Proteaceae: Diverse approaches toward new syntheses

1998 ◽  
Vol 11 (4) ◽  
pp. 631 ◽  
Author(s):  
Barbara G. Briggs
Keyword(s):  
Dna Sequence ◽  
Reproductive Biology ◽  
Fossil Record ◽  
Sequence Data ◽  
Large Body ◽  
Dna Sequence Data ◽  
Wide Range ◽  
Phylogenetic Hypotheses

The 1996 Commemorative Proteaceae Conference drew attention to the large body of work proceeding on all southern continents, the extensive and informative fossil record, and the wide range of studies in ecology and reproductive biology. DNA sequence data and organogeny are producing major insights at the upper taxonomic levels, new phylogenetic hypotheses and classifications are emerging in respect of the recognition of subfamilies and the relationships and composition of tribes, and there is also evidence from morphology and DNA sequence data that several genera are paraphyletic.

scholarly journals Unravelling unexplored diversity of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) in tropical Africa

MycoKeys ◽  
2021 ◽  
Vol 81 ◽  
pp. 69-138
Author(s):  
Yalemwork Meswaet ◽  
Ralph Mangelsdorff ◽  
Nourou S. Yorou ◽  
Meike Piepenbring
Keyword(s):  
West Africa ◽  
Dna Sequence ◽  
Vigna Unguiculata ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Molecular Sequence Data ◽  
Dna Sequence Data ◽  
Wide Range ◽  
Cercosporoid Fungi ◽  
First Time

Cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales, Ascomycota) are one of the largest and most diverse groups of hyphomycetes causing a wide range of diseases of economically important plants as well as of plants in the wild. Although more than 6000 species are known for this group, the documentation of this fungal group is far from complete. Especially in the tropics, the diversity of cercosporoid fungi is poorly known. The present study aims to identify and characterise cercosporoid fungi collected on host plants belonging to Fabaceae in Benin, West Africa. Information on their morphology, host species and DNA sequence data (18S rDNA, 28S rDNA, ITS and tef1) is provided. DNA sequence data were obtained by a simple and non-culture-based method for DNA isolation which has been applied for cercosporoid fungi for the first time in the context of the present study. Among the loci used for the phylogenetic analysis, tef1 provided the best resolution together with the multigene dataset. Species delimitation in many cases, however, was only possible by combining molecular sequence data with morphological characteristics. Based on forty specimens recently collected in Benin, 18 species are presented with morphological descriptions, illustrations and sequence data. Among these, six species in the genus Cercospora and two species in Pseudocercospora are proposed as species new to science. The newly described species are Cercospora (C.) beninensis on Crotalaria macrocalyx, C. parakouensis on Desmodium tortuosum, C. rhynchophora on Vigna unguiculata, C. vignae-subterraneae on Vigna subterranea, C. tentaculifera on Vigna unguiculata, C. zorniicola on Zornia glochidiata, Pseudocercospora sennicola on Senna occidentalis and Pseudocercospora tabei on Vigna unguiculata. Eight species of cercosporoid fungi are reported for Benin for the first time, three of them, namely C. cf. canscorina, C. cf. fagopyri and C. phaseoli-lunati are new for West Africa. The presence of two species of cercosporoid fungi on Fabaceae previously reported from Benin, namely Nothopassalora personata and Passalora arachidicola, is confirmed.

Nerve cells of Xenoturbella bocki (phylum uncertain) and Harrimania kupfferi (Enteropneusta) are positively immunoreactive to antibodies raised against echinoderm neuropeptides

2005 ◽  
Vol 85 (6) ◽  
pp. 1519-1524 ◽  
Author(s):  
Thomas Stach ◽  
Samuel Dupont ◽  
Olle Israelson ◽  
Geraldine Fauville ◽  
Hiroaki Nakano ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Dna Sequence ◽  
Sequence Data ◽  
Nerve Cells ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Close Phylogenetic Relationship ◽  
Positive Immunoreactivity ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

The phylogenetic position of Xenoturbella spp. has been uncertain since their discovery in 1949. It has been recently suggested that they could be related to Ambulacraria within Deuterostomia. Ambulacraria is a taxon that has been suggested to consist of Hemichordata and Echinodermata. The hypothesis that X. bocki was related to Ambulacraria as well as the hypothesis of a monophyletic Ambulacraria is primarily based on the analysis of DNA sequence data. We tested both phylogenetic hypotheses using antibodies raised against SALMFamide 1 and 2 (S1, S2), neuropeptides isolated from echinoderms, on X. bocki and the enteropneust Harrimania kupfferi. Both species showed distinct positive immunoreactivity against S1 and S2. This finding supports the Ambulacraria-hypothesis and suggests a close phylogenetic relationship of X. bocki to Ambulacraria. In particular, the presence of immunoreactivity against S2 can be interpreted as a synapomorphy of Enteropneusta, Echinodermata, and Xenoturbella spp.

scholarly journals A Show of Character—a further response to Wiley et al.

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 29 ◽  
Author(s):  
ANTHONY C. GILL ◽  
RANDALL D. MOOI
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
Sequence Data ◽  
Molecular Data ◽  
Scientific Rigor ◽  
Dna Sequence Data ◽  
Phylogenetic Hypotheses ◽  
Alternative Relationships

Wiley et al. (2011) begin their critique of our paper (Mooi & Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith & Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi & Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi & Gill’s various studies are usually focused on Johnson & Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

Didymella eriobotryae sp. nov. (Didymellaceae) and Arthrinium arundinis (Apiosporaceae) from fruit of Eriobotrya japonica (loquat) in China

Phytotaxa ◽  
2018 ◽  
Vol 382 (1) ◽  
pp. 136 ◽  
Author(s):  
KASUN M. THAMBUGALA ◽  
KEVIN D. HYDE ◽  
JIN-FENG ZHANG ◽  
ZUO-YI LIU
Keyword(s):  
Dna Sequence ◽  
New Record ◽  
Sequence Data ◽  
Eriobotrya Japonica ◽  
Dna Sequence Data ◽  
Wide Range

Arthrinium (Apiosporaceae) and Didymella (Didymellaceae) are species-rich genera and most of the members in these genera are plant pathogenic, saprobic or endophytic species that have been recorded from a wide range of hosts. The present study introduces Didymella eriobotryae sp. nov. and a new record of Arthrinium arundinis which are associated with decaying fruit of Eriobotrya japonica in China. Morphology and DNA sequence data are employed to determine the taxonomic placement of these species.

The phylogenetic and taxonomic position of Lilaeopsis (Apiaceae), with notes on the applicability of ITS sequence data for phylogenetic reconstruction

2002 ◽  
Vol 15 (2) ◽  
pp. 181 ◽  
Author(s):  
Gitte Petersen ◽  
Ole Seberg ◽  
Sidsel Larsen
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Its Sequences ◽  
Its Sequence ◽  
Dna Sequence Data ◽  
Coding Regions ◽  
Phylogenetic Hypotheses

The relationships of the genusLilaeopsis Greene have been difficult to determine primarily due to its simple morphology with entire, linear to spathulate leaves, simple umbels and lack of carpophore. Consequently, the genus has been referred to both Hydrocotyloideae and Apioideae. DNA sequence data from different genes (rbcL and matK) and non-coding regions (rpoC1 intron and ITS) were explored in order to determine the phylogenetic relationships of Lilaeopsis. Separate and combined analyses of rpoC1 intron, rbcL and matK data give almost congruent results with respect to a clade including Lilaeopsis. The three species of Lilaeopsis included in the analyses form a monophyletic group within the Oenanthe clade and hence belong to the Apioideae. Presently, the Mexican genus Neogoezia Hemsl. is considered its most likely sister group. Optimisation alignment of the ITS sequence data results in widely different phylogenetic hypotheses, but on the basis of congruence tests, two very similar trees can be selected. These trees are, however, incongruent with the trees obtained from analyses of the chloroplast sequences. As alignment of the ITS sequences is problematic even within the Oenanthe clade, the reliability of phylogenies on the basis of ITS data of higher taxonomic levels in the Apiaceae is questioned. However, for phylogenetic analysis within Lilaeopsis ITS sequences may prove useful and unproblematic.

Shall we dance or shall we fight? Using DNA sequence data to untangle controversies surrounding sexual selection

Genome ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 925-929 ◽  
Author(s):  
Alberto Civetta
Keyword(s):  
Sexual Selection ◽  
Dna Sequence ◽  
Sequence Data ◽  
Classical Model ◽  
Rapid Evolution ◽  
Large Body ◽  
Evolutionary Genetics ◽  
Reproductive Proteins ◽  
Dna Sequence Data ◽  
Reproductive Genes

Population and evolutionary genetics studies have largely benefitted from advances in DNA manipulation and sequencing, as well as DNA data analysis techniques. Molecular evolution studies of male reproductive genes show a pattern of rapid evolution shaped, in some cases, by an adaptive selective process. Despite the large body of data on male reproductive genes, the female side of the story has remained unexplored. The few cases of female egg receptors analyzed also show rapid evolution. However, to disentangle between competing hypotheses on how selection operates on male × female molecular interaction leading to fertilization, we need to find male and female molecules that are partners in fertilization. A conflict model of sexual selection (similar to a host-parasite model) assumes a male-driven system where females are being forced under suboptimal conditions. This predicts that the amount of divergence at a female receptor depends on the amount of divergence among the male reproductive proteins that it binds (i.e., males are leading). Under a classical model of runaway sexual selection, female protein receptors might be the key to the rapid molecular changes observed in male reproductive proteins and higher divergence should be expected among female receptors than among their respective male binding proteins.Key words: Reproductive genes, DNA sequence data, sexual selection, coadaptation, conflict.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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