A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data

2005 ◽  
Vol 83 (11) ◽  
pp. 1457-1477 ◽  
Author(s):  
Sigisfredo Garnica ◽  
Michael Weiß ◽  
Bernhard Oertel ◽  
Franz Oberwinkler
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Nuclear Rdna ◽  
Ecological Data ◽  
Natural Classification ◽  
Geographical Patterns ◽  
Rdna Sequences ◽  
Molecular Phylogenetic

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable disagreement with earlier morphology-based hypotheses concerning the infrageneric delimitations in Cortinarius. We propose a new base for a more natural classification system in Cortinarius involving the taxonomic rearrangement of the species into the following major lineages that we informally designate as “clades” at this time: (1) phlegmacioid species are included in Alluti, Amarescentes, Arguti, Calochroi, Caerulescentes, Percomes, Phlegmacioides, Phlegmacium, Purpurascentes, Scauri, and Vulpini; (2) the Heterocliti clade includes species of the subgenera Leprocybe and Cystogenes ; (3) most of the Myxacium species are included in the Delibuti and Myxacium clades; (4) part of Rozites are included in the Rozites clade; (5) the north-hemispheric species of subgenus Dermocybe are included in the Dermocybe clade and part of the south-hemispheric species in the Splendidi clade; (6) part of Sericeocybe are integrated in the Anomali and Telamonia clades; (7) members of subgenus Cortinarius are assigned to the Cortinarius clade; (8) telamonioid taxa are included in the Obtusi, Renidentes, and Telamonia clades. Several Cortinarius species with peculiar patterns of morphology and basidiome coloration had isolated positions in the sequence analysis, and the evolutionary relationships among the major lineages remained unresolved. Our results suggest the convergent evolution of certain morphological traits across phylogenetically divergent lineages in Cortinarius. However, combinations of features such as pileipellis anatomy, spore shape, veil coloration, basidiome pigments, and stipe shape appear useful to circumscribe clades. Our molecular phylogenetic analysis allows insights in global geographical patterns of species distribution within the major lineages in the genus Cortinarius. The clade structure proposed here could be used as backbone for further more detailed systematic studies.

Two Erysiphe species associated with recent outbreak of soybean powdery mildew: results of molecular phylogenetic analysis based on nuclear rDNA sequences

Mycoscience ◽  
2002 ◽  
Vol 43 (4) ◽  
pp. 333-341 ◽  
Author(s):  
Susumu Takamatsu ◽  
Yusuke Taguchi ◽  
Hyeon-Dong Shin ◽  
Urailak Paksiri ◽  
Saranya Limkaisang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Molecular Phylogenetic Analysis ◽  
Nuclear Rdna ◽  
Rdna Sequences ◽  
Recent Outbreak ◽  
Molecular Phylogenetic

Pilaira australis sp. nov. (Mucorales, Mucoromycota) isolated from emu faeces in Australia

Phytotaxa ◽  
2017 ◽  
Vol 329 (3) ◽  
pp. 277 ◽  
Author(s):  
ANDREW S. URQUHART ◽  
PAULINE M. L. COULON ◽  
ALEXANDER IDNURM
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Identification ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Unique Combination ◽  
Dromaius Novaehollandiae ◽  
Molecular Phylogenetic ◽  
Carbon Utilisation ◽  
A New Species

Pilaira australis, a new species of fungus in the coprophilous genus Pilaira, was isolated from emu (Dromaius novaehollandiae) faeces and is described. Morphologically, the species resembles other species in the genus, particularly P. moreaui, except differs in its unique combination of sporangiophore height and sporangiospore length. Molecular phylogenetic analysis indicates that P. australis is distinct from other species in the genus with two regions, the internal transcribed spacers (ITS) and a fragment of the pyrG gene, showing 91% and 90% identity to the nearest species, respectively. Ultrastructure features and carbon utilisation were determined for P. australis, and may provide characteristics for species identification in this genus.

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

2008 ◽  
Vol 98 (5) ◽  
pp. 499-507 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Host Specificity ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Primary Host ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

Paleontological data and molecular phylogenetic analysis

Paleobiology ◽  
1994 ◽  
Vol 20 (3) ◽  
pp. 259-273 ◽  
Author(s):  
Andrew B. Smith ◽  
D. T. J. Littlewood
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Sequence Data ◽  
Molecular Data ◽  
Total Evidence ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Sequence Data ◽  
Geological Past ◽  
Molecular Phylogenetic ◽  
Rates Of Molecular Evolution

Molecular data are becoming an indispensable tool for the reconstruction of phylogenies. Fossil molecular data remain scarce, but have the potential to resolve patterns of deep branching and provide empirical tests of tree reconstruction techniques. A total evidence approach, combining and comparing complementary morphological, molecular and stratigraphical data from both recent and fossil taxa, is advocated as the most promising way forward because there are several well-established problems that can afflict the analysis of molecular sequence data sometimes resulting in spurious tree topologies. The integration of evidence allows us to: (1) choose suitable taxa for molecular phylogenetic analysis for the question at hand; (2) discriminate between conflicting hypotheses of taxonomic relationship and phylogeny; (3) evaluate procedures and assumptions underlying methods of building trees; and (4) estimate rates of molecular evolution in the geological past. Paleontology offers a set of independent data for comparison and corroboration of analyses and provides the only direct means of calibrating molecular trees, thus giving insight into rates of molecular evolution in the geological past.

scholarly journals Zehneria grandibracteata (Cucurbitaceae), an overlooked new species from western Kenyan forests

PhytoKeys ◽  
2020 ◽  
Vol 165 ◽  
pp. 85-98
Author(s):  
Neng Wei ◽  
Zhi-Xiang Zhong ◽  
David Kimutai Melly ◽  
Solomon Kipkoech ◽  
Benjamin Muema Watuma ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Western Kenya ◽  
Entire Plant ◽  
Molecular Phylogenetic ◽  
Morphological And Molecular Data ◽  
A New Species

Zehneria grandibracteata, a new species of Cucurbitaceae from western Kenya, is described here, based on morphological and molecular data. It has long been misidentified as the widely-distributed species Z. scabra. However, it differs by its ovate leafy probract at the base of the inflorescences, subglabrous condition of the entire plant, shorter receptacle-tube and filaments, as well as denser and sessile inflorescences. Furthermore, the molecular phylogenetic analysis of Zehneria, based on nrITS sequences, further supports the argument that Z. grandibracteata should be segregated from Z. scabra.

Stellaria multipartita (Caryophyllaceae), a new species from Chongqing, China

Phytotaxa ◽  
2020 ◽  
Vol 442 (3) ◽  
pp. 196-204 ◽  
Author(s):  
YAN-FENG SONG ◽  
MENG LI ◽  
BO XU ◽  
SHUI-FEI CHEN ◽  
LIN CHEN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Morphological And Molecular Data ◽  
A New Species

Stellaria multipartita sp. nov. (Caryophyllaceae) from Chongqing, China, is described and illustrated based on morphological and molecular data. The new species is similar to S. radians by the palmately fimbriate petals with more linear divisions. Different characters are: shape of the leaves (oblong-triangular to ovate-triangular vs. oblong-lanceolate to ovate-lanceolate in S. radians), petals (10–12-cleft vs. 5–7-cleft in S. radians), and seeds (with mamillate ornamentation vs. scrobiculate ornamentation in S. radians). A molecular phylogenetic analysis supports the recognition of Chongqing population as a new species for science.

Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification

2008 ◽  
Vol 21 (1) ◽  
pp. 1 ◽  
Author(s):  
Jacinta M. Burke ◽  
Michael J. Bayly ◽  
Peter B. Adams ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Divergence ◽  
Its Region ◽  
Sister Group ◽  
Main Group ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna ◽  
Sister Relationship ◽  
Asian Clade ◽  
Molecular Phylogenetic

Sequences of the internal transcribed spacers (ITS) of nuclear rDNA were obtained for a broad range of dendrobium orchids for phylogenetic analysis using parsimony. A progressive approach was used to identify functional outgroups for analysis of all taxa in Dendrobium sect. Dendrocoryne. Our first, broadest analysis confirmed the results of other workers that Dendrobium sensu lato includes a major Australasian clade and a sister Asian clade. In the Australasian clade, the New Zealand species D. cunninghamii (=gen. Winika, Clements et al. 1997) was identified as the sister group to a well supported clade that includes the genera Cadetia, Diplocaulobium and Flickingeria, and Dendrobium sects Grastidium, Latouria, Spatulata, Australorchis (=gen. Australorchis), Rhizobium (= gen. Dockrillia) and Dendrocoryne. Sect. Dendrocoryne is probably polyphyletic, with two species, D. aemulum and D. callitrophilum (=gen. Tropilis), outside the main group and sect. Rhizobium (= gen. Dockrillia) nested within it. Sect. Australorchis (= gen. Australorchis) is possibly the sister group to the clade of Rhizobium plus the main group of Dendrocoryne. Thelychiton (a genus reinstated for several species in Dendrocoryne) is polyphyletic, given that Tetrabaculum (=D. tetragonum complex) and Dockrillia fall within the same clade. The splitting of the Australasian dendrobiums into various genera by other authors is excessive and unnecessary, and alternative taxonomic treatments are offered here for debate. Our study included accessions for all varieties in the following three widespread eastern Australian species: D. speciosum, D. kingianum and D. tetragonum. Each of these species showed significant sequence divergence between particular geographic regions, but some varieties had identical sequences. The splitting of D. speciosum into 11 species is not supported. We identified pseudogenes in the ITS region for D. fleckeri and D. finniganense, which appear to have evolved before these two species diverged, but support their sister relationship. Sequences for D. callitrophilum and D. (Grastidium) baileyi (the latter from GenBank) also appear to be pseudogenes, and these taxa need further study.

A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea: Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia: Macropodoidea) 

Zootaxa ◽  
2020 ◽  
Vol 4851 (2) ◽  
pp. 271-288
Author(s):  
I. BEVERIDGE ◽  
A. JABBAR ◽  
A. KOEHLER ◽  
T. SUKEE
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Morphological Characteristics ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Phenetic Classification

A phylogenetic analysis of the genera of the strongyloid sub-family Cloacininae from macropodoid marsupials in Australasia was undertaken based on morphological characteristics and analysis of concatenated sequences (ITS+) of the first (ITS-1) and second (ITS-2) internal transcribed spacers of nuclear ribosomal DNA. Neither approach provided a robust phylogeny, but similarities between the two methods in terms of generic groupings suggested that substantial revision is needed of the current phenetic classification, with some of the key morphological characteristics currently used to define genera and tribes proving to be homoplasious. 

scholarly journals Molecular Phylogenetic Analysis of Vicia L. (Fabaceae) Taxa Growing in the Southeastern Anatolia Region of Turkey: Based on Internal Transcribed Spacer (ITS)

2021 ◽  
Vol 9 (10) ◽  
pp. 1831-1839
Author(s):  
Alevcan Kaplan ◽  
Alaattin Selçuk Ertekin ◽  
Esra Gündüzler
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacers ◽  
Flowering Plant ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic Analysis ◽  
Conservation Strategies ◽  
Attractive Alternative ◽  
Accurate Identification ◽  
Molecular Phylogenetic ◽  
Species Specific

Leguminosae or Fabaceae is the third-largest flowering plant family and is important in terms of both food production and soil fertility. Wild Vicia species and the genetic diversity of the Southeastern Anatolia Region provide an invaluable resource for the improvement of cultivated temperate feed and legume crops. The rapid progress of technology in recent years has nowmade it possible to use modern techniques in phylogenetic studies and to examine plants in a greater detail using biochemical, cytological and molecular methods to supplement purely systematic studies. The use of molecular phylogenetic analysis is the most attractive alternative strategy for a more accurate identification of the species of the Vicia genus. In the current study, some Vicia L. taxa growing naturally in the Southeastern Anatolia Region were investigated using molecular phylogenetic analysis. Internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced in order to study the phylogenetic relationships of Vicia L. taxa. Lathyrus inconspicuous L. and Lathyrus cassius Boiss. were used as an outgroup. The ITS area was determined to be approximately 479- 672 bp. The ITS sequences were submitted to the NCBI database and accession numbers obtained. The resulting tree clearly groups and separates the sect. Narbonensis, Ervilia, Peregrinae, Lathyroides, Vicia and Cracca species but was less able to distinguish species from sect. Hypechusa and Lentopsis. The data acquired were observed to be reliable in terms of solving the taxonomical problems of the Vicia L. taxa. The morphological distinctions are greatly supported by DNA sequence studies. The species-specific markers developed in this study are useful for early detection of targeted Vicia taxa and can act as a guide to the basic data required for the evolution of systematic breeding and conservation strategies, as well as for germplasm resources.

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