A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Abstract

BackgroundDictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa.ResultsWe retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification.ConclusionsThe multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0825-7) contains supplementary material, which is available to authorized users.

Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae

“…1B ). The phylogeny of clade I is generally consistent with the phylogeny of the six species determined using other genes 18 . All species contain one gene in this clade except for D .…”

Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas

“…Groups 1, 2, 3 and 4 have recently been reclassified as families with the names Cavenderiaceae, Acytosteliaceae, Raperosteliaceae and Dictyosteliaceae, while Dlac , Ppal and Dfas have been renamed to Tieghemostelium lacteum , Heterostelium album and Cavenderia fasciculata [14]. However, this classification was based on the single gene small subunit ribosomal DNA phylogeny [4], which was superseded by more robust multi-gene phylogenies, which only partially support the new classification [5, 15]. We therefore continue to use the older nomenclature here.…”

“…We aim to understand how the gene regulatory mechanisms that caused cell-type specialization evolved in early multicellular organisms, using the genetically tractable Dictyostelia to investigate this problem. Molecular phylogenies subdivide Dictyostelia into four major and some minor groups [4, 5], with most novel cell types appearing in group 4 [6, 7], which contains the model organism Dictyostelium discoideum . Following completion of the D. discoideum genome sequence [8], we obtained genome sequences for a representative species in each of the three other taxon groups, which were almost fully assembled by primer walking [9, 10].…”

Evolution of Multicellular Complexity in the Dictyostelid Social Amoebas

“…Their phylogenetic relationships were first reconstructed with molecular data based on SSU rDNA, which established four major groups of Dictyostelids, simply named Group 1, 2, 3 and 4 [26]. Since then, the phylogeny has been revised through phylogenomic studies [27][28][29], but the major groupings stayed the same. Groups 1, 2, 3 and 4 were recently reclassified as Cavenderiaceae, Acytosteliaceae, Raperosteliaceae and Dictyosteliaceae [30], but there are still disagreements with respect to the relationships between a few groups [28], which may lead to further renaming in the near future.…”