Mitochondrial and nuclear ribosomal DNA data do not support the separation of the Antarctic lichens Umbilicaria kappenii and Umbilicaria antarctica as distinct species

2004 ◽  
Vol 36 (3-4) ◽  
pp. 227-234 ◽  
Author(s):  
Sieglinde OTT ◽  
Marcus BRINKMANN ◽  
Nora WIRTZ ◽  
H. Thorsten LUMBSCH
Keyword(s):  
Distinct Species ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Lsu Rdna ◽  
Data Set ◽  
Rdna Sequences ◽  
Group A ◽  
Nuclear Its ◽  
The Antarctic ◽  
Combined Data

The Antarctic endemics Umbilicariakappenii and U. antarctica are morphologically close, but mainly distinguished by their reproductive strategies. Umbilicaria antarctica propagates by means of thalloconidia. Umbilicaria kappenii lacks thalloconidia, but exhibits a variety of asexual propagules: soredia, adventive lobes and thallyles. We have now employed molecular data from three gene regions to examine the phylogenetic relationships of these two morphotypes. The phylogeny of ten samples and four outgroup taxa (Umbilicaria decussata, U. krascheninnikovii, U. nylanderiana, U. umbilicarioides) was reconstructed using Bayesian and maximum parsimony analyses of a combined data set of nuclear ITS, nuclear LSU rDNA and mitochondrial LSU rDNA sequences. Forty two new partial sequences of 14 specimens were generated. Our results indicate that all samples morphologically referred to U. antarctica and U. kappenii form a monophyletic group. A topology separating the two morphotypes as phylogenetic species is significantly rejected with the data set. It is proposed to place U. kappenii into synonymy with U. antarctica.

A comparison of ITS and LSU nrDNA phylogenies of Fulgensia (Teloschistaceae, Lecanorales), a genus of lichenised ascomycetes

2000 ◽  
Vol 78 (12) ◽  
pp. 1580-1589 ◽  
Author(s):  
Thomas Kasalicky ◽  
Heidi Döring ◽  
Gerhard Rambold ◽  
Mats Wedin
Keyword(s):  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Data Set ◽  
Spliceosomal Introns ◽  
Nuclear Its ◽  
Combined Data

The phylogeny of the lichen genus Fulgensia Massal. & De Not. (Teloschistaceae, Lecanorales) is analysed using maximum parsimony and neighbor joining analyses of nuclear ITS and partial large subunit nuclear ribosomal DNA (nrDNA) sequences. Three matrices were analysed with maximum parsimony; an internal transcribed spacer nrDNA matrix, a large subunit nrDNA matrix, and a combined data set. The internal transcribed spacer region contributes 70% of the informative sites to the combined data set. The topology of the trees resulting from the analysis of the internal transcribed spacer region is identical to the tree topology resulting from the combined analysis, but it shows less resolution at basal parts of the tree. Two sites for putative spliceosomal introns in the large subunit nrDNA, at position 808 and 914 (relative to Saccharomyces cerevisiae) are reported. Fulgensia, as currently understood, is polyphyletic and some species have to be excluded. The molecular analyses identified groups of species within the genus that are also supported by anatomical and morphological characters. The results of the analyses are compared with existing classification concepts based on morphological and anatomical data.Key words: LSU, ITS, nrDNA, introns, Fulgensia, phylogeny.

Virulence, cultivating conditions, and phylogenetic analyses of oomycete parasites in Daphnia

Parasitology ◽  
2008 ◽  
Vol 135 (14) ◽  
pp. 1667-1678 ◽  
Author(s):  
J. WOLINSKA ◽  
K. C. KING ◽  
F. VIGNEUX ◽  
C. M. LIVELY
Keyword(s):  
Food Webs ◽  
Phylogenetic Analyses ◽  
Daphnia Pulex ◽  
Distinct Species ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
Aquatic Food Webs ◽  
Close Phylogenetic Relationship ◽  
Aquatic Food ◽  
The Stability

SUMMARYWe describe the infectivity, virulence, cultivating conditions, and phylogenetic positions of naturally occurring oomycete parasites of Daphnia, invertebrates which play a major role in aquatic food webs. Daphnia pulex individuals were found dead and covered by oomycete mycelia when exposed to pond sediments. We were able to extract 4 oomycete isolates from dead Daphnia and successfully cultivate them. Using the ITS and LSU rDNA sequences, we further showed these isolates to be distinct species. The isolates were experimentally demonstrated to be parasitic and not saprobic. After exposure to the parasites, Daphnia mortality was much higher than that reported for Daphnia infected with other known parasite species. Therefore, it is likely that oomycete parasites are important selective pressures in natural Daphnia populations. Moreover, their close phylogenetic relationship to parasites of fish and algae suggests that the stability of aquatic food webs (i.e. fish–Daphnia–algae) might be influenced by the shared parasite communities.

DESCRIPTION OF MUCOR PERNAMBUCOENSIS (MUCORALES, MUCOROMYCOTA), A NEW SPECIES ISOLATED FROM THE BRAZILIAN UPLAND RAINFOREST

Phytotaxa ◽  
2018 ◽  
Vol 350 (3) ◽  
pp. 274 ◽  
Author(s):  
CATARINA L. F. DE LIMA ◽  
DIOGO X. LIMA ◽  
CARLOS A. F. DE SOUZA ◽  
RAFAEL J. V. DE OLIVEIRA ◽  
INGRID B. CAVALCANTI ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
A New Species

The Mucor genus mostly comprises saprobe specimens which are commonly isolated from herbivore dung, fruit and soil. Morphologically, Mucor specimens produce simple or branched sporangiophores without basal rhizoids and non-apophysate sporangia. During a survey of Mucorales in soil from an upland rainforest area in Pernambuco, Brazil, one specimen of Mucor was isolated and characterized based on morphological, physiological and molecular data (ITS1-5.8S-ITS2 and LSU rDNA sequences). The specimen is characterized by producing strongly sympodially branched sporangiophores and sporangiospores which can contain one or more granules at each end. The columellae are frequently globose or obovoid, some ovoid or cylindrical with a truncate base, rarely piriform.  It grew better at 25ºC, with no development at 35ºC. Based on the evidence of the analyzed datasets, a new species of Mucor is proposed.

Morphological and molecular data support the monophyletic nature of the genus Pratylenchoides Winslow, 1958 (Nematoda: Merliniidae) and reveal its intrageneric structuring

Nematology ◽  
2016 ◽  
Vol 18 (10) ◽  
pp. 1165-1183 ◽  
Author(s):  
Kourosh Azizi ◽  
Ali Eskandari ◽  
Akbar Karegar ◽  
Reza Ghaderi ◽  
Sven van den Elsen ◽  
...  
Keyword(s):  
Molecular Data ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
The Family ◽  
Lateral Lines ◽  
Male Head ◽  
Single Transition ◽  
Pharyngeal Gland ◽  
Morphological And Molecular Data ◽  
The Relationship

The genus Pratylenchoides has recently been transferred from the family Pratylenchidae to Merliniidae. To investigate further the relationship between these ‘Pratylenchus-like’ species (residing in the subfamily Pratylenchoidinae) and the subfamily Merliniinae, more than 500 soil samples were collected from various natural and agronomic habitats in the northern and north-western provinces of Iran. In this study, paratypes or populations of 22 species of Pratylenchoides, including the Iranian populations of P. alkani, P. crenicauda, P. erzurumensis, P. laticauda, P. nevadensis, P. ritteri and an undescribed species, were studied. Intra- and interspecies variation of the following characters were investigated: position of the pharyngeal gland nuclei, shape of female and male head, striation of female tail terminus, number of lateral lines at mid-body and in phasmid region for females, presence of intestinal fasciculi, and shape of sperm. Combining morphological and molecular data prompted us to propose two clusters of related Pratylenchoides species. One cluster includes P. crenicauda, P. variabilis and P. erzurumensis, whereas the second cluster consists of P. alkani, P. nevadensis and P. ritteri. Our data point to a sister positioning of P. magnicauda vis-à-vis all Pratylenchoides species included in this research. Analyses of SSU rDNA (for family and subfamily relationships) and partial LSU rDNA sequences (for intrageneric relationships) data revealed: i) the distal and nested positioning of all Pratylenchoidinae within the Merliniidae; ii) the single transition from ectoparasitism to migratory endoparasitism within the family Merliniidae corresponds with the current subfamily partitioning; and iii) support for the monophyletic nature of the genus Pratylenchoides.

scholarly journals Taxonomic Transfer of the Red Algal Genus Gloiosaccion to Chrysymenia (Rhodymeniaceae, Rhodymeniales), Including the Description of a New Species, Chrysymenia pseudoventricosa, for the Gulf of Mexico

Phytotaxa ◽  
2016 ◽  
Vol 243 (1) ◽  
pp. 54 ◽  
Author(s):  
William E Schmidt ◽  
Carlos Frederico D. Gurgel ◽  
Suzanne L. Fredericq
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Gulf Of Mexico ◽  
Caribbean Sea ◽  
Distinct Species ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
Red Algal ◽  
Algal Genus ◽  
A New Species

Gloiosaccion Harvey, with type G. brownii (Rhodymeniaceae, Rhodymeniales), is a red algal genus characterized by the presence of large, hollow and saccate vesicle-shaped thalli arising from small solid axes. Whereas Gloiosaccion has traditionally been viewed as being closely related to Botryocladia (Agardh) Kylin, a multi-marker phylogenetic analysis based on chloroplast-encoded rbcL and UPA and nuclear LSU rDNA sequences instead places Gloiosaccion brownii and G. pumila in the Chrysymenia clade that includes the generitype C. ventricosa (Lamouroux) J. Agardh. Gloiosaccion is reduced to synonymy with Chrysymenia J. Agardh, a taxonomic move first advocated by De Toni in 1900. In addition to C. brownii (Harvey) De Toni, “Gloiosaccion” brownii var. firmum Harvey and “G.” pumilum J. Agardh are recognized as the distinct species Chrysymenia coriacea comb. et stat. nov. and C. pumila (J. Agardh) Weber-van Bosse, respectively. A new species, C. pseudoventricosa sp. nov. is proposed to accommodate specimens going under the name C. ventricosa (J.V. Lamouroux) J. Agardh from the Gulf of Mexico and Caribbean Sea.

Molecular data support rejection of the generic concept in the Coccotremataceae (Ascomycota)

2001 ◽  
Vol 33 (4) ◽  
pp. 315-321 ◽  
Author(s):  
Imke Schmitt ◽  
María Ines Messuti ◽  
G. Benno Feige ◽  
H. Thorsten Lumbsch
Keyword(s):  
Morphological Difference ◽  
Its Region ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Data Sets ◽  
Data Set ◽  
Combined Analysis ◽  
Generic Concept ◽  
Parametric Bootstrapping ◽  
Alternative Topology

AbstractThe Coccotremataceae is a small family including two genera: Coccotrema with a crustose, granulate to verrucose thallus and Lepolichen with terete lobes and rhizines. The generic concept based on this morphological difference was re-evaluated using three molecular markers, mt SSU rDNA, nu LSU rDNA, and the nu ITS region. The analysis of the ITS region does not provide sufficient resolution within the Coccotremataceae, while the other two data sets contradict the current generic concept. The mt SSU and nu LSU data sets and the combined analysis of the two data sets all place Lepolichen within Coccotrema. However, an alternative topology with monophyletic Coccotrema cannot be rejected when the ITS data set is included in the combined analyses. This shortcoming of the ITS data set can be overcome by the combined analysis of all three data sets, where monophyletic Coccotrema can be rejected using parametric bootstrapping, as in the mt SSU and nu LSU data sets and combination thereof. It is proposed to reduce Lepolichen into synonymy with Coccotrema. The correct name for the only species previously placed in Lepolichen is Coccotrema coccophontm (Mont.) I. Schmitt, Messuti & Lumbsch.

scholarly journals A new species of Cryptomonas (Cryptophyceae) from the Western Urals (Russia)

2020 ◽  
Author(s):  
Nikita A. Martynenko ◽  
Evgeniy S. Gusev ◽  
Pavel V. Kulizin ◽  
Elena E. Guseva ◽  
Kevin McCartney ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Nuclear Rdna ◽  
Ural Mountains ◽  
Rdna Its2 ◽  
Rdna Sequences ◽  
Compensatory Base Changes ◽  
Morphological And Molecular Data ◽  
A New Species

A new species, Cryptomonas uralensis Martynenko, Gusev, Kulizin & Guseva sp. nov., is described from western slopes of the Ural Mountains (Russia) based on morphological and molecular data. Phylogenetic relationships inferred from nuclear SSU and LSU rDNA sequences show that the new species forms a clade with C. tetrapyrenoidosa Skuja emend. Hoef-Emden & Melkonian. Comparison of secondary structures of nuclear rDNA ITS2, including analysis of Compensatory Base Changes (CBC), confirms the separation between C. uralensis sp. nov. and C. tetrapyrenoidosa. Cell morphology and sizes of C. uralensis sp. nov. are very similar to C. tetrapyrenoidosa and C. pyrenoidifera, and C. uralensis sp. nov. may thus represent a species that can only be reliably identified using molecular data.

Eutrema racemosum (Eutremeae, Brassicaceae), a new tetraploid species from southwest China

Phytotaxa ◽  
2015 ◽  
Vol 224 (2) ◽  
pp. 185 ◽  
Author(s):  
Guoqian Hao ◽  
Ihsan Al-Shehbaz ◽  
Qian Wang ◽  
Qianlong Liang ◽  
Jianquan Liu
Keyword(s):  
Southwest China ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Distinct Species ◽  
Molecular Data ◽  
Small Genome ◽  
Sequence Variations ◽  
Nuclear Its ◽  
Well Differentiated ◽  
Germination Experiments

The new species Eutrema racemosum is described, and its relationship to the closely related E. heterophyllum and E. edwardsii are discussed based on morphological, cytological, and molecular data.  The novelty differs from E. heterophyllum by having elongated racemes and from E. edwardsii by somewhat reflexed fruiting pedicels. Four chloroplast DNA fragments and nuclear ITS region were sequenced for multiple individuals of each species. Three species show distinct and stable sequence variations. Eutrema racemosum and E. heterophyllum form a clade sister to that of E. edwardsii in phylogenetic analyses of sequence variations. Our cytological studies revealed that E. heterophyllum is a diploid with the small genome size, while E. racemosum is a tetraploid with duplicate genomes. These available data support the recognition of E. racemosum as a distinct species well differentiated morphologically and genetically, as well as well-isolated reproductively from its sister species E. heterophyllum. We further found some interspecific triploid hybrids between tetraploid E. racemosum and diploid E. heterophyllum, which seem to be sterile according to our germination experiments.

Generic Circumscription in Menyanthaceae: A Phylogenetic Evaluation

2008 ◽  
Vol 33 (3) ◽  
pp. 598-612 ◽  
Author(s):  
Nicholas P. Tippery ◽  
Donald H. Les ◽  
Donald J. Padgett ◽  
Surrey W. L. Jacobs
Keyword(s):  
South African ◽  
Sequence Data ◽  
Molecular Data ◽  
Homogeneity Test ◽  
Strict Sense ◽  
Dna Sequence Data ◽  
The Family ◽  
Nuclear Its ◽  
Morphological And Molecular Data ◽  
Combined Data

Menyanthaceae consist of five genera of aquatic and wetland plants distributed worldwide. The three monotypic genera (Liparophyllum, Menyanthes, and Nephrophyllidium) are clearly differentiated morphologically, but the two larger genera (Nymphoides and Villarsia) contain several taxa of uncertain affinity. We undertook a phylogenetic analysis, using a combination of morphological and molecular data, to resolve relationships among species and to evaluate the current circumscription of genera. DNA sequence data for nuclear (ITS) and chloroplast (rbcL and trnK/matK) gene regions were largely congruent (by partition-homogeneity test), and a combined data phylogeny revealed several strongly supported relationships. Analyses using asterid outgroup taxa supported the monophyly of Menyanthaceae. Menyanthes trifoliata and Nephrophyllidium crista-galli comprised a clade sister to the remainder of the family. Species of Nymphoides, except N. exigua, resolved to a single, deeply-nested clade, indicating that the floating-leaved habit is derived evolutionarily within the family. The genus Villarsia comprised a paraphyletic grade toward Nymphoides, wherein the species resolved to three assemblages: (1) a shallowly nested clade containing V. albiflora, V. calthifolia, V. marchantii, V. parnassifolia, V. reniformis, and V. umbricola; (2) an isolated South African clade including V. manningiana and the type species, V. capensis; and (3) a heterogeneous clade of taxa from three genera, including V. exaltata, V. lasiosperma, and V. latifolia, plus the anomalous species V. capitata, V. congestiflora, Liparophyllum gunnii, and Nymphoides exigua. Our results indicate that the genera Menyanthes, Nephrophyllidium, and Nymphoides should be retained as circumscribed, with the exception that Nymphoides exigua should be restored to Villarsia. The genus Villarsia, however, eventually should be subdivided among monophyletic lineages, whereby in the strict sense Villarsia would contain only South African taxa.

scholarly journals Lecanicillium cauligalbarum sp. nov. (Cordycipitaceae, Hypocreales), a novel fungus isolated from a stemborer in the Yao Ren National Forest Mountain Park, Guizhou

MycoKeys ◽  
2018 ◽  
Vol 43 ◽  
pp. 59-74 ◽  
Author(s):  
Ye-Ming Zhou ◽  
Jun-Rui Zhi ◽  
Mao Ye ◽  
Zhi-Yuan Zhang ◽  
Wen-Bo Yue ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Forest Floor ◽  
Sequence Data ◽  
Distinct Species ◽  
National Forest ◽  
Data Set ◽  
Forest Mountain ◽  
A New Species ◽  
Combined Data

A new species of entomopathogenic fungi,Lecanicilliumcauligalbarum, was discovered from a survey of invertebrate-associated fungi in the Yao Ren National Forest Mountain Park in China. The synnemata of this species emerged from the corpse of a stemborer (Lepidoptera), which was hidden amongst pieces of wood on the forest floor. It differs from morphologically similarLecanicilliumspecies mainly in its short conidiogenous cells and ellipsoid to ovoid and aseptate conidia. Phylogenetic analysis of a combined data set comprising ITS,SSU,LSU,TEF,RPB1andRPB2sequence data supported the inclusion ofL.cauligalbarumin theLecanicilliumgenus and its recognition as a distinct species.

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