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. 2022 Jul 1;12(1):11173.
doi: 10.1038/s41598-022-15372-7.

New insights on the evolutionary relationships between the major lineages of Amoebozoa

Yonas I Tekle  1 , Fang Wang  2 , Fiona C Wood  2 , O Roger Anderson  3 , Alexey Smirnov  4
Affiliations

New insights on the evolutionary relationships between the major lineages of Amoebozoa

Yonas I Tekle et al. Sci Rep. .

Abstract

The supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages that have been 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 in the group to date; encompassing 824 genes, including gene sequences not previously analyzed. 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 by adaptive responses to a changing environment, where successful survival and predation resulted from a capacity to disrupt and graze on microbial mats-a dominant ecosystem of the mid-Proterozoic period of the Earth history.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Genome wide phylogeny of the Amoebozoa inferred using Maximum likelihood (ML) in IQ-TREE with LG + G4 + C60 + F model of evolution. The data matrix used to infer this tree consisted of 113,910 amino acid sites from the full dataset, derived from 824 genes and 113 taxa including 10 outgroup taxa. Clade supports at nodes are ML IQ-TREE 1000 ultrafast bootstrap values, obtained using the same model, Internode certainty inferred using QuartetScores and RAxML, respectively. All branches are drawn to scale except branches leading to Archamoebae, and Sapocribrum chincoteaguense, and Parvamoeba monoura, that were reduced to one-third and half, respectively.
Figure 2
Figure 2
A scheme illustrating the loss of kinetosomes and cilia under the different configurations of the phylogenetic tree (A and B). Vertical hash marks on branches show loss of kinetosomes (the number lost as designated by labels on the diagram) depending on the lineage.
See this image and copyright information in PMC

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