1. Exploring fungal disease associations using genomic data and network models
- Author
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Riquelme Medina, Ignacio, Delneri, Daniela, Knight, Christopher, and Mcinerney, James
- Subjects
Fungi ,Networks ,Plasmids ,Phylogeny - Abstract
Convergent evolution is a process by which different distantly related species can evolve the same trait, usually involving adaptation to similar environments, and it is a widespread phenomenon thorough all groups of life. One of the groups where convergent evolution could be common is the fungal kingdom since they have repeatedly and independently adapted to similar environments through their evolutionary history. One way to detect convergent evolution is by using association networks, where groups of genes that appear together more often than expected can be identified. These groups of genes are usually related to a function or process, and by considering the habitat of the species that appear in one set of associated genes we can potentially link the set to a particular phenotype. To exclude traits that are found in different species due to common ancestry, association networks need to be considered in the context of the fungal phylogeny. Fungal phylogenetics is still a very active research area, in large part due to the presence of some problematic taxa such as the Microsporidia, which are intracellular parasites that have lost most of their genome. In this thesis, in order to resolve the phylogenetic positions of problematic groups, I have used tree and data heterogeneous phylogenetic models, that are able to account for different evolutionary processes in different proteins and in different parts of the tree. To investigate and demonstrate the utility of networks for uncovering evolutionary processes, we used bipartite networks to identify evolutionary signals in plasmids. Traditional phylogenetic methodology cannot be used to portray the overall evolutionary history of plasmids, due to the lack of common genes. Therefore, networks allow us to connect plasmids through overlapping gene sets even if there are no genes that are common to all plasmids. Through the investigation of community structure, which emerges throughout evolutionary time as a consequence of the interactions of plasmids with one another, I have been able to associate part of the networks with certain plasmid features, like host taxonomy or function. Finally, I investigated plasmid evolution further by studying how the physical properties of the nucleotide sequences that forms each plasmid can affect plasmid interactions by using Exponential Random Graph Models.
- Published
- 2022