scholarly journals Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

2019 ◽  
Vol 11 (7) ◽  
pp. 2035-2044 ◽  
Author(s):  
Pablo Cruz-Morales ◽  
Camila A Orellana ◽  
George Moutafis ◽  
Glenn Moonen ◽  
Gonzalo Rincon ◽  
...  

Abstract Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here, we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to 1) confirm that the group is composed of more than one genus, 2) detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), 3) identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains, and 4) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria, and highlights the importance of phylogenomics for taxonomic studies.

2019 ◽  
Author(s):  
Pablo Cruz-Morales ◽  
Camila A. Orellana ◽  
George Moutafis ◽  
Glenn Moonen ◽  
Gonzalo Rincon ◽  
...  

AbstractClostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to; (i) confirm that the group is composed of more than one genus (ii), detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains and, (iv) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria and highlights the importance of phylogenomics for taxonomic studies.


1934 ◽  
Vol 11 (2) ◽  
pp. 213-241 ◽  
Author(s):  
A. W. S. Hunter

The history and the present state of the classification of the Gramineae are briefly reviewed and a number of the different characteristics on which phylogenetic systems have been based are considered. The subjects of chromosome morphology and the application of idiograms and karyotypes to taxonomic studies are discussed. Avdulov's recently reported findings on the phylogeny of the grasses are summarized and compared with the results of other workers and those obtained in the present investigation. Three species of bamboos were studied for the first time and evidence secured to indicate that the basic number of the tribe is probably not 12 as has been elsewhere reported. In the Festuceae the chromosome number of Phragmites communis Trin. was definitely ascertained, confirming Avdulov's supposition that the basic number for the genus is 12. The other three species investigated agreed with the arrangement as proposed by Avdulov. The tribe Chlorideae, with the exception of the genus Beckmannia, has been reported to be almost entirely Panicoid with respect to chromosome morphology. This was confirmed in the four species examined. Avdulov's rearrangement of the tribe Hordeae was somewhat altered and a confusion m the nomenclature of the genus Lepturus was corrected. An anomalous situation was cleared up in the tribe Agrostideae by the establishment of the chromosome number of Sporobolus tennuissinus Kuntz as 40. The specimen of Anthoxanthum odoratum L. (tribe Phalarideae) examined provided a very interesting example of secondary splitting in somatic chromosomes. One species was examined in the tribe Melinideae and six in the tribe Paniceae. In the latter tribe no difference could be detected between the several subdivisions of the genus Panicum. The same condition held for the large genus Andropogon in the tribe Andropogoneae. In the tribe Maydeae the chromosome number of Tripsacum dactyloides L. was found to be 9, and the suggestion was made that it may be a link, along with the genus Coix, between the Andropogoneae and the Maydeae. The other four species examined all had a basic number of 10.


2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  

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.


Rodriguésia ◽  
2012 ◽  
Vol 63 (1) ◽  
pp. 227-242 ◽  
Author(s):  
Ricardo de S. Secco ◽  
Inês Cordeiro ◽  
Luci de Senna-Vale ◽  
Margareth F. de Sales ◽  
Letícia Ribes de Lima ◽  
...  

The Euphorbiaceae sensu lato are distributed mainly in the tropics, in various types of vegetation and habitats, being one of the largest, most complex and diverse families of angiosperms. It has recently been divided into four families, according to classification systems based on molecular phylogeny: Euphorbiaceae sensu stricto, Phyllanthaceae, Putranjivaceae, and Picrodendraceae. There is a proposition to establish Peraceae still under discussion. There were also changes in the taxonomic position of genera widely distributed in the Brazilian territory, such as Amanoa, Drypetes, Pera, Phyllanthus, Podocalyx, Pogonophora, and Richeria, among others. In addition, new species have been proposed and the limits of taxa distribution are expanding in Brazil. Thus, the authors provide an overview of recent studies and advances in the taxonomy of Euphorbiaceae s.l. in the Northern, Northeastern, Southeastern and Southern regions of Brazil, concentrating on review works and regional floras, as well as the changes that resulted in setting a new taxonomic family.


2021 ◽  
Vol 13 (5) ◽  
pp. 18257-18282
Author(s):  
Anoop P. Balan ◽  
S.V. Predeep

A checklist of the legumes of Kerala State is presented.  This exhaustive checklist is an outcome of extensive field surveys, collection, identification and documentation of family Leguminosae carried out across Kerala State during the period 2006–2019.  A total of 448 taxa were recorded under five subfamilies and 115 genera.  The majority of the legumes are herbs and shrubs, the rest being trees and woody climbers.  About 81 taxa are endemic to India, especially confined to the Western Ghats biodiversity hotspot, out of which 17 are endemic to  Kerala.  The state is home to two Critically Endangered and six Endangered legumes, facing severe threat of extinction.  Crotalaria is the dominant legume genus in the state with 62 taxa followed by Desmodium and Indigofera.  About 57 genera are represented by single species each.  Legumes are treated according to the latest phylogenetic classification of the Legume Phylogeny Working Group (LPWG).  Updated nomenclature, habit, native countries, voucher specimens, and images of endemic and lesser known legumes found in the state are provided.  Crotalaria multiflora var. kurisumalayana (Sibichen & Nampy) Krishnaraj & N. Mohanan is reduced as a synonym to C. multiflora (Arn.) Benth.


1968 ◽  
Vol 5 (4) ◽  
pp. 801-812 ◽  
Author(s):  
Michael Katz

The fabric of the highly deformed and recrystallized gneisses formed under granulite facies conditions of metamorphism are described from Mont Tremblant Park, Quebec, Canada. These gneisses are termed granulites and are classified into quartzofeldspathic and hypersthene varieties.The term 'cataclastic-gneissose' fabrics is used to imply varying degrees of deformation and recrystallization without micro-brecciation or cataclasis 'sensu stricto' and a classification of these various fabrics is presented. The modifications in these granulites are progressive and are assumed to have the following sequence:[Formula: see text]During the evolution from mortar to granoblastic types, the minerals become flattened and increasingly elongated, while the individual recrystallized grains increase in size. The same deformation produced flaser and granoblastic gneisses in the quartzofeldspathic granulites and mortar and augen gneisses in the hypersthene granulites.The mineral relicts (porphyroclasts) in the mortar and augen gneisses are highly deformed and display evidence of strain, such as undulatory extinction, deformation bands, polygonization, mechanical twins, and bent cleavages. These mortar and augen gneisses display a poor preferred orientation of quartz c axis.In the recrystallized rocks the grains form a clear, fresh, unstrained polygonal mosaic and in the case of quartz, long leaf-like uniform plates are produced. In the flaser and especially the granoblastic gneisses no signs of strain remain and the recrystallized fabric consists of quartz plates alternating on a micro-scale with bands of polygonal fresh feldspar and granular streaks of dark minerals. A petrofabric diagram from a granoblastic gneiss shows a marked preferred orientation of quartz c axis.A review of the relevant literature on the natural and experimental investigations strongly supports the hypothesis that the fabrics of the granulites are produced as a result of the progressive deformation and recrystallization of the mineral constituents.


Author(s):  
Luis M. Rodriguez-R ◽  
Ramon Rosselló-Móra ◽  
Konstantinos T. Konstantinidis

Abstract This book chapter attempts to summarize the major findings from genome-based taxonomic studies in the past two decades, and briefly describe the major genome-based approaches currently available for species identification and classification with special focus on the 'uncultivated majority' and associated limitations, as well as outlines future directions towards a truly genome-based taxonomy for prokaryotes that will equally encompass cultured and uncultivated taxa. Importantly, the need for a system to catalogue uncultivated taxa is very urgent, because the genomes and ecological/functional data that are becoming available are already overwhelming, and alphanumeric identifiers and synonyms are creating confusion of Babylonian dimensions.


2009 ◽  
Vol 34 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Dietmar Quandt ◽  
Sanna Huttunen ◽  
Ray Tangney ◽  
Michael Stech

Although the Lembophyllaceae has undergone considerable revision during the last century, the generic and familial level relationships of this pleurocarpous moss family are still poorly understood. To address this problem, a generic revision of the Lembophyllaceae based on molecular data was undertaken. We analyzed two plastid markers, the trnL-trnF and the psbT-psbH region in combination with the ITS2 of nuclear ribosomal DNA. The molecular data reveal that the current circumscription of the family is too narrow and that several genera previously placed in the Lembophyllaceae should be reincluded. The family includes: Bestia, Camptochaete, Dolichomitra, Dolichomitriopsis, Fallaciella, Fifea, Isothecium, Lembophyllum, Looseria stat. nov., Pilotrichella, Rigodium, Tripterocladium, and Weymouthia. Looseria contains a single species: Looseria orbiculata comb. nov. Acrocladium is excluded and provisionally accommodated in the Lepyrodontaceae. Generic limits supported by the molecular data support a return to the early twentieth century family concept of Brotherus. The analyses indicate that the segregate genus Orthostichella is distinct from its parent genus Pilotrichella, probably at the family level. Whereas Pilotrichella is resolved within the Lembophyllaceae, Orthostichella clusters with Porotrichum and Porothamnium forming a clade (OPP-clade) sister to the remaining Neckeraceae and Lembophyllaceae. Hence, the Neckeraceae is paraphyletic. Recognition of the OPP-clade as a new family is desirable but awaits the results of detailed ongoing morphological studies.


1997 ◽  
Vol 11 (1) ◽  
pp. 1 ◽  
Author(s):  
A. D. Austin ◽  
and S. A. Field

The morphology of the sclerotised components of the ovipositor system is comprehensively surveyed for scelionid and platygastrid wasps, with information being assessed for 120 genera and 220 species. A diagnosis for the ovipositor system is presented for most genera to complement existing generic descriptions. Two previously described and mechanically different forms of the ovipositor system are recognised: (1) the Ceratobaeus-type that is extended and retracted by antagonistic muscles and (2) the Scelio-type that is operated by changes in hydrostatic pressure, where the ovipositor is extended at the end of an elongate telescopic tube derived from expanded intersegmental membrane between metasomal segments 6 and 7. Comparison of these forms with the supposed ground plan for the Scelionidae strongly indicates that the Scelio-type is apomorphic, that it defines a monophyletic group associated with orthopteran host eggs, and that it comprises the tribes Scelionini, Calliscelionini, most Psilanteridini, Aradophagini, Neoscelionini, Platyscelionini, Doddiellini and four genera misplaced within the Sparasionini and Baryconini (Archaeoteleia Masner, Bracalba Dodd, Chromoteleia Ashmead and Oxyscelio Kieffer), as well as Sceliacanthella Dodd. Until a more robust classification of the superfamily is forthcoming, it is proposed that this group be informally referred to as the 'Scelionini sensu lato'. Further, seven genera (Habroteleia Kieffer, Palpoteleia Kieffer, Anteris Foerster, Fusicornia Risbec, Leptoteleia Kieffer, Opisthacantha Ashmead and Styloteleia Kieffer) are misplaced in the Calliscelionini and Psilanteridini because they possess the Ceratobaeus-type system. Nixonia Masner, Sparasion Latreille and Sceliomorpha Ashmead (Sparasionini) are considered to have the most primitive ovipositor system because they possess a Ceratobaeus-type system, and sub-basally fused lateral and latero-ventral apodemes, the latter being loosely attached to sternite 6. Sparasion and Sceliomorpha also have very short lateral apodemes and this, in conjunction with the form of the apodemes, can be considered to be the ground plan for the superfamily. The Platygastridae all possess a modified ovipositor system but, nonetheless, one that in most cases is extended and retracted by musculature (i.e. Ceratobaeus-type). In particular, the system in most platygastrids is typified by having metasomal tergite 8 and associated cerci missing, the lateral apodemes short and forming a U-shape, and the ovipositor assembly generally robust. Only one of approximately 30 genera examined, Acerotella Masner, has very elongate apodemes, as in the Scelionidae. Many platygastrids also have a pair of latero-ventral apodemes, a presumed plesiomorphic character, rather than a single medial apodeme on stemite 6, which is the case for many Scelionidae. The most highly modified system is found in Isostasius Foerster and some Synopeas (Sactogaster) Foerster, where the ovipositor assembly is coiled vertically or partly so and the apodemes are greatly reduced. Generally, characters associated with the ovipositor system do not provide any independent support for the most recent higher-level classification of platygastrids, although they show substantial potential for more accurate definition of genera. A preliminary cladistic analysis of 14 ovipositor characters supports the monophyly of five clades that correspond to the Scelionini s. l., the Scelionidae (minus the Sparasionini sensu stricto), the Sparasionini s. str., the Platygastridae, and the Sparasioriini s. str. + Platygastridae. Overall, results from this study will provide baseline information on the ovipositor system as a prelude to a more complete phylogenetic analysis of the superfamily including external morphological characters. Although no new classification for the Scelionidae and Platygastridae is proposed, their higher-level taxonomy is reviewed and discussed and cases identified where, on the basis of ovipositor morphology, taxa (tribes and/or genera) apparently form monophyletic groups, and where taxa are misplaced. Finally, the status of the major higher-level groups within the superfamily is discussed, as is the available evidence to support their monophyly.


1984 ◽  
Vol 62 (12) ◽  
pp. 2754-2764 ◽  
Author(s):  
Bernard R. Baum ◽  
L. Grant Bailey

The demarcation of the Old World species in Hordeum L. section Hordeastrum Doell. has been the subject of considerable controversy. The present paper reports the results of a morphometric analysis of the wall and sea barleys (H. murinum L., H. marinum Huds., and their allies). A sample of 227 accessions was scored for 39 characters, and the resulting data matrix was divided into three groups on the basis of lodicules and cpiblast characters. These three groups were then subjected to several aspects of discriminant analysis (stepwise discriminant analysis, linear discriminant analysis, canonical analysis of discriminance, and nearest neighbor discriminant analysis) both on untransformed and log-transformed data. The results indicate that the wall and sea barleys consist of five distinct groups worthy of morphological specific rank. These correspond to H. marinum sensu stricto, H. geniculatum All., H. glaucum Steudel. H. murinum sensu stricto, and H. leporinum Link. Ranges for 37 characters within these five taxa are presented. A key to the five species and one hybrid (reported in the first paper of this series) is supplied. Our conclusions are discussed in the context of various taxonomic treatments of the group.


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