Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

Phylogenetic relationships of three tribes of cloacinine nematodes (Strongylida: Chabertiidae) from macropodid marsupials

2018 ◽  
Vol 93 (04) ◽  
pp. 486-493 ◽  
Author(s):  
N.B. Chilton ◽  
F. Huby-Chilton ◽  
A. Koehler ◽  
R.B. Gasser ◽  
I. Beveridge
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Host Genus ◽  
Single Host

AbstractThe phylogenetic relationships of 42 species of cloacinine nematodes belonging to three tribes (Coronostrongylinea, Macropostrongylinea and Zoniolaiminea) were examined based on sequence data of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. All nematodes examined are parasites of Australian macropodid marsupials. None of the three nematode tribes was monophyletic. Paraphyly was also encountered in three genera: Papillostrongylus, Monilonema and Wallabinema. Species within the genus Thallostonema were limited to a single host genus (i.e. Thylogale), whereas species within the five principal genera (Coronostrongylus, Macropostrongylus, Popovastrongylus, Wallabinema and Zoniolaimus) were found to occur in multiple host genera. Potential modes of evolution among these nematodes are discussed.

Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

scholarly journals Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Anson V. Koehler ◽  
Ross Hall ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Sister Relationship

Abstract Background The subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences. Methods The sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets. Results Within the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related to Oesophagostomum spp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae. Conclusion The current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials. Graphical Abstract

scholarly journals Molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus inferred from analysis of internal transcribed spacer sequences

2015 ◽  
Vol 22 (2) ◽  
pp. 111-118 ◽  
Author(s):  
Fahad M.A. Al-Hemaid ◽  
M. Ajmal Ali ◽  
Joongku Lee ◽  
Soo-Yong Kim ◽  
Md. Oliur Rahman
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Evolutionary Relationships ◽  
Local Alignment ◽  
Its Sequence ◽  
Molecular Phylogenetic ◽  
Plant Taxon

The present study explored molecular phylogenetic analysis of 28 species of Euphorbia L. for the identification and establishment of molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus based on the internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA). The sequence similarity search using Basic Local Alignment Search Tool (BLAST) of the ITS sequence of E. scordifolia showed the closest sequence similarity to E. supina Raf. The analysis of ITS sequence data revealed four major clades consistent with subgeneric classifications of the genus. Molecular data support placement of E. scordifolia in the subgenus Chamaesyce.Bangladesh J. Plant Taxon. 22(2): 111-118, 2015 (December)

Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

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