The impact of mutualistic dependence on the evolution interaction-related genes: a case study in the largest ant/plant symbiotic system

Background Mutualisms -cooperation between species- are ubiquitous and linked to major transitions in the history of life, such as the evolution of eukaryotes or the conquest of the land by plants. They have allowed the diversification of new lineages, permitted species to access otherwise inaccessible resources and radically modified Earth's geochemical cycles. Yet, understanding the origins and evolutionary trajectories of mutualistic dependences remains a major challenge. How symbiotic mutualisms impact genomes is poorly known besides microbial endosymbioses. This project proposes to test how mutualistic dependence influences the evolution interaction-related genes in the largest ant/plant symbiotic system. The symbiotic system involves epiphytic plants offering lodging and sometimes food to ants in return for extra nutrients and sometimes defense against herbivores. This system, the Hydnophytinae clade in the coffee plant family (Rubiaceae) is uniquely replicated: specialization and loss of the mutualism occurred recurrently over the group's evolutionary history. Does obligate dependence promote faster rates of molecular evolution following a Red Queen Hypothesis dynamics? Or alternatively, do they rather show evolutionary stasis as predicted if there is no conflict with the partner? Does the complete loss of mutualistic dependence lead to the degradation of symbiotic genes? Using a uniquely replicated system, with a large number of mutualism breakdowns (scaled to size), the student will test these alternative hypotheses.

Aims The student will conduct comparative genomic analyses and phylogenomic analyses across the whole Hydnophytinae clade (~105 species) and appropriate outgroups. A symbiotic toolkit of genes of interest will be identified using transcriptomics and whole genome sequences at hand. The student will generate a solid phylogenomic dataset based on 100s genes (plastome plus hundreds of nuclear genes) using targeted hybrid capture. The student will then reconstruct the evolution of major gene families linked to the mutualism such as nitrogen and phosphorus transporters, and reconstruct their phylogenetic history, unveiling loss and expansions of gene families together with recurrent loss or specialization of the symbiotic mutualism. Using this dataset, the student will perform selection tests across the clade, focusing both on (i) targeted gene families and (ii) genome-wide analyses using complementary approaches, to test the competing hypotheses.

Methodology This project will use (i) targeted-sequencing-based phylogenomics, (ii) comparative genomics using (1) targeted sequencing of a 'symbiotic toolkit' across 120 species, (2) whole genome sequencing for 20 species and (iii) selection tests using complementary methods.
Timetable of Activities Year 1: Generate all sequence data, becoming familiar with the systematics of the group. Year 2: Generate species phylogeny, and phylogenies for key gene families, assemble whole genome data. Year 3: Finish genomic analyses and write up thesis.

Novelty The proposed PhD project is timely for several reasons: the advent of genomics with both sequencing methods and computational tools now allow genome assembly for non-model, wild species; (3) the Hydnophytinae are a promising system to study evolution and ecology of mutualism at various scales because of its highly replicated history. This project is also novel because: (1) it will provide a new reading of the diversity of mutualisms through an essential, unifying aspect: dependence; (2) the comparative genomics of mutualisms is an emerging (outside endosymbioses with microbes), highly promising research field. As a result, I anticipate that this will result in several high-profile publications.

Student Training The student will receive training in (1) molecular methods for next-generation sequencing; (2) phylogenomics; (3) genomic analyses (genome assembly, gene selection test, genome-wide gene selection).