Pontus Skoglund


Evolutionary genomics of the human past

Present-day human biology and disease are outcomes of historical evolutionary processes, and the large-scale retrieval of ancient DNA now provides the opportunity to directly study the dynamics and signatures of these processes in the human genome through time and space. This PhD-studentship will join the new Crick ancient genomics laboratory in reaching back into the deep past to gain insights about the human condition.

The lab is interested in developing molecular and computational tools to retrieve ancient genomes from past populations (Skoglund et al. 2012; Skoglund et al. 2014a) in conjunction with statistical population genetic approaches (Skoglund et al. 2015), with the overarching goal to study how ecological and cultural factors have shaped human population structure and biology during momentous transitions in prehistory. From the emergence of anatomically modern humans to the profound lifestyle changes associated with transitions to agriculture and sedentary societies (Skoglund et al. 2014b; 2016), the research group aims to understand central evolutionary episodes in the human past, and their impact on human societies and health.

Possible projects include:

1.         Integrating functional genomics and statistical population genetics to study human adaptation to new lifestyles and environments

2.         Reconstructing human population history in Africa using ancient DNA

3.         Application and development of molecular and computational methods to retrieve ancient DNA and proteins from deeper in the past

4.         Establishing domestic dogs and their wild progenitor gray wolves as a model system for evolutionary ancient genomics

These are examples of the types of projects that are available in the research group. The precise project will be decided on in consultation with the supervisor.

1.  Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P., Willerslev, E., Gilbert, M. T. P., Götherström, A. and Jakobsson, M. (2012)
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.
Science 336: 466-469. PubMed abstract

2. Skoglund, P., Malmström, H., Omrak, A., Raghavan, M., Valdiosera, C., Günther, T., Hall, P., Tambets, K., Parik, J., Sjögren, K.-G., Apel, J., Willerslev, E., Storå, J., Götherström, A. and Jakobsson, M. (2014)
Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers.
Science 344: 747-750. PubMed abstract

3. Skoglund, P., Mallick, S., Bortolini, M. C., Chennagiri, N., Hünemeier, T., Petzl-Erler, M. L., Salzano, F. M., Patterson, N. and Reich, D. (2015)
Genetic evidence for two founding populations of the Americas.
Nature 525: 104-108. PubMed abstract

4. Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J. and Jakobsson, M. (2014)
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.
Proceedings of the National Academy of Sciences of the United States of America 111: 2229-2234. PubMed abstract

5. Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., Clark, G. R., Reepmeyer, C., Petchey, F., Fernandes, D., Fu, Q., Harney, E., Lipson, M., Mallick, S., Novak, M., Rohland, N., Stewardson, K., Abdullah, S., Cox, M. P., Friedlaender, F. R., Friedlaender, J. S., Kivisild, T., Koki, G., Kusuma, P., Merriwether, D. A., Ricaut, F.-X., Wee, J. T. S., Patterson, N., Krause, J., Pinhasi, R. and Reich, D. (2016)
Genomic insights into the peopling of the Southwest Pacific.
Nature 538: 510-513. PubMed abstract