scholarly journals Stepping stones towards a new prokaryotic taxonomy

2006 ◽  
Vol 361 (1475) ◽  
pp. 1911-1916 ◽  
Author(s):  
Dirk Gevers ◽  
Peter Dawyndt ◽  
Peter Vandamme ◽  
Anne Willems ◽  
Marc Vancanneyt ◽  
...  
Keyword(s):  
Species Concept ◽  
Molecular Data ◽  
Present Species ◽  
Stepping Stones ◽  
Species Definition ◽  
Homogeneous Groups ◽  
Technological Developments ◽  
Prokaryotic Taxonomy ◽  
Species Definitions ◽  
Prokaryotic Evolution

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.

scholarly journals Morphological and Genetic Structure of Two Equivalent Astyanax Species (Characiformes: Characidae) in the Region of Paranaíba Arc

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Renan Rodrigues Rocha ◽  
Rosana de Mesquita Alves ◽  
Rubens Pasa ◽  
Karine Frehner Kavalco
Keyword(s):  
Geometric Morphometrics ◽  
River Basin ◽  
Dna Sequences ◽  
Haplotype Network ◽  
River Basins ◽  
Molecular Data ◽  
The Body ◽  
Present Species ◽  
Body Depth ◽  
Geometric Morphometric

The Astyanax scabripinnis complex is composed of a large number of almost morphological indistinguishable species, including Astyanax paranae and Astyanax rivularis, which exist in the Paraná and São Francisco Basins, respectively, and sometimes are considered subspecies of the A. scabripinnis group or even are cited just as A. scabripinnis. The two river basins are separated by the Upper Paranaíba Arc, likely the main cause of the isolation of these species. We used geometric morphometric tools and DNA analyses of populations of both species to identify the differences between them. Geometric morphometrics separated the two species into distinct groups, whose main difference was the body depth. This is generally related to the speed of the water flow in the river basins. The maximum likelihood phylogram based on mitochondrial DNA sequences formed two main clades: one composed of the population of A. rivularis and the other, of A. paranae. In the haplotype network, the species were similarly separated into two groups from the same ancestral haplotype, with A. rivularis dispersing into two lineages in the São Francisco River Basin. The distribution of A. paranae is a consequence of a secondary dispersion event in the Paraná River Basin. It forms two lineages from a haplotype derived from the ancestor. The vicariant effect of separate basins, through the elevation of the Upper Paranaíba Arc, led to the allopatric speciation of the populations originating the present species. The results of geometric morphometrics and molecular data of the fish show the importance of this geological event in the biogeography and evolutionary history of the ichthyofauna of the region and indicate that the isolation of these species seems to be effective.

scholarly journals Analysis of the Phenotypes in the Rett Networked Database

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Elisa Frullanti ◽  
Filomena T. Papa ◽  
Elisa Grillo ◽  
Angus Clarke ◽  
Bruria Ben-Zeev ◽  
...  
Keyword(s):  
Clinical Presentation ◽  
Molecular Data ◽  
Spectrum Disorder ◽  
Onset Seizure ◽  
Phenotype Correlation ◽  
Causative Gene ◽  
Genetic Characteristics ◽  
Homogeneous Groups ◽  
Severity Scores ◽  
Classic Form

Rett spectrum disorder is a progressive neurological disease and the most common genetic cause of intellectual disability in females. MECP2 is the major causative gene. In addition, CDKL5 and FOXG1 mutations have been reported in Rett patients, especially with the atypical presentation. Each gene and different mutations within each gene contribute to variability in clinical presentation, and several groups worldwide performed genotype-phenotype correlation studies using cohorts of patients with classic and atypical forms of Rett spectrum disorder. The Rett Networked Database is a unified registry of clinical and molecular data of Rett patients, and it is currently one of the largest Rett registries worldwide with several hundred records provided by Rett expert clinicians from 13 countries. Collected data revealed that the majority of MECP2-mutated patients present with the classic form, the majority of CDKL5-mutated patients with the early-onset seizure variant, and the majority of FOXG1-mutated patients with the congenital form. A computation of severity scores further revealed significant differences between groups of patients and correlation with mutation types. The highly detailed phenotypic information contained in the Rett Networked Database allows the grouping of patients presenting specific clinical and genetic characteristics for studies by the Rett community and beyond. These data will also serve for the development of clinical trials involving homogeneous groups of patients.

Fern nothogenera and ×Lepinema, a new hybrid genus between Ellipinema and Lepisorus (Polypodiaceae)

Phytotaxa ◽  
2020 ◽  
Vol 455 (4) ◽  
pp. 262-266
Author(s):  
LIANG ZHANG ◽  
LI-BING ZHANG
Keyword(s):  
Species Concept ◽  
Intergeneric Hybrid ◽  
Molecular Data ◽  
Biological Species ◽  
Biological Species Concept

The biological species concept is not exclusively applicable in many groups of organisms including ferns. Interspecific fern hybrids are not rare: there are 16 intergeneric hybrid genera in ferns confirmed with molecular data. Here we add one more hybrid genus in the tribe Lepisoreae of Polypodiaceae, ×Lepinema, formed via hybridization between parents in two genera: Ellipinema and Lepisorus.

Species limits in Pteruthius (Aves: Corvida) shrike-babblers: a comparison between the Biological and Phylogenetic Species Concepts

Zootaxa ◽  
2009 ◽  
Vol 2301 (1) ◽  
pp. 29-54 ◽  
Author(s):  
FRANK E. RHEINDT ◽  
JAMES A. EATON
Keyword(s):  
Species Concept ◽  
Molecular Data ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Species Status ◽  
Phylogenetic Species Concept ◽  
Sampling Regime ◽  
Morphological And Molecular Data

The question of how to define a species continues to divide biologists. Meanwhile, the application of different species concepts has led to disparate taxonomic treatments that confound conservationists and other biologists. The most widely followed guidelines to species designation in avian and other vertebrate taxonomy are Ernst Mayr’s Biological Species Concept (BSC) and Joel Cracraft’s version of the Phylogenetic Species Concept (PSC). Although the BSC is considered to be more conservative in its assignment of species status, there is a lack of research demonstrating differences in taxonomic treatment between the BSC and the PSC with reference to a multi-taxon multi-trait study system. We examined the case of five traditionally recognized species of shrike-babbler (Pteruthius) that have recently been divided into 19 species under the PSC. Re-analyzing previous morphological and molecular data and adding new vocal data, we propose a BSC classification of 9 species. However, taking into consideration geographic gaps in the sampling regime, we contend that additional data will likely reduce discrepancies between the total numbers of species designated under the PSC and BSC. The current PSC species total is a likely overestimate owing to species diagnosis based on characters that erroneously appear to be unique to a taxon at low sample size. The current BSC species total as here proposed is a likely underestimate on account of the conservative designation of taxa as subspecies in equivocal cases, e.g. where BSC species status is potentially warranted but may be masked by insufficient data.

scholarly journals The bacterial species dilemma and the genomic–phylogenetic species concept

2006 ◽  
Vol 361 (1475) ◽  
pp. 1899-1909 ◽  
Author(s):  
James T Staley
Keyword(s):  
New Species ◽  
Dna Hybridization ◽  
Species Concept ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Phylogenetic Species ◽  
Bacterial Taxonomy ◽  
Species Definition ◽  
Phylogenetic Species Concept

The number of species of Bacteria and Archaea ( ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

The species concept in desmids: the problem of variability, infraspecific taxa and the monothetic species definition

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Frans Kouwets
Keyword(s):  
Related Species ◽  
Species Concept ◽  
Morphological Variability ◽  
Present Contribution ◽  
Species Definition ◽  
Infraspecific Taxa

AbstractDesmid systematics are much confused due to the existence of a very large number of infraspecific taxa, obscuring a clear species concept. The basis of this confusion is the huge morphological variability of desmid cells. Moreover, these ill-defined forms are frequently recombined back and forth with superficially related species, hence constantly changing species characterizations. In the present contribution the author will argue in favour of the utmost reserve with respect to the description of infraspecific taxa in desmids, the strict use of a monothetic species definition and a clear species concept.

A revision of the Trimeresurus puniceus-complex (Serpentes: Viperidae: Crotalinae) based on morphological and molecular data

Zootaxa ◽  
2006 ◽  
Vol 1293 (1) ◽  
pp. 1 ◽  
Author(s):  
PATRICK DAVID ◽  
GERNOT VOGEL ◽  
S. P. VIJAYAKUMAR ◽  
NICOLAS VIDAL
Keyword(s):  
Species Concept ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biological Species ◽  
Valid Species ◽  
Biological Species Concept ◽  
Phylogenetic Species Concept ◽  
Morphological And Molecular Data ◽  
A New Species

The brown Asian pitvipers of the genus Trimeresurus related to Trimeresurus puniceus (informal Trimeresurus puniceus-complex) are revised on the basis of morphological and molecular analyses. Variation in morphological characters were investigated among 119 specimens from 62 populations of the whole range of the pitvipers currently known as Trimeresurus puniceus (Boie, 1827), Trimeresurus borneensis (Peters, 1872) and Trimeresurus brongersmai Hoge, 1969. Molecular and morphological analyses clearly differentiate two groups of taxa, referrable to the informal Trimeresurus puniceus-group and Trimeresurus borneensis-group, and confirm the distinct specific status of T. puniceus and T. borneensis. Morphological univariate and multivariate analyses differentiate six clusters of populations that are morphologically diagnosable, of which five are here considered to represent independent lineages and one is placed incertae sedis pending the availability of further specimens. These clusters are considered to be distinct species following the Biological Species Concept and the Phylogenetic Species Concept. One of them is described as a new species, Trimeresurus andalasensis spec. nov. (T. borneensis-group), which includes populations from northern Sumatra. Trimeresurus wiroti Trutnau, 1981 is revalidated to accommodate populations from Thailand and West Malaysia. Trimeresurus borneensis is here considered endemic to Borneo. Trimeresurus puniceus is known from Java and from South Sumatra, but the taxonomy of this species in Sumatra is left unresolved. Also left unresolved is the taxonomic position of specimens from western Sumatra and the Mentawai Archipelago, and from the Natuna Islands and Anamba Islands. Although belonging to the T. puniceus-group, they show some differences to other specimens of the group. They are not referred to any taxon pending the collection of additional specimens. Lastly, Trimeresurus brongersmai is confirmed as a valid species from the Mentawai Archipelago. A key to these taxa is provided.

scholarly journals On the Diversity of Phyllodocida (Annelida: Errantia), with a Focus on Glyceridae, Goniadidae, Nephtyidae, Polynoidae, Sphaerodoridae, Syllidae, and the Holoplanktonic Families

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 131
Author(s):  
Daniel Martin ◽  
Maria Teresa Aguado ◽  
María-Ana Fernández Álamo ◽  
Temir Alanovich Britayev ◽  
Markus Böggemann ◽  
...  
Keyword(s):  
Species Concept ◽  
Current Knowledge ◽  
Sampling Bias ◽  
Molecular Data ◽  
Nominal Species ◽  
Deep Waters ◽  
European North ◽  
Continental Shelves ◽  
Molecular Barcode ◽  
Group 2

Phyllodocida is a clade of errantiate annelids characterized by having ventral sensory palps, anterior enlarged cirri, axial muscular proboscis, compound chaetae (if present) with a single ligament, and of lacking dorsolateral folds. Members of most families date back to the Carboniferous, although the earliest fossil was dated from the Devonian. Phyllodocida holds 27 well-established and morphologically homogenous clades ranked as families, gathering more than 4600 currently accepted nominal species. Among them, Syllidae and Polynoidae are the most specious polychaete groups. Species of Phyllodocida are mainly found in the marine benthos, although a few inhabit freshwater, terrestrial and planktonic environments, and occur from intertidal to deep waters in all oceans. In this review, we (1) explore the current knowledge on species diversity trends (based on traditional species concept and molecular data), phylogeny, ecology, and geographic distribution for the whole group, (2) try to identify the main knowledge gaps, and (3) focus on selected families: Alciopidae, Goniadidae, Glyceridae, Iospilidae, Lopadorrhynchidae, Polynoidae, Pontodoridae, Nephtyidae, Sphaerodoridae, Syllidae, Tomopteridae, Typhloscolecidae, and Yndolaciidae. The highest species richness is concentrated in European, North American, and Australian continental shelves (reflecting a strong sampling bias). While most data come from shallow coastal and surface environments most world oceans are clearly under-studied. The overall trends indicate that new descriptions are constantly added through time and that less than 10% of the known species have molecular barcode information available.

Morphological and genetic variations of Ommatotriton in Turkey

2013 ◽  
Vol 63 (3) ◽  
pp. 297-312 ◽  
Author(s):  
Ufuk Bülbül ◽  
Bilal Kutrup
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Black Sea ◽  
Sequence Divergence ◽  
Distinct Species ◽  
Molecular Data ◽  
Canonical Variate ◽  
Rrna Gene ◽  
Cytb Gene ◽  
Homogeneous Groups

The classification of European newts has fluctuated throughout history based on morphological and genetic discoveries. In this study, specimens of Ommatotriton from Turkey were compared by using morphometrical features and partial mitochondrial sequences data. When we used the TCS program, 15 haplotypes were found for a 541 bp fragment of the 16S rRNA gene in 118 specimens, while 25 haplotypes were found for a 398 bp fragment of the cytb gene in 112 specimens. The sequence divergence of 16S rRNA gene ranged from 0.18% to 5.70% while for cytb gene it ranged from 0.25% to 12.84%. Combined sequences showed that newts collected in three distinct geographical areas of Turkey (Southern Anatolia, Western Black Sea and Eastern Black Sea) form four distinct lineages (Hatay, Adana-Mersin, Western Black Sea and Eastern Black Sea). A total of 195 adult specimens (94 males and 101 females) from 20 different populations belonging to the three distinct geographic areas were used in the morphometrical comparisons. Canonical Variate Analysis demonstrated that the four groups were successfully separated and formed geographically homogeneous groups in the canonical space. As a conclusion, our molecular data suggest that individuals from Western Black Sea are not conspecific with Eastern Black Sea ones and they could represent a good species (Ommatotriton nesterovi). Finally, we suggest that three distinct species, O. nesterovi, O. ophryticus and O. vittatus should be recognised as banded newts of Turkey.

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