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 Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India

2007 ◽  
Vol 57 (2) ◽  
pp. 414-418 ◽  
Author(s):  
Puja Saluja ◽  
G. S. Prasad
Keyword(s):  
Large Subunit ◽  
Its Region ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Cryptococcus Laurentii ◽  
The Novel ◽  
D2 Domain ◽  
Its Regions ◽  
Anamorphic Yeast ◽  
Physiological Tests

Two novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).

Do skin peptide profiles reflect speciation in the Australian treefrog Litoria caerulea (Anura : Hylidae)?

2000 ◽  
Vol 48 (1) ◽  
pp. 33 ◽  
Author(s):  
Stephen C. Donnellan ◽  
Michael J. Tyler ◽  
Paul Monis ◽  
Adam Barclay ◽  
Anna Medlin
Keyword(s):  
Molecular Genetic ◽  
Molecular Data ◽  
Data Sets ◽  
Tree Frog ◽  
Separate Species ◽  
Data Set ◽  
Skin Gland ◽  
Molecular Genetic Data ◽  
Litoria Caerulea ◽  
Peptide Profiles

Profiles of skin gland peptides of the tree frog Litoria caerulea from Australia show substantial divergence among geographic locations. Indeed, two divergent groups of populations, ‘eastern’ and ‘northern’, are apparent from a phenetic analysis of similarities of skin gland peptide profiles among populations of L. caerulea. We analyse variation in nuclear genes (allozyme frequencies) and the mitochondrial genome (haplotype relationships and frequencies) to test the taxonomic significance of differences apparent among profiles of skin gland peptides. Both molecular genetic data sets identified the same two groups apparent in the profiles of skin gland peptides. However, neither molecular data set, under an evolutionary species concept, provides strong enough evidence to support recognition of these groups as separate species. These data imply that the genetic basis of the inheritance and expression of skin gland peptides requires further characterisation.

Phylogenetic analysis of the druid flies (Diptera: Schizophora: Clusiidae) based on morphological and molecular data

2010 ◽  
Vol 41 (3) ◽  
pp. 231-274 ◽  
Author(s):  
Jinzhong Fu ◽  
Owen Lonsdale ◽  
Brian Wiegmann ◽  
Stephen Marshall
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Cytochrome Oxidase Subunit ◽  
Data Set ◽  
Oxidase Subunit ◽  
Morphological And Molecular Data

AbstractIn this paper, the Clusiidae (Diptera: Schizophora) is analyzed phylogenetically using morphological and molecular data sets, and then redefined on the basis of derived morphological characters. The biology and distribution of the Clusiidae are also reviewed, a key is provided to the World genera, the status of the genus Craspedochaeta Czerny is reevaluated and the type of Heterochroa pictipennis Wulp is discussed. Molecular data sets include genomic DNA sequences from the mitochondrial genes COI (cytochrome oxidase subunit I) and COII (cytochrome oxidase subunit II), the large ribosomal nuclear subunit 28S, and the nuclear protein-coding carbomoylphosphate synthase (CPS) domain of CAD (or “rudimentary”). Genes were analyzed separately, in combination with each other, and in combination with a morphological data set. Although individual molecular data sets often provided conflicting phylogenetic signals, the topologies of the cladograms produced from each data set alone or in combination were largely similar. Most genus-level relationships and several basal divergences were unresolved, but Apiochaeta was very strongly and consistently supported as Sobarocephalinae, not Clusiinae. The Clusiinae and Sobarocephalinae are subsequently redefined using an adjusted morphological tree — retaining Apiochaeta in the Sobarocephalinae — that is only slightly longer (8.4%, or seven steps) than the most parsimonious tree. Our results illustrate the benefits of multiple independent data sets for phylogenetic reconstruction in order to verify and refine existing classifications.

scholarly journals First Report of Downy Mildew of Spider Flower Caused by a Hyaloperonospora sp. in Korea

Plant Disease ◽  
2012 ◽  
Vol 96 (4) ◽  
pp. 588-588 ◽  
Author(s):  
Y. J. Choi ◽  
W. Mulenko ◽  
J. H. Park ◽  
H. D. Shin
Keyword(s):  
Downy Mildew ◽  
Morphological Difference ◽  
Its Region ◽  
The United States ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Ornamental Plant ◽  
Width Ratio ◽  
Public Gardens ◽  
Morphological And Molecular Data

Spider flower, Tarenaya hassleriana (Chodat) H. H. Iltis (synonym Cleome hassleriana; C. spinosa), which is native to South America, is now cultivated as an ornamental plant worldwide. In Korea, this plant has recently become popular in gardens and parks because of its beautiful flowers. During July 2010, plants showing typical symptoms of downy mildew were observed in public gardens along the lakeside in Ganghwa, South Korea. Infection resulted in chlorotic areas on the leaves with a white mildew developing on the abaxial surface and finally leading to necrosis of the lesions. Representative samples of infected leaves were deposited at the herbarium of Korea University, Seoul, Korea (KUS-F25091 and F25462). Microscopic examination of fresh material was performed under a light microscope. Conidiophores emerging from stomata were hyaline, 250 to 650 × 10 to 15 μm, straight, and monopodially branched in five to eight orders. Ultimate branchlets were mostly in pairs, flexuous to sigmoid, 15 to 30 μm long, and had obtuse or subtruncate tips. Conidia were hyaline, subglobose, and measured 23 to 26.5 × 21 to 24 μm with a length/width ratio (L/W) of 1.05 to 1.15. Up to now, the downy mildew pathogen of the spider flower has been considered to be Hyaloperonospora parasitica, Peronospora capparidis or P. cleomes, but the latter two names were considered as synonyms of the former (1). In the current study, the spider flower pathogen was morphologically distinct from H. parasitica; in the Korean specimen, conidia were subglobose with a low L/W value, while in H. parasitica sensu stricto, originated from Capsella bursa-pastoris, conidia were broadly ellipsoidal and measured 22.5 to 26.5 × 18 to 21.5 μm with a L/W ratio of 1.17 to 1.31 (1). To confirm this morphological difference, the amplification and sequencing of the internal transcribed spacer (ITS) region of rDNA of the Korean specimen were performed using procedures outlined by Göker et al. (3). The resulting 874-bp sequence of the region was deposited in GenBank (Accession No. JQ301468). A comparison with the ITS sequences available in the GenBank database revealed that the Korean accession exhibits a high dissimilarity of approximately 11% (99 of 882 characters are different) from that of H. parasitica from C. bursa-pastoris (AY210987). On the basis of morphological and molecular data, the spider flower pathogen found in Korea was clearly distinct from H. parasitica. Therefore, we provisionally indicate this pathogen as a Hyaloperonospora sp. To our knowledge, there is no previous record of a downy mildew on spider flower in Asia, although this disease has been previously recorded in Malawi, South Africa, Uganda, New Zealand, Poland, Romania, the United States, and Venezuela (2). The presence of a downy mildew on spider flower in Asia can be considered a potentially new and serious threat to this ornamental plant. References: (1) O. Constantinescu and J. Fatehi. Nova Hedwigia 74:291, 2002. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , December 13, 2011. (3) M. Göker et al. Mycol. Res. 113:308, 2009.

scholarly journals Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum

2019 ◽  
Vol 69 (2) ◽  
pp. 234-248
Author(s):  
Eric Lewitus ◽  
Leandro Aristide ◽  
Hélène Morlon
Keyword(s):  
Resource Use ◽  
Simulated Data ◽  
Graph Laplacian ◽  
Molecular Data ◽  
Nonparametric Analysis ◽  
Data Sets ◽  
New World Monkeys ◽  
Phenotypic Evolution ◽  
Laplacian Spectrum ◽  
Data Set

Abstract The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

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.

scholarly journals Molecules, morphology, and the monophyly of diapsid reptiles

2001 ◽  
Vol 70 (1) ◽  
pp. 1-22 ◽  
Author(s):  
Michael S.Y. Lee
Keyword(s):  
Nuclear Genes ◽  
Molecular Evidence ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Combined Analysis ◽  
Mitochondrial Data ◽  
Molecular Signal ◽  
Partition Homogeneity Test ◽  
Molecular Characters

The morphological and molecular evidence for higher-level reptile relationships is reassessed. A combined analysis of 176 osteological, 40 soft anatomical, and 2903 (1783 aligned) molecular characters in 28 amniote taxa yields the traditional reptile tree. Synapsids (including mammals) are the sister taxon to all other amniotes, including all extant reptiles. Turtles group with anapsid parareptiles and fall outside a monophyletic Diapsida. Within diapsids, squamates and Sphenodon form a monophyletic Lepidosauria, and crocodiles plus birds form a monophyletic Archosauria. This tree is identical to the tree strongly supported by the osteological data alone when fossils are included. In a combined analysis the strong osteological signal linking turtles with anapsids is sufficient to override a soft anatomical signal placing turtles next to a heterodox archosaur-mammal clade, and a weaker molecular signal linking turtles with archosaurs. However, the turtle-archosaur clade cannot be statistically rejected. When fossils are ignored, the signal in the osteological data set disappears and, in a combined analysis of morphology and molecules, the molecular (turtle-archosaur) signal prevails. These results highlight the importance of fossils, not just in osteological studies, but even in “combined” analyses where they cannot be scored for the majority of characters (soft anatomy and molecules). Although the total number of molecular traits (2903) is much greater than the total number of morphological taits (216), when only characters informative at the relevant levels are considered, the two data sets are approximately equal in size. The partition homogeneity test yields unreliable results unless uninformative (invariant and autapomorphic) characters are excluded. Analyses of the mitochondrial data suggest that recent evidence from nuclear genes for a heterodox turtlecrocodile clade (excluding birds) might be an artefact of inadequate sampling of a diverse outgroup (mammals) and thus, problems with rooting the reptile tree.

Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

2000 ◽  
Vol 31 (1) ◽  
pp. 71-90 ◽  
Author(s):  
Nils Møller Andersen ◽  
Jakob Damgaard ◽  
Felix A.H. Sperling
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Published Data ◽  
Data Sets ◽  
Gene Encoding ◽  
Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

Morphological data, molecular data, and total evidence in phylogenetic analysis

1995 ◽  
Vol 73 (S1) ◽  
pp. 667-676 ◽  
Author(s):  
Anders Tehler
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Molecular Data ◽  
Sister Species ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Data Set ◽  
Morphological And Molecular Data ◽  
Congruence Test

Two data sets, one morphological and one molecular, for ascolocular fungi have been analysed separately for taxonomic congruence and in combination for total evidence. Data were analysed with cladistic parsimony, the total support test, and the congruence test. The morphological data set comprised 15 characters and four species, Arthonia radiata, Dendrographa leucophaea, Lecanactis abietina, and Schismatomma pericleum (Arthoniales). The molecular data include the same species and comprised sequence data with 21 informative sites from approximately half of the 18S ribosomal RNA gene. The morphological phylogeny is corroborated by the molecular phylogeny with regard to relationships of Arthonia radiata, Schismatomma pericleum, and Dendrographa leucophaea. But in the molecular phylogeny Lecanactis abietina is placed as a sister species to the former three species. In the phylogeny inferred from morphological data Lecanactis abietina and Dendrographa leucophaea constitute a sister pair with Schismatomma pericleum followed by Arthonia radiata as subsequent sister taxa. The consensus obtained from the taxonomic congruence method was fully collapsed and uninformative. The combined morphological and molecular data in total evidence produced one most parsimonious cladogram. In total evidence Lecanactis abietina is placed as sister species to Schismatomma pericleum and Dendrographa leucophaea all with Arthonia radiata as sister species. The most resolved and phylogenetically informative hypothesis was obtained from cladistic parsimony analysis using total evidence. A review of congruence between morphological and molecular data in determining gross relationships within the Eumycota and Ascomycetes is also given. Key words: Ascomycetes, Arthoniales, phylogeny, cladistics, taxonomic congruence, total evidence, 18SrDNA.

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