EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

Zhang, Huangkai; Gao, Shenghan; Lercher, Martin J.; Hu, Songnian; Chen, Wei‐Hua

doi:10.1093/nar/gks576

Cited by 379 publications

(278 citation statements)

References 18 publications

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“…This trimmed phylogeny was used to define the evolutionary relationships and distances between species for the phylogenetic correction of the raw data. Characters were mapped onto the trimmed Huang (2012) phylogeny using Mesquite 2.75 (Maddison & Maddison 2011) and visualized with Evolview (Zhang et al 2012). Homoplasy in the categorical character-state and bleaching data was assessed using the Retention Index (RI, ranges from 0−1, where 0 is homoplastic) in Mesquite.…”

Section: Methodsmentioning

confidence: 99%

Physiological integration of coral colonies is correlated with bleaching resistance

Swain¹,

Bold²,

Osborn³

et al. 2018

Mar. Ecol. Prog. Ser.

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Inter-module physiological integration of colonial organisms can facilitate colony-wide coordinated responses to stimuli that strengthen colony fitness and stress resistance. In scleractinian corals, whose colonial integration ranges from isolated polyps to a seamless continuum of polyp structures and functions, this coordination improves re sponses to injury, predation, disease, and stress and may be one of the indications of an evolutionary origin of Symbiodinium symbiosis. However, observations of species-specific coral bleaching patterns suggest that highly integrated coral colonies may be more susceptible to thermal stress, and support the hypothesis that communication pathways between highly integrated polyps facilitate the dissemination of toxic byproducts created during the bleaching response. Here we reassess this hypothesis by parameterizing an integration index using 7 skeletal features that have been historically employed to infer physiological integration. We examine the relationship between this index and bleaching response across a phylogeny of 88 diverse coral species. Correcting for phylogenetic relationships among species in the analyses reveals significant patterns among species characters that could otherwise be obscured in simple crossspecies comparisons using standard statistics, whose assump tions of independence are violated by the shared evolutionary history among species. Similar to the observed benefits of in creased coloniality for other types of stressors, the results indicate a significantly reduced bleaching response among coral species with highly integrated colonies.KEY WORDS: Colony integration · Colony form · Coral bleaching · Phylogenetically corrected analysis Stylized representation of the phylogeny and morphologies that allowed detection of decreased thermal bleaching with greater polyp integration (coloniality).

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Section: Methodsmentioning

confidence: 99%

Physiological integration of coral colonies is correlated with bleaching resistance

Swain¹,

Bold²,

Osborn³

et al. 2018

Mar. Ecol. Prog. Ser.

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“…The reliability for the internal branches of NJ was assessed using the bootstrapping method (1000 bootstrap replicates). Graphical representation and editing of the phylogenetic trees were performed with EvolView (Zhang et al, 2012). The accession numbers and geographic origins of the isolates used in the phylogenetic analysis are shown in the phylogenetic trees.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Detection and phylogenetic characterization of Theileria spp. and Anaplasma marginale in Rhipicephalus bursa in Portugal

Ferrolho

Antunes

Santos

et al. 2016

Ticks and Tick-borne Diseases

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a b s t r a c tTicks are obligatory blood-sucking arthropod (Acari:Ixodida) ectoparasites of domestic and wild animals as well as humans. The incidence of tick-borne diseases is rising worldwide, challenging our approach toward diagnosis, treatment and control options. Rhipicephalus bursa Canestrini and Fanzago, 1877, a two-host tick widely distributed in the Palearctic Mediterranean region, is considered a multi-host tick that can be commonly found on sheep, goats and cattle, and occasionally on horses, dogs, deer and humans. R. bursa is a species involved in the transmission of several tick-borne pathogens with a known impact on animal health and production. The aim of this study was to estimate R. bursa prevalence in Portugal Mainland and circulating pathogens in order to contribute to a better knowledge of the impact of this tick species. Anaplasma marginale and Theileria spp. were detected and classified using phylogenetic analysis. This is the first report of Theileria annulata and Theileria equi detection in R. bursa ticks feeding on cattle and horses, respectively, in Portugal. This study contributes toward the identification of currently circulating pathogens in this tick species as a prerequisite for developing future effective anti-tick control measures.

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“…Similar sequences from NCBI were also used for the phylogenetic analysis, which were redeemed from the environment where the source material was collected to check the relationship between the isolates from T. elegans and the bacteria of another environment. For generation of the phylogenetic tree, EvolView (Zhang et al, 2012) was used.…”

Section: Estimation Of Genetic Distance Of the Isolatesmentioning

confidence: 99%

Phylogenetic analysis of endophytic bacterial isolates from leaves of the medicinal plant Trichilia elegans A. Juss. (Meliaceae)

Rhoden

García

Silva³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Various organisms such as fungi and bacteria can live inside plants, inhabiting the aerial parts (primarily the leaves) without causing damage. These microorganisms, called endophytes, produce an extensive variety of compounds that can be useful for medical and agronomic purposes. Trichilia elegans A. Juss., belonging to the Meliaceae family, shows wide dispersion in South America, and phytochemical analyses from these plants and endophyte isolates have shown biological activity. Accordingly, the aim of this study was to verify the diversity of bacterial endophytes from T. elegans using partial sequencing of 16S rRNA, followed by phylogenetic analysis. Isolation was performed by cutting the leaves, after disinfection with 5% sodium hypochlorite (NaOCl), in 1-2-mm 2 fragments, which were equally placed on dishes containing TSA and fungicide BENLATE at 75 μg/mL. All dishes were incubated at 28°C in the biochemical oxygen demand system for 5 days and periodically checked. Afterwards, the colonization frequency (%) was determined: (number of fragments colonized by bacteria/total number of fragments) x 100. Three isolations between September 2011 and March 2012 were performed; the growth frequency ranged between 1.6 and 13.6%. Following sequencing of 16S rRNA and phylogenetic analysis, the genera identified were: Staphylococcus, Bacillus, Microbacterium, Pseudomonas, and Pantoea. These results will provide important knowledge on the diversity of endophytic bacteria inhabiting medicinal plants, and a better understanding of the microbiome of T. elegans would reinforce the necessity of endophyte studies with a focus on their future applications in biotechnological areas of agriculture, medicine, and the environment.

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EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

Cited by 379 publications

References 18 publications

Physiological integration of coral colonies is correlated with bleaching resistance

Physiological integration of coral colonies is correlated with bleaching resistance

Detection and phylogenetic characterization of Theileria spp. and Anaplasma marginale in Rhipicephalus bursa in Portugal

Phylogenetic analysis of endophytic bacterial isolates from leaves of the medicinal plant Trichilia elegans A. Juss. (Meliaceae)

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