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Archaic human ancestry in East Asia
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2011 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 45, 18301-18306 p.Article in journal (Refereed) Published
Abstract [en]

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisovagenome-a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

Place, publisher, year, edition, pages
2011. Vol. 108, no 45, 18301-18306 p.
Keyword [en]
human origins, ancient DNA
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-162448DOI: 10.1073/pnas.1108181108ISI: 000296700000034OAI: oai:DiVA.org:uu-162448DiVA: diva2:460815
Available from: 2011-12-01 Created: 2011-11-30 Last updated: 2017-12-08Bibliographically approved
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.

Place, publisher, year, edition, pages
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 from: 2013-09-27 Created: 2013-09-04 Last updated: 2014-01-23

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Skoglund, PontusJakobsson, Mattias

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