African history and genomic diversity
African populations harbor the greatest genomic diversity, and the ancestry of the African continent encompasses the ancestry outside of Africa as a consequence of the expansion into Eurasia by an African subpopulation after 100,000 years ago. We are committed to extending the ancient genomic record to Africa, with the first step including mapping population history and evolutionary adaptations over the past 20,000 years since the last Ice Age. Our preliminary analyses of 15 prehistoric individuals (Skoglund et al. 2017, Cell) provided the first glimpse of African population diversity prior to the transformations conveyed by agricultural expansions in the past few thousand years, documenting an interconnected hunter-gatherer population in eastern and southern Africa from 8,100 years ago. 

The origin of modern humans
How, when, and where did anatomically modern humans originate and how did they interact with archaic human populations such as Neandertals? Our research has provided evidence that the earliest diverging modern human population lineages are present in western Africa today (Skoglund et al. 2017, Cell) . Previous research has provided evidence for natural selection targeting genes associated with skeletal development in this time period around the emergence of anatomically modern humans (Schlebusch, Skoglund et al. 2012, Science) .

Agricultural expansions
A major research question has been whether farming culture spread 
through Europe and other parts of the world by migrating human groups or as a viral idea. In Scandinavia, cultures practicing farming and foraging coexisted during
the same time, separated by less than 400km. In the first ancient genomic data from Europe, we showed that prehistoric hunter-gatherers and farmers in Scandinavia were separate populations (Skoglund et al. 2012, Science), solving an 100 year-old debate in archaeology. Since then, we have observed similar population processes in Oceania (Skoglund et al. 2016. Nature). We have also documented that European hunter-gatherers had low effective population size, and that farming populations migrating through Europe absorbed ancestry from local hunter-gatherer groups (Skoglund, Malmström et al. 2014, Science).

The natural history of dogs and wolves
We have published the first genome sequencing of a 35,000 year old wolf—which through our analysis provided the first direct evidence of a Pleistocene divergence between dogs and wolves as well as evidence for ancient Siberian wolf ancestry in present-day Husky-type breeds (Skoglund et al. 2015, Current Biology). We our currently leading an effort sequence more ancient dog and wolf genomes from across Eurasia to understand this history in greater detail.

The peopling of the Americas
When and how did people first reach the Americas, as the last continent to be colonized by humans? My research has discovered an unexpected genetic link between isolated indigenous groups in the South American Amazon and Australasian groups such as aboriginal Australians, an ancient connection which suggests entirely unexpected stories in the first peopling of the Americas (Skoglund et al. 2015, Nature). I have also been involved in research on a 24,000 year-old anatomically modern human from the Lake Baikal region in Siberia (Raghavan, Skoglund et al. 2014, Nature), which deep ancestry both the ancient hunter-gatherers of Europe and present-day Native Americans whose ancestors carried it with them as they traversed the thin landbridge that connected Alaska to Siberia in ancient times, as we were able to demonstrate by analyzing the genome of a 12,600 year old individual from a Clovis burial in the state of Montana (Rasmussen et al. 2014, Nature).

Improving ancient genomics
Ancient DNA studies are vulnerable to contamination from humans and other sources during excavation, analysis, and laboratory preparation of fossils. I developed a computational solution to this problem in the form of statistical models for isolating DNA sequences that show unambiguous evidence of the postmortem damage that is typical of ancient molecules. This has allowed not only authentication of some of the first ancient human genomes analyzed (Skoglund et al. 2012, Science), but also the rescue of specimens that are widely contaminated, such as that of a Siberian Neandertal (Skoglund et al. 2014, PNAS). I am the principal developer of PMDtools, a software for analysis of postmortem DNA damage patterns: