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Sunday, December 28, 2014

UISPP Burgos 2014 abstracts book


This really isn't much more than a big tease, but here's the download link anyway: UISPP Burgos 2014 abstracts book. The conference website is here. I'd like to see the following papers online ASAP:

THE UNUSUAL HUMAN CONSUMPTION OF EQUIDS FROM THE EARLY BRONZE AGE OF THE EL PORTALÓN SITE (SIERRA DE ATAPUERCA, BURGOS, SPAIN)

Galindo-Pellicena et al., page 54

The horse has played an important role in the prehistoric societies along the time. During the Paleolithic the horse was frequently hunted and consumed by man. In the Iberian Peninsula, the horse was a common element at the end of the Late Pleistocene, after which there was a long period during the Early Holocene when sites containing horse remains were very rare. It was not until the Chalcolithic or Bell Beaker culture when more equine remains were found in certain regions. The horse was exploited for various reasons in the Iberian Peninsula during the Bronze Age. In some cases, horses were used for their meat. They were also used as pack or draft animals, and only after they fulfilled this purpose, were eventually consumed. Another possible purpose of horse exploitation could be to obtain milk. Nonetheless, no evidence has been found at any site in Iberia that indicates mare’s milk consumption.

Lastly, during the Bronze Age, horses could have been considered goods that represented prestige. The possession and consumption of horses could have served to distinguish between different social classes living in settlements in that period. This is difficult to verify with the zooarchaeological record. In this study, an exceptional consumption of horse remains in Early Bronze Age is documented. These remains were discovered during the sixth excavation campaign of the El Portalón site directed by J. M. Apellániz in 1979. The material consists of 103 bones and teeth, belonging to a minimum number of six individuals of Equus sp., recovered in a thin stratigraphic interval (around 70 centimeters) and a 2 m2 of area (called Horse stratigraphic unit: HSU). It is dated c. 2000 yr cal B.C. The mortality profile (three of the six individuals were slaughtered before reaching four years of age), butchery marks (on 27.18% of the bone remains), thermal alteration and the percussion marks suggest horse meat as an important resource for the inhabitants from the Bronze Age of El Portalón. This is unusual among other Iberian sites where ovicaprines, bovids and suids provide the majority of the meat. The high percentage of equid remains identified in the HSU (43% of total NISP) makes this place one of few Holocene Iberian sites (with Cerro de La Encinaand the phase III of Pic del Corbs) where the horse is the most abundant species.

The mentioned evidences and the low representation of the equid remains in the other levels of the whole site’s stratigraphic sequence bring forward the exceptional character of equid consumption represented in this site, and, together with other contextual evidences, suggest that this accumulation of horse remains could be the result of a feast.


ONCE UPON A TIME IN THE WEST? NEW ANCIENT DNA DATA FROM PREHISTORIC IBERIA

Roth et al., page 980

Ancient DNA studies focusing on the Iberian Peninsula have mainly investigated the Mesolithic-Neolithic transition in few areas due to the limited data available. Within a comprehensive international project founded by the German Research Foundation, we genetically analysed more than 300 Mesolithic to Early Bronze Age individuals from the Iberian Peninsula. Altogether, mitochondrial results of 250 individuals could be successfully reproduced.

Together with published data from the Iberian Peninsula, results were pooled into 19 groups of different chronological and regional context all over the research area. We applied several statistical methods to reveal continuities and discontinuities among populations on chronological as well as spatial level and will here present the results for the first time.


CHALCOLITHIC MITOCHONDRIAL DNA DIVERSITY IN IBERIAN HORSES FROM EL PORTALÓN SITE (ATAPUERCA, BURGOS): INSIGHTS INTO HORSE DOMESTICATION

Lira et al., page 1013

Horse domestication was a complex process with a principal episode in the Eurasian steppes around 5.000 years BP, enriched with recurrent introgression events from local wild populations through Eurasia. Archaeological studies as well as genetic analyses with modern samples have pinpointed the Iberian Peninsula as an important area involved in the horse domestication process. Mitochondrial DNA analyses with horse ancient remains have supported this hypothesis. In this context, a Bronze Age sample sequences from El Portalón site (sierra de Atapuerca, Burgos), showed the significance of a specific maternal lineage among others, a lineage currently found exclusively on Iberian horse populations and horses from Iberian origin.

With the aim to know in detail the presence and diversity of this Iberian lineage in Iberian Peninsula in earlier times, in this study we analyse the mitochondrial DNA from 22 Chalcolithic and Early Bronze Age horse remains recovered from El Portalón site. Furthermore, we study their relationships with the 19 Iberian Bronze Age Portalón samples previously published, and the persistence of their maternal lineages in the Iberian populations through the time.


TRACING THE GENETIC HISTORY OF FARMING POPULATIONS OF EL PORTALÓN CAVE IN THE SIERRA DE ATAPUERCA, SPAIN

Valdiosera et al., page 1016

One of the most important and influential changes in human behaviour has been the change from small hunter-gathering/fishing bands to sedentary agrarian societies. This transition is generally characterised by the contrast between the two subsistence strategies and the accompanying cultural, technological and behavioural changes that occurred, and can be generalised (in Eurasia) as the Mesolithic-Neolithic transition. One of the characteristic features of this transition is how quickly the agrarian lifestyle spread and its impact on the demographic patterns of Europe; however, the nature of how it was spread remains open to debate. Ancient genomics applied to human skeletal remains from well-dated contexts allow us a precise understanding of population origins, genetic variation, migrations and admixture and comparisons between populations over time. Previous studies have shown close relationships between early Scandinavian and modern-day southern Europeans, as well as strong differences between hunter-gatherers and early farmers. However, with migration routes from the south and the modern mitochondrial DNA composition on the Iberian peninsula, the population history of southwestern Europe appears to have been different.

We sampled bone remains corresponding to 10 individuals excavated from El Portalón Cave. Radiocarbon dates were obtained for each sample. DNA was isolated using a conventional silica-based extraction method. DNA extracts were further converted into multiplexing illumina libraries and shotgun sequenced on a HiSeq platform.

Five of the 10 individuals analysed have not yielded sufficient coverage for genomic analysis. We present low coverage genomic sequences (average depth between 0.2 and 1%) of five early Iberian farmers dated to between 4,000 and 5,000 years old, from El Portalón. These individuals display a similar pattern to that observed for central and northern European farmers and all show genetic similarities to modern-day southern Europeans, particularly to Sardinians, in contrast to the recently published 7,000 year old hunter-gatherer from near-by La Brana in Spain.

Our results are important to uncover the genetic origin of farming populations in the Iberian peninsula as well as the impact on demographic patterns. Moreover, these results will contribute to the clarification of the complete demographic picture of the neolithisation in Europe. This is an on-going study and we are currently increasing genome coverage and sample numbers to obtain a higher resolution of the patterns observed.

Friday, December 26, 2014

The fateful triangle


Not long ago Lazaridis et al. proposed that most present-day Europeans were derived from three distinct ancestral populations: Ancient North Eurasians (ANE), Early European Farmers (EEF) and Western European Hunter-Gatherers (WHG).

However, this is essentially a stop-gap model, which will in all likelihood be replaced by a partly revised and more robust model once someone manages to sequence a genome or two from the Neolithic Near East. That's because EEF is clearly a hybrid component, largely made up of ancient Near Eastern ancestry and something very WHG-like, sometimes in very different proportions depending on the location and archeological context of the EEF genomes being analyzed.

So what will this new model look like, you might ask? Probably like this, where EEF is replaced by an Early Neolithic Farmer (ENF) component from the ancient Near East, or something very similar:


The diagram above is basically a Principal Component Analysis (PCA) based on output from my new West Eurasia K8 test (see here), in which the Near Eastern component is synonymous with ENF.

I'm quite certain that these results are very close to the truth. However, just in case the Near Eastern ancestry proportions are a little bit too high (and we won't know until we see those ancient genomes from the Near East), I've got another version that offers lower bound Near Eastern estimates.


It might be useful to keep in mind that I rotated the plots to fit geography. As a result, Component 1, which packs around 85% of the variance on both plots, appears smaller than Component 2, which only carries around 10% of the variance.

A spreadsheet with West Eurasia K8 results for a wide variety of populations is available here. Please note that there are two sheets, with the second sheet showing the lower bound Near Eastern ancestry proportions.

We'll probably learn of more ancient European meta-populations as many more genomes are sequenced from across Eurasia. Nevertheless, I doubt this will affect the model outlined above. That's because I'm expecting all such meta-populations to be mixtures of ANE, ENF and/or WHG, as well as, in some cases, extra-West Eurasian components.

However, I suspect that West Eurasia will have to be modeled in a different way from Europe, with, amongst other things, the so called Basal Eurasian component replacing ENF. But for this to happen we'll need at least one ancient genome that is in large-part of Basal Eurasian origin. In any case, that's a whole different subject.

See also...

4mix: four-way mixture modeling in R

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

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

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 realistic, because the Scandinavian forager genomes sequenced to date have very 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. The datasheet is available here. You can view a spreadsheet of the results with extra samples here.

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 any proportions, will not produce a result even vaguely similar to present-day Swedes (ie. the outcome will 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. 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 options 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 of 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

See also...

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

Monday, December 15, 2014

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


Here's a Principal Component Analysis (PCA) and an accompanying biplot based on output from an improved version of my ANE K7 ancestry test. Let's call it the West Eurasia K8. 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 with extra samples 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, who 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 may have carried even higher levels of ANE than they do today, before newcomers 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)

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

Stuttgart (Neolithic)

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

NE1 (Neolithic)

ANE 0
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...

The fateful triangle

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

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 until the mid 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).


Citation...

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 (LN/BA) individuals from across West Eurasia. Admittedly, the sampling is very sparse, but like I've said before on these blogs, the LN/BA was a time of profound changes in Europe, so every scrap of data from this period is very valuable.

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 LN/BA, mostly as a result of migrations from the east.


Citation...

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...

Lactase persistence and ancient DNA

Ancient genomes from the Great Hungarian Plain

Friday, December 5, 2014

The Y-chromosome tree bursts into leaf


Update 20/05/2015: Large-scale recent expansion of European patrilineages

...

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.


Citation...

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

Monday, December 1, 2014

Latest speculation about R1b


The events outlined on the map below purportedly took place during the Neolithic. Perhaps, but we simply don't have enough ancient DNA yet to be sure of much as far as the spread of R1b into Europe is concerned. Nevertheless, I'm just wondering, what's the chance that R1b was established in Western and/or Central Europe before the very late Neolithic, which is what this paper is suggesting, as far as I can tell, but has not shown up in any of the relevant ancient samples to date?

Citation...

Hovhannisyan et al.: Different waves and directions of Neolithic migrations in the Armenian Highland. Investigative Genetics 2014 5:15. doi:10.1186/s13323-014-0015-6

See also...

The story of R1b: it's complicated

Sunday, November 30, 2014

Short clip: The making of modern Europe


Simple but, I think, very cool animation: ten ancient genomes analyzed with the Eurogenes K15. More elaborate clips are on the way.



And this is basically the same thing, but restricted to samples from Hungary.

Tuesday, November 25, 2014

Admixture and migration patterns along the former Silk Road


This Mezzavilla et al. paper is currently up for public comment at bioRxiv. My comment is that we really need ancient genomes to be able to answer the sorts of questions that the authors of this paper are trying to answer. Nevertheless, it's an interesting read.

Background: The ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition "Marco Polo" has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes.

Results: We characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era.

Conclusions: We clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes.

Massimo Mezzavilla et al., Genetic landscape of populations along the Silk Road: admixture and migration patterns, bioRxiv, Posted November 24, 2014, doi: http://dx.doi.org/10.1101/011759

Tuesday, November 18, 2014

Review paper: Human paleogenetics of Europe - The known knowns and the known unknowns


Many of us are waiting impatiently for the new manuscript from the Reich Lab on the genetic shifts in Central and Eastern Europe during the late Neolithic/early Bronze Age, which will apparently include genome-wide data from Bell Beaker, Corded Ware and Yamnaya remains (see here). Rumor has it that it'll appear at bioRxiv within a few weeks.

Meantime, it might be useful to check out this review paper by Guido Brandt et al. on the present state of play in European paleogenetics.

Human paleogenetics of Europe - The known knowns and the known unknowns

It's a thorough summary of almost all ancient DNA results to date from Europe, and includes some very nice maps and other figures that look like updates on the stuff from Brandt et al. 2013 (see here). However, there are a couple of major problems with this paper that drag it down a few notches in my estimation.

Firstly, the authors leave open the possibility that Indo-European languages were introduced into Europe by early Neolithic farmers from Anatolia. Maybe they're trying to be diplomatic and humor those that won't let this failed hypothesis finally die, because otherwise I have no idea why they even considered it?

There are some very good reasons now why this is indeed a failed hypothesis. For one, linguistic evidence shows that all Indo-European languages in Europe include similar loans of non-Indo-European origin associated with farming, like the words for bean, carrot, hemp, oats and pea (for instance, see here).

These words were in all likelihood borrowed by the early Indo-Europeans from someone else as they spread out across Europe well after agriculture had been established throughout much of the continent. So who was this someone else? Probably the non-Indo-European descendants of the non-Indo-European early farmers from Anatolia.

Ancient DNA shows something similar. All ancient European genomes in a farming context sequenced to date from the Neolithic to the Copper Age are clearly distinct from present-day Indo-European speaking Europeans. But they resemble very closely present-day Sardinians, whose ancestors only became Indo-European speakers during the late Iron Age.

The other serious problem with this paper is the suggestion that present-day Northeast Europeans show the highest genome-wide affinity to Pitted Ware hunter-gatherers because the eastern Baltic acted as a refugium during the Last Glacial Maximum (LGM). It's on page 10 of the PDF.

This must be some sort of oversight, because I refuse to believe that the authors aren't aware of the fact that the eastern Baltic was covered in a big fuck off ice sheet during the LGM. Here's a map from Mangerud et al 2004.


A much more plausible explanation why present-day Northeast Europeans show the highest genome-wide affinity to Pitted Ware hunter-gatherers, and indeed all European hunter-gatherers for whom we have data, is that their ancestors were amongst the last people in Europe to take up farming and Christianity.

Citation...

Brandt, G., et al., Human paleogenetics of Europe - The known knowns and the known unknowns, Journal of Human Evolution (2014), http://dx.doi.org/10.1016/j.jhevol.2014.06.017

Thursday, November 13, 2014

TreeMix graphs with Kostenki14 and Ust'-Ishim


First of all, here's a map with some basic info about these two Upper Paleolithic North Eurasian genomes. They're separated by less than 10,000 years and a couple thousand kilometers, so in theory they shouldn't be all that different.


Let's see what TreeMix has to say on the matter. Note that the graphs also include five other ancient genomes: Denisova, Altai Neanderthal, Loschbour, Stuttgart and BR2 (LBA_Hungary).







Admittedly, I'm still learning to use TreeMix. But with that in mind, I'd say the graphs above appear very reasonable, and show outcomes that generally fit with what I've seen elsewhere.

For instance, Denisova harbors something chimp-like that isn't shared with the Altai Neanderthal. This might be a signal of the introgression from an unidentified archaic hominin that has already been reported in scientific literature.

In regards to Kostenki14, the graphs back one of the main conclusions of Seguin-Orlando et al. (ie. the people who first analyzed and published this genome), in that it appears basal to later Europeans. However, the last two graphs suggest that this basal ancestry is not the same thing as the Stuttgart-related Basal Eurasian component described in Lazaridis et al., which, if I understand correctly, is what Seguin-Orlando et al. were saying.

In fact, the basal stuff carried by Kostenki14 seems to be related to the greater part of Ust'-Ishim's genetic makeup. I say the greater part, because Ust'-Ishim also appears to harbor Papuan-like ancestry not shared with Kostenki14.

Is there anything I can do to make these graphs more informative? Perhaps add or take away some samples? Feel free to let me know in the comments below.

By the way, I downloaded the Kostenki14, LBA_Hungary and Ust'-Ishim genomes from Genetic Genealogy Tools. The rest of the samples came from the Reich Lab's Human Origins dataset, available here.

Update 14/11/2014: After looking over the results above and reading the comments below, I made a few changes to the dataset and came up with a couple more graphs that I think are worth sharing. I'm quite certain now that the so called Basal Eurasian ancestry carried by Stuttgart and Kostenki14 can't be lumped into a single component.





See also...

Kostenki14: first genome of an Upper Paleolithic European

Ust'-Ishim belongs to K-M526

Thursday, November 6, 2014

Kostenki14: first genome of an Upper Paleolithic European


At last, we have an ancient genome from pre-LGM Europe: Kostenki14 (K14) from the famous Kostenki Upper Paleolithic site in southern Russia. The paper, Seguin-Orlando et al. 2014, is locked away behind a paywall, but at least the supplementary materials are open access.

K14 is dated at 38,700-36,200 cal BP and belongs to Y-chromosome haplogroup C-M130, a basal and widespread paternal marker that has already been reported in three other ancient European genomes: La Brana-1 from Mesolithic Spain and NE5 and NE6 from Neolithic Hungary. It also belongs to mitochondrial (mtDNA) haplogroup U2, but we've actually known this since 2010 (see here).

The shared drift stats of the form f3(Mbuti;K14,X), where X is the test population, reveal that from among present-day Eurasians, this early European is most similar to Northeast Europeans, such as Lithuanians, Estonians and Belarusians, and some Western Europeans, like Basques and Orcadians (ie. people from the Orkney Isles). This is also what we've seen from other indigenous European hunter-gatherer genomes sequenced to date.


As far as Eurasians are concerned, Papuans and Melanesians are the most distinct from K14, somewhat paradoxically so, considering the ancient genome's Oceanian-like Y-haplogroup. The authors speculate that this might be because they carry ancestry from a very basal lineage that went its own way before the split between West Eurasians and East Asians. But I'm wondering whether this result can't simply be explained by the inflated Denisovan admixture among Oceanians (usually reported at around 5%)?

Indeed, there's no mention anywhere in the paper that K14 has Denisova ancestry. However, much like the recently published Ust'-Ishim genome, it shows significantly larger genomic tracts of Neanderthal origin than present-day Eurasians. The implication of this is obvious, and well covered elsewhere, so I won't go into it here.

Arguably the most controversial outcome of the study is that it shows K14 to be partly of Basal Eurasian origin. This is a highly divergent Eurasian clade first described in Lazaridis et al. (see here), and associated with Neolithic farmers. Seguin-Orlando et al. came to their conclusion via two sets of D-statistics and an ADMIXTURE run, which showed K14 to carry a component specific to the Middle East.

If true, then this finding debunks one of the main premises in Lazaridis et al., which is that Basal Eurasian admixture first arrived in Europe from the Middle East with Neolithic farmers. However, it doesn't debunk this paper's model of the formation of the modern European gene pool. Basically, for that to happen we'd need the Basal Eurasian component to show up in pre-Neolithic samples from Western and Central Europe.

Nevertheless, David Reich (one of the co-authors of Lazaridis et al.) seemed so taken aback by the news that he suggested K14 might be contaminated. Or at least, he was reported to have made this suggestion (scroll down to the last paragraph here)

This is interesting because Reich is currently working on a paper that includes ancient genomes from the Samara Valley, which isn't too far away from the Kostenki site (see here). Judging by his reaction to K14's purported Basal Eurasian admixture, we can probably assume that the pre-Neolithic genomes he's analyzed from Russia don't show any signals of this type of ancestry.

In any case, the model devised by Seguin-Orlando et al., set out in the figure below, is actually very similar to the one in Lazaridis et al., with NEOL basically standing in for EEF (Early European Farmer) and MHG for WHG and SHG (Western European Hunter-Gatherer and Scandinavian Hunter-Gatherer, respectively).


However, the suggestion that the Yenisei Siberians carry MHG rather than ANE doesn't look right to me. Why would Siberians carry European rather than Siberian hunter-gatherer ancestry? I suspect the problem is that MHG is a composite of WHG and ANE (because, as we know, SHG are partly ANE). Thus, if the Yenisei Siberians do carry both ANE and WHG, because they might indeed harbor some ancient European admixture, then perhaps this is simply being classified as MHG? If so, then I suppose it's not technically wrong, but it does look confusing.

Citation...

Seguin-Orlando et al., Genomic structure in Europeans dating back at least 36,200 years, Published Online November 6 2014, Science, DOI: 10.1126/science.aaa0114

Friday, October 31, 2014

Genetic continuity and shifts across the metal ages in the Carpathian Basin: analysis of ancient Hungarian genomes CO1, BR1 and IR1


The recent Gamba at el. paper on the genetic prehistory of the Great Hungarian Plain was an excellent piece of paleogenomic detective work. However, I feel that the authors could have done a little better with characterizing the genetic origins of their samples.

For instance, the Principal Component Analysis (PCA) appears to suffer from subtle projection bias, which is a common problem in ancient DNA studies (see here). Also, the model-based analyses, like the ADMIXTURE run, leave me wanting a lot more.

However, all of the samples are freely available online, including in user friendly genotype format at Genetic Genealogy Tools. So I thought it might be useful to take a closer look at three of the genomes, spanning a 2,000-year period from the Copper Age to the Iron Age: CO1, BR1 and IR1.

The metal ages are a critical period of prehistory and early history in the making of modern Europe. It's a time of profound cultural changes, and as we now know, large-scale genetic shifts across the continent (see here). Indeed, the three aforementioned genomes clearly show that major genetic shifts took place on the Great Hungarian Plain from the Copper Age to the Iron Age. However, they also suggest strong genetic continuity in the region throughout this period.

CO1, the Copper Age genome from a Baden Culture burial, appears ridiculously Western European, and could easily pass for a present-day Sardinian in most analyses, even though it's most likely of Balkan and Near Eastern origin. It's very similar in that respect to another Copper Age sample, Oetzi the Iceman from the Tyrolean Alps.

One of the main reasons for this Sardinian-like genetic character is certainly its very low level of Ancient North Eurasian (ANE) admixture, probably much less than five per cent. Almost everyone in West Eurasia has more these days, so they appear a lot more eastern.




Shared drift stats of the form f3(Mbuti;CO1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;CO1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

BR1 represents the Early Bronze Age (EBA) Mako Culture. It looks roughly like a cross between CO1 and someone from northeastern Europe with an unusually high level of hunter-gatherer ancestry, and also a fair whack of ANE. Indeed, after running a variety of tests, I'd say that BR1 has around 12% of ANE (in other words, more than Basques but less than British, which fits with its position on the West Eurasian PCA).

So as far as I can see, the most parsimonious explanation for this result is a population movement into present-day Hungary from the northeast during the EBA, perhaps associated with the early Indo-Europeans and the not-so-pleasant effects of the 4.2 kiloyear event (see here).

Interestingly, the 4A Oracle suggests that BR1 might in large part be a mixture of CO1 and KO1, which is another sample from Gamba et al., assigned to the Koros Culture of early Neolithic Balkan farmers, but with typically hunter-gatherer genetic structure. This opens up the possibility that people with unusually high levels of hunter-gatherer ancestry lived on the Great Hungarian Plain throughout the Neolithic, and the sampling by Gamba et al. was too patchy to find them.

However, it's not possible to get a genome like BR1 simply by mixing CO1 with KO1, because the hunter-gatherer-like sample is not eastern enough. In other words, it lacks ANE. I know this just by eyeballing a couple of PCA, featuring KO1 and Motala12, a Scandinavian sample estimated by Lazaridis et al. to have a ratio of ~19% ANE (see here and here).

So there might well have been a resurgence in local hunter-gatherer DNA on the Great Hungarian Plain, and perhaps throughout much of Central Europe, after the Neolithic. Nevertheless, in my opinion this alone cannot explain the results in this case.




Shared drift stats of the form f3(Mbuti;BR1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;BR1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

IR1, the Iron Age genome, is clearly mixed. In some ways, much like CO1 and BR1, it's also deceptively similar to present-day Western Europeans, which suggests that it's in large part of local origin. However, its uniparental markers (Y-haplogroup N-M231 and mitochondrial haplogroup G2a1) actually fit better in Siberia than anywhere in Europe, and its genome-wide DNA shows influences from the North Caucasus and Volga-Ural regions (refer to the 4A Oracle results below).

Because of its complex ancestry, I can't accurately estimate the level of ANE admixture in this genome. Nevertheless, the PCA and Eurogenes K15 suggest that it easily surpasses BR1 in this respect. Note, for instance, its position among the Kargopol Russians and North Ossetians on the global PCA plot, as well as its high Eastern Euro score in the Eurogenes K15.

What I think this hints at is that the present levels of ANE across Europe aren't the result of a single early Indo-European migration, but multiple population movements around the continent spanning the entire metal ages, although usually involving Indo-European groups, and the effects of isolation-by-distance.

By the way, IR1 comes from a burial site of the Mezocsat Culture, which is generally accepted to be of Cimmerian origin. The Cimmerians are usually described as a nomadic Indo-European people from the Kuban steppe, just north of the Caucasus, who were pushed west by the expanding Scythians. Apparently, they founded a variety of cultures in the Carpathian Basin and Balkans by imposing themselves as the ruling elite over the locals. It's remarkable how closely IR1's genetic structure fits this narrative.




Shared drift stats of the form f3(Mbuti;IR1,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;IR1,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

Also, here's a really cool map of Identity-by-Descent (IBD) hits of over 3 cM shared between IR1 and a wide range of present-day populations. It comes from a recent post at Vadim's blog (see here). The shared IBD peaks are found in East Central Europe and the Volga-Ural region, which makes sense.


Sunday, October 26, 2014

Hinxton ancient genomes roundup


Most visitors here are probably aware by now that the Iron Age genomes from Hinxton are the two male samples 1 and 4 (ERS389795 and ERS389798, respectively). You can find confirmation of this at the link below.
The researchers were surprised to find that the older Iron Age men were genetically more similar to people living in Britain today than the Anglo-Saxon women were. Stephan Schiffels of the Wellcome Trust Sanger Institute reported the results October 20 at the annual meeting of the American Society of Human Genetics.

“It doesn’t look like these Anglo-Saxon immigrants left a big impact on the genetic makeup of modern-day Britain,” Schiffels said.

The finding raises an intriguing possibility that indigenous people in Britain may have repelled the Anglo-Saxons but adopted the invaders’ language and culture, says Eimear Kenny, a population geneticist at the Icahn School of Medicine at Mount Sinai in New York City, who was not involved in the work. More ancient samples from other times and parts of Britain should give a clearer picture of that episode of history, she said.

Anglo-Saxons left language, but maybe not genes to modern Britons

In regards to the main thrust of the article above, I'm not sure if there's much point discussing whether the British today are mostly of Celtic or Anglo-Saxon stock based on just five ancient genomes from a single location in England. However, if I was told that Hinxton4, the only high coverage genome in this collection, was a modern sample, I'd say it belonged to an Irishman from western Ireland, rather than an Englishman from eastern England.

Thus, unless Hinxton4 was an ancient migrant from Ireland, then it does seem to me as if there was a fairly significant admixture event in England between the indigenous Irish-like Celts and newcomers from the east, which eventually resulted in the present-day English population.

In any case, there are indeed some noticeable differences between the two sets of samples, and these can be visualized by plotting their f3 shared drift statistics.

For instance, plotting the f3-statistics of Hinxton2, which actually looks like the genome of someone straight off the boat from the Jutland Peninsula, against those of Hinxtons 1 and 4, we see that the former shares most drift with the Danes. Moreover, the Danes, Swedes and Germans, all Germanic-speakers of course, deviate strongly on both graphs from the lines of slope that run from the Erzya to the Irish. The reason they deviate from these lines is because they don't share enough drift with Hinxtons 1 and 4 compared to the other reference populations from Northwestern Europe, especially the Irish.



A similar pattern can be seen when plotting the average results of Hinxtons 1 and 4 against those of 2, 3 and 5. However, the effect isn't nearly as pronounced, possibly because Hinxtons 3 and 5 are of mixed Celtic/Germanic origin.


See also...

Analysis of an ancient genome from Hinxton

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton3 - ERS389797

Analysis of Hinxton4 - ERS389798

Analysis of Hinxton5 - ERS389799

Friday, October 24, 2014

Analysis of Hinxton5 - ERS389799


Hinxton5, or ERS389799, is one of five ancient English genomes stored at the Sequence Read Archive under accession number ERP003900. However, this analysis is based on the genotype file of Hinxton5 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

Despite its relatively low North Sea score in the Eurogenes K15, and pronounced western shift on the Principal Component Analysis (PCA) plots, this genome appears mostly Germanic. In my opinion, the shared drift stats and also oracle results are quite convincing in this regard. If this were a modern sample it could probably pass for 3/4 north Dutch and 1/4 Irish. By the way, the Sub-Saharan admixture just looks like noise; this is, after all, a low coverage genome.



Shared drift stats of the form f3(Mbuti;Hinxton5,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton5,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton3 - ERS389797

Analysis of Hinxton4 - ERS389798

Hinxton ancient genomes roundup

Wednesday, October 22, 2014

Ust'-Ishim belongs to K-M526


Not long ago I predicted that Ust'-Ishim belonged to a basal form of Y-chromosome haplogroup P (see here). As it turns out, the 45,000 year-old western Siberian genome belongs to K(xLT) or K-M526, which is actually pretty close to my guess. The Ust'-Ishim paper was published today and is behind a paywall here, but the extensive supp info is free.

Here's a map to help visualize the information, featuring Ust'-Ishim as well as Mal'ta boy, another North Eurasian Upper Paleolithic genome published recently.


The Ust'-Ishim genome was sequenced from the fossil of a femur bone found on the right bank of the Irtysh River. This area is very close to the Urals, and almost in the middle of the former Mammoth steppe that once stretched across North Eurasia from Iberia to Alaska. Interestingly, M526 is an ancestral mutation to the markers that define Y-chromosome haplogroups N, Q and R, which possibly dominated North Eurasia since the Upper Paleolithic (note that the 24,000 year-old Mal'ta boy belongs to a basal form of R).

Moreover, R1a and R1b are the most frequent haplogroups in Europe today. Thus, it would seem that most European males derive their paternal ancestry from North Eurasian hunter-gatherers whose ancestors spread out across Eurasia from the Middle East over 45,000 years ago.

I know that a lot of people have been arguing recently that K-M526 and the derived P-M45 originated and diversified in Southeast Asia, and then migrated north well within the last 45,000 years (for instance, see here). However, considering that K-M526 was already in reindeer country 45,000 years ago, as well as the Denisovan (ancient Siberian hominin) admixture among Southeast Asians, that might well turn out to be the equivalent of arguing that up is down and down is up.

By the way, Ust'-Ishim also belongs to pan-Eurasian mitochondrial (mtDNA) haplogroup R*, and in terms of genome-wide genetic structure appears roughly intermediate between West and East Eurasians. These outcomes fit very nicely with its Y-haplogroup.

However, it's slightly closer to Mesolithic Iberian genome La Brana-1, Upper Paleolithic Siberian MA-1 (or Mal'ta boy), and present-day East Asians, than to present-day West Eurasians, including Europeans. That's because it lacks "ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia". This is obviously the so called Basal Eurasian admixture discussed in Lazaridis et al. (see here), which is probably associated with early Neolithic farmers.

Also worth mentioning is that Ust'-Ishim harbors longer stretches of Neanderthal chromosomal segments than present-day Eurasians, which suggests that admixture between modern humans and Neanderthals took place in the Middle East not long before the ancestors of Ust-Ishim moved into Siberia (50-60,000 years ago). But this was already covered months ago, and you'll find lots of links on the topic on Google.

Citation...

Qiaomei Fu et al., Genome sequence of a 45,000-year-old modern human from western Siberia, Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810

Tuesday, October 21, 2014

Ancient genomes from the Great Hungarian Plain


This open access paper on the genetic prehistory of the Great Hungarian Plain is full of surprises. Here are a few of my observations:

- Four of the genomes from a Neolithic farming context produced two Y-haplogroups previously identified in Mesolithic European hunter-gatherers (I2a and C6), and one of the samples (KO1) could probably pass for a Mesolithic hunter-gatherer overall, suggesting that males of hunter-gatherer origin played a major role in early European Neolithic societies. But what's happened to the C6 since then?

- The two Bronze Age genomes, BR1 and BR2, look very present-day French, and probably western French at that, in both the Principal Component and Admixture analyses. Indeed, they clearly show a northern influence relative to all of the Neolithic farmers and the Iron Age IR1. And yet, BR2 belongs to Y-haplogroup J2a1, which is generally seen as a Near Eastern marker.

- IR1 is described as a pre-Scythian genome with both East Eurasian and North Caucasian affinities (it's not clear in the paper whether it belongs to Y-haplogroup N and mtDNA G2a1, or vice versa, although either way works in this context). However, it also shows significant Northern European-like ancestry, and is even inferred to have fair hair, which makes me think that its eastern shift might be in large part due to Eastern Hunter-Gatherer (EHG) or Yamnaya-related admixture, which is now pervasive across Northern Europe (see here).

- Many people, including myself nowadays, see the Carpathian Basin as potentially a major staging point for the expansion of Y-chromosome haplogroup R1b into Central and Western Europe during the Bronze Age. And yet, it's again missing from the line-up.

- The T allele at SNP rs4988235, associated with lactase persistence into adulthood in Europeans, is only present among the two most recent genomes: BR2 and IR1. This suggests that selection for this allele, which now reaches frequencies of well over 50% in much of Europe, post dates not only the Neolithic but also the early Indo-European period, and was possibly most intense during the metal ages.

- Some of the Neolithic samples are clearly shifted towards the Bedouins (Bed) in Figure 2, relative to Oetzi the Iceman, a Copper Age genome from the Tyrolean Alps, which is generally considered to be typical of European Neolithic farmers (see below). So perhaps further sampling of Neolithic remains from southern Europe, in particular the southern Balkans, might reveal early farmers who actually cluster with Near Eastern populations, rather than Europeans?

- The authors found a sweetspot for extracting ancient DNA from humans: "the petrous portion of the temporal bone, the densest bone in the mammalian body". The amount of endogenous DNA salvaged from this part of the skull exceeds those from other bones by up to 183-fold. This is obviously great news, and probably means we can expect many more ancient genomes to be published in the near future.



Citation...

Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5:5257 doi:10.1038/ncomms6257 (2014).

See also...

First I1-M253 from prehistoric Europe

Genetic continuity and shifts across the metal ages in the Carpathian Basin: analysis of ancient Hungarian genomes CO1, BR1 and IR1

Monday, October 20, 2014

PIE homeland update: paleogenomics supports the steppe hypothesis


Several people tweeted from Iosif Lazaridis' talk at the ASHG earlier today, which focused on ancient DNA from 65 Neolithic and Bronze Age Europeans. Here are a couple of the tweets that caught my eye:
There was an influx from north Eurasian steppe into Europe after advent of farming. Consistent w linguistic evidence.Link

Admixture shows multiway admixture among late Neolithic ancient samples. Yamnaya good source as 3rd ancestral reference.Link

So it seems that latest paleogenomics data support the linguists and archeologists who see the Proto-Indo-European (PIE) homeland on the Eastern European steppe. For some background on that, check out the videos here.

Razib also tweeted a few times from the talk, and as far as I can tell, his main point was that the Yamnaya samples showed affinity to the Ancient North Eurasian (ANE) proxy Mal'ta boy, but were also partly of Near Eastern origin, and indeed could be modeled as a 50/50 mixture between present-day Armenians and ancient Karelian hunter-gatherers. He also said that the ancient Karelians were classified as eastern hunter-gatherers (let's call them EHG for now), along with the hunter-gatherers from the Samara Valley, which probably means they carried a lot of ANE admixture.

Moreover, he added that Corded Ware genomes from late Neolithic Germany could be modeled as 75% Yamnaya, while another source from the talk revealed to me that they carried a minimum of 36% EHG.

All of this makes sense, considering that during the Neolithic much of present-day Ukraine west of the Dnieper was home to the Cucuteni-Trypillian farmers, probably of Near Eastern origin, while at the same time large groups of indigenous hunter-gatherers still foraged east of the Dnieper. Based on archeological data, it seems these two groups mixed at some point, becoming mobile pastoralists associated with the Yamnaya culture, and then expanded in all directions during the late Neolithic/early Bronze Age, potentially spreading Indo-European culture and languages as they went.

The Cucuteni-Trypillian farmers might well have been very similar to present-day Armenians, although probably without the 10-15% of ANE carried by them, which likely arrived in eastern Anatolia with the early Indo-Europeans from the steppe.

By the way, it's possible that the Karelian hunter-gatherers are the same samples as those featured in Der Sarkissian et al. 2013., where they were reported to carry mitochondrial (mtDNA) haplogroups C1 (3 instances), U2e (x2), U4 (x2), U5a and H.

Here's a spatial map from that study showing genetic distances between the ancient Karelian mtDNA and that of modern populations.


Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, et al. (2013) Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. PLoS Genet 9(2): e1003296. doi:10.1371/journal.pgen.1003296

See also...

Corded Ware Culture linked to the spread of ANE across Europe

Coming soon: genome-wide data from more than forty 3-9K year-old humans from the ancient Russian steppe

Analysis of Hinxton4 - ERS389798


Hinxton4, or ERS389798, is one of five ancient English genomes stored at the Sequence Read Archive under accession number ERP003900. However, this analysis is based on the genotype file of Hinxton4 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

I still don't know who these samples represent exactly, but in all likelihood, this is one of the two Iron Age sequences from the collection, and probably belongs to a Briton of Celtic stock. Note, for instance, its high affinity to the present-day Irish, relatively low North Sea score in the Eurogenes K15, and pronounced western shift on the second Principal Component Analysis (PCA) plot below.

Interestingly, Lithuanians top its shared drift list based on the Human Origins dataset and more than 360K SNPs. I'm not entirely sure what this means, but it's probably related in some way to the unusually high level (>45%) of indigenous European hunter-gatherer ancestry carried by Lithuanians.



Shared drift stats of the form f3(Mbuti;Hinxton4,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton4,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton3 - ERS389797

Analysis of Hinxton5 - ERS389799

Hinxton ancient genomes roundup

Friday, October 17, 2014

Analysis of Hinxton3 - ERS389797


Hinxton3, or ERS389797, is one of five ancient English genomes stored at the Sequence Read Archive under accession number ERP003900. However, this analysis is based on the genotype file of Hinxton3 available at Genetic Genealogy Tools. For more information and some speculation about these genomes see my earlier blog post here.

Despite the exaggerated North Sea score in the Eurogenes K15, Hinxton3 could easily pass for a present-day Briton from the eastern coast of England or Scotland, albeit with a stronger than usual pull towards Scandinavia. Indeed, the f3-statistics show that it shares most genetic drift with the British and Icelanders from Eurogenes and Human Origins, respectively.



Shared drift stats of the form f3(Mbuti;Hinxton3,Test) - Eurogenes dataset

Shared drift stats of the form f3(Mbuti;Hinxton3,Test) - Human Origins dataset



Eurogenes K15 4 Ancestors Oracle results

See also...

Analysis of Hinxton2 - ERS389796

Analysis of Hinxton4 - ERS389798

Analysis of Hinxton5 - ERS389799

Hinxton ancient genomes roundup