A well supported multi gene phylogeny of 52 dictyostelia

Christina Schilde, Hajara M. Lawal, Koryu Kin, Ikumi Shibano-Hayakawa, Kei Inouye, Pauline Schaap (Lead / Corresponding author)

Research output: Contribution to journalArticle

Abstract

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.

LanguageEnglish
JournalMolecular Phylogenetics and Evolution
Early online date31 Jan 2019
DOIs
Publication statusE-pub ahead of print - 31 Jan 2019

Fingerprint

Phylogeny
phylogeny
gene
Genes
genome
Ribosomal DNA
Genome
genes
protein
group process
developmental biology
Dictyostelium
Developmental Biology
Proteins
Amoeba
Systems Biology
proteins
cells
ribosomal DNA
topology

Keywords

  • phylogenomics
  • ancestral state reconstruction
  • phylogenetic marker genes
  • Dictyostelia
  • Polysphondylium multicystogenum
  • Dictyostelium caveateum

Cite this

Schilde, Christina ; Lawal, Hajara M. ; Kin, Koryu ; Shibano-Hayakawa, Ikumi ; Inouye, Kei ; Schaap, Pauline. / A well supported multi gene phylogeny of 52 dictyostelia. In: Molecular Phylogenetics and Evolution. 2019.
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A well supported multi gene phylogeny of 52 dictyostelia. / Schilde, Christina; Lawal, Hajara M.; Kin, Koryu; Shibano-Hayakawa, Ikumi; Inouye, Kei; Schaap, Pauline (Lead / Corresponding author).

In: Molecular Phylogenetics and Evolution, 31.01.2019.

Research output: Contribution to journalArticle

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KW - Dictyostelium caveateum

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