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Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Recent ancient DNA studies have provided new evidence for prehistoric population structure associated with the contentious transition to an agricultural lifestyle in Europe. In this study, we infer human population structure and history in Holocene Europe by generating ancient genomic sequence data from 9 Scandinavian individuals associated with the foraging Pitted Ware Culture and the agricultural Funnel Beaker Culture (TRB). We obtained up to 1.1x coverage of the genomes for the nine individuals allowing direct comparisons of the two groups. We show that the Neolithic Scandinavian individuals show remarkable population structure corresponding to their cultural association. Looking beyond Scandinavia, we integrate this data with ancient genomes from Southern Europe and find that the Tyrolean Iceman from an agricultural context is most similar to Scandinavian individuals from a farming context, whereas Mesolithic Iberian hunter-gatherers are most similar to Scandinavian hunter-gatherers, opposite to what would have been predicted from their geographical origins. This finding shows that among these individuals, lifestyle is the major determinant of genetic ancestry rather than geography. Comparisons with modern populations reveal a latitudinal relationship where Southern European populations such as Sardinians are closely related with the genetic variation of the agricultural groups, whereas hunter-gatherer individuals appear to have the closest relationship with Baltic populations such as Lithuanians and present-day Scandinavians. Our results also demonstrate that while Middle Eastern populations are not the most similar to Neolithic farmers, this observation can be explained by African-related admixture in more recent times for Middle Eastern groups, which, once accounted for, reveals that the other major component of their ancestry resembles Neolithic farmers. While present-day Scandinavian populations are intermediate between the two groups, consistent with admixture, they appear genetically slightly closer to Neolithic hunter-gatherers than Neolithic farmers. This suggests a model where initial colonization by agricultural populations was followed by later admixture with hunter-gatherer populations or gene flow from other regions.

National Category
Biological Sciences
Research subject
Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-206770 (URN)oai:DiVA.org:uu-206770 (OAI)diva2:645429 (DiVA)
Available from2013-09-04 Created:2013-09-04 Last updated:2014-01-23
In thesis
1. Reconstructing the Human Past using Ancient and Modern Genomes
Open this publication in new window or tab >>Reconstructing the Human Past using Ancient and Modern Genomes
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

Publisher, range
Uppsala: Acta Universitatis Upsaliensis, 2013. 68 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1069
Keyword
population genetics, paleogenomics, human evolution
National Category
Evolutionary Biology Genetics
Research subject
Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-206787 (URN)978-91-554-8744-7 (ISBN)
Public defence
2013-10-18, Zootissalen, Evolutionary Biology Centre, Norbyvägen 18C, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from2013-09-27 Created:2013-09-04 Last updated:2014-01-23

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Skoglund, PontusMalmström, HelenaOmrak, AyçaRhagavan, MaanasaValdiosera, CristinaHall, PerWillerslev, EskeStorå, JanGötherström, AndersJakobsson, Mattias
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Evolutionary BiologyDepartment of Archaeology and Classical studies, Stockholm University, Stockholm, Sweden
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