A reader alerts me to the availability of this comprehensive summary (pdf) which references a number of new manuscripts. A quite interesting picture which extends the author's previous work on ancient DNA from Sweden. Note the addition of a "a Mesolithic individual from Stora Förvar cave on the Stora Karlsö Island in the Baltic Sea" and more Ajv Neolithic hunters and Go:k Neolithic TRB farmers compared to the Science paper.
Reconstructing the Human Past using Ancient and Modern Genomes
Skoglund, P. 2013. Reconstructing the Human Past using Ancient and Modern Genomes. Acta
Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from
the Faculty of Science and Technology 1069. 68 pp. Uppsala. ISBN 978-91-554-8744-7.
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, modernday 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.