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.

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.

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 An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species

2010 ◽  
Vol 60 (8) ◽  
pp. 1962-1977 ◽  
Author(s):  
Chitchai Chantangsi ◽  
Brian S. Leander
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Morphological Features ◽  
Molecular Signature ◽  
Nucleotide Sequence Analysis ◽  
Heterotrophic Flagellates ◽  
Rdna Sequences

Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera Cryothecomonas and Protaspis. Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of Protaspis obliqua and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5′ end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7 % and very low intraspecific sequence divergences of 0–0.5 %; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.

scholarly journals Cryptic species in sympatry: Nonrandom small-scale distribution patterns in Bostrychia intricata (Ceramiales, Rhodophyta)

2020 ◽  
Author(s):  
N Muangmai ◽  
U Von Ammon ◽  
Giuseppe Zuccarello
Keyword(s):  
Cryptic Species ◽  
Algal Species ◽  
Sun Exposure ◽  
Distribution Patterns ◽  
Molecular Data ◽  
Small Scale ◽  
Ecological Resources ◽  
Intertidal Habitats ◽  
Multiple Species ◽  
Multiple Samples

© 2016 International Phycological Society. Sympatric coexistence of cryptic species, indistinguishable morphological taxa, has increasingly been detected on the basis of molecular data. This discovery raises the interesting question of how cryptic species can coexist, as hypothetically they would need identical ecological resources. The red alga Bostrychia intricata is commonly found along New Zealand shores. Previous studies indicated several cryptic species within this morphospecies, and that some populations have multiple species. This study aimed to determine how coexisting cryptic B. intricata distribute at a small scale. Along the shore of Moa Point, Wellington, we conducted intensive sampling of B. intricata in different habitats with respect to tidal position, wave and sun exposure levels. Our genetic data clearly documented the coexistence of three cryptic species of B. intricata: N2, N4 and N5. Multiple samples from individual algal patches indicated that each patch was made of the same ramet. Our analyses revealed a habitat-related pattern in small-scale distribution of different cryptic B. intricata, suggesting that the distribution of these cryptic species was not random. Cryptic species N4 was found at a higher tidal position than species N2 and N5, whereas cryptic species N2 occurred in more wave-exposed areas than the other species. Discriminant analysis indicated that tidal height strongly influenced the distribution pattern among these cryptic species. Our observations demonstrated that the co-occurrence of three cryptic B. intricata can partly be explained by their occupation of different intertidal habitats, highlighting the nonrandom distribution of coexisting cryptic algal species.

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).

scholarly journals Cryptic species in sympatry: Nonrandom small-scale distribution patterns in Bostrychia intricata (Ceramiales, Rhodophyta)

2020 ◽  
Author(s):  
N Muangmai ◽  
U Von Ammon ◽  
Giuseppe Zuccarello
Keyword(s):  
Cryptic Species ◽  
Algal Species ◽  
Sun Exposure ◽  
Distribution Patterns ◽  
Molecular Data ◽  
Small Scale ◽  
Ecological Resources ◽  
Intertidal Habitats ◽  
Multiple Species ◽  
Multiple Samples

© 2016 International Phycological Society. Sympatric coexistence of cryptic species, indistinguishable morphological taxa, has increasingly been detected on the basis of molecular data. This discovery raises the interesting question of how cryptic species can coexist, as hypothetically they would need identical ecological resources. The red alga Bostrychia intricata is commonly found along New Zealand shores. Previous studies indicated several cryptic species within this morphospecies, and that some populations have multiple species. This study aimed to determine how coexisting cryptic B. intricata distribute at a small scale. Along the shore of Moa Point, Wellington, we conducted intensive sampling of B. intricata in different habitats with respect to tidal position, wave and sun exposure levels. Our genetic data clearly documented the coexistence of three cryptic species of B. intricata: N2, N4 and N5. Multiple samples from individual algal patches indicated that each patch was made of the same ramet. Our analyses revealed a habitat-related pattern in small-scale distribution of different cryptic B. intricata, suggesting that the distribution of these cryptic species was not random. Cryptic species N4 was found at a higher tidal position than species N2 and N5, whereas cryptic species N2 occurred in more wave-exposed areas than the other species. Discriminant analysis indicated that tidal height strongly influenced the distribution pattern among these cryptic species. Our observations demonstrated that the co-occurrence of three cryptic B. intricata can partly be explained by their occupation of different intertidal habitats, highlighting the nonrandom distribution of coexisting cryptic algal species.

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.

Dinobryon taiyuanensis (Chrysophyta, Dinobryaceae), a new freshwater species described from Shanxi province, China

Phytotaxa ◽  
2019 ◽  
Vol 404 (1) ◽  
pp. 41 ◽  
Author(s):  
XIAO-DIE JIANG ◽  
FANG-RU NAN ◽  
JUN-PING LV ◽  
QI LIU ◽  
SHU-LIAN XIE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Molecular Data ◽  
Small Subunit ◽  
Shanxi Province ◽  
Freshwater Species ◽  
5.8S Rdna ◽  
Single Clade ◽  
Small Subunit Ribosomal Dna

A new freshwater species of Chrysophyceae, Dinobryon taiyuanensis, is described from Linde Lake in Shanxi province, China. This new species is similar to D. sertularia, the type species of the genus, in the shape of the lorica and organization of the colony. The cells have two heterokont flagella surrounded by a lorica and occurred both as free-living, solitary cells or in branched colonies. The lorica of our new species like a bent or S-shaped cone, and shorter than the lorica in D. sertularia. In addition to describing the morphological features of D. taiyuanensis, a phylogenetic analysis based on sequences of the nuclear small subunit ribosomal DNA (SSU rDNA) and internal transcribed spacer (including internal transcribed spacer 1, 5.8S rDNA and internal transcribed spacer 2) placed this alga in single clade with a considerable sequence distance from the other Dinobryon species. Thus, results of both morphological comparisons and phylogenetic analysis based on molecular data suggest this alga as a new species, increasing the total number of recognized freshwater Chrysophyta species in China.

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.

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