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The ancient past of Africa: reconstructing paleobiomes over the last 800k years

Supervisor: Professor Andrea Manica

Project summary:

This project will reconstruct the role that environemtal change had in shaping genetic and biodiveristy in Africa. By leveraging a new set of climatic reconstructions for the last 800k years, together with published as well as novel genetic data on birds and mammals provided by collaborators, we will reconstruct the extent of different biomes through time, and how changes in climate led population divergence and, eventually, speciation. By considering two lines of evidence simultaneously, we will compensate for the limited paleoclimatic proxies available for this continent, and aim to achieve a climatic history that is consistent with the evolutionary signals from the African fauna.

The response of biodiversity to global change is one of the most concerning issues facing our society. Yet, our ability to predict adaptation and biological change in the face of environmental change is limited at best. Past climatic changes provide the idea testing ground for ideas and tools. However, reconstructing the past is full of challenges due to the scarce data available.

What the student will be doing:

The student will work with a novel spatial modelling framework that allows to investigate the role of climatic change on demography and genetics. By exploring the coherence between climatic reconstructions and genetic data, the student will be able to investigate whether different lines of evidence provide a coherent story. The student will be able to explore the uncertainties on both climatic and genetic reconstructions. The work is fully computational, handling large data and working with Next Generation Sequence.

The student will join a large lab with an expertise in advanced statistical and computation techniques. Training in processing Next Generation Sequence data will also be provided. Whilst the project will mostly require programming in R, there will be the opportunity to gain training in python and C++.

References:

Eriksson, A. et al. Late Pleistocene climate change and the global expansion of anatomically modern humans. Proceedings of the National Academy of Sciences 109, 16089–16094 (2012).

Leonardi, M. et al. Late Quaternary horses in Eurasia in the face of climate and vegetation change. Science Advances 4, eaar5589 (2018).

Somveille, M., Rodrigues, A. S. L. & Manica, A. Energy efficiency drives the global seasonal distribution of birds. Nature Ecology & Evolution 2, 962–969 (2018)