Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Abstract

Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses.

Exploring the evolutionary history of centrosomes

“…Choanoflagellates, which are unicellular or colonial free-living uniflagellates, are considered the closest living relatives of animals [45,[47][48][49][50][51]. Filasterea comprise only two known species of filose amoebae completely lacking centrioles and cilia: the free-living marine protist Ministeria vibrans and Capsaspora owczarzaki, an endosymbiont of Biomphalaria glabrata, the intermediate snail host for intestinal schistosomiasis [46,[51][52][53]. Ichthyosporeans comprises unicellular species living in parasitic or commensal relationships with animals, mostly fish.…”

“…In addition, they form pseudopodia from their ventral surface, which are involved in prey capture but not motility [66]. Recent molecular phylogenies support that either the whole phylum, which comprises the genera Apusomonadida and Ancyromonadida, or Apusomonadida only, is the sister group to Opisthokonta, and hence that they branched off of the main amorphean lineage later than Amoebozoa [47,53,81] ( figure 1). This suggests that the last common ancestor of Apusozoa and opisthokonts was itself an excavate-like biflagellate, and hence that Amoebozoa and opisthokonts evolved from two different flagellated ancestors.…”

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

“…Choanoflagellates are a group of heterotrophic aquatic protists that are the closest unicellular relatives of the animals [15,16]. Within choanoflagellates, the Acanthoecidae are a monophyletic group [17] characterized by the possession of an extracellular lorica constructed from a series of costal strips [18].…”

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

“…This lack of knowledge of eukaryotic diversity also occurs in Opisthokonta, the superclade that comprises Metazoa, Fungi and several unicellular lineages (Ruiz-Trillo et al, 2008;Paps and Ruiz-Trillo, 2010;Torruella et al, 2012). These unicellular opisthokonts are understudied compared to their multicellular relatives, even though they are essential for better understanding key evolutionary transitions, including those that took place at the origins of both animals and fungi (Ruiz-Trillo et al, 2007;Richter and King, 2013;Brunet and King, 2017;Richards et al, 2017;Sebé-Pedrós et al, 2017).…”