Phylogeny and Biogeography of Chara (Charophyta) Inferred from 18S rDNA Sequences

1999 ◽  
Vol 47 (3) ◽  
pp. 347 ◽  
Author(s):  
S. T. Meiers ◽  
V. W. Proctor ◽  
R. L. Chapman
Keyword(s):  
Maximum Likelihood ◽  
Morphological Characters ◽  
Small Subunit ◽  
Monophyletic Clade ◽  
Rdna Sequences ◽  
Extant Species ◽  
Likelihood Analysis ◽  
18S Rdna Sequences ◽  
Break Up ◽  
Fossil Data

Competing hypotheses concerning the relationships among subsections of the genus Chara were tested with parsimony and maximum likelihood analysis of small subunit (18S) ribosomal DNA gene (rDNA) sequences. The traditional hypothesis as stated by Wood and Imahori (1965) separates Chara into subgenera and subsections based primarily on stipulode and cortication characters, whereas Proctor’s (1980) hypothesis proposed subgenera based on the break-up of Pangea into Laurasia and Gondwana, and subsections based on the subsequent break-up of these two supercontinents. Both parsimony and maximum likelihood analyses strongly refuted Wood and Imahori’s hypothesis, as well as the importance traditionally placed on stipulode and cortication characters. Partial or total loss of cortication may occur within a subsection, as demonstrated by C. imperfecta, C. braunii, C. muelleri and C. brittonii. Although the nodal stem cell gives rise to the branchlets, stipulodes and axial cortex, stipulodes can be retained despite the loss of cortication as demonstrated by C. hydropitys, which is placed solidly within Willdenowia by both analyses. Proctor’s hypothesis was supported with Gondwanan subsections basal (except for C. tomentosa) and Laurasian subsections placed together in a monophyletic clade in both analyses, although the placement of subsection Grovesia is uncertain. Monophyly of subsections Wallmania and Willdenowia and Lamprothamnium are strongly supported. Lamprothamnium is placed within the genus Chara, which disagrees with previous (McCourt et al. 1996) rbcL analyses. Further studies are needed to identify phylogenetically informative morphological characters for extant taxa, and a method is needed to link extant species to the extensive fossil data for a fuller understanding of the phylogeny and biogeography of this distinctive genus.

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

scholarly journals Taxonomic justification of the pathogenic strongylid infecting the Arabian camel Camelus dromedarius as Haemonchus longistipes by morphological and molecular phylogeny

2019 ◽  
Vol 63 (1) ◽  
pp. 51-61
Author(s):  
Saad Dajem ◽  
Kareem Morsy ◽  
Mohammed Al-Kahtani ◽  
Rewaida Abdel-Gaber
Keyword(s):  
Electron Microscopy ◽  
Saudi Arabia ◽  
Maximum Likelihood ◽  
Sequence Alignment ◽  
Maximum Likelihood Analysis ◽  
Phylogenetic Information ◽  
Multiple Sequence ◽  
Rdna Sequences ◽  
Likelihood Analysis ◽  
Arabian Camel

Abstract Introduction: There is still lack of morphological and phylogenetic information on the pathogenic nematode of the camel Haemonchus longistipes. In the present study, this parasite was isolated in Saudi Arabia and described. Material and Methods: The abomasa of two Arabian camels were collected from a slaughterhouse in Abha province and examined for nematode infection. Worms were described morphologically and morphometrically by electron microscopy. Multiple sequence alignment and the phylogenetic tree of the parasite were constructed from maximum likelihood analysis of its ITS-2 rDNA sequences. Results: These nematodes had a slender body terminating anteriorly at a conspicuous dorsal lancet. A pair of lateral cervical papillae distant from the anterior end was observed. The buccal aperture was hexagonal and surrounded by two amphids, six externo-labial papillae, and four cephalic papillae. Males terminated posteriorly at a bursa supported by spicules and lateral and dorsal rays. Females were linguiform and knobbed morphotypes with distinct ovijectors and a dorsal rim covering the anal pore. The taxonomy was confirmed by the morphology and number of the longitudinal cuticular ridges in a 43–46 range. The sequence alignment and phylogeny revealed 92% homology with H. longistipes (AJ577461.1), and the sequence was deposited into GenBank. Conclusion: The present study describes H. longistipes morphologically and molecularly which facilitates further discrimination of this species worldwide.

Myxobolus jialingensis n. sp. (Myxozoa: Myxobolidae) infecting urinary bladder and hepatopancreas of yellowhead catfish Tachysurus fulvidraco from China

Zootaxa ◽  
2020 ◽  
Vol 4819 (1) ◽  
pp. 179-186
Author(s):  
LEI GAO ◽  
JING ZHANG ◽  
CHENGZHONG YANG ◽  
YUANJUN ZHAO
Keyword(s):  
Urinary Bladder ◽  
18S Rdna ◽  
Polar Capsule ◽  
Small Subunit ◽  
Rdna Sequences ◽  
Multiple Origins ◽  
Close Phylogenetic Relationship ◽  
18S Rdna Sequences ◽  
Tachysurus Fulvidraco ◽  
Myxosporean Species

In the present study, we described a novel myxosporean species, Myxobolus jialingensis n. sp. (Myxozoa: Myxobolidae), which infected the urinary bladder and hepatopancreas of yellowhead catfish Tachysurus fulvidraco in China. The mature spores of M. jialingensis n. sp. were pyriform with the length of 15.8 ± 0.7 (15.4–17.0) μm and width of 8.0 ± 0.3 (7.8–8.9) μm. Two pyriform polar capsules were slightly unequal in size: the larger polar capsule was 7.4 ± 0.3 (6.7–8.0) μm in length and 3.1 ± 0.2 (2.8–3.6) μm in width; and the smaller polar capsule measured 7.3 ± 0.3 (6.6–8.1) μm in length and 3.3 ± 0.2 (2.9–3.6) μm in width. The polar capsules were directed toward the apex of the spore, packing seven to eight spirals of the polar filaments. The small subunit ribosomal RNA gene (18S rDNA) sequence of M. jialingensis n. sp. was unique among all myxozoans, and the highest similarity was 96.1% with M. voremkhai. Phylogenetic analysis based on 18S rDNA sequences revealed that myxosporeans infecting the close host affinity (belonging to the same order) had close phylogenetic relationship and, some myxosporeans infecting the same host order might have multiple origins.

scholarly journals Description of a new marine predatory nematode Latronema dyngi sp. nov. (Nematoda, Chromadorida, Selachinematidae) from the west coast of Sweden and an updated phylogeny of Chromadoria

2020 ◽  
Vol 50 (6) ◽  
Author(s):  
Mohammed Ahmed ◽  
Oleksandr Holovachov
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
West Coast ◽  
18S Rdna ◽  
Nematode Species ◽  
The West ◽  
Spicule Length ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
Circular Outline

AbstractA new nematode species, Latronema dyngi sp. nov., is described from Skagerrak off the west coast of Sweden with the type locality near Dyngö island. Latronema dyngi sp. nov. is characterized by multispiral amphideal fovea with circular outline, 0.2–0.3 corresponding body diameters wide in males and 0.1–0.2 corresponding body diameters wide in females, 12 cuticular longitudinal ridges and 18–27 precloacal supplements in males. Latronema dyngi sp. nov. most closely resembles L. orcinum in terms of body length; demanian ratios a, b, c and c′; number of amphid turns in males; and the ratio of spicule length to cloacal body diameter. The two species can be differentiated by the number longitudinal ridges on the cuticle (12 for Latronema dyngi sp. nov. vs 20–22 for L. orcinum) and spicule length (65–78 μm for L. dyngi vs 60 for L. orcinum) and shape (weakly arcuate for L. dyngi sp. nov. vs strongly arcuate for L. orcinum). We also performed a maximum likelihood phylogenetic analysis on over 250 nematodes of the subclass Chromadoria based on their nearly full-length 18S rDNA sequences. In agreement with previous studies, our analysis supported Selachinematidae as a monophyletic group and placed Richtersia Steiner, 1916 within Desmodoridae Filipjev, 1922 or just outside of the main Desmodorida clade with the latter placement not well supported.

scholarly journals Endocranial preservation of a Carboniferous actinopterygian from Lancashire, UK, and the interrelationships of primitive actinopterygians

1999 ◽  
Vol 354 (1382) ◽  
pp. 435-462 ◽  
Author(s):  
Michael I. Coates
Keyword(s):  
Brain Structure ◽  
Morphological Characters ◽  
Taxonomic Group ◽  
Brain Morphology ◽  
Monophyletic Clade ◽  
Upper Carboniferous ◽  
Fossil Material ◽  
Muscle Insertion ◽  
Fossil Data ◽  
Enamel Composition

The gross brain structure of an Upper Carboniferous ( ca . 310 Myr ago) ray–finned fish (Actinopterygii) is described from exceptionally well–preserved fossil material from the Burnley region of Lancashire, UK. Previously identified as ‘ Rhadinichthys ’ planti , the species is reassigned to the genus Mesopoma . Morphological characters derived from these data are combined with reviews of cranial skeletal anatomy, enamel composition, oculomoter muscle insertion and paired fin morphology to test and reanalyse hypotheses of primitive actinopterygian interrelationships. Results indicate that ancestral chondrostean (sturgeon and paddlefish) and neopterygian (teleost, amiid and gar) lineages diverged earlier than current theories suggest. Palaeonisciformes, a taxonomic group widely used to include most Palaeozoic actinopterygians, include a significant number of primitive neopterygians, several of which may form a distinct monophyletic clade. Within this revised phylogenetic context, changes in gross brain morphology from primitive conditions, as revealed by fossil data, highlight likely specializations in extant non–teleostean actinopterygians.

scholarly journals First detection of Eimeria species in Myanmar domestic goats with both microscopic and molecular methods

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 38
Author(s):  
Saw Bawm ◽  
Tay Zar Bhone Win ◽  
Shwe Yee Win ◽  
Lat Lat Htun ◽  
Ryo Nakao ◽  
...  
Keyword(s):  
18S Rdna ◽  
Eimeria Species ◽  
Morphological Characters ◽  
Farm Animals ◽  
Detection Rates ◽  
Rdna Sequences ◽  
Faecal Samples ◽  
18S Rdna Sequences ◽  
Flotation Method ◽  
Coi Sequences

Coccidiosis is of great economic importance in many farm animals. This study involved analysis of 280 faecal samples collected from 12 traditional goat farms from Nay Pyi Taw area, Myanmar. Faecal samples were examined by the flotation method and concentrated oocysts were identified on the basis of morphological characters. Of 280 faecal samples examined, 168 (60.0%) were positive for Eimeria oocysts. Three different Eimeria species were identified and their positive detection rates in the herd were: E. arloingi (25.4%), followed by E. hirci (20.7%) and E. christenseni (13.9%). Identifications were confirmed by 18S rDNA and COI sequences. 18S rDNA sequences showed 100% homology with, respectively, E. christenseni reported from Australia, E. arloingi reported from Australia and Iran, and E. hirci from Australia. COI sequences of E. christenseni, E. hirci, and E. arloingi, respectively, exhibited 98.9%, 98.4%, and 98.5% similarities with those reported from Australia. This is the first report of Eimeria infection in Myanmar goats.

scholarly journals Partially incorrect fossil data augment analyses of discrete trait evolution in living species

2016 ◽  
Vol 12 (8) ◽  
pp. 20160392 ◽  
Author(s):  
Mark N. Puttick
Keyword(s):  
Morphological Characters ◽  
Ancestral State Reconstruction ◽  
Character State ◽  
Ancestral State ◽  
Trait Evolution ◽  
State Reconstruction ◽  
Extant Species ◽  
Likelihood Model ◽  
Living Species ◽  
Fossil Data

Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model. Under simulated phylogenies and data, likelihood-based models are generally accurate when estimating ancestral node values. Analyses with combined fossil and extant data always outperform analyses with extant species alone, even when around one quarter of the fossil information is incorrect. These results are especially pronounced when model assumptions are violated, such as when there is a trend away from the root value. Fossil data are of particular importance when attempting to estimate the root node character state. Attempts should be made to include fossils in analysis of discrete traits under likelihood, even if there is uncertainty in the fossil trait data.

Parasitodiplogaster species associated with Pharmacosycea figs in Panama

Nematology ◽  
2014 ◽  
Vol 16 (5) ◽  
pp. 607-619 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
Weimin Ye ◽  
Edward Allen Herre ◽  
Barbara J. Center
Keyword(s):  
Ribosomal Rna ◽  
Morphological Study ◽  
Large Subunit ◽  
Morphological Characters ◽  
Small Subunit ◽  
Nominal Species ◽  
Monophyletic Clade ◽  
Male Tail ◽  
Stomatal Morphology ◽  
Rna Genes

Parasitodiplogaster species that are associated with figs in the Ficus subsection Pharmacosycea, i.e., Ficus maxima, F. yoponensis, F. insipida and F. glabrata, were studied using morphological characters and molecular sequences. Some nematodes isolated from the fig sycones were casually observed and recorded as morphospecies according to their morphotype, and were then digested for their DNA, while others were fixed in formalin-glycerin for additional morphological study. High resolution microscopic observation of the morphological materials yielded five morphospecies including two nominal species, P. maxinema and P. pharmaconema. The morphospecies were distinguished from each other by male tail characters. By contrast, five and six genotypes were recognised by D2/D3 expansion segments of the large subunit (LSU) and near-full-length sequences of small subunit (SSU) ribosomal RNA genes, respectively. Except for two nominal species, genotypes and morphospecies were not clearly correlated because of limitations in the microscopic resolution in the initial morphotyping. Although the morphospecies and genotypes were not clearly paired, Pharmacosycea-associated Parasitodiplogaster species, which are tentatively referred to as the ‘P. maxinema group’, formed a monophyletic clade in both D2/D3 LSU and SSU analyses and are morphologically characterised by their stomatal morphology, i.e., a tube-shaped stoma with two stick-like teeth and male tail morphology, presence of nine paired papillae and relatively slender spicule.

scholarly journals SEQUENCE ANALYSIS OF 18s DNA OF Melosira sp., Dunaliella sp., Isochrysis sp. AND Porphyridium sp.

2015 ◽  
Vol 2 (1) ◽  
pp. 592
Author(s):  
Lucia Kusumawati ◽  
Ruben Wahyudi ◽  
Reinhard Pinontoan ◽  
Maria Gorreti Lily Panggabean
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Rdna Sequences ◽  
Pcr Products ◽  
18S Rdna Sequences ◽  
Pcr Method ◽  
High Level

<p>Phytoplankton has high level of biodiversity. In previous years phytoplankton was identified by their morphological characters. However, their morphology might change in different environments. These difficulties can be overcome by comparing their 18S rDNA sequences. This research is aimed to verify the identity of Melosira sp., Dunaliella sp., Isochrysis sp. and Porphyridium sp. Here, PCR method was used to amplify 18s DNA sequences. Three primer pairs were used, i.e. 18S-F and 18S-R; 501F and 1700R; 18S-2F and 18S-2R. PCR products were sequenced. MEGA5 was used to make phylogenetic tree. Genus verification for Isochrysis sp., Dunaliella sp. and Melosira sp. were conducted successfully using Blast and phylogenetic tree. 18s DNA sequence of Porphyridium sp. shows an interesting result and needs further verification.</p><p><br /><strong>Keywords</strong>: Phytoplankton, Melosira sp., Dunaliella sp., Isochrysis sp., Porphyridium sp.</p>

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