Influence of admixture histories on the genetic evolution of hybrid populations

Informations

Funding country

France

Acronym

METHIS

URL

-

Start date

12/1/2015

End date

-

Budget

278,676 EUR

Fundings

Abstract

Hybrid populations from numerous plant and animal species, including humans, have been extensively studied by population geneticists to infer historical migrations, detect signatures of natural selection, and identify genomic regions related to phenotypes of interest. Most of these studies considered a simple statistical framework describing the admixture levels of hybrid populations and inferred the influence of a single founding admixture event on their genetic diversity. However, these statistical models do not capture the known complexity of admixture processes in which several source populations can contribute in varying amounts to the hybrid population over many generations. For example, in the case of biodiversity conservation, reintroduction programs often involve complex admixture processes over time with recurrent introductions and hybridizations with pre-existing populations. In humans, isolated populations have historically come into contact through colonization waves, forced displacements, and population migrations. Finally, admixture between communities is often determined by sociocultural rules on intermarriages in contexts of ethnic conflicts or discrimination, slavery, and clan or caste systems. Realistic models of admixture are needed to accurately reconstruct the histories of admixture of hybrid populations from genetic data, and to understand and predict how complex admixture processes influence genetic diversity within and among hybrid populations. To accurately model complex historical admixture, we recently published a general admixture model that considers multiple source populations contributing to the gene-pool of a hybrid population, with potentially variable contributions over time. Theoretically, we have shown that this model allows reconstructing unknown histories of admixture from genetic data. The METHIS project aims to develop a novel comprehensive population-genetic framework for studying, reconstructing and predicting how complex admixture events influence the genetic diversity and evolution of hybrid populations. First, we will expand our admixture model to incorporate several often neglected forces, such as assortative mating and natural selection, known to influence the genetic diversity of hybrid populations. This will allow us to capture these frequently-occurring processes and widen the application spectrum of our approach. Second, we will develop several computer programs to facilitate the application of these theoretical models to the study of admixed populations using genetic data. In particular, we will develop a simulator of genome-wide genetic data based on our admixture models, which can be used to predict the admixture structure and genetic diversity patterns expected in hybrid populations for specific scenarios of interest to researchers. We will integrate this new simulator into an Approximate Bayesian Computation framework that we will specifically adapt to infer, using genetic data, the parameters of complex admixture processes that gave rise to hybrid populations. We will make these new tools publically available. We will apply this new methodology to two case-studies. First, using available genetic data, we will reconstruct and predict the influence of admixture processes on the survival and adaptation of Arenaria grandiflora, a plant species targeted by a hybrid re-introduction program conducted since 1999 in the Fontainebleau forest to restore its nearly extinct population. Second, we will investigate recent histories of admixture in human populations. Indeed, we will generate genome-wide genotypes for 400 individuals from Cape Verde. Merging this new data with publicly available data from African, European, Caribbean and American populations we will reconstruct how variable admixture histories influenced the genomic diversity of these populations descending, on each side of the Atlantic, from the history of European colonization and the Atlantic Slave Trade.