Embedding CIPRES science gateway capabilities in phylogenetics software environments

Miller, Mark A.; Schwartz, Terri; Pfeiffer, Wayne

doi:10.1145/2484762.2484806

Cited by 20 publications

(17 citation statements)

References 30 publications

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“…Ambiguously aligned regions were excluded, and gaps were treated as missing data. Maximum likelihood phylogenetic analyses were performed in the CIPRES web portal [ 127 ] using RAxML-HPC2 on XSEDE (8.2.12) tool [ 128 ]. The bootstrap analysis for each ML tree was performed with 1000 thorough bootstrap replicates with the same parameter settings using the GTR+G+I substitution model selected by MrModel Test 2.2 [ 129 ].…”

Section: Methodsmentioning

confidence: 99%

A Review of the Fungi That Degrade Plastic

Ekanayaka

Tibpromma

Dai

et al. 2022

JoF

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Plastic has become established over the world as an essential basic need for our daily life. Current global plastic production exceeds 300 million tons annually. Plastics have many characteristics such as low production costs, inertness, relatively low weight, and durability. The primary disadvantage of plastics is their extremely slow natural degradation. The latter results in an accumulation of plastic waste in nature. The amount of plastic waste as of 2015 was 6300 million tons worldwide, and 79% of this was placed in landfills or left in the natural environment. Moreover, recent estimates report that 12,000 million tons of plastic waste will have been accumulated on the earth by 2050. Therefore, it is necessary to develop an effective plastic biodegradation process to accelerate the natural degradation rate of plastics. More than 400 microbes have been identified as capable of plastic degradation. This is the first paper of the series on plastic-degrading fungi. This paper provides a summary of the current global production of plastic and plastic waste accumulation in nature. A list is given of all the plastic-degrading fungi recorded thus far, based on the available literature, and comments are made relating to the major fungal groups. In addition, the phylogenetic relationships of plastic-degrading fungi were analyzed using a combined ITS, LSU, SSU, TEF, RPB1, and RPB2 dataset consisting of 395 strains. Our results confirm that plastic-degrading fungi are found in eleven classes in the fungal phyla Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes, Saccharomycetes, and Sordariomycetes), Basidiomycota (Agaricomycetes, Microbotryomycetes, Tremellomycetes, Tritirachiomycetes, and Ustilaginomy-cetes), and Mucoromycota (Mucoromycetes). The taxonomic placement of plastic-degrading fungal taxa is briefly discussed. The Eurotiomycetes include the largest number of plastic degraders in the kingdom Fungi. The results presented herein are expected to influence the direction of future research on similar topics in order to find effective plastic-degrading fungi that can eliminate plastic wastes. The next publication of the series on plastic-degrading fungi will be focused on major metabolites, degradation pathways, and enzyme production in plastic degradation by fungi.

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Section: Methodsmentioning

confidence: 99%

A Review of the Fungi That Degrade Plastic

Ekanayaka

Tibpromma

Dai

et al. 2022

JoF

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“…BI analyses were conducted in MrBayes 3.2.7a [122] employing the CIPRES Science Gateway [123]. The Mkv model (with rates of the character evolution model set to a lognormal distribution) with one partition was run under the following settings: four separated runs each with one cold and five heated chains, three swaps and heated chain temperature set to 0.09; burn-in fraction set at 0.25 for 10 7 generations sampled every 1000 generations.…”

Section: Methodsmentioning

confidence: 99%

Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria

et al. 2022

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The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.

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“…A majority consensus tree was reconstructed after discarding the first 2,500 sampled trees as burn-in. All analyses were run in the public resource CIPRES Science Gateway v.3.3 (Miller et al 2009).…”

Section: Methodsmentioning

confidence: 99%

Different Perspectives on the Phylogeny of Mordellidae (Coleoptera) Provided by Two Regions of the mtDNA COI Gene

Sanz-laParra,

García-París,

López-Estrada

2023

Annales Zoologici

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The cytochrome c oxidase subunit I (COI) gene has been used broadly as a DNA barcoding region or and relevant molecular marker for phylogenetic reconstruction. The exact region that has been standardized as a universal barcode is the one amplified by Folmer's primers HCO-LCO. Nevertheless, many other primers have been developed for the amplification of the COI gene, among them the Jerry-Pat primers. This paper aims to analyze the performance of different regions of the COI, in particular those amplified by Folmer's and Jerry-Pat primers, on different taxonomic levels by using specimens from a complex and homogeneous beetle family, Mordellidae Latreille, 1802. To achieve this goal, we used two different datasets: Jerry-Pat matrix included 48 sequences from specimens sampled in the field and 19 sequences from GenBank, whereas Folmer's matrix included 91 sequences from BOLD; representing 24 and 85 species respectively. Our results show different properties of both COI regions regarding GC content (3.7% lower in Jerry-Pat fragment), sequence length, interspecific divergence, evolutionary models, and saturation analyses. We also found that the two studied regions of the COI perform differently, showing notable differences in the topology of the reconstructed trees. Finally, a discussion of the pros and cons of each region is provided. This is a first glance at the molecular data of Mordellidae, where we provided a general picture of the evolutionary history of the family and included new sequences for Mediimorda Méquignon, 1946 and Stenalia Mulsant, 1856.

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Embedding CIPRES science gateway capabilities in phylogenetics software environments

Cited by 20 publications

References 30 publications

A Review of the Fungi That Degrade Plastic

A Review of the Fungi That Degrade Plastic

Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria

Different Perspectives on the Phylogeny of Mordellidae (Coleoptera) Provided by Two Regions of the mtDNA COI Gene

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