Phylogenetic analysis of these near full-length genome sequences revealed that all genotype 5 sequences formed a close cluster with high bootstrap support.
Surprisingly, all mRNA-derived sequences formed a tight monophyletic group, which fell into large Shallow Marine Group I cluster with sequences retrieved from shallow (up to 200 m) waters, sediments and corals.
Together with two other Ethiopian sequences, the new sequences formed a geographic cluster when the complete genome was analyzed.
These sequences formed a moderately supported subclade (ML = 84%%, MP = 88%%, PP = 56%%) which was basal to Palythoa mutuki and Palythoa tuberculosa sequences.
However, the remaining sequences formed a polytomic node, in which apicomplexans were only resolved at genus levels.
All F. speciosa sequences formed a clade in MP trees of the unedited alignment and clustered together in UPGMA trees.
Interestingly, with only a few exceptions, BceS-like sequences formed a monophyletic group in the maximum likelihood BceS tree (Figure S1).
The CTree algorithm yielded an ARI of 0.955; in this case two subtype D sequences formed a cluster apart, similarly to the TBC.
In these trees the modern human, Neanderthal, Numt-1 and Numt-2 sequences formed a macroclade that we called the macroclade Homo.
However, 27 UK sequences formed a single well-supported group displaying short branch lengths suggestive of a local transmission chain [31].
In our phylogenetic analysis, eukaryotic PFO sequences formed a single, poorly-supported clade (Figure S1), in which the Trimastix sequence emerged as a sister lineage to two cytosolic Entamoeba sequences (1.00 PP/67% BP).
