Mots-Clés

Genomic architecture, Primates, speciation

Description

Funding Status:

Funding is in competition with other projects and students through Doctoral Training Programs (NERC and BBSRC DTPs, Darwin Trust)

Project Description

The chromosomal theory of speciation stipulates that differences in karyotypes, consisting of fissions and fusions, and intrachromosomal structural variants, are strong barriers to gene flow. This is supported by the observations that closely related species often differ in karyotype. Guenons, the most genetically diverse African primates, seem

to defy many of the general rules of speciation. Despite the presence of pronounced karyotypic differences, with diploid chromosome numbers ranging from 48 to 72, guenons hybridise in captivity and the wild, producing viable and at least partially fertile offspring between species that have diverged millions of years ago. This is not a new phenomenon, as guenons hybridised extensively throughout their 10 million years of evolutionary history, despite the presence of chromosomal differences.

The aim of this project is to study the genomic mechanisms underlying the rapid karyotypic evolution and preservation of genetic compatibilities despite deep evolutionary divergence. Karyotypic differences have been proposed to be both the driver of speciation and the consequence of gene flow, but we have very limited understanding of how they emerge, from the evolution of chromosomal breakpoints to the emergence of novel centromeres. In this project, we will use long-read sequencing and chromosome-resolved genome assemblies to study these fundamental evolutionary processes in a unique system of close human relatives.

Key research questions

- Are certain chromosomes or chromosomal regions more prone to breaking and are some genomic features, e.g., the presence of specific repeats, a prerequisite for chromosomal fissions and fusions?

- How do novel centromeres emerge on newly generated chromosomes and what are their precursors on the ancestral chromosomes?

- What consequences do chromosome fissions and fusions have on the landscape of recombination and evolutionary processes that depend on it?

- Given extensive ancestral hybridisation in guenons, how does genomic architecture influence the exchange of genetic material? Which specific genomic features facilitate or hinder gene flow?

- What explains the difference in the rate of evolution, including rearrangements, across guenon chromosomes?.

The project relies on newly generated long-read PacBio HiFi and Hi-C data for up to 14 guenon species (8 are already available and another 6 are currently being produced). The focal species span the entire breadth of guenon chromosomal diversity, with representatives of all genera and species groups, including all major participants in ancient gene flow events and karyotypic extremes. We will also include publicly available genome assemblies from closely related primates. This is a computational project and it will be conducted in collaboration with researchers in the UK, Sweden, and France.

Candidate requirements

To be eligible for a PhD-student position, the applicant should have at least an upper 2.1 degree in evolutionary biology, bioinformatics, or a related field. In the British system, candidates who have successfully finished their undergraduate degree (Honours) are eligible to apply. The technical skills of the candidates will be evaluated based on the experience with large-scale sequencing analyses and bioinformatics proficiency. Experience with genome assembly will be an advantage. The ideal candidate will have a strong interest and documented knowledge in evolutionary biology, with a drive to understand processes involved in speciation. Perseverance and high intrinsic motivation are necessary to successfully complete a PhD project and overcome the unavoidable obstacles with data and analyses. You will be highly reliable, driven and well-organised, curious and willing to think outside the box, with the ability to quickly acquire new skills, and enjoy working both independently and as part of a team.

The position will begin Fall 2025. The deadlines for the DTPs are in early January, but supervisors have to propose candidates to be considered, particularly for candidates applying from outside of the UK. Interested students should send a CV and a brief letter of interest to Dr. Katerina Guschanski (Katerina.Guschanski@ed.ac.uk). Please also reach out with informal questions.

E5 DTP (NERC), deadline January 6, 2025

https://e4-dtp.ed.ac.uk/e5-dtp/supervisor-led-projects/project?item=1679

Darwin Trust, deadline January 3, 2025

https://darwintrust.bio.ed.ac.uk/edinburgh

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th'ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.