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POPULATION REPLACEMENT OR CONTINUITY?
A GENOMIC CONTRIBUTION TO THE NEOLITHISATION DEBATE

Final Report Summary - NEOLITHISATION (POPULATION REPLACEMENT OR CONTINUITY?<br/>A GENOMIC CONTRIBUTION TO THE NEOLITHISATION DEBATE)

Summary of project objectives

The original overall objective of this project was to provide a detailed genomic characterisation of the ancient human Stone Age populations in Scandinavia, and the potential population migrations that accompanied the transition from Mesolithic hunter-gathering to Neolithic farming. Early in the process this objective was extended to also include migrations in the Bronze Age period. This decision was made based on three grounds. Firstly, many of the Danish Stone Ages samples displayed much worse DNA preservation than anticipated, making it difficult to fulfill the genome-scale ambitions of the project. Secondly, a number of papers on Stone Age genomics were published from other research groups, making my original research questions slightly less novel and thus less attractive to pursue as the only objective. Thirdly, archaeologists and linguists have argued for decades that the cultural and demographic transformations occurring in the Bronze Age had a major impact on the population of Eurasia and are a key events to understand the formation of the present day populations. We set out to test this hypothesis using ancient DNA data.

Description of work
The work has involved several intensive sampling periods, travelling to museums across Europe to gather suitable sample material - mainly well-preserved teeth from Stone Age and Bronze Age human material. In total we have collected samples from more than 700 humans. The samples have all been processed with ancient DNA technology in our dedicated clean lab facilities. They were passed through an inital screening phase to assess the DNA preservation and hence the suitability for genome scale research. Based on this, more than 100 samples were selected for in-depth genomic characterization. Population genomic analyses have been finalized for a large subset of the samples and we are in the process of publishing these results.


Description of main results
I have divided the main results under four themes.

1) Method improvements
By sampling and sequencing a very large number of ancient specimens, the project has provided me with extensive empirical insights into the strenghts and weaknesses of ancient DNA methodologies. This has resulted in several publications describing new improvement on aspects such as field work(1), sampling and ancient DNA extraction protocols(2), and human DNA capture methods(3).

2) Identification of Stone Age genomic candidates
By taking advantage of these new improved methods, and by targeting teeth rather than bones, it has been possible to identify >10 specimens from the Stone Age that display extremely good DNA preservation and are thus suitable for whole genome characterization.The deep genomic sequencing of these candidate samples is ongoing and the orginal main objective of the project can now be fulfilled.

3) The first Mesolithic genome
In 2014 we characterized for the first time the full genome sequence of a 7,500 year old Mesolithic hunter-gatherer (4). This was not part of the original project, but given the exceptional DNA preservation in this sample, we used the data to address many of the questions related to the Neolithic transition. For example we showed that this individual has no close genetic resemblance to any modern European population, supporting the population replacement theory during the Neolithisation. We also showed that he was poor at digesting starch and milk, suggesting that these traits were selected for during the Neolithisation. These are key insights of direct relvance to the objectives in the original proposal. The study was published in the journal Nature.

4) Bronze Age population genomics
Owing to a change in strategy, as outlined above, the Bronze Age ended up being the main focus area throughout 2014/2015. This has resulted in the generation of genome-wide data from more than 100 Bronze Age Eurasians and hence the largest ancient DNA study ever undertaken. The study has provided detalied insigths into the large-scale population migrations during this time period and allowed us to describe how the present day Eurasian gene pools were formed. This study has now been accpeted for publication in the journal Nature.


Impact
The improved laboratory protocols are of immediate value to the field of ancient DNA and result in an increased proportion of ancient samples being suitable for genomic research. I believe that several of these simple but efficient improvements within long will be implemented as standard procedures in most ancient DNA laboratories worldwide. As for the population genomic data, they have been used to uncover the underlying demographic events in two of the most transforming periods in European prehistory, namely the Stone Age and the Bronze Age. The results have significantly increased the understanding of our shared history and what it means to be European.


References

1 Allentoft, M. E. Recovering samples for ancient DNA research—guidelines for the field archaeologist. Antiquity 87 (2013).
2 Damgaard, P. d. B. et al. Improving access to endogenous DNA in ancient bones and teeth. bioRxiv (2015).
3 Carpenter, Meredith L. et al. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. American Journal of Human Genetics 93, 852-864, doi:10.1016/j.ajhg.2013.10.002 (2013).
4 Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225-228, doi:10.1038/nature12960 (2014).