Project proposal and aims:
Whole genome duplication (WGD, polyploidization) is a ubiquitous genome-wide mutation and a dominant force in sympatric speciation, particularly in plants including many crops. It is usually assumed that polyploidy poses an instant barrier to gene flow between diploid and its polyploid derivative. Our genomic survey in wild Arabidopsis, however, recently demonstrated rampant gene flow across the presumable ploidy 'barrier'. Yet evolutionary consequences of such unexpected genome permeability and generality of this finding across plant diversity remain elusive. 

Here, we aim to determine genomic signatures of the action of selection during inter-ploidy introgression in seven plant species varying in ploidy, i.e. cases of incipient polyploid speciation. We will test the hypothesis that selection promotes inter-ploidy introgression in certain genomic regions while it operates against gene flow in different parts of the genome. Firstly, based on available short-read data from all species backed by long read data in three cases, we will infer the strength and directionality of the inter-ploidy introgression. Then, we will test if selection shapes the differentiation landscape of admixed polyploid genomes using the state-of-the art population genomic tools. Finally, we will test for congruence across the species in order to provide a general synthesis on the strength, direction and evolutionary consequences of interploidy gene flow. The results have the potential to shift our perception of polyploidy towards speciation-with-gene-flow scenarios and inform breeding programs involving polyploid crops. 

We seek a highly motivated, independent early career researcher interested in developing a research program within the context of an ERC-funded project. Keen interest in in leading an independent research program and a strong background in structural, statistical, and/or population genetics/genomics are required. There will be possibility to expand to analyses towards experimental validation of the findings of population genomic analyses (crossing experiments, transformation of candidate genes) in some of the studied species. Alongside head-start with available data, the candidate is expected to be fully involved in the overall project design and lead the analytical part of the project. Student (co-)supervison and lecturing at the faculty is not required but supported as well as the development of further independent self-funded research projects.

The successful candidate will join the team of Ecological Genomics lead by Filip Kolář (https://botany.natur.cuni.cz/ecolgen). This project will involve close collaboration with other labs focused on ecological and evolutionary genomics of polyploidy ain introgression: Levi Yant (University of Nottingham, UK) and Simon Martin (University of Edinburgh, UK).

I declare that:
● co-founding 1000 EUR/month is ensured
● project is approved by head of corresponding department

Co-founding resources:
ERC Starting grant, European Research Council (850852) DOUBLE ADAPT: Whole genome duplication – the gateway to adaptation?

Contact details:
Filip Kolář
department: Department of Botany, Faculty of Sciences
email: filip.kolar@natur.cuni.cz
telephone number: +420 221 95 1645

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