The lab: Chikhi group

Instituto Gulbenkian de Ciência

Lab's research themes:

Genetic and genomic data are influenced by the demographic history of populations. This history is the result of events that include population collapses, expansions, or admixture processes. It also involves the connection and disconnection of populations (i.e. varying population structure). Such changes in population structure and connectivity can be caused by many factors, including climate change over short or long periods of human activities in both the most recent and ancient past.
Our group is interested in the genetic consequences of such events. We are thus interested in the methods used to improve our understanding of the recent evolutionary history of species and in the development of new methods or approaches to that aim. The species we are interested in are either endangered species, or the human species. In the case of humans, we try to understand whether genomic data can be used to reconstruct the major events such as expansions and admixture events in the last hundreds of thousands of years.

Merits of the lab:

The group mixes approaches that go from field work (in Madagascar), lab work (DNA extraction, sequencing) to data analysis and computer simulations. It therefore provides a "multi-cultural environment" in which people with very different backgrounds meet and discuss.

Country: Portugal
Supervisor: Lounes Chikhi
Research group website

The position

What’s the main purpose of our research?

Our group develops research projects in which we aim at interpreting patterns of genomic diversity in terms of spatial patterns, and temporal and spatial processes. For instance, we ask whether genomic data obtained from humans are better explained by models assuming changes in population size (expansions, bottlenecks) or by models assuming changes in connectivity between populations. The long-term objective is to integrate the two types of changes but much work is still required to reach that objective.

How we will do it?

Thus projects currently developed in the group require the identification of adequate genomic data, their analysis and interpretation and the validation of the inferences. For endangered species, we use published data and generate new data whereas for humans we mainly work on published data. Thus projects currently developed in the group require the identification of adequate genomic data, their analysis and interpretation and the validation of the inferences. For endangered species, we use published data and generate new data whereas for humans we mainly work on published data.

Why is this important?

In a period where climate change and habitat loss and fragmentation are among the greatest threats to wild species and humans, understanding whether and how our genomes have been influenced by ancient environmental changes may be more important than the academic exercise may suggest. Are the polymorphisms we observe today the result of selective processes or the simple random results of a complex history where changes in connectivity were important. The interpretation of polymorphisms observed in humans and endangered species depends on the demographic history inferred. Under some history, some polymorphism suggests past selective pressures, whereas in others they are nothing but the result of that complex demography.

Who is a good fit for the project?

The person interested in joining the groups should be:

  • Interested in working in an interdisciplinary environment
  • interested in population and quantitative thinking
  • Interested in learning, applying and developing quantitative skills
  • Willing to work on science projects that are not directly related to applied medicine

Medical doctors interested in human polymorphism and genetic diseases might potentially feel more comfortable with the research we do, but any background could be interested if they are interested in the points mentioned above.

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