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Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).

Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M, Cavalier-Smith T - PLoS ONE (2013)

Bottom Line: We discuss possible evolutionary pathways.Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding.We report a new group I intron insertion site for Myxomycetes in one Licea.

View Article: PubMed Central - PubMed

Affiliation: Zoology Department, University of Oxford, Oxford, United Kingdom. afiore-donno6@infomaniak.ch

ABSTRACT
Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

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Bayesian phylogeny of Lucisporidia inferred from concatenated alignments of SSU rRNA and EF-1α genes, based on 41 sequences and 1705 positions, with Ceratiomyxa fruticulosa as outgroup.Clades are highlighted as in Fig. 1. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; a dot on the line indicates maximum support in both analyses. In Trichiida, classical families (according to [12]) are indicated by an ellipse with the initials (Arc = Arcyriidae; Dia = Dianemidae; Tri = Trichiidae). The scale bar indicates the fraction of substitutions per site.
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pone-0062586-g002: Bayesian phylogeny of Lucisporidia inferred from concatenated alignments of SSU rRNA and EF-1α genes, based on 41 sequences and 1705 positions, with Ceratiomyxa fruticulosa as outgroup.Clades are highlighted as in Fig. 1. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; a dot on the line indicates maximum support in both analyses. In Trichiida, classical families (according to [12]) are indicated by an ellipse with the initials (Arc = Arcyriidae; Dia = Dianemidae; Tri = Trichiidae). The scale bar indicates the fraction of substitutions per site.

Mentions: We obtained 66 new sequences, 37 SSU and 29 EF-1α for 35 taxa (Table S1). We assembled them with the few publicly available genuine, good-quality lucisporidian sequences in two separate alignments and a combined one. The results of our phylogenetic analyses are presented as a SSU tree (Fig. 1) and a combined SSU+EF-1α tree with fewer taxa (Fig. 2). Both trees presented the same topology, but the second had increased support for the basal branches. On the other hand, the EF-1α gene alone is too conserved to provide enough informative sites, resulting in a tree with mainly unresolved branches, provided in Fig. S2. Both SSU and two-gene trees strongly place Cribrariidae as a monophyletic lineage sister to all other Lucisporidia (Bayesian posterior probabilities (BPP) 1.0; ML bootstrap replicates (MLB) 0.98%). These are divided into seven clades, with the holophyletic Reticulariidae sister to all the others (BPP 1.0; MLB 0.85). The remaining clades are named Liceidae (pro parte) (BPP 1.0; MLB 0.81), new clade 1, new clade 2, Arcyria, Perichaena and “Trichia and allied genera” (Fig. 1 and Fig. 2).


Two-gene phylogeny of bright-spored Myxomycetes (slime moulds, superorder Lucisporidia).

Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M, Cavalier-Smith T - PLoS ONE (2013)

Bayesian phylogeny of Lucisporidia inferred from concatenated alignments of SSU rRNA and EF-1α genes, based on 41 sequences and 1705 positions, with Ceratiomyxa fruticulosa as outgroup.Clades are highlighted as in Fig. 1. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; a dot on the line indicates maximum support in both analyses. In Trichiida, classical families (according to [12]) are indicated by an ellipse with the initials (Arc = Arcyriidae; Dia = Dianemidae; Tri = Trichiidae). The scale bar indicates the fraction of substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646832&req=5

pone-0062586-g002: Bayesian phylogeny of Lucisporidia inferred from concatenated alignments of SSU rRNA and EF-1α genes, based on 41 sequences and 1705 positions, with Ceratiomyxa fruticulosa as outgroup.Clades are highlighted as in Fig. 1. Bayesian posterior probabilities (BPP)/ML bootstrap replicates (MLB) are shown for each branch; a dot on the line indicates maximum support in both analyses. In Trichiida, classical families (according to [12]) are indicated by an ellipse with the initials (Arc = Arcyriidae; Dia = Dianemidae; Tri = Trichiidae). The scale bar indicates the fraction of substitutions per site.
Mentions: We obtained 66 new sequences, 37 SSU and 29 EF-1α for 35 taxa (Table S1). We assembled them with the few publicly available genuine, good-quality lucisporidian sequences in two separate alignments and a combined one. The results of our phylogenetic analyses are presented as a SSU tree (Fig. 1) and a combined SSU+EF-1α tree with fewer taxa (Fig. 2). Both trees presented the same topology, but the second had increased support for the basal branches. On the other hand, the EF-1α gene alone is too conserved to provide enough informative sites, resulting in a tree with mainly unresolved branches, provided in Fig. S2. Both SSU and two-gene trees strongly place Cribrariidae as a monophyletic lineage sister to all other Lucisporidia (Bayesian posterior probabilities (BPP) 1.0; ML bootstrap replicates (MLB) 0.98%). These are divided into seven clades, with the holophyletic Reticulariidae sister to all the others (BPP 1.0; MLB 0.85). The remaining clades are named Liceidae (pro parte) (BPP 1.0; MLB 0.81), new clade 1, new clade 2, Arcyria, Perichaena and “Trichia and allied genera” (Fig. 1 and Fig. 2).

Bottom Line: We discuss possible evolutionary pathways.Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding.We report a new group I intron insertion site for Myxomycetes in one Licea.

View Article: PubMed Central - PubMed

Affiliation: Zoology Department, University of Oxford, Oxford, United Kingdom. afiore-donno6@infomaniak.ch

ABSTRACT
Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Show MeSH
Related in: MedlinePlus