Genomics of ancient hybridization

We are looking for a strongly motivated graduate student interested in pursuing a PhD degree in Evolutionary Genomics in collaboration between CIBIO-InBIO, University of Porto (https://cibio.up.pt/) and ISEM, University of Montpellier (http://www.isem.univ-montp2.fr/en/).

The selected candidate will be invited to apply to a 4-year PhD Fellowship of Fundação para a Ciência e a Tecnologia (FCT, Portugal), in the call expected for the first trimester of 2022 (see information about the previous call at https://www.fct.pt/apoios/bolsas/concursos/individuais2021.phtml.en). Monthly salary is compatible with living costs in Portugal ("BD” in https://www.fct.pt/apoios/bolsas/docs/Tabela_Valores_SMM_LOE_2021.pdf), and the fellowship covers social security and tuition fees. If the fellowship is granted, the PhD project is expected to start in October 2022.

Application deadline: 21 January 2022

Project Description
It is now well documented that related species often exchange genetic material in the wild. Interspecific genetic introgression is thus a potentially important player in biodiversity evolution, yet poorly quantified and characterised. Modern genomics offers unprecedented opportunities to fill this gap and address several questions of great importance for our understanding of evolution: under what conditions does introgression occur, what is the role of natural selection in promoting or impeding it, and the origin selection? The project will focus on three species of south European hares (genus Lepus) that were affected by introgression from an arctic/boreal species that they replaced in this region during the current deglaciation. Analysing a collection of full genome sequences and additional population genetics data, this project will aim to detect and quantify all factors modulating introgression, related for example with sex-linked transmission and behaviour, the interplay between recombination rate variation and genetic incompatibilities, positive natural selection, and coadaptation between genomic regions. This project will allow the acquisition of skills in bioinformatics and sophisticated cutting-edge population and evolutionary genomics, by handling large-scale genomic datasets. This work is expected to have a general impact on the understanding of speciation and evolution through genetic exchange, broadening our understanding of biodiversity beyond species inventories.

Supervision:
- The PhD project will be supervised by José Melo-Ferreira (CIBIO-InBIO, University of Porto - https://cibio.up.pt/; https://sites.google.com/site/meloferreiraj; https://scholar.google.com/citations?hl=en&user=YYMR-gMAAAAJ) and Pierre Boursot (ISEM, University of Montpellier; http://www.isem.univ-montp2.fr/en/personnel/teams/sex-and-speciation/boursot-pierre.index/; https://scholar.google.com/citations?hl=en&user=fslosr0AAAAJ) and developed in both labs. It will integrate the long-term collaboration between the institutions (see http://www.lia-bioevol.org/).
- If the Fellowship is granted, the Student will register in the BIODIV – Biodiversity, Genetics and Evolution – PhD program at the University of Porto, Portugal. A cotutelle between the Universities of Porto and Montpellier is envisioned.
- The successful candidate will integrate the EVOCHANGE – Genomics of Evolutionary Change – research group at CIBIO-InBIO (https://cibio.up.pt/research-groups-1/details/evochange).

Required Qualifications:
- A Master (MSc) degree in Biology, Evolution, Genetics, Bioinformatics or related fields is required. If any of the stated degrees was obtained abroad, the formal recognition of the degree in Portugal and the conversion of the obtained grades to the Portuguese scale are required at the time of the application to FCT (more information at https://www.dges.gov.pt/en/pagina/degree-and-diploma-recognition).
- Candidates should be highly motivated and demonstrate strong interest in Evolutionary Biology.
- Preference will be given to candidates with experience in analyses of high-throughput sequencing data, and knowledge of programming languages, such as Unix, Python/Perl and/or R, and with a track record demonstrating these skills.
- Good writing and communication skills in English, excellent teamwork skills, and ability to work independently.
- Availability for mobility between CIBIO-InBIO (Vairão, Portugal) and ISEM (Montpellier, France). Specific funds are available to sustain such mobility.
- The successful applicant must be resident in Portugal at the start of the PhD.

How to Apply:
- Application deadline: 21 January 2022 or until the position is filled, whichever comes first;
- Inquiries and Applications should be directed to José Melo-Ferreira (jmeloferreira@cibio.up.pt; meloferreiraj@gmail.com) indicating the research subject "Genomics of ancient hybridization”.
- Applications should be written in English and must include the following information:
1) a motivation letter describing the candidate’s profile, research interests and suitability for the role;
2) a Curriculum Vitae, summarizing the academic path, research experience, publications and other qualifications deemed relevant;
3) copy of the BSc and MSc certificates, and course grades;
4) names and contact information of two referees.