search this blog

Thursday, April 18, 2013

Hundreds of prehistoric North European skeletons to be genotyped for Y-DNA, mtDNA and autosomal DNA

Update 10/08/2015: 101 ancient Eurasian genomes (Allentoft et al. 2015)


It looks like we'll soon be inundated with ancient DNA from across Northern Europe thanks to a project called The Rise, focusing on the formation of Bronze Age societies in Southern Scandinavia. The exciting news for me is that prehistoric skeletons from Poland are also being studied as part of the effort. Below are a few quotes about the part of the project dealing with ancient DNA, called "Human Mobility".

The study will be based on burials with preserved skeletal material from southern Scandinavia, from the late middle Neolithic, late Neolithic and early Bronze Age periods. This is a material which is essential for many of the questions discussed, but that so far has received little systematic treatment. Comparisons will also be made with reference material from earlier periods and other regions, such as Germany and Poland. A systematic comparison of bio-archaeological data with variations in burial practices and artifact compositions will provide us with new insights on socially effective ways of classifying people during these periods, and contribute to our understanding of how gender, ethnicities and elites were constructed.


The key focus of the ancient DNA study will be to exploit recent technological and computational developments, in order to reconstruct the genetic history, and origins, of the Nordic and north European populations of the 3rd and 2nd millennium BC. When compared with pre-existing European Neolithic ancient DNA datasets, and modern DNA datasets, the new data will supplement and add historical depth to the strontium isotope analyses, as well as resolve kinship between the ancient samples. Three strategies will be employed:

1. Several hundred south Scandinavian and central European (German and Polish) skeletons from the 3rd and 2nd millennium BC will be pre-screened for appropriate DNA survival and quality, in order to generate a test dataset. Based on previous result, combined with new techniques that significantly enhance success rates, we anticipate subsequently genotyping between 100 and 150 samples for both mitochondrial (complete mtDNA genomes), Y chromosome and autosomal DNA (15,000 informative SNPs). This data will be compared against both published and unpublished ancient datasets and with modern datasets, in order to establish the geographical location and possible origin of primarily the new Corded Ware (CW), Single Grave (SG) and Battle Axe (BA) culture groups of the early 3rd millennium BC, but also of later Bronze Age groups of the same regions. The CW, SG and BA cultures are candidates for some major migrations that introduced a completely new social organization, and possibly Indo-European languages, that persisted into the Bronze Age. Did they have a steppe origin, a Nordic origin, a Polish/central European or a mixed origin? Did the later Bronze Age people of Scandinavia share genetic relations with these groups? The ancient DNA data will contribute to resolving this.

2. Using the data generated above, we will be able to investigate the kinship of skeletons within barrows and burials, in order to document whether they were family barrows, and whether some individuals were foreigners.

3. The complete nuclear genome sequence will be generated from hair sampled from one of the most well preserved skeletons – in particular that of an oak coffin burial of Jutland from 1400 BC. Recent technical developments published out of the Copenhagen group have demonstrated that not only is this feasible, but that such data can provide fine scale details about ancient humans – including resolving sample genetic origins to unprecedented detail, but also incidentally offer insights into functionally important genetic traits of the ancient people.

But that's not all. Recently we saw the announcement of a cutting-edge project called The Genomic History of Denmark. Its aim is to sequence 100 ancient Danish genomes from the Neolithic (including 7,000-year-old hunter-gatherers), metal ages, Viking Age, and the early Industrial Age. These samples will be compared to the genomes of 1000 modern Danes.

The project will likely add new views to Danish and European debates on heritage and national affiliations by re-addressing when and from where our ancestors came. At the same time results will allow Denmark as the first country to understand its genetic disease risk and drug suitability (personal genomics) from historical/evolutionary perspectives.

Thus, the data should allow us understanding when and possibly why current highly frequent genetic diseases, like haemochromatosis and cystic fibrosis, and increased HIV resistance became abundant in Denmark.

There are several other ancient DNA projects underway in Europe which I haven't got around to blogging about yet. I'll do that as soon as they produce some results. But I should probably mention that one of the most promising efforts, called BEAN (aka. Bridging the European and Anatolian Neolithic), recently launched a new website.

See also...

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

Monday, April 15, 2013

R1a and R1b as markers of the Proto-Indo-European expansion: a review of ancient DNA evidence

Y-DNA haplogroup R1a is arguably the best candidate for a genetic signal of the Proto-Indo-Europeans, who are thought to have expanded across Eurasia during the Copper Age. It's been characterized as such in several academic papers during the past 15 years, and the theory now looks more plausible than ever thanks to recent discoveries about its structure and phylogeography (for example, see here and here). Moreover, it's been found in numerous ancient remains supposedly belonging to early Indo-Europeans.

R1a's brother clade, R1b, has also been proposed as a marker of the Proto-Indo-European dispersals, mostly by hobby genetic genealogists on various online forums. Among other things, they argue that it shows a high correlation with the so called Centum Indo-European languages, and probably expanded rapidly across Europe at exactly the right time (ie. during and/or after the Copper Age). However, there are also several problems with this theory, such as the fact that R1b is the dominant Y-DNA haplogroup in one of Europe's few non-Indo-European speaking groups, the Basques. Moreover, there is very little R1b in South Asia - where the early Indo-Europeans are thought to have arrived en masse from Central Asia during the early Iron Age - and much of that can be explained by historic Turkic incursions anyway.

Eventually, probably in the not too distant future, next-generation sequencing of a wide range of C14 dated Eurasian remains will solve the mystery of who the Proto-Indo-Europeans were genetically. However, as already mentioned, we've now seen a reasonable number of ancient Eurasian remains tested for Y-DNA, so perhaps it might be useful to review how R1a and R1b stack up as potential Proto-Indo-European markers based on these results? In the lists below, I describe all the samples from archaeological cultures usually suspected or known to be of Indo-European origin as simply "Indo-European", while I tag those that derive from archeological cultures generally not regarded as Indo-European as "non-Indo-European".

Ancient R1a recovered to date

- Corded Ware, Copper Age, Germany, Indo-European

- Tocharian?, Bronze Age, Tarim Basin, Indo-European

- Andronovo, Bronze Age, South Siberia, Indo-European

- Urnfield, Bronze Age, Germany, Indo-European

- Tagar Scythian, Iron Age, South Siberia, Indo-European

- Pazyrk Scythian, Iron Age, Alati Republic, Indo-European

- Xiongnu, Iron Age, Mongolia, non-Indo-European

- Tachtyk Scythian, Iron Age, South Siberia, Indo-European

- Slavic or Germanic, Middle Ages, Germany, Indo-European

- Spanish, Modern (17th–18th centuries), Canary Islands, Indo-European

Ancient R1b recovered to date

- Bell Beaker, Copper Age, Germany, non-Indo-European

- Urnfield, Bronze Age, Germany, Indo-European

- Guanches, Iron Age and/or Middle Ages, Canary Islands, non-Indo-European

- Basque, Middle Ages, Spain, non-Indo-European

- Merovingian, Middle Ages, Germany, Indo-European

- Czech, Middle Ages, Czech Republic, Indo-European

- Spanish, Modern (17th–18th centuries), Canary Islands, Indo-European

Obviously, the scope of the sampling could be a lot better, but I think that already it's possible to tease out some very interesting patterns from these results. For instance, the R1a list is overwhelmingly "Indo-European". Only one sample qualifies as non-Indo-European in this scheme, and that's the Xiongnu individual from Mongolia. However, in the paper where this result was reported, Kijeong Kim et al. 2010, the R1a result was actually explained as a genetic signal of West Eurasian and indeed Indo-European influence in the Xiongnu population.

In comparison, the R1b list came out significantly "non-Indo-European", starting with the Copper Age Bell Beaker sample. The oldest supposedly Indo-European R1b reported so far is the one from the Urnfield burial site. However, it's important to note that R1a was found in two remains from that site. Note also the presence of R1b in the non-Indo-European indigenous Canary Island sample, and the appearance of R1a on the islands only after they were Indo-Europeanized by the Spanish.

Based on these ancient DNA results, I'd say it's easy to argue that R1a was an important Proto-Indo-European marker. It's much more difficult to argue the same for R1b. Indeed, taking all evidence into account, the most plausible scenario at the moment is that R1b became an important feature of the early Indo-European gene pool during the Bronze Age, after complex interactions between Corded Ware and Bell Beaker cultures in Central Europe.


New Vistas on the Distant Past: Ancient Western Eurasian DNA

Kijeong Kim et al., A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia, American Journal of Physical Anthropology, Published Online: 20 Jan 2010, doi: 10.1002/ajpa.21242

Rosa Fregel, Demographic history of Canary Islands male gene-pool: replacement of native lineages by European, BMC Evolutionary Biology, 2009, 9:181, doi:10.1186/1471-2148-9-181

See also...

Lots of ancient Y-DNA from China

Ancient Siberians carrying R1a1 had light eyes

Ancient Siberians carrying R1a1 had light eyes - take 2

First R1b from Neolithic Europe...and it ain't from the steppe

The story of R1b: it's complicated