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Monday, June 29, 2015

K8 results for selected Allentoft et al. genomes


Running the ancient genomes from Allentoft et al. in ADMIXTURE is proving a challenge. The reasons for this are covered in the paper; see section 6 in the supp info. Fortunately, I managed to obtain robust outcomes using my K8 model for ten samples representing almost all of the main archeological groups studied by the authors.

The spreadsheet with the new results is here. The full K8 spreadsheet is here. Below you can see a Principal Component Analysis (PCA) produced with the data. Click on the image to go to my drive, where you can download a high quality copy.



Some of the outcomes might look unusual, but as I say, they are solid. I double checked each one with an unsupervised ADMIXTURE test and genotype-based PCA. For instance, the genotype-based PCA featuring RISE247 and RISE479, respectively, look like this:



Citation...

Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

See also...

Bell Beaker, Corded Ware, EHG and Yamnaya genomes in the fateful triangle

Sunday, June 28, 2015

R1b from Vučedol period Hungary


Via the Bell Beaker Blogger:

It is noteworthy that the R1b occurred first after the Middle Chalcolithic in Transdanubia. (Late Chalcolithic has not been not examined yet, and so a hiatus remains between the Middle Chalcolithic and the Early Bronze Age data.) The two R1b samples are dated to the Vučedol period (~2,870-2,580 cal BC) and to the Gáta/Wieslburg culture (~1,950- 1,760 cal BC). R1b is the most frequent haplogroup in today’s Europe, with a frequency peak in Western Europe (Balaresque et al., 2010). From prehistoric context, this haplogroup is known from the Late Neolithic Central Germany (Bell Beaker culture, Lee et al., 2012). The theory that R1b reached Central Europe (and possibly the Carpathian Basin as well) with the Bell Beaker migration, starting from southwestern Europe (Brandt et al., 2014) seems to be collapsing, as R1b (M269) has recently been found in Yamnaya (3,300-2,700 cal BC) population on the Russian steppe as well (Haak et al., 2015).

The other Vučedol period sample belongs to I2a2. Also worth noting is the J2 from the Late Neolithic Sopot/Lengyel remains.


Source: Szecsenyi-Nagy, Anna (2015) Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin, Dissertation

Friday, June 26, 2015

Genetic substructures among Late Neolithic/Bronze Age Scandinavians


I may have discovered an interesting pattern in the Allentoft et al. data. It seems that during the Late Neolithic/Bronze Age, Scandinavia was populated by two somewhat different populations; one characterized by Y-Chromosome haplogroup R1b and a genome-wide genetic structure typical of present-day Northwestern Europeans, and another by Y-Chromosome haplogroup R1a and a relatively more eastern genome-wide genetic profile.

Below are two Principal Component Analyses (PCA), both featuring ancient Swedish genomes classified as part of the Late Neolithic Battle-Axe archeological culture. However, the first sample clusters near present-day Norwegians and belongs to Y-haplogroup R1b-U106, which is nowadays typically known as a Germanic paternal marker. On the other hand, the second sample clusters among present-day Russians and Mordovians, from all the way near the Volga, and belongs to Y-haplogroup R1a-Z645, which very likely expanded from Eastern Europe during the Late Neolithic.




Here's another example of basically the same thing, but this time with two ancient genomes from Denmark. If you're having trouble finding the ancient samples, download the PDF files and type their IDs in the PDF search field.



Coincidence? Probably not, but we obviously need more samples to confirm these results and establish that there is indeed a pattern.

Citation...

Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Monday, June 22, 2015

First look at an ancient genome from Neolithic Anatolia


Felix at GGT is in the process of uploading the genomes from the recent Pinhasi et al. paper. The file for the early Neolithic sample from Barcin, Turkey, is basically ready. I analyzed it with my K8 model and got these results (click on the image to enlarge).


I was only able to use a couple hundred SNPs for the test, so the outcome can't be taken too seriously. But it does make sense. The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.

Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border.

I also ran an Identical-by-State (IBS) affinity test using the Human Origins dataset and around 1800 SNPs. The results broadly back up the K8 analysis, with southern Europeans topping the list.


Citation...

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

See also...

The Near East ain't what it used to be

Oase 1: An early modern human from Romania with a recent Neanderthal ancestor


The Y-chromosome belongs to macrohaplogroup F and the mtDNA to macrohaplogroup N. For details see the supp info PDF here.

Abstract: Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Citation...

Qiaomei Fu et al., An early modern human from Romania with a recent Neanderthal ancestor, Nature (2015) doi:10.1038/nature14558

Update 05/07/2015: This is how Oase 1 comes out in the Eurogenes K15. Forcing ancient genomes into modern variation like this isn't the ideal way to analyze them, but in this case the relatively low affinity of Oase 1 to present-day Europe and the Near East makes sense.

North_Sea 8.12
Atlantic 13.45
Baltic 9.65
Eastern_Euro 0
West_Med 4.51
West_Asian 0.4
East_Med 0
Red_Sea 0
South_Asian 26.1
Southeast_Asian 7.65
Siberian 0
Amerindian 0
Oceanian 9.36
Northeast_African 4.16
Sub-Saharan 16.6

Thursday, June 18, 2015

Paul Heggarty: desperate or clueless?


Over at Diversity Linguistics Comment, Paul Heggarty of the Max Planck Institute for Evolutionary Anthropology (Leipzig) puts his foot in his mouth with a long-winded and rather whiny comment piece about two recent ancient genomics papers, Haak et al. and Allentoft et al., and the PIE question.

I don't have the time or energy right now to pick apart in detail Heggarty's ramblings, so I'll only focus on a couple of points. Firstly, here's a modified figure from Haak et al. that Heggarty put up with his post, and below that a couple of quotes with his explanation.

These data imply that Uralic-speakers too would have been part of the Yamnaya > Corded Ware movement, which was thus not exclusively Indo-European in any case. And as well as the genetics, the geography, chronology and language contact evidence also all fit with a Yamnaya > Corded Ware movement including Uralic as well as Balto-Slavic.

Both papers fail to address properly the question of the Uralic languages. And this despite — or because? — the only Uralic speakers they report rank so high among modern populations with Yamnaya ancestry. Their linguistic ancestors also have a good claim to have been involved in the Corded Ware and Yamnaya cultures, and of course the other members of the Uralic family are scattered across European Russia up to the Urals.

These are exceedingly naive and stupid comments from someone representing the Max Planck Institute. Perhaps as an ardent supporter of the Anatolian hypothesis he's feeling more than a little desperate at this point and clutching at straws? That's because anyone with even a basic grasp of European linguistics and genetics should know that:

- present-day Hungarians and Estonians speak Uralic languages, but they are of course overwhelmingly of Indo-European origin, which is easily seen in their genome-wide and uniparental DNA

- other Uralic speakers, further to the north and east, in the forest zone away from Indo-European influence, are clearly distinct from the vast majority of Indo-European speaking Europeans, because they show significant levels of recent Siberian ancestry, which was missing among the Yamnaya and Corded Ware people, and appears to be an Uralic-specific genetic signature

- therefore, it's highly unlikely that Uralic-speakers were also part of the Yamnaya > Corded Ware movement; rather, early Uralics in all likelihood began to move west across the forest zone well after the Yamnaya and related expansions from the steppe.

Heggarty also can't get over the fact that not all Indo-European speaking Europeans harbor as much Yamnaya-related ancestry as Northern and Eastern Europeans.

Above all, the Yamnaya > Corded Ware impact is much less widespread in Europe than Indo-European languages are. Much of southern Europe has spoken Indo-European languages from our earliest records (Latin and its ‘Italic’ relatives, Greek, Albanian and various other Indo-European languages of the Balkans, now extinct).

Some (low) proportions of apparent ‘Yamnaya’, ‘Corded Ware’ and north European ancestry do appear in present-day populations of southern Europe (Haak et al. 2015 Figure 3b). But such north to south population admixture is in any case expected from the historical period. The collapse of the Roman Empire and the migrations of the early medieval period were defined by major invasions and settlements of Slavic and Germanic-speaking populations into southern Europe.

The levels of Yamnaya-related admixture among present-day Southern Europeans are significant and plenty enough to explain why most of them speak Indo-European languages. All of this Yamnaya-related admixture cannot be explained by Germanic and Slavic incursions into Southern Europe during the early medieval period, because:

- most Southern European populations show very little admixture from Northern and Eastern Europe dating to this time frame (see Ralph and Coop 2013)

- R1b-M269 is the most common Y-chromosome haplogroup across much of Southern Europe, and its subclade structure among Southern Europeans, as well as the ancient DNA data from Haak et al. and Allentoft et al., suggest that the vast majority of it arrived there from somewhere in the east before the historical period but after the Neolithic.

About the only worthwhile point that Heggarty makes is that we need more ancient DNA, especially from more southerly regions, to help solve the PIE riddle once and for all.

He probably thinks that the new data will back up the Anatolian hypothesis. It won't. If Heggarty could actually understand the data from Haak et al. and Allentoft et al., he'd already know that the jig was up for his pet theory.

See also...

The ancient DNA case against the Anatolian hypothesis

Population genomics of Early Bronze Age Europe in three simple graphs

Wednesday, June 10, 2015

101 ancient Eurasian genomes (Allentoft et al. 2015)


It'll take me a while to digest all of the information in this massive new Allentoft et al. paper. But I've already noticed that, just like in Haak et al. 2015, the Yamnaya samples are again from the eastern half of the Yamnaya horizon. This time, however, not all of the Yamnaya individuals carry Y-haplogroup R1b; one of the five samples belongs to Y-haplogroup I2a (see here).

So I'm wondering what more westerly Yamnaya sites will reveal in the future, considering the predominance of Y-haplogroup R1a among the Corded Ware individuals sampled to date, and the close genome-wide relationship between the Yamnaya and Corded Ware?

Abstract: The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

See also...

Population genomics of Early Bronze Age Europe in three simple graphs

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

Sunday, June 7, 2015

101 ancient Eurasian genomes?


Update 10/06/2015: 101 ancient Eurasian genomes (Allentoft et al. 2015)

...

I'm hearing rumors that Nature is about to publish an important ancient DNA paper on the Late Neolithic to Bronze Age transition in West Eurasia. The paper is one of the main outcomes of The Rise, a Gothenburg University-based project focusing on the rise of Bronze Age societies in Northern Europe.

Below is a Google translation of a recent article from NovostiNK which is almost certainly about the imminent publication of this paper.

It's interesting to note the claim by one of the Armenian researchers that present-day Armenians are almost indistinguishable from the Bronze Age samples from what is now the Republic of Armenia.

This sounds very reasonable based on what we've learned to date from present-day Armenian variation (for instance, see here and here), but it's difficult to know what it means exactly without knowing what types of analyses were carried out and thresholds used. Hopefully we'll learn that in "a few days".

Today Armenians are descendants of people who lived in the territory of Armenia 5 thousand years ago, told reporters on Friday the head of the Laboratory of Molecular Biodiversity Institute of the National Academy of Sciences Levon Yepiskoposyan, referring to the international genetic study.

Genetic analysis of 101 DNA samples from different parts of Eurasia was made to clarify the genetic portrait of a man of the Bronze Age.

Eight DNA samples were taken from various archaeological sites throughout Armenia. They date back to the middle and late Bronze and Iron ages.

"The results of genetic studies have shown that DNA samples from the Bronze Age have been found on the territory of Armenia have a genetic portrait that is almost indistinguishable from the genetic portrait of people living today in our territory," said Yepiskoposyan.

He stressed that based on the results, we can conclude that modern people living in the territory of Armenia has enough deep roots.

"By participating in this study, we were able to solve not only the question of the genetic, historical and archaeological analysis, but also to some extent to respond to allegations that the Armenians living in the territory of Eastern Armenia only 200 years" said Yepiskoposyan.

He also noted that Armenia was the only country in the region that participated in the study. "Perhaps the reason is that we do not have the problems associated with our history and our neighbors apparently have such problems," said Yepiskoposyan.

"The study was conducted to study the genetic portrait of generations past and solve one of the most important questions - are we, modern people, direct descendants of the peoples living on the territory of a 5 thousand years ago," said Yepiskoposyan.

In turn, the director of the Institute of Archeology and Ethnography of the National Academy of Sciences Pavel Avetisyan added that the results of this study, conducted at Copenhagen University, will be published a few days later in a scientific paper, authored by 44 experts from 13 countries.

"Armenia for the first time take part in this kind of program, and the results we got were quite interesting," said Avetisyan.

Source: Современные армяне являются потомками людей, населявших территорию Армении 5 тыс. лет назад

Wednesday, June 3, 2015

Mitochondrial DNA from medieval Bulgaria


Human Biology has a new preprint on ancient mitochondrial DNA (mtDNA) from three medieval Bulgar sites. It includes data for 13 samples belonging to 10 different haplogroups: H, H1, H5, H13, HV1, J, J1, T, T2 and U3.

Abstract: Ancient (proto-) Bulgarians have long been thought to as a Turkic population. However, evidence found in the past three decades show that this is not the case. Until now, this evidence does not include ancient mitochondrial DNA (mtDNA) analysis. In order to fill this void, we have collected human remains from the VIII-X century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in Northeast Bulgaria and Tuhovishte (Satovcha region) in Southwest Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and Western Eurasian populations. Our results suggest a Western Eurasian matrilineal origin for proto-Bulgarians as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data which will further clarify proto-Bulgarian origins; thereby adding new clues to current understanding of European genetic evolution.


Nesheva, D V.; Karachanak-Yankova, S; Lari, M; Yordanov, Y; Galabov, A; Caramelli, David; and Toncheva, Draga, Mitochondrial DNA Suggests a Western Eurasian origin for Ancient (Proto-) Bulgarians (2015). Human Biology Open Access Pre-Prints. Paper 69.

Tuesday, June 2, 2015

Ancient cattle DNA hints at early Neolithic trade contacts between Europe and the Near East


A new paper at BMC Genetics on the origins of European cattle argues that European and Near Eastern farmers maintained trade links during the early Neolithic. This is very interesting if true, because it suggests that there was also regular movement of people between Europe and the Near East at this time.

Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

...

According to our demographic modelling, migration between Anatolia/the Near East and Europe was greatly reduced, essentially to zero, in the period after 5,000 BCE.

...

The pattern of decreasing diversity in the direction of the Neolithic expansion and the correlation of genetic and geographical distances is considerably weaker in modern-day cattle breeds than in the Neolithic. It is not clear yet to which extent human migrations from the East as postulated for the Bronze Age [61] influenced the already existing cattle stock in Europe.


Citation...

Scheu et al., The genetic prehistory of domesticated cattle from their origin to the spread across Europe, BMC Genetics (2015) 16:54 DOI 10.1186/s12863-015-0203-2