PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

Multi-gene and genomic datasets have become commonplace in the field of phylogenetics, but many of the existing tools are not designed for such datasets, which makes the analysis time-consuming and tedious. We therefore present PhyloSuite, a user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It employs a plugin-based system that integrates a number of useful phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation, with the following features: (i) point-and-click and drag-and-drop graphical user interface, (ii) a workspace to manage and organize molecular sequence data and results of analyses, (iii) GenBank entries extraction and comparative statistics, (iv) a phylogenetic workflow with batch processing capability, (v) elaborate bioinformatic analysis for mitochondrial genomes. The aim of PhyloSuite is to enable researchers to spend more time playing with scientific questions, instead of wasting it on conducting standard analyses. The compiled binary of PhyloSuite is available under the GPL license at https://github.com/dongzhang0725/PhyloSuite/releases, implemented in Python and runs on Windows, Mac OSX and Linux.

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The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera

Genes ◽

10.3390/genes10020108 ◽

2019 ◽

Vol 10 (2) ◽

pp. 108 ◽

Cited By ~ 3

Author(s):

Nan Song ◽

Xin-xin Li ◽

Qing Zhai ◽

Hakan Bozdoğan ◽

Xin-ming Yin

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Genomic Data ◽

Considerable Progress ◽

Mitochondrial Genomes ◽

Special Focus ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Taxonomic Sampling ◽

Inference Methods

The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.

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PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

Molecular Ecology Resources ◽

10.1111/1755-0998.13096 ◽

2019 ◽

Vol 20 (1) ◽

pp. 348-355 ◽

Cited By ~ 104

Author(s):

Dong Zhang ◽

Fangluan Gao ◽

Ivan Jakovlić ◽

Hong Zou ◽

Jin Zhang ◽

...

Keyword(s):

Data Management ◽

Sequence Data ◽

Molecular Sequence Data ◽

Molecular Sequence

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The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽

10.11646/phytotaxa.176.1.22 ◽

2014 ◽

Vol 176 (1) ◽

pp. 219 ◽

Cited By ~ 10

Author(s):

ASHA J. DISSANAYAKE ◽

RUVISHIKA S. JAYAWARDENA ◽

SARANYAPHAT BOONMEE ◽

KASUN M. THAMBUGALA ◽

QING TIAN ◽

...

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

The Family ◽

The Status ◽

Sexual State ◽

Morphological And Molecular Data ◽

Asexual State ◽

Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

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Apertochrysa (Neuroptera: Chrysopidae): A heterogeneric phantom?

Zootaxa ◽

10.11646/zootaxa.4238.1.4 ◽

2017 ◽

Vol 4238 (1) ◽

pp. 58 ◽

Cited By ~ 5

Author(s):

ATSUSHI MOCHIZUKI ◽

CHARLES S. HENRY ◽

PETER DUELLI

Keyword(s):

Type Species ◽

Morphological Traits ◽

New Genus ◽

Sequence Data ◽

New Combination ◽

Wing Venation ◽

Monophyletic Clade ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Group Relationships

The small lacewing genus Apertochrysa comprises species from Africa, Asia and Australia. All lack a tignum, but otherwise resemble distantly related genera. We show that Apertochrysa does not form a monophyletic clade, based on analyses of molecular sequence data and morphological traits such as the presence and shape of the male gonapsis, wing venation, and larval setae. Apertochrysa kichijoi forms a clade with Eremochrysa, Suarius and Chrysemosa, whereas A. albolineatoides belongs to a clade that includes Cunctochrysa. Apertochrysa albolineatoides should become a new combination as Cunctochrysa albolineatoides, while A. kichijoi will have to be transferred to a new genus. The Australian A. edwardsi, the African A. eurydera and the type species of the genus Apertochrysa, A. umbrosa, join the large Pseudomallada group. Relationships of A. umbrosa are less certain, because for it we could amplify only one of the three nuclear genes used in the overall analysis. However, in all morphological traits tested, that species strongly resembles A. edwardsi and A. eurydera and thus is very likely just another exceptional Pseudomallada lacking a tignum. The fate of the genus name Apertochrysa depends on additional molecular and morphological analyses of A. umbrosa.

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The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0034 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2197-2207 ◽

Cited By ~ 82

Author(s):

Peter G. Foster ◽

Cymon J. Cox ◽

T. Martin Embley

Keyword(s):

Sequence Data ◽

Phylogenetic Signal ◽

Amino Acid Sequences ◽

Rate Variation ◽

Molecular Sequence Data ◽

Protein Coding ◽

Molecular Sequence ◽

Heterogeneous Models ◽

Matrix Heterogeneity ◽

Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

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Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽

10.11646/phytotaxa.514.3.5 ◽

2021 ◽

Vol 514 (3) ◽

pp. 247-260

Author(s):

KASUN THAMBUGALA ◽

DINUSHANI DARANAGAMA ◽

SAGARIKA KANNANGARA ◽

THENUKA KODITUWAKKU

Keyword(s):

Sri Lanka ◽

Camellia Sinensis ◽

Endophytic Fungi ◽

Sequence Data ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tea Leaves ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

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Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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A widespread distribution for Arostrilepis tenuicirrosa (Eucestoda: Hymenolepididae) in Myodes voles (Cricetidae: Arvicolinae) from the Palearctic based on molecular and morphological evidence: historical and biogeographic implications

Acta Parasitologica ◽

10.2478/s11686-013-0170-6 ◽

2013 ◽

Vol 58 (4) ◽

Cited By ~ 6

Author(s):

Kurt Galbreath ◽

Kristina Ragaliauskaite ◽

Leonas Kontrimavichus ◽

Arseny Makarikov ◽

Eric Hoberg

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Intraspecific Diversity ◽

Myodes Glareolus ◽

Morphological Evidence ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Biogeographic History ◽

Mitochondrial Cytochrome B ◽

The Republic

AbstractHymenolepidid cestodes in Myodes glareolus from Lithuania and additional specimens originally attributed to Arostrilepis horrida from the Republic of Belarus are now referred to A. tenuicirrosa. Our study includes the first records of A. tenuicirrosa from the European (western) region of the Palearctic, and contributes to the recognition of A. horrida (sensu lato) as a complex of cryptic species distributed broadly across the Holarctic. Specimens of A. tenuicirrosa from Lithuania were compared to cestodes representing apparently disjunct populations in the eastern Palearctic based on structural characters of adult parasites and molecular sequence data from nuclear (ITS2) and mitochondrial (cytochrome b) genes. Morphological and molecular data revealed low levels of divergence between eastern and western populations. Phylogeographic relationships among populations and host biogeographic history suggests that limited intraspecific diversity within A. tenuicirrosa may reflect a Late Pleistocene transcontinental range expansion from an East Asian point of origin.

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Two new genera and twelve new species of Graphidaceae from Puerto Rico: a case for higher endemism of lichenized fungi in islands of the Caribbean?

Phytotaxa ◽

10.11646/phytotaxa.189.1.14 ◽

2014 ◽

Vol 189 (1) ◽

pp. 186 ◽

Cited By ~ 8

Author(s):

JOEL A. MERCADO-DÍAZ ◽

ROBERT LÜCKING ◽

SITTIPORN PARNMEN

Keyword(s):

Puerto Rico ◽

New Species ◽

Sequence Data ◽

New Combination ◽

New Genera ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Biodiversity Knowledge ◽

Three New Species ◽

High Level

Two new genera and twelve new species of Graphidaceae are described from Puerto Rico. The two new genera, Borinquenotrema and Paratopeliopsis, are based on a combination of molecular sequence data and phenotype characters. Borinquenotrema, with the single new species B. soredicarpum, features rounded ascomata developing beneath and persistently covered with soralia and with an internal anatomy reminescent of Carbacanthographis; it is close to the tribe Ocellularieae. Paratopeliopsis, including the single new species P. caraibica, resembles a miniature Topeliopsis but differs in the distinctly farinose thallus and the small, brown ascospores; it is not closely related to the latter genus but belongs in tribe Thelotremateae. The other ten new species belong in the genera Acanthotrema, Clandestinotrema, Compositrema, Fissurina, Ocellularia, and Thalloloma. Acanthotrema alboisidiatum is closely related to A. brasilianum but differs in the short, white isidia resembling insect eggs. Clandestinotrema portoricense has a unique ascospore type with a longitudinal septum only in the proximal cell. Compositrema borinquense resembles a species of Stegobolus but belongs in Compositrema based on sequence data, and is characterized by ascomata with a unique columella composed of thick, irregularly radiating strands. The second new species in this genus, C. isidiofarinosum, differs by its ecorticate, farinose thallus with scattered, corticate isidia and by its small ascomata with inconspicuous columella. The three new species of Fissurina all have 3-septate ascospores and are otherwise characterized by an isidiate thallus and stellate, orange-yellow lirellae (F. aurantiacostellata), a verrucose thallus strongly encrusted with calcium oxalate crystals and white, irregularly branched lirellae (F. crystallifera), and myriotremoid ascomata arranged in short lines (F. monilifera). Ocellularia portoricensis belongs in the core group of Ocellularia and differs from O. cavata in the white medulla and the larger ascospores becoming brown, whereas O. vulcanisorediata produces prominent soralia and immersed ascomata with apically carbonized excipulum and columella and small, transversely septate, hyaline ascospores; it is closely related to O. conformalis. Finally, Thalloloma rubromarginatum resembles T. haemographum in the brownish lirellae with bright red margin but differs from that and other species in the corticate thallus and the norstictic acid chemistry. The new combination Ampliotrema rimosum (Hale) Mercado-Díaz, Lücking & Parnmen is also proposed. Considering the current biodiversity knowledge on this family, the high level of endemism observed in other groups of organisms in the island, and the relatively high number of Graphidaceae described, it is highly likely that at least some of these new taxa are endemic to the island. This view is further supported by the unique features of several of the new species, representing novel characters in the corresponding genera.

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