Exploring the evolutionary relationships amongst eukaryote groups using comparative genomics, with a particular focus on the excavate taxa

Abstract

Large-scale genomic data have provided new insights into the evolutionary relationships of various eukaryotes. Of particular interest were the excavates, a group of morphologically similar protists whose placement within the eukaryote Tree of Life (eToL) has long been problematic for researchers. The protein
sequences of different taxa, representing all major lineages within Eukaryota, were here compared to identify the number of orthologous sequences that are shared amongst pairs of lineages. A high number of proteins shared uniquely between two eukaryote groups was proposed as evidence that the gene families encoding these proteins represented synapomorphies. This approach is an alternative to conventional phylogenetic analyses which do not always provide consistent results when inferring deep relationships amongst eukaryotes.
Analysis of the three excavate lineages Metamonada, Discoba and Malawimonadidae did not return a significant number of uniquely shared orthogroups in any pairwise comparison, therefore lending no support to the idea of a monophyletic Excavata. Other groups shared a considerably greater number
of orthogroups, however. The orphan lineage Telonemia, comprising the sole genus Telonema, was inferred to have a specific relationship with another recently discovered orphan species, Ancoracysta twista. Similarly, Ancyromonadida was found to be related to members of the CRuMs (Collodictyonidae, Rigifilida, and Mantamonas) lineage, specifically Diphylleia rotans and Rigifila ramosa. Phylogenetic constraint analyses were performed to test these relationships. Neither the topology constraining Telonemia + A. twista nor that constraining Ancyromonadida + CRuMs could be rejected by the approximately unbiased (AU) test at a significance of 5%. 
Based on these results, and the presence of a collection of ’excavate-like’ morphological characters found with punctate distribution throughout the eToL, it is suggested here that the excavates may be a paraphyletic lineage and that the last eukaryotic common ancestor (LECA) may have been an excavate-like organism.

Date of Award	11 May 2021
Original language	English
Awarding Institution	The University of Bristol
Supervisor	Davide Pisani (Supervisor) & Tom Williams (Supervisor)