Description of the pseudocryptic species Conticribra weissflogiopsis sp. nov. (Thalassiosirales, Bacillariophyta) isolated from brackish waters in Korea, based on its cingulum structure and molecular analysis

Phytotaxa ◽  
2014 ◽  
Vol 191 (1) ◽  
pp. 115 ◽  
Author(s):  
JOON SANG PARK ◽  
JIN HWAN LEE
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Diatom Species ◽  
Brackish Waters ◽  
Valve Structure ◽  
Small Subunit Ribosomal Dna ◽  
Pseudocryptic Species

We describe the new fultoportulate diatom species, Conticribra weissflogiopsis, isolated from brackish waters in Korea, based on morphological characters and molecular data. The new species is characterized by having areolae venation with internal (semi-) continuous cribra, a flat valve face, a single marginal rimoportula replacing a marginal fultoportula, a subcentral ring of the valve face fultoportulae, and a dextral pattern of cingulum structure. The overall valve structure of C. weissflogiopsis resembles that of C. weissflogii; however, the cingulum structure differs between the two species—C. weissflogiopsis has a dextral offset of band opening in the cingulum, whereas C. weissflogii has a sinistral offset. Phylogenetic analysis of the nuclear small subunit ribosomal DNA (SSU rDNA) revealed that C. weissflogiopsis is located in the Conticribra clade. Further, the pairwise genetic distance based on the SSU rDNA and the internal transcribed spacer 2 (ITS2) indicated that C. weissflogiopsis is a distinct Conticribra species. On the basis of the morphology and molecular phylogeny, we expand the hypothesis regarding the morphological evolution of Conticribra species.

Molecular identification of cryptic species of Ceratomyxa Thélohan, 1892 (Myxosporea: Bivalvulida) including the description of eight novel species from apogonid fishes (Perciformes: Apogonidae) from Australian waters

2013 ◽  
Vol 58 (3) ◽  
Author(s):  
Holly Heiniger ◽  
Robert Adlard
Keyword(s):  
Cryptic Species ◽  
Genetic Markers ◽  
Novel Species ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Phylogenetic Relatedness ◽  
Biological Characters ◽  
Multiple Species ◽  
Small Subunit Ribosomal Dna

AbstractCeratomyxa parasites from the gall bladders of 23 species of cardinalfishes (family Apogonidae) from Australian waters were examined for their taxonomic identity and phylogenetic relatedness. We identified 15 of the 23 apogonid fish species infected with species of Ceratomyxa. Although the majority of apogonid species harboured only a single Ceratomyxa species, four were found with multiple species of Ceratomyxa. This study describes eight novel species using a combination of morphological, small subunit ribosomal DNA (SSU rDNA) and biological characters. Six Ceratomyxa species are reported from single apogonid species, while two are reported from multiple host species. Molecular data were critical in identifying several morphologically cryptic species. However, our results suggest that SSU rDNA was not capable of distinguishing all the species present in the current study system and alternative genetic markers should be investigated in the future.

scholarly journals Small Subunit Ribosomal DNA-Based Phylogenetic Analysis of Foliar Nematodes (Aphelenchoides spp.) and Their Quantitative Detection in Complex DNA Backgrounds

2012 ◽  
Vol 102 (12) ◽  
pp. 1153-1160 ◽  
Author(s):  
Katarzyna Rybarczyk-Mydłowska ◽  
Paul Mooyman ◽  
Hanny van Megen ◽  
Sven van den Elsen ◽  
Mariëtte Vervoort ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Developmental Stages ◽  
Nematode Species ◽  
Morphological Characters ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rapid Screening ◽  
Quantitative Detection ◽  
Small Subunit Ribosomal Dna ◽  
Plant Parasitic

Foliar nematodes, plant-parasitic representatives of the genus Aphelenchoides, constitute a minority in a group dominated by fungivorous species. Distinction between (mostly harmless) fungal feeding Aphelenchoides species and high impact plant parasites such as A. besseyi, A. fragariae, A. ritzemabosi, and A. subtenuis is severely hampered by the scarcity of informative morphological characters, some of which are only observable in specific developmental stages. Poor description of a number of non-plant-parasitic Aphelenchoides species further complicates identification. Based on (nearly) full-length small subunit ribosomal DNA (SSU rDNA) sequences (≈1,700 bp), a phylogenetic tree was generated, and the four target species appeared as distinct, well-supported groups. Notably, this genus does not constitute a monophyletic group: A. besseyi and A. ritzemabosi cluster together and they are phylogenetically isolated from A. fragariae, A. subtenuis, and most other fungivorous species. A phylum-wide SSU rDNA framework was used to identify species-specific DNA motifs. For the molecular detection of four plant-parasitic Aphelenchoides species, polymerase chain reaction primers were developed with high, identical annealing temperatures (63°C). Within the molecular framework presented here, these primers can be used for the rapid screening of plant material and soil for the presence of one or multiple foliar nematode species.

scholarly journals Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils

2020 ◽  
Author(s):  
Ludovic Le Renard ◽  
André L. Firmino ◽  
Olinto L. Pereira ◽  
Ruth A. Stockey ◽  
Mary. L. Berbee
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Small Subunit ◽  
Leaf Surfaces ◽  
The Matrix ◽  
Character Matrix ◽  
Phylogenetic Framework ◽  
Single Hypha ◽  
Objective Basis ◽  
Ancestral Character States

AbstractPREMISE OF THE STUDYFossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ∼250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.METHODSWe placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.KEY RESULTSThyriothecia evolved convergently in multiple lineages of superficial, leaf- inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes.CONCLUSIONSThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.

scholarly journals Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida)

2015 ◽  
Vol 2 (12) ◽  
pp. 150414 ◽  
Author(s):  
Angela M. Oliverio ◽  
Daniel J. G. Lahr ◽  
Jessica Grant ◽  
Laura A. Katz
Keyword(s):  
Testate Amoebae ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Coi Gene ◽  
Testate Amoeba ◽  
Phenotypic Evolution ◽  
Gene Sequences ◽  
Small Subunit Ribosomal Dna ◽  
Mitochondrial Cytochrome Oxidase ◽  
Phenotypic Convergence

This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for ‘core Nebela ’ species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.

scholarly journals The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858

Parasitology ◽  
2003 ◽  
Vol 126 (3) ◽  
pp. 203-224 ◽  
Author(s):  
A. E. LOCKYER ◽  
P. D. OLSON ◽  
P. ØSTERGAARD ◽  
D. ROLLINSON ◽  
D. A. JOHNSTON ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Good Deal ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Asian Origin ◽  
The Family ◽  
Veterinary Importance

Schistosomes are digenean flukes, parasitic of birds, mammals and crocodiles. The family Schistosomatidae contains species of considerable medical and veterinary importance, which cause the disease schistosomiasis. Previous studies, both morphological and molecular, which have provided a good deal of information on the phylogenetics of this group, have been limited in the number of species investigated or the type or extent of molecular data used. This paper presents the most comprehensive phylogeny to date, based on the sequences of 3 genes, complete ribosomal small subunit rRNA and large ribosomal subunit rRNA, and mitochondrial cytochrome oxidase 1, sequenced from 30 taxa including at least 1 representative from 10 of the 13 known genera of the Schistosomatidae and 17 of the 20 recognized Schistosoma species. The phylogeny is examined using morphological characters, intermediate and definitive host associations and biogeography. Theories as to the origins and spread of Schistosoma are also explored. The principal findings are that Ornithobilharzia and Austrobilharzia form a sister group to the Schistosoma; mammalian schistosomes appear paraphyletic and 2 Trichobilharzia species, T. ocellata and T. szidati, seem to be synonymous. The position of Orientobilharzia within the Schistosoma is confirmed, as is an Asian origin for the Schistosoma, followed by subsequent dispersal through India and Africa.

scholarly journals First record of Nocturama (Batrachospermales, Rhodophyta) in South America, with the description of a new species N. novamundensis

Phytotaxa ◽  
2016 ◽  
Vol 278 (3) ◽  
pp. 273
Author(s):  
ORLANDO NECCHI JR ◽  
TIMOTHY J. ENTWISLE ◽  
CIRO C.Z. BRANCO ◽  
MONICA O. PAIANO
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
First Record ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Evidence ◽  
Southern Brazil ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

Specimens from southeastern and southern Brazil previously identified as Sheathia arcuata (= Batrachospermum arcuatum) are shown to be members of the recently described genus Nocturama, previously known only from Australia and New Zealand. Morphological and molecular evidence support recognizing the Brazilian specimens as a new species, described here as Nocturama novamundensis, sp. nov. Comparison of DNA sequences of the plastid-encoded ribulose-1,5-bisphosphatecarboxylase–oxygenase large subunit (rbcL) and the nuclear small subunit ribosomal DNA (SSU rDNA) markers showed Nocturama as a well supported clade. The sequence divergences between the new and the type species were high (95-98bp, 7.4–7.6%) for rbcL and 19bp, 1.1% for SSU), and those within each species were extremely low (0-1 bp, 0-0.1%). The new species can be distinguished from N. antipodites in having curved primary fascicles composed of non-‘audouinelloid’ cells (compared to straight primary fascicles with audouinelloid—cylindrical—cells) and in being always dioecious (only rarely is N. antipodites dioecious).

Phylogenetic analysis of Rhizoclonium (Cladophoraceae, Cladophorales), and the description of Rhizoclonium subtile sp. nov. from China

Phytotaxa ◽  
2018 ◽  
Vol 383 (2) ◽  
pp. 147 ◽  
Author(s):  
ZHI-JUAN ZHAO ◽  
HUAN ZHU ◽  
GUO-XIANG LIU ◽  
ZHENG-YU HU
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Gene Markers ◽  
Long Time ◽  
Small Subunit Ribosomal Dna

The genus Rhizoclonium (Cladophoraceae, Cladophorales) accommodates uniserial, unbranched filamentous algae, closely related to Cladophora and Chaetomorpha. Its taxonomy has been problematic for a long time due to the lack of diagnostic morphological characters. To clarify the species diversity and taxonomic relationships of this genus, we collected and analyzed thirteen freshwater Rhizoclonium specimens from China. The morphological traits of these specimens were observed and described in detail. Three nuclear gene markers small subunit ribosomal DNA (SSU), large subunit ribosomal DNA (LSU) and internal transcribed spacer 2 (ITS2) sequences were analyzed to elucidate their phylogenetic relationships. The results revealed that there were at least fifteen molecular species assignable to Rhizoclonium and our thirteen specimens were distributed in four clades. On the basis of morphological and molecular evidence we propose the new species, R. subtile sp. nov.

scholarly journals Trypanosoma culicavium sp. nov., an avian trypanosome transmitted by Culex mosquitoes

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 745-754 ◽  
Author(s):  
Jan Votýpka ◽  
Jana Szabová ◽  
Jana Rádrová ◽  
Lenka Zídková ◽  
Milena Svobodová
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Ficedula Albicollis ◽  
Small Subunit Rrna ◽  
Comprehensive Description ◽  
Dehydrogenase Gene ◽  
Natural Hosts ◽  
Mosquito Females

A novel avian trypanosome, Trypanosoma culicavium sp. nov., isolated from Culex mosquitoes, is described on the basis of naturally and experimentally infected vectors and bird hosts, localization in the vector, morphological characters and molecular data. This study provides the first comprehensive description of a trypanosome species transmitted by mosquitoes, in which parasites form plugs and rosettes on the stomodeal valve. Trypanosomes occurred as long epimastigotes and short trypomastigotes in vectors and culture and as long trypomastigotes in birds. Transmission of parasites to bird hosts was achieved exclusively by ingestion of experimentally infected Culex mosquito females by canaries (Serinus canaria), but not by Japanese quails (Coturnix japonica), nor by the bite of infected vectors, nor by ingestion of parasites from laboratory cultures. Transmission experiments and the identity of isolates from collared flycatchers (Ficedula albicollis) and Culex mosquitoes suggests that the natural hosts of T. culicavium are insectivorous songbirds (Passeriformes). Phylogenetic analyses of small-subunit rRNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase gene sequences demonstrated that T. culicavium sp. nov. is more related to Trypanosoma corvi than to other avian trypanosomes (e.g. Trypanosoma avium and Trypanosoma bennetti).

scholarly journals Evidence for Interspecies Gene Transfer in the Evolution of 2,4-Dichlorophenoxyacetic Acid Degraders

1998 ◽  
Vol 64 (10) ◽  
pp. 4089-4092 ◽  
Author(s):  
Catherine McGowan ◽  
Roberta Fulthorpe ◽  
Alice Wright ◽  
J. M. Tiedje
Keyword(s):  
Gene Transfer ◽  
Burkholderia Cepacia ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Dichlorophenoxyacetic Acid ◽  
Rdna Genes ◽  
Degrading Bacteria ◽  
Pcr Products ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
Small Subunit Ribosomal Dna

ABSTRACT Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the classProteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the α-Proteobacteria yieldedtfdA PCR products. A comparison of the dendrogram of thetfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains withtfdA sequences highly similar to the tfdAsequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to aBurkholderia cepacia recipient.

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