A Case Study for Effects of Operational Taxonomic Units from Intracellular Endoparasites and Ciliates on the Eukaryotic Phylogeny: Phylogenetic Position of the Haptophyta in Analyses of Multiple Slowly Evolving Genes

<div><p>Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs), intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates]) was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA), disruption of the monophyly between haptophytes and SAR (or SA) in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA) clade in the absence of intracellular endoparasite/ciliate OTUs.</p> </div

Eukaryotic phylogeny based on nuclear-encoded protein sequences using 6,048 aa (modified from the data matrix of Nozaki et al.[<b>27</b>]), including (A) and excluding (B) the intracellular endoparasites apicomplexans.

<p>The analysis is based on the concatenated dataset of slowly evolving nuclear proteins (21 proteins; 6,048 amino acid positions). The tree was determined using RAxML with the WAG+I+4G model. Numbers on the left, middle, or right side at the branches represent BV (≥50%) obtained using 1,000 replicates with the RAxML, PhyML (WAG+I+4G), or MP analysis, respectively. Asterisks at the branches indicate 100% BV by all three methods.</p

Eukaryotic phylogeny based on nuclear-encoded protein sequences plus nucleotide sequences of 18S rRNA genes using M 10:16 (modified from the data matrix by Parfrey et al.[<b>29</b>]), including (A) and excluding (B) intracellular endoparasite/ciliate OTUs.

<p>The analysis is based on the concatenated dataset of slowly evolving nuclear proteins (15 proteins; 5710 amino acid positions) and 18S rRNA genes (868 nucleotide positions). The tree was prepared using RAxML with the WAG+4G model (for amino acid positions) and the GTR+4G model (for nucleotide positions). Numbers at the left or right side at the branches represent BV (≥50%) obtained using 1,000 replicates with the RAxML or MP analysis, respectively. Asterisks at the branches indicate 100% BV by all three methods.</p