New Insights on the Evolutionary Relationships Between the Major Lineages of Amoebozoa

Abstract

The supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages recalcitrant to modern phylogenetics. Deep divergences, taxonomic placement of some key taxa and character evolution in the group largely remain poorly elucidated or controversial. We surveyed available Amoebozoa genomes and transcriptomes to mine conserved putative single copy genes, which were used to enrich gene sampling and generate the largest supermatrix (824 genes) in the group to date. We recovered a well-resolved and supported tree of Amoebozoa, revealing novel deep level relationships and resolving placement of enigmatic lineages congruent with morphological data. In our analysis the deepest branching group is Tubulinea. A recent proposed major clade Tevosa, uniting Evosea and Tubulinea, is not supported. Based on the new phylogenetic tree, paleoecological and paleontological data as well as data on the biology of presently living amoebozoans, we hypothesize that the evolution of Amoebozoa probably was driven with the need to disrupt and graze on microbial mats - a dominant ecosystem of the mid-Proterozoic period of the Earth history.

Coronamoeba villafranca gen. nov. sp. nov. (Amoebozoa, Dermamoebida) challenges the correlation of morphology and phylogeny in Amoebozoa

“…The studied amoeba species shows a typical limax locomotive form of Tubulinea that is surprising given its evolutionary relationships, but contributes to the growing evidence that this morphotype may not be restricted to Tubulinea contrasting to the proposal by Tekle et al 22 . Instead, it is present in a diverse set of lineages broadly scattered over the tree.…”

“…Monoaxial flow of the cytoplasm in every pseudopodium or in the entire cell” 14 , p. 138. This clade of Amoebozoa has been retrieved since the first single-gene molecular phylogenetic works with a reasonable dataset size 14 – 17 to multigene phylogenetic studies 18 – 22 . The cells’ ability to adopt a cylindrical shape or produce cylindrical projections with monoaxial cytoplasmic flow is considered as a synapomorphy of Tubulinea, and it is broadly assumed that this set of morphotypes does not occur in the other clades of amoebae.…”

The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa

“…Some isolates, believed to be parasites, have been described from fish organs 18 . Cochliopodium is among the fast-evolving amoeboid lineages and its phylogenetic position within the supergroup as a member of Centramoebia (Discosea) has only been recently resolved using phylogenomic analysis 13 , 19 , 20 . Cochliopodium has been a subject of extensive study due to the unusual behavior of cell-to-cell interaction it exhibits in actively growing cultures during its life cycle 6 , 21 , 22 .…”

Omics of an enigmatic marine amoeba uncovers unprecedented giant viruses gene trafficking and provides insights into its complex life cycle

“…Up to four species of Trichosphaerium are described, mainly based on spicule morphology (Angell 1976; Angell 1975; Page 1983; Schaudinn 1899; Schuster 1976). The phylogenetic position of Trichosphaerium was controversial (Adl, et al 2019; Smirnov, et al 2011; Tekle, et al 2008) but most recent phylogenomic studies place it under the clade Tubulinea (Cavalier-Smith, et al 2016; Kang, et al 2017; Tekle, et al 2022; Tekle and Wood 2017). Trichosphaerium (Order Trichosida) is set apart from the rest of the amoebozoans by its unique features including multiporous test and a characteristic non-locomotroy digitiform, dactylopodium, that likely serves as a sensory structure (Angell 1976; Angell 1975; Schuster 1976).…”