus, in theory, if northern Spain experienced gene flow from the steppe when ATP3 was alive, this should register in ATP2.

Indeed, ATP2 also shows an eastern shift relative to Sardinians and Neolithic farmers in the PCA in Gunther et al. (refer to Figure S5 in the Supplementary Information here). But as far as I can tell after analyzing ATP2 myself, this is not real.

ATP2 is very similar to Middle Neolithic samples from Spain (Spain_MN from Haak et al. 2015) and Copper Age samples from Italy and Hungary (Remedello_CA from Allentoft et al. 2015 and Hungary_CA or CO1 from Gamba et al. 2014). You can see this on the graphs and plots below, produced with transversion (high confidence) SNPs and D-stats. The D-stats can be downloaded here and here.

So does this mean that ATP3 also lacks Yamnaya-related ancestry? Probably, but not necessarily. Large-scale population turnovers were common in ancient Europe, and ATP3 may have been the result of an early migration from the east that didn't leave a lasting impact on Sierra de Atapuerca. I'll need a higher quality sequence of ATP3 to sort this out properly. By the way, thanks to Sergey for the ATP2 genotype data.

Please note, the ancient samples in the PCA below are mostly composites in large part made up of the highest quality sequences from each population group. The reason I chose to run composites was to ensure that missing markers and low coverage calls didn't skew the results in the higher eigenvectors, which are super sensitive to such artifacts in the data.

See also...

Steppe-related admixture in Bronze Age northern Spain

Tuesday, September 15, 2015

Early Bronze Age migrants and ethnicity in the Middle Eastern mountain zone

Open access at PNAS:

Abstract: The Kura-Araxes cultural tradition existed in the highlands of the South Caucasus from 3500 to 2450 BCE (before the Christian era). This tradition represented an adaptive regime and a symbolically encoded common identity spread over a broad area of patchy mountain environments. By 3000 BCE, groups bearing this identity had migrated southwest across a wide area from the Taurus Mountains down into the southern Levant, southeast along the Zagros Mountains, and north across the Caucasus Mountains. In these new places, they became effectively ethnic groups amid already heterogeneous societies. This paper addresses the place of migrants among local populations as ethnicities and the reasons for their disappearance in the diaspora after 2450 BCE.

Mitchell S. Rothman, Early Bronze Age migrants and ethnicity in the Middle Eastern mountain zone, PNAS, July 28, 2015 vol. 112 no. 30, doi: 10.1073/pnas.1502220112

Sunday, September 13, 2015

ASHG 2015 abstracts

The abstract search is here. Feel free to post your picks in the comments. Lots of detail in this one, which is very much appreciated.

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

I. Lazaridis, D. Fernandes, N. Rohland, S. Mallick, K. Stewardson, S. Alpaslan, N. Patterson, R. Pinhasi, D. Reich, Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic. ASHG 2015 abstract. Talk to be held on October 9.

See also...

The ancient DNA case against the Anatolian hypothesis

Monday, September 7, 2015

Copper & Bronze Age genomes from northern Spain

Update: the paper is now available and open access here.

See also: Steppe-related admixture in Bronze Age northern Spain


A paper titled "Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques", by Günther et al., will appear shortly in PNAS early edition. Here's the press release from Uppsala University.

An international team led by researchers at Uppsala University reports a surprising discovery from the genomes of eight Iberian Stone-Age farmer remains. The analyses revealed that early Iberian farmers are the closest ancestors to modern-day Basques, in contrast previous hypotheses that linked Basques to earlier pre-farming groups.

The team could also demonstrate that farming was brought to Iberia by the same/similar groups that migrated to northern and central Europe and that the incoming farmers admixed with local, Iberian hunter-gather groups, a process that continued for at least 2 millennia.

The study is published today, ahead of print, in the leading scientific journal Proceedings of the National Academy of Sciences of the USA, PNAS.

Most of the previous studies about the transition from small and mobile hunter-gatherer groups to larger and sedentary farming populations have focused on central and northern Europe, however much less in known about how this major event unfolded in Iberia. This time, the research team investigated eight individuals associated with archaeological remains from farming cultures in the El Portalón cave from the well-known Anthropological site Atapuerca in northern Spain.

“The El Portalon cave is a fantastic site with amazing preservation of artefact material,” says Dr. Cristina Valdiosera of Uppsala University and La Trobe University, one of the lead authors.

“Every year we find human and animal bones and artifacts, including stone tools, ceramics, bone artefacts and metal objects, it is like a detailed book of the last 10,000 years, providing a wonderful understanding of this period. The preservation of organic remains is great and this has enabled us to study the genetic material complementing the archaeology,” Dr. Cristina Valdiosera continues.

From these individuals who lived 3,500-5,500 years ago, the authors generated the first genome-wide sequence data from Iberian ancient farmers and observed that these share a similar story to those of central and northern Europe. That is, they originate from a southern wave of expansion, and also admixed with local hunter-gatherer populations and spread agricultural practices through population expansions. The authors noticed that although they share these similarities with other European farmers, this early Iberian population has its own particularities.

“We show that the hunter-gatherer genetic component increases with time during several millennia, which means that later farmers were genetically more similar to hunter-gatherers than their forefathers who brought farming to Europe,” says Dr. Torsten Günther of Uppsala University and one of the lead authors.

“We also see that different farmers mixed with different hunter-gatherer groups across Europe, for example, Iberian farmers mixed with Iberian hunter-gatherers and Scandinavian farmers mixed with Scandinavian hunter-gatherers.” Dr. Cristina Valdiosera adds.

The study also reports that compared to all modern Spanish populations, the El Portalón individuals are genetically most similar to modern-day Basques. Basques have so far – based on their distinct culture, non-indo-European language, but also genetic make-up – been thought of as a population with a long continuity in the area, probably since more than 10,000 years ago.

“Our results show that the Basques trace their ancestry to early farming groups from Iberia, which contradicts previous views of them being a remnant population that trace their ancestry to Mesolithic hunter-gatherer groups,” says Prof. Mattias Jakobsson of Uppsala University, who headed the study.

“The difference between Basques and other Iberian groups is these latter ones show distinct features of admixture from the east and from north Africa.” he continues.

These findings shed light into the demographic processes taking place in Europe and Iberia during the last 5,000 years which highlights the unique opportunities gained from the collaborative work of archaeologists, anthropologists and geneticists in the analysis of ancient DNA.

“One of the great things about working with ancient DNA is that the data obtained is like opening a time capsule. Seeing the similarities between modern Basques and these early farmers directly tells us that Basques remained relatively isolated for the last 5,000 years but not much longer,” says Dr. Torsten Günther.

Source: Ancient genomes link early farmers to Basques

Sunday, September 6, 2015

CB13: 7,400 year-old Cardial genome from near Barcelona

CB13 looks practically indistinguishable from the early Neolithic Spanish samples from Haak et al. 2015, which makes sense. The paper is open access.

Abstract: The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: an initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK tradition, which followed the Danube River into Central Europe. While genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.


Olalde et al., A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures, MBE Advance Access published September 2, 2015, doi: 10.1093/molbev/msv181

Wednesday, September 2, 2015

A multidimensional approach

This is arguably the most interesting Principal Component Analysis (PCA) I've run to date. Note that overall the ancient steppe genomes appear to be the crucial link in the Indo-European chain, basically bridging the gap between European and South Asian Indo-European-speakers. A plot with all of the samples labeled individually can be downloaded here. If you have any questions about the methodology, just ask in the comments.

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.

See also...

No significant genetic substructures within (eastern) Yamnaya