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

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.

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Redefinition of Cornexcisia Fan & Kano, 2000 (Diptera: Sarcophagidae), with the first description of the female of Sarcophaga kurahashii (Shinonaga & Tumrasvin, 1979)

Zootaxa ◽

10.11646/zootaxa.4668.3.6 ◽

2019 ◽

Vol 4668 (3) ◽

pp. 410-420

Author(s):

CHAO WANG ◽

YUNYUN GAO ◽

THOMAS PAPE ◽

DONG ZHANG

Keyword(s):

Cytochrome Oxidase ◽

Coi Gene ◽

Mitochondrial Cytochrome ◽

Gene Sequences ◽

Cytochrome Oxidase Subunit ◽

Cytochrome Oxidase Subunit I ◽

Mitochondrial Cytochrome Oxidase Subunit ◽

Senior Synonym ◽

First Time ◽

Mitochondrial Cytochrome Oxidase

Sarcophaga Meigen, 1826 is proposed as a senior synonym of Cornexcisia Fan & Kano, 2000, syn. nov. and Fanzideia Xue, Verves & Du, 2011, syn. nov. Cornexcisia Fan & Kano, 2000, stat. rev. is given status as a subgenus and is considered a senior synonym of Fanzideia Xue, Verves & Du, 2011, syn. nov. at the subgeneric level. Cornexcisia is argued to contain S. (Cornexcisia) longicornuta (Fan & Kano, 2000), comb. nov., S. (C.) cygnocerca (Xue, Verves & Du, 2011), comb. nov., S. (C.) kurahashii (Shinonaga & Tumrasvin, 1979), subgen. comb. nov. (from Phallosphaera Rohdendorf) and S. (C.) suthep Pape & Bänziger, 2003, subgen. comb. nov. (from Rosellea Rohdendorf). Sarcophaga (C.) kurahashii is newly recorded from China (Yunnan), the male is redescribed and the female is described for the first time, supported by photographs, illustrations and mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Species of Cornexcisia share an exceptionally long postpedicel in the female and the following apomorphic distiphallic appendages in the male: juxta ventro-proximally with an apically divided arm with cuticular pile, and lateral styli bifurcated from the base with each branch elongate, gently curved and slightly expanded apically. A key to the species of Cornexcisia is provided.

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

Phytotaxa ◽

10.11646/phytotaxa.278.3.7 ◽

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).

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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 ◽

10.11646/phytotaxa.191.1.7 ◽

2014 ◽

Vol 191 (1) ◽

pp. 115 ◽

Cited By ~ 5

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.

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Relationships of the Insect-Pathogenic Order Entomophthorales (Zygomycota, Fungi) Based on Phylogenetic Analyses of Nuclear Small Subunit Ribosomal DNA Sequences (SSU rDNA)

Fungal Genetics and Biology ◽

10.1006/fgbi.1998.1063 ◽

1998 ◽

Vol 24 (3) ◽

pp. 325-334 ◽

Cited By ~ 58

Author(s):

Annette Bruun Jensen ◽

Andrea Gargas ◽

Jørgen Eilenberg ◽

Søren Rosendahl

Keyword(s):

Ribosomal Dna ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Ssu Rdna ◽

Small Subunit Ribosomal Dna

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

Applied and Environmental Microbiology ◽

10.1128/aem.64.10.4089-4092.1998 ◽

1998 ◽

Vol 64 (10) ◽

pp. 4089-4092 ◽

Cited By ~ 90

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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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

Acta Parasitologica ◽

10.2478/s11686-013-0149-3 ◽

2013 ◽

Vol 58 (3) ◽

Cited By ~ 22

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.

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

Phytopathology ◽

10.1094/phyto-05-12-0114-r ◽

2012 ◽

Vol 102 (12) ◽

pp. 1153-1160 ◽

Cited By ~ 37

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.

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Phylogenetic relationships, based on SSU rDNA sequences, among the didelphic genera of the family Trichodoridae from Portugal

Nematology ◽

10.1163/156854109x461721 ◽

2010 ◽

Vol 12 (2) ◽

pp. 171-180 ◽

Cited By ~ 16

Author(s):

Isabel M. Duarte ◽

Maria Teresa M. de Almeida ◽

Derek J.F. Brown ◽

Isabel Marques ◽

Roy Neilson ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Small Subunit ◽

Ssu Rdna ◽

Indigenous Populations ◽

Molecular Analyses ◽

Rdna Sequences ◽

The Family ◽

Northern Regions ◽

First Time ◽

Small Subunit Ribosomal Dna

Abstract A survey of virus vector trichodorid nematodes was carried out in the central and northern regions of Portugal. Morphobiometric identification showed the presence of trichodorid species previously reported from Portugal, except for Paratrichodorus porosus, which is reported for the first time in Continental Europe. Small subunit ribosomal DNA (SSU rDNA) sequences of ten different species occurring in Portugal were obtained and a phylogenetic analysis based on their alignment was performed to infer relationships among the different Portuguese trichodorid species and three non-indigenous populations (Nanidorus minor, P. allius and P. teres). The resulting phylogenetic tree is in agreement with the currently accepted classification for Trichodoridae, except for Nanidorus, which clusters together with Trichodorus species, while the genera Paratrichodorus and Trichodorus appear as two distinct groups. A better understanding of the generic groupings in the family Trichodoridae was found. Based on the new molecular analyses we herein accept Nanidorus as a valid genus.

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Genetic diversity analysis of an isolate of microsporidia infesting Athetis lepigone

10.1101/526368 ◽

2019 ◽

Author(s):

Haijian Zhang ◽

Jian Song ◽

Yunhe Yang ◽

Jingjie An ◽

Hongxia Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Pcr Amplification ◽

Small Subunit ◽

Ssu Rdna ◽

Sequencing Analysis ◽

Multiple Sequence ◽

Intergenic Spacers ◽

Link Type ◽

Close Relationship ◽

Small Subunit Ribosomal Dna

AbstractIn this study, PCR amplification, cloning and sequencing analysis were adopted to explore genetic diversity of microsporidia (LEP9557) infecting Athetis lepigone. The small subunit ribosomal DNA (SSU rDNA), internal transcribed spacer (ITS) and intergenic spacers (IGS) of ribosomal RNA (rRNA) were cloned from the strain and sequenced. By means of multiple sequence alignment, we found that the three gene regions had different levels of polymorphism. There was greater polymorphism in ITS (74 variable sites) and IGS (55.59%) regions than in the SSU rDNA (17 variable sites). Phylogenetic analysis was performed using Kimura 2-parameter with neighbor joining and the results showed that LEP9557 had a close relationship with Nosema bombycis. Sequences of each clone were submitted to Genbank (Accession number: MF150254-MF150258). All of the results indicated the presence of genetic diversity in LEP9557, which established the foundation for identifying the phylogeny and relationships with other microsporidian strains, and had significant biological meaning for maintaining the survival and population continuity of the strain.

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