Masters Thesis

Intron evolution and the origin of animals

The relationship between molecular complexity and organismal complexity is a central question in biology’s quest to understand the phenotype-genotype connection. Several recent studies tackled this problem on a genome-wide scale in the context of the origin of animal multicellularity. A study by Grau-Bove et al. (2017) leveraged newly- available genomes of lineages closely related to Metazoa in order to characterize spliceosomal intron evolution in animal ancestors. The authors reconstructed an “explosion” of introns in the branch leading to the last common ancestor of metazoa. Notably, they also reconstructed an independent proliferation of intron gains in the lineage of another Eukaryote, the Ichthyosporea. Scrutiny of their reconstructions revealed that they infer a surprisingly high number of intron gains at the same site, or parallel gains, in these two lineages. Given that previous results suggest that parallel gain can be overestimated by models that fail to account for differences in evolutionary rates across sites, I sought to reanalyze these data using more appropriate models. In this thesis, reanalysis of Grau-Bove et a/.’s intron presence-absence data using the intron reconstruction software Malin, the same statistical program used by Grau-Bove et al., suggests that the method may systematically underestimate ancestral intron density. Furthermore, attempts to incorporate rate variation across sites resulted in unstable behavior by Malin, perhaps due to over-parameterization of the likelihood with more taxa, particularly across deep macroevolutionary timescales. Finally, reanalysis with an alternative likelihood method suggests, in contrast, that the last common ancestor of animals and their sister group, choanoflagellates, already had an intron density comparable to modem, intron-rich animals. More work will be necessary to resolve this controversy.

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