Comparative Genomics of Divergence for linking speciation to species life-history traits – CoGeDiv

A standardized population genomic approach will be implemented to evaluate the rate at which speciation proceeds in these different taxa.

In the first part of the project, a reference genome will be generated for each species using an approach based on long read sequencing. Genome-wide polymorphism data will then be used to document the recombination landscape across the genome of each species. Finally, a comparative genomics analysis will be performed to describe how recombination patterns are conserved or vary among species. This analysis should provide a detailed description of architectural constraints affecting the intensity of linked-selection within fish genomes.

The second part of the project will specifically address the role of demography during the speciation history of each species-pair, and try to relate species’ demography with life history traits. Genome-wide differentiation patterns will be characterized for each species-pair using whole-genome resequencing. For each species-pair, inference methods that separately capture historical, demographic and selective effects will be used. The inferred selective and demographic parameters will be finally compared across species-pairs with contrasted life history traits to understand how these influence the unfolding of speciation.

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Speciation is the process by which populations diverge and accumulate reproductive isolation barriers up to the point they become separate species. Although evolutionary biologists are now able to score genetic differentiation at the whole genome scale, the factors determining the rate of divergence and the likelihood of speciation still remain elusive. The main objective of the CoGeDiv project is to address the unknown role of demographic factors in speciation using a multispecies comparative genomic framework.
Major biogeographic suture zones offer ideal study systems to implement such a comparative approach. They concentrate across a wide variety of taxa the coexistence of cryptic species-pairs separated by physical or ecological barriers, which continue to exchange genes despite being partially reproductively isolated. Because these semi-species have originally diversified in a shared historical and ecological context, they provide a suitable framework to identify the evolutionary processes which affect species diversification in phylogenetically diverse groups.
The CoGeDiv project will focus on 16 littoral marine species-pairs distributed across a major biogeographic boundary comprising dispersal and ecological barriers: the Atlantic-Mediterranean transition zone. These species-pairs display variable degrees of reproductive isolation and are characterized by a wide range of life-history traits that impact their demography in different ways.
A standardized population genomic approach will be implemented to evaluate the rate at which speciation proceeds in these different taxa. Genome-wide differentiation patterns will be characterized for each species-pair using individual RNA-Sequencing in population samples. An integrated bioinformatic pipeline will be used to score polymorphisms and compute population genetic statistics. For each species-pair, the joint demographic history will be inferred using statistical methods that separately capture historical, demographic and selective effects. Estimated divergence parameters will be compared among species-pairs to link species biology and ecology with their propensity to speciate in a shared biogeographical context. By generating a comprehensive and high-dimensional dataset to address testable predictions, we expect to bring significant progress beyond the state-of-the-art on several fundamental questions that remain unanswered.

(i) How the balance between selection and gene flow affects divergence across the speciation continuum?
(ii) Is heterogeneous genomic divergence shaped by differential gene flow and/or linked selection?
(iii) What is the role of cytonuclear incompatibilities in speciation?
(iv) How life-history traits and species demographic characteristics affect speciation?

By generating an unprecedented analysis of species genetic diversity beyond the classically recognized conservation units, we expect to provide a mechanistic understanding of species responses to contemporary climate change, and to improve our knowledge of cryptic diversity in a littoral marine diversity hotspot.