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Cambridge NERC Doctoral Training Partnerships

Graduate Research Opportunities
 

Lead Supervisor: Guy Jacobs, Archaeology

Brief summary: 
The project will analyse genetic data to understand how genetic mixing of ancient hominins - humans, Neanderthals, Denisovans and potentially others - occurred, and what impacts it had on our evolution and genetic diversity.
Importance of the area of research concerned: 
Modern genomic data is increasingly revealing admixture between divergent populations as a widespread and important process in evolution. The hominin clade offers many exciting examples – between Neanderthal, Denisovans and modern humans as well as other, presently little-known groups. The evolutionary implications of a more network-like phylogeny are profound, impacting genetic diversity as well as the course of adaptation and speciation. However, little is known about the detailed process of admixture – models tend to describe mixing as single, discrete events between panmictic populations, with limited reference to ecology, geography or context. This project will combine existing ancient genome data with newly generated modern data and simulation modelling to investigate how admixing groups were living, what social processes structured contact, and the evolutionary consequences of admixture. Using humans as an especially rich and interesting case study, it will develop methods to interpret and understand admixture signals between divergent populations – an increasingly important topic in a world where human influence is dramatically impacting species distributions and contacts.
Project summary : 
This is a highly computational project that will analyse existing ancient hominin genome data and newly generated modern human data to infer lesser-known properties of the admixture process. The goal is to develop and apply methods to infer more ecologically realistic demographies, more socially realistic admixture processes (for example, detecting sex-biases and the degree to which admixture occurs as discrete events), and more nuanced interpretations of immediate and longer-term adaptive impacts of admixture. Both genetic signals of admixture and the theoretical implications of the process will be profiled using extensive simulations. Together, the project will both propel understanding of the evolutionary impact of admixture on the hominin clade, and provide a toolkit to study the detailed process of admixture in other species.
What will the student do?: 
The student will assemble a genetic dataset from existing (Neanderthal, Denisovan and human) and newly generated (modern human) genetic data, and prepare this for analysis. They will then conduct demographic inference, replicating known signals and assessing confidence in ‘standard’ models of admixture. With this understanding as a baseline, the student will begin to design and test methods to infer more subtle details of the admixture process, and apply these to the dataset. Testing will be achieved through simulation modelling (coalescent and forward-time). The focus will be, as above, on more realistic demographic inference, the impact of social behaviour on admixture, and the process of adaptation. A particular approach will be the inference of evolutionary and ecological processes more than the specific sequence of events usually inferred – distributions of metapopulation sizes, frequencies of contact, extent of sex-biases etc. They will use their simulations and results to understand the broader evolutionary impact of – and ecological requirements for – phylogenetic networks characterised by divergence and contact.
References - references should provide further reading about the project: 
Dannemann, M. and Racimo, F., 2018. Something old, something borrowed: admixture and adaptation in human evolution. Current opinion in genetics & development, 53, pp.1-8.
Iasi, L.N., Ringbauer, H. and Peter, B.M., 2021. An extended admixture pulse model reveals the limitations to Human-Neandertal introgression dating. bioRxiv.
Jacobs, G.S. et al. 2019. Multiple deeply divergent Denisovan ancestries in Papuans. Cell, 177(4), pp.1010-1021.
Applying
You can find out about applying for this project on the Department of Archaeology page.
Dr Guy Jacobs
Department of Archaeology Graduate Administrator