Research

Detecting episodes of positive selection in complex histories

We have designed several model-based tests for selection that use patterns of allele frequency differentiation in a three-population tree to scan the genome for regions under ancient positive selection. One of these methods - called 3P-CLR - can serve to distinguish selective events that occurred before two populations split from each other from those that occurred after the split. A more recent method we developed - called Graph Aware Retrieval of Selective Sweeps (GRoSS) - can identify past episodes of positive selection events in arbitrarily complex admixture histories. Below is an example looking at genes under positive selection in the complex history of bovine breeds.

Paleobiological modelling (ERC-STAMP)

Radical changes in the Earth’s biome as a consequence of climate change will fundamentally affect human society and its relation to the natural world. How can we best model species dynamics, to make predictions for the future? What are the main drivers underlying these dynamics, and how are these changing as we enter the Anthropocene? A great compass for biotic changes we will see in coming decades is the study of changes the Earth has experienced before – from alterations in the distribution of terrestrial and marine mammals, to the dynamic changes in the range and connectivity of forests. There is now a wealth of historic and prehistoric records documenting past evolutionary processes, including pollen and fossil records, ancient genomes and sedimentary DNA. Together with members of my research group, I am working on an ERC-funded research project called “STAMP” (Spatiotemporal analytical modelling for paleobiology) to link these disparate types of paleobiological records with the methodological tools of spatiotemporal process analysis. We are focusing on three empirical research areas: 1) reconstruction of megafauna species ranges across the late Pleistocene and Holocene; 2) reconstruction of boreal paleo-forest dynamics; 3) study of the historical resilience and mobility of arctic marine mammals.

Spatio-temporal genomics

The genomes of organisms contain information about their past history: migrations, displacements and expansions of populations can be discerned from the footprints they left in genetic sequences – including our own genomes. Space is thus a crucial dimension of evolution: organisms interact, mate and compete with organisms that are closest to them in their landscape. Yet, tools for analyzing genomes in space are scarce or highly limited in scope. Which types of genetic patterns are most informative of spatial aspects of the history of a species? And how can we best harness them to better understand the movement and past distribution of those species? To answer these questions, we are working on an NNF-funded project to generate computational tools - like slendr - for simulating, analyzing and modelling genomes on real geographic landscapes. Using these tools, we are working to infer the spatial distribution and expansion of ancient pathogens and their hosts, using a combination of present-day and ancient genomic data. We are seeking to understand how past epidemics have affected human populations over the last 50,000 years, how humans – in turn – have responded to these epidemics, and how future epidemics might unfold over time, as a consequence of climate change and ecological breakdown.

Academic activism

We are currently working on an in-depth study on academic activism, to understand why more and more scientists are shifting from mere passive observers of climate breakdown, to active communicators of governmental inaction. We have co-authored a paper together by several scientist-activists on the urgent need for scientists to change the way we engage with society. More recently, Fernando Racimo has written a book called Science in Resistance, in which he provides a first-person account of the Scientist Rebellion, an international movement of researchers stepping beyond conventional roles to alert the public about the need for action in the climate emergency. Combining personal stories, interviews with scientist-activists, and insights from research on direct action and academia, he explores the challenges scientists face when taking a stand for climate and ecological justice.

Archaic human demographic history

We have a broad interest in paleogenomics. Fernando was involved in the data processing and analysis of the first high-coverage Neanderthal and Denisova genomes (Meyer et al. 2012, Prüfer et al. 2014). One of these analyses consisted in elucidating a signal of super-archaic admixture into the Denisova genome, which is likely to have come from a hominin group that diverged before Neaderthals, Denisovans and modern humans diverged from each other (Prüfer et al. 2014).

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