INFERRING THE EVOLUTIONARY HISTORY OF SPECIES WITH POPULATION GENOMICS
The study of natural populations has been revolutionized by Next Generation Sequencing (NGS), which enables us to obtain genome-wide data from multiple individuals. Currently, we can obtain data not only from present-day samples from different geographic regions but also from ancient DNA at different time points. Such data hold the potential to resolve questions about the evolutionary history of a given species. However, even though we are facing a flood of genomic data, we currently lack tools to analyse such large datasets. I will illustrate how model-based approaches can be useful to reconstruct the evolutionary history of populations. I will describe a flexible composite likelihood method based on the site frequency spectrum (SFS). This method allows us to use genome-wide data to test alternative demographic scenarios and infer relevant parameters, such as migration rates, population sizes and times of divergence. I will exemplify and discuss the application of this method to different questions, ranging from speciation genetics in insects, to the genetic basis of coat colour adaptation in deer mice (Peromyscus maniculatus), and inferring human demographic history with modern and ancient DNA. I will focus on quantifying past gene flow levels, and on the interaction of gene flow with natural selection. I will exemplify how models and simulations offer us the possibility to interpret genome-wide patterns, and learn about the roles of demography and natural selection in the structuring of natural populations.
Vítor Sousa has a background in Biology and a post-graduation in Bioinformatics. He conducted his Ph.D. in Evolutionary Biology at the Gulbenkian Science Institute (IGC, Oeiras, Portugal) and received his degree from the University of Lisbon in 2010, under the supervision of Manuela Coelho and Lounès Chikhi. Vítor Sousa was then a postdoctoral researcher in Jody Hey’s lab (Rutgers University, New Jersey, USA) from 2010 to 2013, and in Laurent Excoffier’s lab (University of Bern and Swiss Institute of Bioinformatics, Switzerland) from 2013 to 2016. Since October 2016 that he is a researcher at the centre for ecology, evolution and environmental changes (cE3c) at FCUL, University of Lisbon. Since March 2018 Vítor is a Marie Sklodowska-Curie fellow. Currently, he is the group leader of the Evolutionary Genetics group at cE3c. In his research Dr Sousa addresses biological questions arising in the fields of speciation, molecular ecology, conservation and human genetics from a population genomics perspective. In particular, he is interested in characterizing the interplay between demographic processes (e.g. migration and gene flow, population expansions) and natural selection in the structure and divergence of populations.
[Host: Catarina Pinho, Phenotypic Evolution]
Image credits: Vítor Sousa