scholarly journals Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7662 ◽  
Author(s):  
Xiangyu Tian ◽  
Junwei Ye ◽  
Yu Song
Keyword(s):  
Species Identification ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Variable Regions ◽  
The Core ◽  
The Family ◽  
Close Relationship ◽  
Lindera Obtusiloba ◽  
Hypervariable Loci

Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.

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.

Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 1. Evidence for the Plocamiales ord.nov.

1994 ◽  
Vol 72 (9) ◽  
pp. 1250-1263 ◽  
Author(s):  
G. W. Saunders ◽  
G. T. Kraft
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Chain Reaction ◽  
Small Subunit Rrna Gene ◽  
New Information ◽  
The Family ◽  
Close Relationship ◽  
Polymerase Chain

Nucleotide sequences of the nuclear, small-subunit (SSU) ribosomal RNAs, as inferred from polymerase chain reaction (PCR)-amplified products, are presented for Areschougia congesta (Turner) J. Agardh (Solieriaceae), Dasyphloea insignis Montagne (Dumontiaceae), Sarcothalia crassifolia (C. Agardh) Edyvane & Womersley (Gigartinaceae), Nizymenia australis Sonder (Nizymeniaceae), Phacelocarpus peperocarpos (Poiret) Wynne, Ardré & Silva (Phacelocarpaceae), Plocamiocolax pulvinata Setchell, Plocamium angustum (J. Agardh) J.D. Hooker, Plocamium cartilagineum (Linnaeus) Dixon (Plocamiaceae), Rhodymenia linearis J. Agardh (Rhodymeniaceae), and Sphaerococcus coronopifolius Stackhouse (Sphaerococcaceae). Phylogenetic analyses of the SSU sequences between the Plocamiaceae and members of the Sphaerococcaceae, Phacelocarpaceae, and Nizymeniaceae, with which the Plocamiaceae has been associated historically, show SSU differences of between 87 and 105 nucleotides and do not indicate a close relationship. A review of anatomical knowledge of the Plocamiaceae and Pseudoanemoniaceae and new information on vegetative and tetrasporangial development in Plocamium and Plocamiocolax are presented to buttress a case for the Plocamiales ord.nov. Representatives of the Nizymeniaceae and Phacelocarpaceae differ from one another by only nine nucleotides, suggesting that these two taxa are very closely related and perhaps not distinct at the family rank. Key words: Gigartinales, PCR, phylogeny, Plocamiales ord.nov., Pseudoanemoniaceae, Rhodophyta, small-subunit rRNA, systematics.

Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data

1998 ◽  
Vol 30 (4-5) ◽  
pp. 463-472 ◽  
Author(s):  
Jan-Eric Mattsson ◽  
Mats Wedin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Slight Variation ◽  
Hypogymnia Physodes ◽  
Nuclear Rdna ◽  
Future Studies ◽  
The Family ◽  
Rdna Sequence Data ◽  
Close Relationship

AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

Genetic and morphological data support placement of Myrmotherula gularis (Spix) in the monotypic genus Rhopias Cabanis and Heine (Aves: Passeriformes: Thamnophilidae)

Zootaxa ◽  
2012 ◽  
Vol 3451 (1) ◽  
pp. 1 ◽  
Author(s):  
RICARDO BELMONTE-LOPES ◽  
GUSTAVO A. BRAVO ◽  
MARCOS R. BORNSCHEIN ◽  
GIOVANNI N. MAURÍCIO ◽  
MARCIO R. PIE ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Character State ◽  
Monotypic Genus ◽  
Ancestral Reconstruction ◽  
The Family ◽  
Close Relationship ◽  
Phylogenetic Resolution ◽  
Phylogenetic Affinities

Recent DNA-based phylogenetic analyses of the family Thamnophilidae have shown that the genus Myrmotherula is polyphyletic. Traditional plumage-based taxonomy has been misleading in terms of identifying independently evolving lineages within the complex. Here, we integrate a molecular phylogeny with morphometric information and ancestral reconstruction of syringeal character states of the Musculi vocales ventrales, to investigate the taxonomic position of M. gularis, a species for which phylogenetic affinities have long been uncertain. We show that M. gularis represents a long branch in the tribe Thamnophilini that is not closely related to any other member of the Myrmotherula complex. Its relationships within the tribe remain uncertain because of the lack of phylogenetic resolution at the base of the tribe. M. gularis shares a derived character state of the M. vocalis ventralis with Taraba, Hypoedaleus, and Mackenziaena, which supports a close relationship between M. gularis and the large antshrikes. M. gularis can be diagnosed from Myrmotherula and Epinecrophylla by this condition of its M. vocalis ventralis, and from Isleria by plumage and other morphological traits. The phylogenetic and morphological distinctiveness of M. gularis does not warrant merging it into any other genus. We propose that this species be placed in a monotypic genus, for which the available name Rhopias applies.

scholarly journals Resurrecting the genus Geomorium: Systematic study of fungi in the genera Underwoodia and Gymnohydnotrya (Pezizales) with the description of three new South American species

2020 ◽  
Vol 44 (1) ◽  
pp. 98-112
Author(s):  
N. Kraisitudomsook ◽  
R.A. Healy ◽  
D.H. Pfister ◽  
C. Truong ◽  
E. Nouhra ◽  
...  
Keyword(s):  
South America ◽  
Southern Hemisphere ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Fungal Species ◽  
Molecular Dating ◽  
Phylogenetic Study ◽  
South American Species ◽  
New Family ◽  
The Family

Molecular phylogenetic analyses have addressed the systematic position of several major Northern Hemisphere lineages of Pezizales but the taxa of the Southern Hemisphere remain understudied. This study focuses on the molecular systematics and taxonomy of Southern Hemisphere species currently treated in the genera Underwoodia and Gymnohydnotrya. Species in these genera have been identified as the monophyletic/gymnohydnotrya lineage, but no further research has been conducted to determine the evolutionary origin of this lineage or its relationship with other Pezizales lineages. Here, we present a phylogenetic study of fungal species previously described in Underwoodia and Gymnohydnotrya, with sampling of all but one described species. We revise the taxonomy of this lineage and describe three new species from the Patagonian region of South America. Our results show that none of these Southern Hemisphere species are closely related to Underwoodia columnaris, the type species of the genus Underwoodia. Accordingly, we recognize the genus Geomorium described by Spegazzini in 1922 for G. fuegianum. We propose the new family, Geomoriaceae fam. nov., to accommodate this phylogenetically and morphologically unique Southern Hemisphere lineage. Molecular dating estimated that Geomoriaceae started to diverge from its sister clade Tuberaceae c. 112 MYA, with a crown age for the family in the late Cretaceous (c. 67 MYA). This scenario fits well with a Gondwanan origin of the family before the split of Australia and South America from Antarctica during the Paleocene-Eocene boundary (c. 50 MYA).

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.

Remarkable cases of parallel evolution of the placodioid thallus growth form in the Lecanographaceae (Arthoniales) with the description of a new species of Alyxoria from Mexico

2020 ◽  
Vol 52 (6) ◽  
pp. 415-424
Author(s):  
Damien Ertz ◽  
Alejandro Huereca ◽  
Sergio Manuel Salcedo-Martínez ◽  
Anders Tehler
Keyword(s):  
New Species ◽  
Growth Form ◽  
Phylogenetic Analyses ◽  
Parallel Evolution ◽  
Systematic Position ◽  
Growth Forms ◽  
The Family ◽  
Lichenized Fungus ◽  
A New Species ◽  
Lichen Growth

AbstractThe new species Alyxoria sierramadrensis is described from Mexico where it inhabits limestone rocks. The lichen developing from this fungus is characterized by a placodioid to subfoliose thallus with a white pruinose surface; rounded to shortly elongated ascomata with a black epruinose margin and a widely exposed, white pruinose hymenial disc; hyaline, 3-septate ascospores, 17–25 × 7–9 μm; the presence of anthraquinones rendering the medulla orange. Phylogenetic analyses of nuLSU, mtSSU and RPB2 sequences place this species in the genus Alyxoria (Lecanographaceae). This generic affiliation is surprising because all known Alyxoria species have a crustose thallus. Lecanographaceae mainly includes species without a thallus (lichenicolous taxa) or with a thin crustose thallus, the only exception being Simonyella variegata with a fruticose thallus. The new species belongs to the Alyxoria ochrocheila subgroup, which includes lichens also frequently known to have anthraquinones, white pruinose hymenial discs and 3-septate ascospores. Phylogenetic analyses further determined the systematic position of the monotypic genus Phoebus. This genus, considered as an Arthoniales of uncertain family affiliation, is shown to belong to the Lecanographaceae. With its placodioid thallus, it is another example of a lichenized fungus with a deviating morphology in thallus structure for the family, increasing the number of remarkable cases of parallel evolution of lichen growth forms within the Arthoniales. Phoebus hydrophobius is newly recorded for Mexico.

scholarly journals Reassessment and systematic position of the sinistral snails of genus Hemiplecta from Thailand (Eupulmonata: Ariophantidae), with description of two new species

2020 ◽  
pp. 1-33
Author(s):  
Chirasak Sutcharit ◽  
Ekgachai Jeratthitikul ◽  
Piyoros Tongkerd ◽  
Somsak Panha
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Comparative Morphology ◽  
Systematic Position ◽  
Reproductive Organ ◽  
Peninsular Malaysia ◽  
Land Snails ◽  
The Family ◽  
Two New Species ◽  
Molecular Phylogenetic

Indochina land snails of the family Ariophantidae are in need of thorough systematic revision. Here we comprehensively revise the systematics of the large-shelled, sinistral (counterclockwise) coiling snails from Thailand and Peninsular Malaysia. Molecular phylogeny based on mitochondrial (coi and 16S) and nuclear (28S) gene sequences demonstrates that these sinistral snails are not members of Dyakiidae as previously thought, but instead are more closely related to the genus Hemiplecta in the family Ariophantidae. Comparative morphology also reveals similarity of reproductive organ features (globular gametolytic organ, well-developed dart apparatus, and lack of amatorial organ complex). Based on this evidence, we propose to transfer these sinistral snails to the genus Hemiplecta. Molecular phylogenetic analyses further strongly support the monophyly of this sinistral lineage with respect to other members of Hemiplecta. This monophyletic clade consists of five members including three species that were previously classified as “Dyakia”, H. lahatensis, H. retrorsa and H. salangana, and two new species described herein, H. ligorica n. sp. and H. thailandica n. sp. This study also suggests that the anatomy of the gametolytic organ in the genus Hemiplecta corresponds well with the phylogenetic relationships and appears to be a taxonomically informative character, while the penial verge has little utility for generic recognition.

An opisthorchiid concept of the genus Liliatrema (Trematoda: Plagiorchiida: Opisthorchioidea): an unexpected systematic position

2020 ◽  
Author(s):  
Sergey Sokolov ◽  
Evgeniy Frolov ◽  
Semen Novokreshchennykh ◽  
Dmitry Atopkin
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Systematic Position ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Family ◽  
Using Data ◽  
Terminal Genitalia ◽  
Rdna Analysis

Abstract Liliatrema is a small genus of trematodes consisting of two species. Its systematic position has long been debated, partly because of the confusing reports about the structure of male terminal genitalia. Here we test the phylogenetic position of the genus Liliatrema using data on complete 18S rRNA and partial 28S rRNA gene sequences obtained for Liliatrema skrjabini. We also provide a detailed description of terminal genitalia in adult specimens of L. sobolevi and metacercariae of both Liliatrema species. The results of the 28S rDNA-based phylogenetic analysis indicate that Liliatrema falls within a well-supported clade, which also includes Apophallus and traditional opisthorchiids. This clade, in turn, is nested within a well-supported clade, containing Euryhelmis, Cryptocotyle and Scaphanocephalus. In the 18S+8S rDNA analysis, Liliatrema appears as a sister-taxon to the Cryptocotyle + Euryhelmis group. The Liliatrema + (Cryptocotyle + Euryhelmis) clade is a well-supported sister-group to the traditional opisthorchiids. The morphology of the terminal genitalia of the liliatrematids also corresponds to that of the opisthorchioids. Thus, the results of our morphological and phylogenetic analyses favour an unexpected conclusion that the genus Liliatrema belongs to the Opisthorchioidea. We propose that the genera Liliatrema, Apophallus, Euryhelmis, Cryptocotyle and Scaphanocephalus belong, respectively, within the subfamilies Liliatrematinae, Apophallinae, Euryhelminthinae and Cryptocotylinae of the family Opisthorchiidae.

scholarly journals Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts

2011 ◽  
Vol 392 (1-2) ◽  
Author(s):  
Soledad Funes ◽  
Frank Kauff ◽  
Eli O. van der Sluis ◽  
Martin Ott ◽  
Johannes M. Herrmann
Keyword(s):  
Phylogenetic Analyses ◽  
Core Region ◽  
Functional Specialization ◽  
Gene Duplications ◽  
Hydrophobic Core ◽  
Core Domain ◽  
The Core ◽  
Independent Gene ◽  
The Family ◽  
Substrate Spectrum

Abstract Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.

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