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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

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