scholarly journals Phylogenetic position of the Diadromus pulchellus ascovirus DNA polymerase among viruses with large double-stranded DNA genomes

2000 ◽  
Vol 81 (12) ◽  
pp. 3059-3072 ◽  
Author(s):  
Karine Stasiak ◽  
Marie-Véronique Demattei ◽  
Brian A. Federici ◽  
Yves Bigot
Keyword(s):  
Dna Polymerase ◽  
Trichoplusia Ni ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Virus Species ◽  
Diadromus Pulchellus ◽  
The Family ◽  
Virion Structure ◽  
Primary Means ◽  
Insect Viruses

The Ascoviridae is a family of large double-stranded (ds) DNA insect viruses that contains four species, the Spodoptera frugiperda (SfAV1), Trichoplusia ni (TnAV2), Heliothis virescens (HvAV3) and Diadromus pulchellus (DpAV4) ascoviruses. These are unique among insect viruses in that the primary means of transmission among their lepidopteran hosts is generally by being vectored mechanically by hymenopteran parasitoids. Ascoviruses are similar in virion structure, but their relationships with their parasitoid vectors vary from being opportunistic to obligate. Little is known, however, about the relatedness of these viruses to one another or to other large dsDNA viruses. We therefore cloned and sequenced the δ DNA polymerase gene of DpAV4, characterized it and compared it to 59 eukaryotic and viral δ and ϵ DNA polymerases. Phylogenetic analyses based on these genes revealed that the ascoviruses DpAV4 and SfAV1 formed a group of virus species distinct from, but closely related to, species of the family Iridoviridae. Detailed analyses of the relatedness of ascovirus species based on conserved δ DNA polymerase motifs showed two groups within the family Ascoviridae, one containing DpAV4 and the other containing SfAV1, TnAV2 and HvAV3, which was consistent with their host–vector relationships. Despite significant differences in capsid symmetry between ascoviruses and iridoviruses, these results suggest that these viruses may have originated from a common ancestral virus.

scholarly journals The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer from Niphargidae to Pseudoniphargidae

2021 ◽  
Vol 151 ◽  
Author(s):  
Dieter Weber ◽  
Fabio Stoch ◽  
Lee R.F.D. Knight ◽  
Claire Chauveau ◽  
Jean-François Flot
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Ribosomal Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Monotypic Genus ◽  
Centre Of Origin ◽  
Phylogenetic Studies ◽  
The Family

Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469 km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200 km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

The Phylogenetic Position of Crenea in the Lythraceae Based on Molecular Evidence, and the Transfer of Its Two Species to Ammannia

2021 ◽  
Vol 106 ◽  
pp. 325-339
Author(s):  
Shirley A. Graham ◽  
Peter W. Inglis ◽  
Taciana B. Cavalcanti
Keyword(s):  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
The Family ◽  
Mangrove Vegetation ◽  
Molecular Phylogenetic ◽  
Globally Distributed

Crenea Aubl. (Lythraceae) is a ditypic genus of subshrubs occurring in mangrove vegetation on the coasts of northern South America. Phylogenetic analyses based on morphology have offered unresolved and conflicting phylogenetic positions for the genus in the family. This study presents the first molecular sequences for Crenea, from nrITS, rbcL, trnL, trnL-F, and matK regions. Molecular phylogenetic analyses find full support for Crenea within Ammannia L., a relationship not previously recognized. Ammannia is a globally distributed genus of terrestrial to amphibious herbs mostly occurring in freshwater marshes and wetlands. It was recently reconfigured based on phylogenetic evidence to include the genera Nesaea Comm. ex Kunth and Hionanthera A. Fern. & Diniz. The transfer of Crenea to Ammannia further extends the morphological, ecological, and biogeographical diversity of Ammannia and provides the final evidence defining Ammannia as a monophyletic lineage of the Lythraceae. A revised circumscription of Ammannia s.l. adds several new morphological character states and the first species in the genus restricted to mangrove vegetation. Two changes in taxonomic status are made: Ammannia maritima (Aubl.) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov., and Ammannia patentinervius (Koehne) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov. The new combinations are described, a list of exsiccatae examined is provided, and the effects of the reconfiguration to the morphology and biogeography of the genus are detailed.

scholarly journals Phylogenetic placement of Paratrichaptum and reconsideration of Gloeophyllales

2020 ◽  
Vol 5 (1) ◽  
pp. 119-130 ◽  
Author(s):  
C.-C. Chen ◽  
B. Cao ◽  
T. Hattori ◽  
B.-K. Cui ◽  
C.-Y. Chen ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Brown Rot ◽  
Phylogenetic Position ◽  
Nuclear Rdna ◽  
Protein Coding ◽  
Phylogenetic Placement ◽  
The Family ◽  
Ancestral States ◽  
Relic Species

Paratrichaptum accuratum is a large conspicuous polypore fungus growing on dead or living angiosperm trees in subtropical-boreal areas of China, Indonesia, Japan, and Taiwan. The present study places P. accuratum in the family Gloeophyllaceae that belongs to the order Gloeophyllales within Agaricomycetes (Basidiomycota), based on evidence derived from morphological and ecological characteristics, and phylogenetic analyses of sequences of nuclear rDNA regions (5.8S, nuc 18S, nuc 28S) and protein-coding genes (rpb1, rpb2, and tef1). The analyses presented in this study also give strong support for including Jaapia in Gloeophyllaceae and Gloeophyllales. Thus, the names Jaapiaceae and Jaapiales are considered here as synonyms of Gloeophyllaceae and Gloeophyllales. Since Paratrichaptum represents the earliest diverging lineage in Gloeophyllales, pileate basidiocarps and brown rot appear to be ancestral states of Gloeophyllales. Paratrichaptum accuratum may represent a relic species, according to its phylogenetic position, peculiar distribution pattern and rare occurrence.

scholarly journals Phylogeny and morphology of genus Nephrocytium (Sphaeropleales, Chlorophyceae, Chlorophyta) from China

Phytotaxa ◽  
2017 ◽  
Vol 319 (1) ◽  
pp. 84 ◽  
Author(s):  
XUDONG LIU ◽  
HUAN ZHU ◽  
BENWEN LIU ◽  
GUOXIANG LIU ◽  
ZHENGYU HU
Keyword(s):  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Taxonomic Position ◽  
Phylogenetic Position ◽  
Phytoplankton Communities ◽  
Close Phylogenetic Relationship ◽  
The Family ◽  
Close Relationship ◽  
Molecular Phylogenetic

The genus Nephrocytium Nägeli is a common member of phytoplankton communities that has a distinctive morphology. Its taxonomic position is traditionally considered to be within the family Oocystaceae (Trebouxiophyceae). However, research on its ultrastructure is rare, and the phylogenetic position has not yet been determined. In this study, two strains of Nephrocytium, N. agardhianum Nägeli and N. limneticum (G.M.Smith) G.M.Smith, were identified and successfully cultured in the laboratory. Morphological inspection by light and electron microscopy and molecular phylogenetic analyses were performed to explore the taxonomic position. Ultrastructure implied a likely irregular network of dense and fine ribs on the surface of the daughter cell wall that resembled that of the genus Chromochloris Kol & Chodat (Chromochloridaceae). Phylogenetic analyses revealed that Nephrocytium formed an independent lineage in the order Sphaeropleales (Chlorophyceae) with high support values and a close phylogenetic relationship with Chromochloris. Based on combined morphological, ultrastructural and phylogenetic data, we propose a re-classification of Nephrocytium into Sphaeropleales, sharing a close relationship with Chromochloris.

scholarly journals The phylogenetic position of the solitary zoanthid genus Sphenopus (Cnidaria: Hexacorallia)

2012 ◽  
Vol 81 (1) ◽  
pp. 43-54 ◽  
Author(s):  
James D. Reimer ◽  
Meifang Lin ◽  
Takuma Fujii ◽  
David J.W. Lane ◽  
Bert W. Hoeksema
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Solid Substrate ◽  
Ancestral State Reconstruction ◽  
Phylogenetic Position ◽  
Ancestral State ◽  
State Reconstruction ◽  
Unique Character ◽  
The Family ◽  
Southern Taiwan

The zoanthid genus Sphenopus (Cnidaria: Anthozoa: Zoantharia), like many other brachycnemic zoanthids, is found in shallow subtropical and tropical waters, but is uniquely unitary (solitary, monostomatous), azooxanthellate, and free-living. With sparse knowledge of its phylogenetic position, this study examines the phylogenetic position of Sphenopus within the family Sphenopidae utilizing specimens from southern Taiwan and Brunei collected in 1999-2011, and furthermore analyzes the evolution of its unique character set via ancestral state reconstruction analyses. Phylogenetic analyses surprisingly show Sphenopus to be phylogenetically positioned within the genus Palythoa, which is colonial (polystomatous), zooxanthellate, and attached to solid substrate. Ancestral state reconstruction strongly indicates that the unique characters of Sphenopus have evolved recently within Palythoa and only in the Sphenopuslineage. These results indicate that zoanthid body plans can evolve with rapidity, as in some other marine invertebrates, and that the traditional definitions of zoanthid genera may need reexamination.

Phylogenetic position of Sphaerospora testicularis and Latyspora scomberomori n. gen. n. sp. (Myxozoa) within the marine urinary clade

Parasitology ◽  
2010 ◽  
Vol 138 (3) ◽  
pp. 381-393 ◽  
Author(s):  
PAVLA BARTOŠOVÁ ◽  
MARK A. FREEMAN ◽  
HIROSHI YOKOYAMA ◽  
MONICA CAFFARA ◽  
IVAN FIALA
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dicentrarchus Labrax ◽  
Sensu Stricto ◽  
Phylogenetic Position ◽  
Species Cluster ◽  
The Family ◽  
Sutural Line ◽  
Taxonomic Changes

SUMMARYAn amendment of the family Sinuolineidae (Myxosporea) is proposed in order to include a newly described genus Latyspora n. gen. The type species Latyspora scomberomori n. gen. n. sp. is a coelozoic parasite in the kidney tubules of Scomberomorus guttatus. In addition to the morphological and molecular characterization of L. scomberomori n. gen. n. sp., we also present novel SSU rDNA data on Sphaerospora testicularis, a serious parasite of Dicentrarchus labrax. Performed phylogenetic analyses revealed that both species cluster within the marine urinary clade encompassing the representatives with a shared insertion within their V4 SSU rRNA region and grouping according to the shape of their spores’ sutural line and their similar tissue tropism in the host. Sphaerospora testicularis is the closest relative to Parvicapsula minibicornis within the Parvicapsula subclade and L. scomberomori n. gen. n. sp. is the basal species of the Zschokkella subclade. The phylogenetic position of S. testicularis, outwith the basal Sphaerospora sensu stricto clade, and its morphology suggest it being a non-typical Sphaerospora. The sequence data provided on S. testicularis can help in future revisions of the strongly polyphyletic genus Sphaerospora. We recommend re-sequencing of several sphaerosporids as an essential step before such taxonomic changes are accomplished.

A new predatory leech from Vietnam (Hirudinida : Arhynchobdellida : Salifidae): its phylogenetic position with comments on the classification of the family

2015 ◽  
Vol 29 (5) ◽  
pp. 473 ◽  
Author(s):  
Takafumi Nakano ◽  
Son Truong Nguyen
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
The Family ◽  
Morphological And Molecular Data ◽  
First Time

The family Salifidae is a predaceous leech taxon in the suborder Erpobdelliformes. Although Salifidae is widely distributed in the African, Oriental, Indo-Malayan, Sino-Japanese and Australasian regions, the phylogenetic relationships of the family Salifidae have never been tested using molecular data obtained from leeches collected from the family distributional range. A salifid species was collected for the first time in Vietnam, and relevant morphological and molecular data are presented here. Because the Vietnamese salifid species possesses unique morphological characteristics among the known salifid species, this species is herein described as a new species, Salifa motokawai, sp. nov. Phylogenetic analyses based on nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers demonstrate that the Vietnamese salifid species is a close congener with the African Salifa perspicax and the Malagasy Linta be. Furthermore, molecular data revealed non-monophyly of the Asian salifid leeches. According to the observed phylogenetic relationships and morphological characteristics of the Vietnamese Salifa motokawai, sp. nov., the current classification of salifid taxa should be revised.

scholarly journals Novel Mammalian Herpesviruses and Lineages within the Gammaherpesvirinae: Cospeciation and Interspecies Transfer

2008 ◽  
Vol 82 (7) ◽  
pp. 3509-3516 ◽  
Author(s):  
Bernhard Ehlers ◽  
Güzin Dural ◽  
Nezlisah Yasmum ◽  
Tiziana Lembo ◽  
Benoit de Thoisy ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Mammalian Host ◽  
Virus Species ◽  
Branching Pattern ◽  
Long Distance ◽  
Bayesian Monte Carlo ◽  
Long Distance Pcr

ABSTRACT Novel members of the subfamily Gammaherpesvirinae, hosted by eight mammalian species from six orders (Primates, Artiodactyla, Perissodactyla, Carnivora, Scandentia, and Eulipotyphla), were discovered using PCR with pan-herpesvirus DNA polymerase (DPOL) gene primers and genus-specific glycoprotein B (gB) gene primers. The gB and DPOL sequences of each virus species were connected by long-distance PCR, and contiguous sequences of approximately 3.4 kbp were compiled. Six additional gammaherpesviruses from four mammalian host orders (Artiodactyla, Perissodactyla, Primates, and Proboscidea), for which only short DPOL sequences were known, were analyzed in the same manner. Together with available corresponding sequences for 31 other gammaherpesviruses, alignments of encoded amino acid sequences were made and used for phylogenetic analyses by maximum-likelihood and Bayesian Monte Carlo Markov chain methods to derive a tree which contained two major loci of unresolved branching details. The tree was rooted by parallel analyses that included alpha- and betaherpesvirus sequences. This gammaherpesvirus tree contains 11 major lineages and presents the widest view to date of phylogenetic relationships in any subfamily of the Herpesviridae, as well as the most complex in the number of deep lineages. The tree's branching pattern can be interpreted only in part in terms of the cospeciation of virus and host lineages, and a substantial incidence of the interspecies transfer of viruses must also be invoked.

The first troglobitic species of Gymnobisiidae (Pseudoscorpiones : Neobisioidea), from Table Mountain (Western Cape Province, South Africa) and its phylogenetic position

2016 ◽  
Vol 30 (1) ◽  
pp. 75 ◽  
Author(s):  
Mark S. Harvey ◽  
Joel A. Huey ◽  
Mia J. Hillyer ◽  
Erin McIntyre ◽  
Gonzalo Giribet
Keyword(s):  
South Africa ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Strong Support ◽  
Phylogenetic Position ◽  
28S Rrna ◽  
Cave System ◽  
Table Mountain ◽  
The Family ◽  
Afrotropical Region

Fully troglobitic pseudoscorpions are rare in the Afrotropical Region, and we explored the identity and phylogenetic relationships of specimens of a highly modified troglobite of the family Gymnobisiidae in the dark zone of the Wynberg Cave system, on Table Mountain, South Africa. This large pseudoscorpion – described as Gymnobisium inukshuk Harvey & Giribet, sp. nov. – lacks eyes and has extremely long appendages, and has been found together with other troglobitic fauna endemic only to this cave system. Phylogenetic analyses using the nuclear ribosomal genes 18S rRNA and 28S rRNA and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I unambiguously place the new species with other surface Gymnobisium from South Africa. This placement receives strong support and is stable to analytical treatments, including static and dynamic homology, parsimony and maximum likelihood, and data removal for ambiguously aligned sites. This species is the first troglobitic species of the family and one of the most highly modified pseudoscorpions from the Afrotropical Region. http://zoobank.org/urn:lsid:zoobank.org:pub:5227092B-A64B-4DB3-AD90-F474F0BA6AED

Thelopsis challenges the generic circumscription in the Gyalectaceae and brings new insights to the taxonomy of Ramonia

2021 ◽  
Vol 53 (1) ◽  
pp. 45-61
Author(s):  
Damien Ertz ◽  
Neil Sanderson ◽  
Marc Lebouvier
Keyword(s):  
Phylogenetic Analyses ◽  
Saint Paul ◽  
Morphological Characters ◽  
Systematic Position ◽  
Sister Species ◽  
Phylogenetic Position ◽  
Generic Type ◽  
The Family ◽  
Fungal Dna ◽  
First Time

AbstractThe genus Thelopsis was classified in the family Stictidaceae but its systematic position has never been investigated by molecular methods. In order to determine its family placement and to test its monophyly, fungal DNA of recent collections of Thelopsis specimens was sequenced. Phylogenetic analyses using nuLSU, RPB2 and mtSSU sequences reveal that members of Thelopsis form a monophyletic group within the genus Gyalecta as currently accepted. The placement of Thelopsis, including the generic type T. rubella, within the genus Gyalecta challenges the generic circumscription of this group because Thelopsis is well recognized by the combination of morphological characters: perithecioid ascomata, well-developed periphysoids, polysporous asci and small, few-septate ellipsoid-oblong ascospores. The sterile sorediate Opegrapha corticola is also placed in the Gyalectaceae as sister species to Thelopsis byssoidea + T. rubella. Ascomata of O. corticola are illustrated for the first time and support its placement in the genus Thelopsis. The hypothesis that O. corticola might represent the sorediate fertile morph of T. rubella is not confirmed because the species is phylogenetically and morphologically distinct. Thelopsis is recovered as polyphyletic, with T. melathelia being placed as sister species to Ramonia. The new combinations Thelopsis corticola (Coppins & P. James) Sanderson & Ertz comb. nov. and Ramonia melathelia (Nyl.) Ertz comb. nov. are introduced and a new species of Gyalecta, G. amsterdamensis Ertz, is described from Amsterdam and Saint-Paul Islands, characterized by a sterile thallus with discrete soralia. Petractis luetkemuelleri and P. nodispora are accommodated in the new genus Neopetractis, differing from the generic type (P. clausa) by having a different phylogenetic position and a different photobiont. Francisrosea bicolor Ertz & Sanderson gen. & sp. nov. is described for a sterile sorediate lichen somewhat similar to Opegrapha corticola but having an isolated phylogenetic position as sister to a clade including Gyalidea praetermissa and the genera Neopetractis and Ramonia. Gyalecta farlowii, G. nidarosiensis and G. carneola are placed in a molecular phylogeny for the first time. The taxonomic significance of morphological characters in Gyalectaceae is discussed.

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