Genomic signatures of domestication in the fungus-farming ant mutualism

Abstract

The fungus-farming ants and their fungal crop represent a classic example of mutualism and coevolution, in which it was thought, both parts were necessarily dependent on the other, the ants being responsible for the clonal propagation of fungi, and the fungi providing ants’ nourishment. However, recent studies have called these mandatory associations into question, showing the fungi can survive outside some symbiosis. In turn, two species of the family Pterulaceae that are grown by Apterostigma ants were never registered producing fertile basidiomes, what could indicate two scenarios: 1) sexual reproduction is rare in these organisms and not enough sampling have been done to register these fungi during their reproductive stage or 2) these fungi might not survive outside the symbiosis and could have lost their ability to reproduce sexually. Phylogenetically, the two species cultivated by Apterostigma do not form a monophyletic lineage and few free-living species are placed among them. These conditions have opened the way for us to try to answer two key questions about this mutualism: 1) Who are the closest free-living relatives of the two species of Pterula cultivated by Apterostigma ants? and 2) Do the genomes of pterulaceous fungi cultivated by the ants exhibit traits of domestication? Prior to the genomic analyses for the comparisons proposed in this thesis to answer the second question, the first question has to be addressed, thus this thesis proposes a thorough comprehensive reclassification of Pterulaceae in which two new genera Baltazaria (Russulales) and Myrmecopterula (Pterulaceae) are proposed, Radulomycetaceae is proposed as a new sister family to Pterulaceae, Phaeopterula (Pterulaceae) is reintroduced, Deflexula is synonymized into Pterulicium alongside to several Pterula spp. and finally the closest free living of both cultivars need to be identified. To answer the second question, a genomic evaluation of domestication traits is presented in which dN/dS and codon usage bias are measured to compare with predictions for lack of recombination. It is also analysed the deficiency of CpG dinucleotides that is traditionally related to methylation processes, the CpG profile was compared with a range of fungal species and it is shown that fungal symbionts tend to present a higher CpG deficiency

Date of Award	2020
Original language	English
Awarding Institution	Aberystwyth University
Supervisor	Gareth Griffith (Supervisor)