raxmlGUI: a graphical front-end for RAxML

Silvestro, Daniele; Michalak, Ingo

doi:10.1007/s13127-011-0056-0

Cited by 2,579 publications

(1,530 citation statements)

References 13 publications

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“…Loci were analyzed in concatenation using Maximum Likelihood (ML) and Bayesian Inference (BI). The ML analyses were performed using RAxMLGUI (Silvestro & Michalak, 2012) using the ML ? thorough bootstrap option with 100 runs and autoMRE bootstrapping.…”

Section: Resultsmentioning

confidence: 99%

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

et al. 2017

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Megalonaias is the most geographically widespread genus of the subfamily Ambleminae and is distributed across much of the eastern half of North America, from Minnesota to Nicaragua. Despite the large geographic distribution, the species-level diversity of Megalonaias is quite depauperate (2 spp.), suggesting the genus may not be constrained by the same physical, ecological, or physiological barriers that limit dispersal in many other amblemines. However, this hypothesis is contingent on the assumption that the current taxonomy of Megalonaias accurately reflects its evolutionary history, which remains incompletely understood due to the marginalization of Mesoamerican populations in systematic research. Using one mitochondrial (COI) and one nuclear marker (ITS1) sequenced from 41 individuals distributed across both the Nearctic and Mesoamerican ecoregions, we set out to better understand the species boundaries and genetic diversity within Megalonaias. The reconstructed molecular phylogeny and the observed genetic diversity suggests that Megalonaias is a monotypic genus and that Megalonaias nickliniana, currently considered a federally endangered species, is not a valid species. These results are discussed in the context of their systematic and conservation implications, as well as how the unusual life history strategy of Megalonaias may be influencing its molecular diversity.

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Section: Resultsmentioning

confidence: 99%

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

et al. 2017

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“…Tree scores, including tree length, consistency index (CI), retention index (RI) and rescaled consistency index (RC), also were calculated. The ML analysis was done with raxmlGUI (Silvestro and Michalak 2012), under a GTRGAMMA model. The BS supports and trees were obtained by running rapid bootstrap analysis of 1000 pseudoreplicates followed by a search for the tree with the highest likelihood.…”

Section: Methodsmentioning

confidence: 99%

First comprehensive phylogenetic analysis of the genus Erysiphe (Erysiphales, Erysiphaceae) II: the Uncinula lineage

Takamatsu¹,

Ito²,

Shiroya

et al. 2015

Mycologia

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Phylogenetic relationships of the Uncinula lineage, which is the basal group in the genus Erysiphe, were investigated with 167 sequences of nuc ITS1-5. 8S-ITS2 and the 28S rDNA regions. Backbone tree analyses with six datasets and two tree-constructing methods revealed that the Uncinula lineage is divided into seven distinct clades. Clades 1-5 each contained a representative powdery mildew species, namely E. australiana in Clade 1, E. liquidambaris in Clade 2, E. adunca in Clade 3, E. fraxinicola in Clade 4 and E. actinidiae in Clade 5. Clade 6 comprises 71 sequences including the Microsphaera lineage and 17 species of the Uncinula lineage, such as E. carpinicola, E. carpinilaxiflorae, E. miyabei, E. glycines and E. necator. Topology tests supported the Microsphaera lineage forming a monophyletic clade in Clade 6, suggesting that Microsphaera-type appendages appeared only once in this clade to diverge into the Microsphaera lineage. Clade 7 consists of 72 sequences containing 30 species, including species of sects. Californiomyces and Typhulochaeta, four species from Nothofagus, species of sect. Erysiphe parasitising herbaceous plants belonging to the Asteraceae, Rosaceae and Saxifragaceae. Molecular clock analysis suggests that the major seven clades appeared 50-30 million years ago (Ma) in the Paleogene Period. The Microsphaera lineage may have split from the Uncinula lineage at the boundary of the Paleogene and Neogene, when appendages with dichotomously branched tips appeared. The clade of the species on Nothofagus split from the northern hemisphere species about 20-10 million years ago (Ma) in the Miocene Epoch, and host-shift from trees to herbs also might have occurred in this period.

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“…For ML analyses the program RAxML 7.3.0 (Stamatakis, 2006) was operated via raxmlGUI version 1.0 (Silvestro and Michalak, 2011). Settings were ML+ thorough bootstrap, 100 runs, 1000 replicates, a GTR model of substitution with a GAMMA (Yang, 1994) model of rate heterogeneity among sites and a proportion of invariable sites (this option was chosen because modelling the parameter 'invariable sites' was recommended by the best-fit models obtained for COI, see below).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Molecular phylogeny of the Notostraca

Korn

Rabet

Ghate³

et al. 2013

Molecular Phylogenetics and Evolution

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a b s t r a c tWe used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minor Trusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensis Gand et al., 1997.

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raxmlGUI: a graphical front-end for RAxML

Cited by 2,579 publications

References 13 publications

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

First comprehensive phylogenetic analysis of the genus Erysiphe (Erysiphales, Erysiphaceae) II: the Uncinula lineage

Molecular phylogeny of the Notostraca

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