Phylogenetic relationships among taxa in the Jahnulales inferred from 18S and 28S nuclear ribosomal DNA sequences

Jahnulales is an order of freshwater, lignicolous, bitunicate ascomycetes characterized by wide (10–40 μm), brown, septate hyphae, stalked and (or) sessile ascomata, ascomal walls of 2–6 layers of large cells, and 1-septate ascospores. A variety of ascospore modifications are represented among the species in the order, including wall roughening, gelatinous sheaths, appendages and (or) pads, and apical caps or spines. To clarify generic boundaries and phylogenetic relationships within the Jahnulales and to assess the taxonomic significance of various morphological characters, a molecular study was carried out using 18S and 28S rDNA sequence data from 15 species representing the four genera in the order. In addition, Brachiosphaera tropicalis Nawawi and Xylomyces chlamydosporus Goos, R.D. Brooks & Lamore, two mitosporic species that co-occur with Jahnula Kirschst., species and have wide (>10 μm), brown, septate hyphae were included in the study to determine whether these species are members of this order. Maximum likelihood analyses confirmed the monophyly of the Jahnulales and resolved four clades. Two robustly supported clades comprise the genera Aliquandostipite Inderb. and Megalohypha A. Ferrer & Shearer. A third well-supported clade encompassed species of Brachiosphaera , Jahnula , and Xylomyces . The fourth clade contained isolates of the type species of the genus Jahnula, Jahnula aquatica (Plöttn. & Kirschst.) Kirschst., and two other members of this genus, but this clade was weakly supported. Our data suggest that the presence of very wide, brown, septate hyphae is an important character defining the Jahnulales. Based on molecular and morphological data, we propose the transfer of Jahnula siamensiae Sivichai & E.B.G. Jones and Patescospora separans Abdel-Wahab & El-Shar. to Aliquandostipite and emend the description of the Jahnulales.

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Phylogeny of the genus Bryoria

The Lichenologist ◽

10.1017/s0024282911000132 ◽

2011 ◽

Vol 43 (6) ◽

pp. 617-638 ◽

Cited By ~ 32

Author(s):

Leena MYLLYS ◽

Saara VELMALA ◽

Håkon HOLIEN ◽

Pekka HALONEN ◽

Li-Song WANG ◽

...

Keyword(s):

Growth Form ◽

Sequence Data ◽

Molecular Study ◽

Morphological Characters ◽

Ssu Rdna ◽

Species Status ◽

Infrageneric Classification ◽

Rdna Sequence Data ◽

Cladistic Analyses ◽

Current Species

AbstractThe phylogenetic relationships of the genus Bryoria were examined using ITS, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and mitochondrial SSU rDNA sequence data in addition to 20 chemical and morphological characters. This first comprehensive molecular study to assess Bryoria phylogeny includes representatives from all the traditionally recognized four sections. Combined cladistic analyses of 88 Bryoria specimens representing at least 25 species resulted in highly resolved phylogenies. Based on the results, a new infrageneric classification for the genus is proposed. Five sections are recognized, largely corresponding to the existing classification, with the addition of section Americanae. The study shows that while most species with an erect growth-form are clearly monophyletic, current species status of many pendent taxa can be questioned.

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Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization ofEphesiella,EphesiopsisandSphaerodorum

PeerJ ◽

10.7717/peerj.5783 ◽

2018 ◽

Vol 6 ◽

pp. e5783 ◽

Cited By ~ 1

Author(s):

María Capa ◽

Torkild Bakken ◽

Karin Meißner ◽

Arne Nygren

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Intraspecific Variability ◽

Morphological Data ◽

Nominal Species ◽

Type Specimens ◽

Diagnostic Features ◽

28S Rdna Sequence

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms:Ephesiella,EphesiopsisandSphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members ofEphesiellaare characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers),Sphaerodorumbear only simple chaetae, andEphesiopsishave both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified asEphesiellaandSphaerodorum,based on chaeta morphology, were performed.SphaerodorumandEphesiellawere recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization ofEphesiopsis.

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Phylogeny of infraorder Sejina (Acari: Mesostigmata)

Zootaxa ◽

10.11646/zootaxa.629.1.1 ◽

2004 ◽

Vol 629 (1) ◽

pp. 1 ◽

Cited By ~ 13

Author(s):

MARIAM LEKVEISHVILI ◽

HANS KLOMPEN

Keyword(s):

Dna Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Sister Group ◽

Morphological Characters ◽

Morphological Data ◽

Data Sets ◽

Dna Sequence Data

Phylogenetic relationships among the families in the infraorder Sejina and the position of Sejina relative to other infraorders of Mesostigmata are re-examined based on molecular and morphological data. Data sets included DNA sequence data for complete 18S, EF-1 , partial CO1genes, and 69 morphological characters. The two families of Heterozerconina consistently group within Sejina, and we propose to synonymize Heterozerconina with Sejina (Sejina s.l). Microgyniina is not the closest relative of Sejina. Rather, Sejina s.l. most often groups with Gamasina. Uropodellidae and Ichthyostomatogasteridae are sister groups and this lineage forms the sister group to Discozerconidae plus Heterozerconidae. Overall, we recognize 5 families within Sejina: Uropodellidae, Ichthyostomatogasteridae, Sejidae, Discozerconidae, and Heterozerconidae.

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A Phylogenetic Investigation of the New Zealand Pteridaceae Ferns

10.26686/wgtn.16934449.v1 ◽

2021 ◽

Author(s):

◽

Whitney L M Bouma

Keyword(s):

New Zealand ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Native Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Taxonomic Confusion ◽

Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

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Further phylogenetic studies of the Polychaeta using 18S rDNA sequence data

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315404010240h ◽

2004 ◽

Vol 84 (5) ◽

pp. 949-960 ◽

Cited By ~ 31

Author(s):

Kathryn A. Hall ◽

Pat A. Hutchings ◽

Donald J. Colgan

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Cladistic Analysis ◽

Sister Group ◽

Morphological Data ◽

Phylogenetic Studies ◽

Rdna Sequence Data ◽

Substantial Progress ◽

18S Rdna Sequence

The integration of molecular and morphological approaches has produced substantial progress in understanding the higher classification of most major invertebrate groups. The striking exception to this is the Polychaeta. Neither the membership nor the higher classification of this group has been robustly established. Major inconsistencies exist between the only comprehensive cladistic analysis of Polychaeta using morphological data and the DNA sequence studies covering all or part of the taxon.We have compiled a dataset of available nearly complete 18S ribosomal DNA sequences and collected an additional 22 sequences (20 Polychaeta in 19 taxa, one Myzostomida and one Phoronida) to obtain more comprehensive coverage of polychaete diversity for this gene. Analyses of the data do not resolve all inconsistencies among current hypotheses of polychaete phylogeny. They do support the recognition (in whole or part) of some clades such as the Eunicida, Phyllodocida and Terebellida that have been proposed on morphological grounds. Our analyses contradict the Canalipalpata and the Scolecida. Although the polychaete sister-group to the Clitellata is not clearly resolved in our analyses, the clitellates are always recovered as a derived clade within the Polychaeta. Increased taxon sampling is required to elucidate further the phylogeny of the Polychaeta.

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Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

Antarctic Science ◽

10.1017/s0954102009990253 ◽

2009 ◽

Vol 21 (6) ◽

pp. 565-570 ◽

Cited By ~ 15

Author(s):

Kristen L. Kuhn ◽

Thomas J. Near

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Single Copy ◽

Morphological Characters ◽

Mitochondrial Genes ◽

Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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Description and experimental transmission of Tetracapsuloides vermiformis n. sp. (Cnidaria: Myxozoa) and guidelines for describing malacosporean species including reinstatement of Buddenbrockia bryozoides n. comb. (syn. Tetracapsula bryozoides)

Parasitology ◽

10.1017/s0031182016001931 ◽

2016 ◽

Vol 144 (4) ◽

pp. 497-511 ◽

Cited By ~ 4

Author(s):

SNEHA PATRA ◽

ASHLIE HARTIGAN ◽

DAVID J. MORRIS ◽

ALENA KODÁDKOVÁ ◽

ASTRID S. HOLZER

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Morphological Characters ◽

Experimental Transmission ◽

Rdna Sequence Data ◽

Differential Characters ◽

Present Description ◽

Fredericella Sultana ◽

18S Rdna Sequence ◽

Molecular Characters

SUMMARYThis paper provides the first detailed description of a Tetracapsuloides species, Tetracapsuloides vermiformis n. sp., with vermiform stages in the bryozoan host, Fredericella sultana, and its experimental transmission from F. sultana to Cyprinus carpio. The suitability of morphological, biological and 18S rDNA sequence data for discrimination between malacosporean species is reviewed and recommendations are given for future descriptions. Presently, malacosporean species cannot be differentiated morphologically due to their cryptic nature and the lack of differential characters of spores and spore-forming stages in both hosts. We examined biological, morphological and molecular characters for the present description and for revising malacosporean taxonomy in general. As a result, Buddenbrockia plumatellae was split into two species, with its sac-like stages being ascribed to Buddenbrockia bryozoides n. comb. In addition to ribosomal DNA sequences multiple biological features rather than morphological characters are considered essential tools to improve malacosporean taxonomy in the future according to our analysis of the limited traits presently available.

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Studies on Wrightoporia from China 3. Wrightoporia subavellanea sp. nov. based on morphological characters and rDNA sequence data

Phytotaxa ◽

10.11646/phytotaxa.175.4.4 ◽

2014 ◽

Vol 175 (4) ◽

pp. 225 ◽

Cited By ~ 6

Author(s):

JIA-JIA CHEN ◽

Bao-Kai Cui

Keyword(s):

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Growth Habit ◽

Sequence Data ◽

Southern China ◽

Molecular Study ◽

Morphological Characters ◽

Molecular Data ◽

Internal Transcribed Spacer Region ◽

Rdna Sequence Data

Wrightoporia subavellanea sp. nov. is described and illustrated from southern China on the basis of morphological characters and molecular data. It is characterized by an annual growth habit, resupinate basidiocarps with white rhizomorphs, large pores, narrow and strongly dextrinoid skeletal hyphae, broadly ellipsoid to subglobose, thick-walled, finely asperulate and strongly amyloid basidiospores (3.8–4.2 × 2.8–3.2 µm), and presence of gloeoplerous hyphae in trama. A molecular study based the combined ITS (internal transcribed spacer region) and nLSU (the large nuclear ribosomal RNA subunit) dataset supported the position of the new species in Wrightoporia. A key to accepted species of Wrightoporia in China is provided.

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A preliminary phylogenetic analysis of the genus Fulvius Stål (Hemiptera:Miridae: Cylapinae) based on molecular data

Insect Systematics & Evolution ◽

10.1163/187631208788784291 ◽

2008 ◽

Vol 39 (4) ◽

pp. 407-417 ◽

Cited By ~ 8

Author(s):

Izabela Sadowska-Woda ◽

Tobias Malm ◽

Frédéric Chérot

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Large Subunit ◽

Morphological Characters ◽

Molecular Data ◽

Dna Sequence Data ◽

Species Groups ◽

Coi Sequences ◽

Preliminary Phylogenetic Analysis

AbstractThe systematics and phylogeny of the genus Fulvius Stål remains unclear. We present herein the first analysis of the phylogenetic relationships within the genus Fulvius based on DNA sequences. The phylogenetic interrelationships in the genus Fulvius are investigated using partial DNA sequence data from two mitochondrial genes, the 16S ribosomal large subunit and the cytochrome oxidase I (COI). DNA sequences for Fulvius species representing three different subgroups distinguished previously on the base of morphological characters alone are compared to sequences from the closely related genera Rhinocylapidius and Cylapus. The data are analyzed using parsimony and Bayesian inference. The results confirm that on the basis of molecular data we can distinguish the same congruent groups of Fulvius species as using morphological characters, however with inclusion of the specimens of the genus Rhinocylapidius in the bifenestratus-group. Additional studies are needed to clarify the phylogenetic relationships within the tribe Fulviini, as well as within the genus Fulvius and its relation to Rhinocylapidius. However, the results of this study suggest that 16S and COI sequences will be very useful as molecular markers for such studies among these species-groups.

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Phylogenetic relationships in the tribe Alysseae (Brassicaceae) based on nuclear ribosomal ITS DNA sequences

Botany ◽

10.1139/b08-013 ◽

2008 ◽

Vol 86 (4) ◽

pp. 315-336 ◽

Cited By ~ 45

Author(s):

Suzanne I. Warwick ◽

Connie A. Sauder ◽

Ihsan A. Al-Shehbaz

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Morphological Characters ◽

Data Support ◽

Its Dna Sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 85 species (131 accessions) were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the tribe Alysseae (Brassicaceae). Both maximum parsimony and maximum likelihood analyses support the recognition of the tribe Alysseae s. str. (12 genera: Alyssoides , Alyssum , Aurinia , Berteroa , Bornmuellera , Clastopus , Clypeola , Degenia , Fibigia , Galitzkya , Hormathophylla , and Physoptychis ). Six well-supported clades were recognized within the Alysseae clade, including two Alyssum clades (one of which includes Clypeola ), an Alyssoides and allies clade (includes Alyssoides , Bornmuellera , Clastopus , Degenia , Fibigia , Hormathophylla , and Physoptychis ), a Berteroa and allies clade (includes Aurinia , Berteroa , and Galitzkya ), a Bornmuellera clade, and a Hormathophylla clade. Morphological and cytological support for these clades is reviewed. The ITS data support the exclusion of the following taxa from the Alysseae, with appropriate tribal assignment given in parentheses: Alyssum klimesii Al-Shehbaz (Camelineae), Asperuginoides (unresolved), Athysanus (Arabideae), Botschantzevia (Arabideae), Didymophysa (unresolved), Farsetia (Malcolmieae), Lobularia (Malcolmieae), and Ptilotrichum (Arabideae). Farsetia and Lobularia are inferred to be monophyletic, and based on molecular and morphological characters they are assigned to Malcolmieae, a recently described tribe.

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