The general stochastic model of nucleotide substitution

166

121

Previous environmental surveys of eukaryotic diversity using the small subunit ribosomal RNA (SSU rRNA) gene have revealed many clone sequences that branch near the base of Fungi. In this work, we demonstrate that many of these sequences, including those of the environmental clade LKM11, form a monophyletic and strongly supported group that also includes two sequences derived from the parasitic genus Rozella. This novel clade, called here ''Rozellida'', is the deepest branch of true fungi so far identified, and appears to be extremely diverse in the environment.

Section: Methodsmentioning

confidence: 99%

“…The first 5000 trees were discarded as the burn in. In addition, a maximum likelihood analysis was carried out using the program TREEFINDER (Jobb et al 2004), applying a GTR+G+I model of nucleotide substitution (Rodríguez et al 1990). All necessary parameters were estimated from the data sets.…”

Section: Methodsmentioning

confidence: 99%

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

Lara¹,

Moreira²,

López‐García³

2010

166

121

“…These analyses were performed with the software MrBayes v. 3.1.2 (Huelsenbeck and Ronquist 2001). The model chosen here was the GTR model of substitution (Lanave et al 1984;Rodriguez et al 1990), the number of invariable sites being estimated, and a gamma-shaped distribution of variable sites with five rate categories. The values of alpha and the proportions of invariable sites, were respectively, 0.467 and 0.269, for the general Tubulina tree, 0.170 and 0.816 for the short-branching arcellinids, and 0.744 and 0.705 for the ''core Nebelas'' tree.…”

Section: Apodera Vasmentioning

confidence: 99%

Ribosomal RNA Genes Challenge the Monophyly of the Hyalospheniidae (Amoebozoa: Arcellinida)

Lara

Heger

Ekelund

et al. 2008

To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphological characters of uncertain value, which causes confusion in the phylogeny, taxonomy and the debate on cosmopolitanism of free-living protists. Here we present a SSU rRNA-based phylogeny of the Hyalospheniidae including the most common species. Similar to the filose testate amoebae of the order Euglyphida the most basal clades have a terminal aperture; the ventral position of the pseudostome appears to be a derived character. Family Hyalospheniidae appears paraphyletic and is separated into three clades: (1) Heleopera sphagni, (2) Heleopera rosea and Argynnia dentistoma and (3) the rest of the species from genera Apodera, Hyalosphenia, Porosia and Nebela. Our data support the validity of morphological characters used to define species among the Hyalospheniidae and even suggest that taxa described as varieties may deserve the rank of species (e.g. N. penardiana var. minor). Finally our results suggest that the genera Hyalosphenia and Nebela are paraphyletic, and that Porosia bigibbosa branches inside the main Nebela clade.

“…Four simultaneous chains were run for 1,000,000 generations, and 10,000 trees were sampled, 50 of which were discarded as the burn-in. The model chosen here was the GTR model of substitution, with five rate categories (Lanave et al 1984;Rodriguez et al 1990), the number of invariable sites being estimated, and a gamma-shaped distribution of variable sites. Posterior probabilities at all nodes were estimated from the 9950 remaining trees.…”

Section: Article In Pressmentioning

confidence: 99%

SSU rRNA Reveals a Sequential Increase in Shell Complexity Among the Euglyphid Testate Amoebae (Rhizaria: Euglyphida)

Lara

Heger

Mitchell

et al. 2007

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a study aiming to fill several important gaps and better understand the relationships among the main euglyphid testate amoebae and the evolutionary steps that led to the present diversity at a higher level. We obtained new SSU rRNA sequences from five genera and seven species. This new phylogeny obtained shows that (1) the clade formed by species of genera Assulina and Placocista branches unambiguously at the base of the subclade of Euglyphida comprising all members of the family Trinematidae and genus Euglypha, (2) family Trinematidae (Trachelocorythion, Trinema, and Corythion) branches as a sister group to genus Euglypha, (3) three newly sequenced Euglypha species (E. cf. ciliata, E. penardi, and E. compressa) form a new clade within the genus. Since our results show that Assulina and Placocista do not belong to the Euglyphidae (unless the Trinematidae are also included in this family), we propose the creation of a new family named Assulinidae. Consequently, we give a family status to the genera Euglypha and (tentatively) Scutiglypha, which become the new family Euglyphidae. The evolutionary pattern suggested by SSU rRNA phylogeny shows a clear tendency towards increasing morphological complexity of the shell characterised by changes in the symmetry (migration of the aperture to a ventral position and/or compression of the shell) and the appearance of specialised scales at the aperture (in families Trinematidae and Euglyphidae).