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.

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

scholarly journals Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Wei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Louse Species ◽  
Mt Genome ◽  
Rna Genes

Abstract Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659 bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract

scholarly journals Highly Rearranged Mitochondrial Genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from Endangered Eagles

2021 ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Ya Tu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

Abstract Background: Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is available about the mt genomes from the family Philopteridae that is the most species-rich family within the suborder Ischnocera. Methods: Herein, we use next-generation sequencing to decode the mt genome sequences of Falcolipeurus suturalis and compared it with the mt genome sequences of F. quadripustulatus. Phylogenetic relationship of the concatenated amino acid sequence data for 13 protein-coding genes of the two Falcolipeurus lice and selected members of the family Philopteridae was evaluated using Bayesian inference (BI).Results: The complete mt genome of F. suturalis is a circular double-stranded DNA molecule of 16,659 bp, and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, as well as three putative non-coding regions. The gene order in F. suturalis mt genome was rearranged compared with that of F. quadripustulatus, and they were radical different from other louse species and the ancestral insect. Phylogenetic analyses revealed that the clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0), and the genus Falcolipeurus is more closely related to the genus Ibidoecus than to other genera (Bayesian posterior probabilities=1.0). Conclusions: These novel datasets will help to better understand the gene rearrangements and phylogenetic position of Falcolipeurus and provide useful genetic markers for systematics and phylogenetic studies of bird lice.

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.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae)

2010 ◽  
Vol 61 (9) ◽  
pp. 980 ◽  
Author(s):  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Stuart J. Rowland ◽  
Peter R. Baverstock
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Allopatric Populations ◽  
Murray Darling Basin ◽  
Murray Cod ◽  
Australian Freshwater

Determining the phylogenetic and taxonomic relationships among allopatric populations can be difficult, especially when divergence is recent and morphology is conserved. We used mitochondrial sequence data from the control region and three protein-coding genes (1253 bp in total) and genotypes determined at 13 microsatellite loci to examine the evolutionary relationships among Australia’s largest freshwater fish, the Murray cod, Maccullochella peelii peelii, from the inland Murray–Darling Basin, and its allopatric sister taxa from coastal drainages, the eastern freshwater cod, M. ikei, and Mary River cod, M. peelii mariensis. Phylogenetic analyses provided strong support for taxon-specific clades, with a clade containing both of the eastern taxa reciprocally monophyletic to M. peelii peelii, suggesting a more recent common ancestry between M. ikei and M. peelii mariensis than between the M. peelii subspecies. This finding conflicts with the existing taxonomy and suggests that ancestral Maccullochella crossed the Great Dividing Range in the Pleistocene and subsequently diverged in eastern coastal drainages. Evidence from the present study, in combination with previous morphological and allozymatic data, demonstrates that all extant taxa are genetically and morphologically distinct. The taxonomy of Maccullochella is revised, with Mary River cod now recognised as a species, Maccullochella mariensis, a sister species to eastern freshwater cod, M. ikei. As a result of the taxonomic revision, Murray cod is M. peelii.

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.

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