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Tuesday, March 24, 2015

Live reports from AAPA 2015

Chad Rohlfsen is heading off to St. Louis tomorrow for the annual American Association of Physical Anthropologists (AAPA) conference, and will be posting updates from the big event in the comments below. Most of you will know Chad from the comments section on this blog. He's yet to finalize his program, but I know he'll be at this talk on the population history of the Aegean.

The origins of the Aegean palatial civilizations from a population genetic perspective

MARTINA UNTERLÄNDER1,2, SUSANNE KREUTZER2 and CHRISTINA PAPAGEORGOPOULOU1. 1 Department of History and Ethnology, Demokritus University of Thrace, 2 Palaeogenetics Group, Institute of Anthropology, Johannes Gutenberg-University of Mainz.

The present paper investigates the origins of the Aegean pre-palatial civilizations (5th-3rd millennium BC) by applying cutting-edge methods of molecular biology and population genetics. The term Aegean Civilizations refers to the novel human lifeway (agriculture and craft specialization, redistribution systems, intensive trade) that appeared during the end of the Neolithic and the beginning of the Bronze Age in the Aegean. Although many studies exist on archaeological constructions of ethnic and cultural identity on mainland Greece, the Cyclades and Crete, not enough efforts have been made to explore this direction on a population history basis. We have investigated Late, Final Neolithic and Early Bronze Age human skeletons (n=127) from the Aegean using ancient DNA methods, next generation sequencing (NGS) technology and statistical population genetic inferences to i) gather information on diversity, population size, and origin of the pre-palatial Aegean Cultures, ii) to compare them on a genetic basis, in terms of their cultural division (Helladic, Cycladic, Minoan) and iii) to investigate their ancestral/non-ancestral status to the Early and Middle Neolithic farmers from Greece. In addition to mitochondrial DNA genomes, by applying a capture-NGS approach we collected information on functional traits of the early Aegean communities in southeastern Europe. Considering the International Spirit that overwhelms the Aegean during the 3rd millennium BC, seen by the wide distribution of artifacts, this palaeogenetic approach provides valuable new insights on population structure of the groups involved in the Neolithic-Bronze Age transition and the spread of specific alleles in this part of Europe.

Feel free to help Chad plan the rest of his itinerary. The AAPA 2015 website is here. You can download a PDF book with all of the abstracts here.

By the way, Chad is paying for the trip himself. If anyone wants to help him cover the costs, please send contributions via PayPal to c_rohlfsen [at] hotmail [dot] com.

Monday, March 23, 2015

Indian genetic structure in the context of ancient European DNA

Let's turn our attention to South Asia for a moment. I was hoping that someone better informed than myself about India's history and genetics could help me interpret these D-stats:

Dravidian & Indo-Aryan D-stats

I ran the tests using qpDstat and genotype data from Haak et al. 2015 and Metspalu et al. 2011. The Indian samples I chose for the analysis are listed here.

Note that I didn't run any groups from northwest of Uttar Pradesh, because this part of India has an even more complex population history than the rest of the country, and I was just trying to focus on the Neolithic and early Indo-European migrations into South Asia.

Interpreting D-stats in the context of ancient migrations and admixture events is often not a straightforward task, but at least they're east to read. If the Z-score is +ve, then the gene flow occurred between W and Y and/or X and Z. If it's -ve, then the gene flow occurred between W and Z and/or X and Y.

Below are some of my observations and (potentially wild) suppositions based on the D-stats. Feel free to correct me in the comments section if I have misinterpreted the data in any way:

- the Indo-Aryans share significantly more gene flow with LBK, MA1 and Yamnaya than the Dravidians do (analyses 1-3), which correlates with their more northerly geographic location, and also with the generally accepted idea that their West Eurasian ancestors arrived in India later than those of the Dravidians, and thus had less time to mix with the locals

- the West Eurasian ancestry of the Indo-Aryans is more Yamnaya-like than that of the Dravidians (analysis 4), which fits with linguistics data, because the Indo-Aryans are obviously Indo-Europeans, while the Yamnaya were supposedly late Proto-Indo-Europeans

- the West Eurasian ancestry of the Dravidians is more LBK-like than that of the Indo-Aryans (again, analysis 4), which suggests that proto-Dravidian languages might have been introduced into South Asia by Neolithic farmers

- the West Eurasian ancestry of the Dravidians is also more MA1-like than that of the Indo-Aryans (analyses 5 & 6), which might mean that MA1-related admixture was already present in South Asia before the Indo-Europeans arrived there

- the Near Eastern ancestors of the Dravidians possibly came from Iran and/or the southern Near East, as opposed to the northern Near East or the Caucasus (analyses 7-13)


Haak et al., Massive migration from the steppe was a source for Indo-European languages in Europe, Nature, Advance online publication, doi:10.1038/nature14317

Metspalu M et al., Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia, Am J Hum Genet. 2011 Dec 9; 89(6): 731–744. doi: 10.1016/j.ajhg.2011.11.010

Saturday, March 21, 2015

Mitogenomes reveal post-Neolithic gene flow from the Near East to Tuscany

Europeans probably received their Ancient North Eurasian (ANE) admixture from at least a couple of different sources. Most of it no doubt came from the Eurasian steppe during the late Neolithic/early Bronze Age, very likely with the early Indo-Europeans. But I'd say that a significant amount of the ANE in southern Europe arrived there from the Near East during and after the late Bronze with a wide variety of groups, possibly including the proto-Etruscans. Here's a new paper from PLoS One focusing on Tuscan mitogenomes that adds weight to my argument.

Background: Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the longstanding debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000).

Results: Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.

Conclusions: Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.


Gómez-Carballa A, Pardo-Seco J, Amigo J, Martinón-Torres F, Salas A (2015) Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans. PLoS ONE 10(3): e0119242. doi:10.1371/journal.pone.0119242

Sunday, March 15, 2015

Modeling the Yamnaya with qpAdm

I've been playing around with the new qpAdm program and the Haak et al. dataset over the past few days and managed to come up with what I think are some very promising results. For instance, the Yamnaya genomes from the Samara Valley and surrounds fit rather well as 0.514 Samara hunter-gatherer + 0.486 Georgian (std. errors 0.032, chisq 3.890, p-value 2.20661e-22).

This is an intriguing outcome, mainly because Georgian is a Kartvelian language, and linguistics data suggest that the early Indo-Europeans - presumably the Yamnaya nomads or their ancestors - were in close contact with Proto-Kartvelian speakers. Moreover, even though the Yamnaya males tested to date all belong to Y-chromosome haplogroup R1b, which they probably inherited from their hunter-gatherer ancestors, because the Samara forager also belonged to this haplogroup, some of their mtDNA lineages appear to be derived from the Caucasus and/or nearby areas of the Near East.

However, the main problem with this analysis is that it's attempting to model an ancient population as a mixture of a modern one. Indeed, my estimate is that present-day Georgians harbor around 20% of the so called Ancient North Eurasian (ANE) component, which probably arrived in the Caucasus from the Eurasian steppe (see here). If so, then the qpAdm run might be overestimating the non-steppe admixture in the Yamnaya genomes by at least 10%. Nevertheless, I'm quite happy with this result as I await ancient DNA from the Caucasus and Near East.

By the way, I also pretty much nailed the Corded Ware sample: 0.73 Yamnaya + 0.27 Esperstedt_MN (std. errors 0.060, chisq 2.621, p-value 9.74968e-06). Admittedly, an identical result for the same genomes was reported months ago at the ASHG 2014 conference (see here), but that's OK, because it means I'm on the right track.

qpAdm is easy to run, but the quality of its output heavily reliant on the outgroup or "right set" of populations picked by the user. As far as I can see, the following ten populations (a subset of the "magic set" of 15 from Haak et al.) produce the most robust outcomes when analyses are limited to West Eurasian groups.


Why do they work so well? I really have no idea, but through simple trial and error I found that some of the others from the "magic set", in particular the Ami, produced much poorer results.

I'll probably end up posting a whole catalog of qpAdm output in the comments section below over the next couple of weeks. I'm open to suggestions about the models to test and how to improve my runs.


Haak et al., Massive migration from the steppe was a source for Indo-European languages in Europe, Nature, Advance online publication, doi:10.1038/nature14317

First genome-wide scan for selection using ancient DNA

A new preprint at bioRxiv reports on the first genome-wide scan for selection using ancient DNA, with a couple of unexpected outcomes:

The SNP (rs4988235) responsible for lactase persistence in Europe gives the strongest signal in our analysis. We estimated the selection coefficient on the derived allele to be 0.015 (95% confidence interval; CI=0.010-0.034) using a method that fits a hidden Markov model to the population allele frequencies as they change over time. Our data strengthens previous reports of the late appearance of lactase persistence in Europe, with the earliest appearance of the allele in a central European Bell Beaker sample (individual I0112) who lived approximately 4,300 years ago. We detect no evidence of lactase persistence in Early Neolithic farming populations like the Linearbandkeramik (LBK), or in the steppe pastoralist Yamnaya, despite their use of domesticated cattle (Figure 2).

We find a surprise in seven Scandinavian hunter-gatherers from the Motala site in southern Sweden who lived around 7,700 years before present. While the western hunter-gatherers of central and southern Europe largely have the ancestral allele at the two major European skin pigmentation loci, the closely related Scandinavian hunter-gatherers have both the derived alleles contributing to light skin pigmentation at high frequency (Figure 2B). Thus, the derived allele of SLC24A5 was common in both the Scandinavian hunter-gatherers and Early European farmers, but not in the geographically intermediate western hunter-gatherers. Further, in four out of seven Motala samples, we observe the derived allele of rs3827760 in the EDAR gene, which has effects on tooth morphology and hair thickness. This allele has been the subject of a selective sweep in East Asia, and today it is at high frequency in East Asians and Native Americans.


The derived allele in the Motala samples lies on the same haplotype as in modern East Asians (Extended Data Figure 4) implying a shared origin. The statistic f4(Yoruba, Scandinavian hunter-gatherers, Han, Onge Andaman Islanders) is significantly negative (Z=-3.9) implying gene flow between the ancestors of Scandinavian hunter-gatherers and Han so this shared haplotype is likely the result of ancient gene flow between groups ancestral to these two populations.

The high frequency of the East Asian-specific EDAR allele among the Motala foragers is even more surprising for me than their inferred light skin. But it does at least gel with the earlier finding that Scandinavian hunter-gatherers did not contribute significant ancestry to modern Europeans (see here).


Mathieson et al., Eight thousand years of natural selection in Europe, bioRxiv preprint first posted online March 14, 2015; doi:

Friday, March 13, 2015

Yamnaya-related ancestry proportions in Europe and west Asia

Here's a quick and dirty attempt to flush out a Yamnaya-specific ancestral component with the ADMIXTURE software and a few Yamnaya genomes from the recent Haak et al. paper: K6 spreadsheet.

Obviously, we'll need many more ancient samples from the vast Yamnaya horizon to be able to estimate direct Yamnaya ancestry in modern populations with any great confidence. But I'd say this looks like a very reasonable attempt, with more or less comparable results to those published by Haak et al. (for instance, see Figure 3 from the study here).

Please note that this wasn't a supervised run. In other words, I didn't mark the Yamnaya genomes as reference samples with the aim of creating a cluster from them.

However, I initially excluded all individuals from northeastern Europe, the north Caucasus and South Asia from the analysis. The reason I did this was because samples from these regions have a peculiar habit of creating very robust clusters in ADMIXTURE, which is useful when looking at recent variation and wanting low cross validation errors, but not so great when trying to resurrect genetic components from the depths of prehistory.

Once I had a dataset that was forcing the algorithm to focus its attention on the ancient genomes and producing consistent results, I tested the problem samples in batches of 5-10, thus making sure they didn't skew the analysis.

Interestingly, the Yamnaya-specific component peaks in Udmurts, who live close to where the Yamnaya samples came from. This can hardly be a coincidence.

In any case, I'm hoping to look at this issue in more detail soon with the help of qpAdm, a new program released recently with the updated ADMIXTOOLS package (see here). Based on f4 statistics, qpAdm is specifically designed for analyzing ancient admixture events.


Haak et al., Massive migration from the steppe was a source for Indo-European languages in Europe, Nature, Advance online publication, doi:10.1038/nature14317

Wednesday, March 11, 2015

New release of ADMIXTOOLS with two additional programs

ADMIXTOOLS 3.0 is now available at github via the Reich Lab site. The updated package includes minor bugfixes and improvements and two new programs: qpWave and qpAdm for studying migration and admixture. Scroll down the page at the link below.

Reich Lab software

Documentation is minimal, but I'm told that users of the old ADMIXTOOLS should be able to get things running. I haven't had a chance to check it out yet, but I'm looking forward to trying qpWave and qpAdm, hopefully this weekend.

Update 16/03/2015: Modeling the Yamnaya with qpAdm