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Sunday, December 21, 2014

Gokhem2 + Motala12 =/= present-day Swedes

I've seen quite a few comments on this blog suggesting that most of the Ancient North Eurasian (ANE) admixture found in Northern Europe today might come from Scandinavian hunter-gatherers like Motala12 and Ajvide58.

It's probably obvious to most that this is not a realistic option, because the Scandinavian forager genomes sequenced to date have impossibly high ratios of Western European Hunter-Gatherer (WHG) ancestry (>80%), so basically the math doesn't add up. Nevertheless, I thought it might be useful to drive the point home using this Principal Component Analysis (PCA) based on my new West Eurasia K8 test.

Please note that neither Motala12 nor Gokhem2, a late Neolithic farmer from south Sweden belonging to the Funnelbeaker culture, can pass for present-day Swedes. Moreover, mixing Gokhem2 with Motala12, in whatever proportions you might choose, will not produce a result even vaguely similar to present-day Swedes (ie. the outcome has to fall somewhere along the dotted line).

I'd say one of the most obvious ways to get the right result would be to blend the Scandinavian forager and farmer with at least one other sample from somewhere below (ie. geographically speaking, east or southeast) of the Swedish cluster.

It might be possible to come up with a more precise plot location, and thus perhaps geographic origin, for this putative third source of Swedish ancestry by running some complex tests with the PCA datasheet (available here). If anyone wants to have a go at that, and you actually manage to come up with a coherent outcome, then feel free to post your findings in the comments below.

I've decided not to bother, because as far as I can see, the possibilities are infinite. What we really need are more genomes from the Swedish late Neolithic/early Bronze Age (LN/EBA), preferably belonging to one of the local spin-offs from the Corded Ware culture, which is thought to have originated in Eastern Europe, to provide more datapoints and help narrow down the options.

On a related note, I'm catching up on some reading this holiday season, and currently going through this book chapter which discusses the upheavals during the LN/EBA in south Scandinavia as seen through its archeology.

Rune Iversen, Beyond the Neolithic transition - the "de-Neolithisation" of south Scandinavia

Monday, December 15, 2014

ANE is the primary cause of west to east genetic differentiation across West Eurasia

What we have here is a Principal Component Analysis (PCA) and an accompanying biplot based on output from an improved version of my Ancient North Eurasian (ANE) ancestry test. Unlike the previous version of this test (described here), this one gives more accurate estimates of Western European Hunter-Gatherer (WHG) and Near Eastern admixture proportions, thanks to the use of new ancient samples.
When rotated accordingly (like here), the results are basically indistinguishable from those I get with genotype data (for instance, see here and here), which suggests that they're correct and based on ancestry proportions that are close to the truth. The Past3 data sheet used to create the PCA is available here. You can view a spreadsheet of the results here.

Clearly, ANE is the main agent causing the west to east differentiation in dimension 2. Note that even a small rise in ANE, say, 4-5%, creates significant distance between samples on the PCA plot.

East and South Eurasian admixture has a similar effect, but must be more considerable to make an impact on a West Eurasian-specific PCA like this (and it does with the obvious Volga-Ural outliers, which come from Chuvashia and Tatarstan).

On the other hand, Near Eastern admixture without ANE creates almost the opposite effect. Note, for instance, that Neolithic genomes Stuttgart and NE1 show much higher levels of Near Eastern ancestry than most Europeans, and yet they're amongst the most western samples on the plot.

This suggests that the Near East, and in particular the Caucasus, experienced a significant rush of ANE admixture after early Neolithic farmers left the region for Europe. Alternatively, Caucasus populations might carried even higher levels of ANE than they do today, before migrants from the Near East mixed with them. But either way, a lot of ANE arrived in the Near East at some point.

It also suggests that, overall, the populations that moved west across northern Europe after the Neolithic, and shifted northern European genetic structure to the east, did not carry high ratios of Near Eastern ancestry. Instead, they harbored high ratios of ANE and WHG. What these ratios were exactly I haven't a clue, but ancient DNA should tell us that soon.

Below are the ancestry proportions for the five ancient genomes in this analysis, in chronological order. It's interesting to note (yet again) the rising and falling Near Eastern admixture, from the Mesolithic to Neolithic and then from the Neolithic to Bronze Age, respectively, as well as the steady rise of ANE from the Bronze Age to the Iron Age.

Loschbour (Mesolithic)

South_Eurasian 0
Near_Eastern 0
East_Eurasian 0
WHG 99.5
Oceanian 0.5
Pygmy 0
Sub-Saharan 0

Stuttgart (Neolithic)

South_Eurasian 0
Near_Eastern 72.19
East_Eurasian 0
WHG 27.8
Oceanian 0
Pygmy 0
Sub-Saharan 0

NE1 (Neolithic)

South_Eurasian 0
Near_Eastern 69.82
East_Eurasian 0
WHG 30.17
Oceanian 0
Pygmy 0
Sub-Saharan 0

BR2 (Bronze Age)

ANE 9.62
South_Eurasian 0.08
Near_Eastern 43.96
East_Eurasian 0
WHG 45.44
Oceanian 0.48
Pygmy 0.23
Sub-Saharan 0.19

Hinxton4 (Iron Age)

ANE 15.08
South_Eurasian 0.06
Near_Eastern 35.44
East_Eurasian 0.46
WHG 48.5
Oceanian 0
Pygmy 0
Sub-Saharan 0.46

See also...

Short clip: The making of modern Europe

Sunday, December 14, 2014

Tigers and Proto-Indo-Europeans

Indo-European languages lack a cognate for the word tiger. In fact, it seems that not even the early Indo-Aryans were familiar with these big cats, because they borrowed their word for tiger from the Dravidians.

I've always found this fascinating, because tigers were once much more widespread than they are today, and found in the Caucasus, eastern Turkey, northern Iran and Afghanistan, and the riverine forests and wetlands of Kazakhstan right up until the late 1900s. Here's an old postcard from Berlin Zoo showing a tiger caught in Georgia, western Caucasus.

What this tells me is that the Proto-Indo-Europeans didn't live very close to the Caucasus, Iran, the wetter parts of Kazakhstan, or in fact in any part of Asia inhabited by tigers.

By the way, here's some more reading:

Linguistics, archaeology and the human past

Tuesday, December 9, 2014

Pit-Grave (Yamnaya) kurgans are as old as Maykop kurgans

Many people believe that Maykop kurgans of the North Caucasus are older than those of the Eastern European steppe, and thus ancestral to them. I've seen this claim made in the comments section of this blog and elsewhere, and regularly cited as evidence for a more southerly Proto-Indo-European (PIE) homeland than the steppe. But this appears to be false:

Abstract: We studied the chronology and periodization of the Pit-Grave (Yamnaya) culture at the Volga and Ural interfluve. Establishing the chronology of the Pit-Grave culture by archaeological methods is difficult due to the lack of artifacts in the burials. Therefore, we excavated 3 kurgan groups in the Orenburg region of Russia during the last decade. Eighteen kurgans of the Pit-Grave culture were studied using archaeological and paleopedological methods and radiocarbon dating. The funeral complexes studied were divided into 3 stages. A variety of carbon-containing materials from the same complexes were dated by different laboratories to increase the accuracy of the obtained dates. In addition, from the excavations of the last years some monuments of the Repino stage, the earliest period of the Pit-Grave culture, were dated using ceramics. Together with archaeological and paleopedological data, 14C dating helped to clarify and, in general, to confirm the 3-stage periodization of the Pit-Grave culture in the Volga-Ural interfluve: the early (Repino) stage, 4000–3300 BC; the advanced (classical) stage, 3300–2600 BC, which is divided into substages A and B at 3300–2900 and 2900–2600 BC, respectively; and the late (Poltavkinsky) stage, 2600–2300 BC.


Thus, on the basis of 14C dating, the chronological limits of the early (Repino) stage of the Pit-Grave culture in the Volga-Ural region are approximately between 4000 and 3300 cal BC. This is ~500 yr older than previously thought (Chernykh and Orlovskaya 2004). At this stage, the Pit-Grave culture developed synchronously with the early stage of the Maikop culture in the northern Caucasus, according to the archaeological evidence and the calibrated 14C dates obtained for the early stage of the Maikop culture (Korenevsky 2004).


Nina Morgunova, Olga Khokhlova, Chronology and Periodization of the Pit-Grave Culture in the Area Between the Volga and Ural Rivers Based on 14C Dating and Paleopedological Research, Radiocarbon, Vol 55, No 2–3 (2013), DOI: 10.2458/azu_js_rc.55.16087

Sunday, December 7, 2014

Milk consumption in late Neolithic/Bronze Age West Eurasia

The map below is based on data from Warinner et al. 2014. It shows the consumption of milk, or lack of, among late Neolithic/Bronze Age (LNE/BA) individuals from across West Eurasia. Admittedly, the sampling is very sparse, but like I've said before on these blogs, the LNE/BA was a time of profound changes in Europe, so every scrap of data from this period is very valuable.

It's interesting to note the lack of milk consumption among the samples from north of the Alps, where today the vast majority of people consume milk as adults, and can do so because they carry the Lactase Persistence Allele (T-13910). This doesn't look like a coincidence, considering the mounting evidence of a major population turnover across much of Europe during the LNE/BA, mostly as a result of migrations from the east.


Warinner, C. et al. Direct evidence of milk consumption from ancient human dental calculus. Sci. Rep. 4, 7104; DOI:10.1038/srep07104 (2014).

See also...

Ancient genomes from the Great Hungarian Plain

Friday, December 5, 2014

The Y-chromosome tree bursts into leaf

I wonder what the hardcore Y-DNA genetic genealogists will say about this effort? I know that many of those guys have been working with full Y-chromosome sequences for a while now. It's open access with lots of supplementary info.

Abstract: Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes.

Here are a couple of interesting quotes. You can see the samples they're talking about on the tree below. As per the second paragraph, it seems there's a paper about to be published at Nature Communications on European Y-chromosome haplogroups based on some heavy resequencing data (see Batini et al. in the references list). Can't wait for that.

(viii) Rare deep-rooting hg Q lineages in NW Europe: Hg Q has been most widely investigated in terms of the peopling of the Americas from NE Asia (Karafet et al. 1999). Here, as well as an example of the common native American Q-M3 lineage, we included examples of rare European hg Q chromosomes. One of the English chromosomes belongs to the deepest-rooting lineage within Q (Q-M378) and may reflect the Jewish diaspora (Hammer et al. 2009); the other is distantly related, shares a deep node with the Mexican Q-M3 chromosome, and has an STR-haplotype closely related to those of scarce Scandinavian hg Q chromosomes (unpublished data).

(ix) Structure within the west Eurasian hg R: The TMRCA of hg R is 19 KYA, and within it both hgs R1a and R1b comprise young, star-like expansions discussed extensively elsewhere (Batini et al. submitted). The addition of Central Asian chromosomes here contributes a sequence to the deepest subclade of R1b-M269, while another, in a Bhutanese individual, forms an outgroup almost as old as the R1a/R1b split.


Hallast et al., The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades, Molecular Biology & Evolution, published online December 2, 2014, doi: 10.1093/molbev/msu327

Wednesday, December 3, 2014

Worst paper of the year?

I reckon this is the worst population genetics paper I've seen in a long time. It's yet another attempt to use modern DNA to untangle ancient population movements:

Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry

The authors are under the illusion that running enough samples with the ADMIXTURE software can reveal pure ancestral components from thousands of years ago, and thus uncover the story of the peopling of the world in all of its glory. That's an incredibly naive view, to put it mildly.

There's not much else I can add. The paper is open access so you can make up your own mind. However, I'd say your time will be better spent reading this paper instead, if you haven't already.

Towards a new history and geography of human genes informed by ancient DNA