A well supported multi gene phylogeny of 52 dictyostelia

• Published in: Molecular phylogenetics and evolution 2019-05, Vol.134, p.66-73
• Main Authors: Schilde, Christina, Lawal, Hajara M., Kin, Koryu, Shibano-Hayakawa, Ikumi, Inouye, Kei, Schaap, Pauline
• Format: Article
• Language: English
• Subjects: Ancestral state reconstruction; Dictyostelia; Dictyostelium caveatum; Dictyostelium discoideum; genes; phenotype; Phylogenetic marker genes; Phylogenomics; phylogeny; Polysphondylium multicystogenum; proteins; social behavior; topology
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2019.01.017

[Display omitted] •A Dictyostelium phylogeny inferred from 18 genomes resolves positions of all major and minor groups.•A tree based on amplified sequences for 6 proteins over 34 species subdivides group 4 into five clades.•Scenarios for trait evolution are more likely over the 6-protein tree than over an SSU rDNA tree. The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality. Small subunit (SSU) ribosomal DNA-based phylogenies subdivide the known 150 species into four major and some minor groups, but lack resolution within groups, particularly group 4, and, as shown by genome-based phylogenies of 11 species, showed errors in the position of the root and nodes separating major clades. We are interested in the evolution of cell-type specialization, which particularly expanded in group 4. To construct a more robust phylogeny, we first included 7 recently sequenced genomes in the genome-based phylogeny of 47 functionally divergent proteins and next selected 6 proteins (Agl, AmdA, PurD, PurL, RpaA, SmdA) that independently or in sets of two fully reproduced the core-phylogeny. We amplified their coding regions from 34 Dictyostelium species and combined their concatenated sequences with those identified in the 18 genomes to generate a fully resolved phylogeny. The new AAPPRS based phylogeny (after the acronym of the 6 proteins) subdivides group 4 into 2 branches. These branches further resolve into 5 clades, rather than the progressively nested group 4 topology of the SSU rDNA tree, and also re-orders taxa in the other major groups. Ancestral state reconstruction of 25 phenotypic traits returned higher “goodness of fit” metrics for evolution of 19 of those traits over the AAPPRS tree, than over the SSU rDNA tree. The novel tree provides a solid framework for studying the evolution of cell-type specialization, signalling and other cellular processes in particularly group 4, which contains the model Dictyostelid D. discoideum.