Fungal taxonomy and nomenclature

2017 ◽  
Author(s):  
Andrew M. Borman
Keyword(s):  
Cryptic Species ◽  
Structural Features ◽  
Fungal Taxonomy ◽  
New Genera ◽  
Molecular Approaches ◽  
Dual Nomenclature ◽  
Fungal Identification ◽  
Phenotypic Features ◽  
Genetic Entity

This chapter summarizes historical and modern approaches to fungal taxonomy, the current taxonomic standing of medically important fungi, and the implications for fungal nomenclature following the recent Amsterdam Declaration on Fungal Nomenclature, which prohibits dual nomenclature. Fungi comprise an entire kingdom, containing an estimated 1–10 million species. Traditionally, fungal identification was based on examination of morphological and phenotypic features, including the type of sexual spores they form, and method of formation, and structural features of their asexual spores. Thus, many fungi have been described and named independently several times based on either their sexual or asexual stages, resulting in a single genetic entity having multiple names. Recent molecular approaches to fungal identification have led to profound changes in fungal nomenclature and taxonomy. Certain phyla have now been disbanded, cryptic species have been identified via molecular approaches, and long-recognized species have been transferred to new genera based on genotypic comparisons.

Fungal taxonomy and nomenclature

2018 ◽  
pp. 8-16
Author(s):  
Andrew M. Borman
Keyword(s):  
Cryptic Species ◽  
Structural Features ◽  
Fungal Taxonomy ◽  
New Genera ◽  
Molecular Approaches ◽  
Dual Nomenclature ◽  
Fungal Identification ◽  
Phenotypic Features ◽  
Genetic Entity

This chapter summarizes historical and modern approaches to fungal taxonomy, the current taxonomic standing of medically important fungi, and the implications for fungal nomenclature following the recent Amsterdam Declaration on Fungal Nomenclature, which prohibits dual nomenclature. Fungi comprise an entire kingdom, containing an estimated 1–10 million species. Traditionally, fungal identification was based on examination of morphological and phenotypic features, including the type of sexual spores they form and method of formation, and structural features of their asexual spores. Thus, many fungi have been described and named independently several times, based on either their sexual or asexual stages, resulting in a single genetic entity having multiple names. Recent molecular approaches to fungal identification have led to profound changes in fungal nomenclature and taxonomy. Certain phyla have now been disbanded, cryptic species have been identified via molecular approaches, and long-recognized species have been transferred to new genera, based on genotypic comparisons.

Quo Vadis Tyrannosaurus?: The Future of Dinosaur Studies

1989 ◽  
Vol 2 ◽  
pp. 175-183 ◽  
Author(s):  
Daniel J. Chure
Keyword(s):  
Public Relations ◽  
Earth Science ◽  
Structural Features ◽  
The Other ◽  
Canada Geese ◽  
New Genera ◽  
Research Activity ◽  
Detailed Understanding ◽  
The Public ◽  
Quo Vadis

“Although I work a lot with fossils in my own research on fishes, I do not care to be called a paleontologist; and I am turned off by many aspects of the public-relations hoopla surrounding paleontology, especially dinosaurs…. One could easily argue that the schools' fascination with dinosaurs might also detract from the other aspects of earth science and biological science and, in the end, weaken paleontology's image as an activity for hard-nosed grown-ups.”K.S. Thomson, 1985: p. 73“Let dinosaurs be dinosaurs. Let the Dinosauria stand proudly alone, a Class by itself. They merit it. And let us squarely face the dinosaurness of birds and the birdness of the Dinosauria. When the Canada geese honk their way northward, we can say: “The dinosaurs are migrating, it must be spring!”R.T. Bakker, 1986: p. 462It is a now oft-repeated statement that we are in the Second Golden Age of dinosaur studies. This may at first seem to be yet another overstatement by dinosaur fanatics; in fact, it is substantiated on a number of fronts. Research activity is certainly at an all-time high, with resident dinosaur researchers on every continent (except Antarctica) and dinosaurs known from every continent (including Antarctica). This activity has resulted in a spate of discoveries, including not only new genera and species, but entirely new types of dinosaurs, such as the segnosaurs. Well-known groups are producing surprises, such as armored sauropods and sauropods bearing tail clubs. Good specimens of previously named genera are revealing unsuspected structural features that almost defy explanation, as in the skull of Oviraptor. However, dinosaur studies extend far beyond the traditional emphasis on dinosaur morphology, and encompass paleobiogeography, paleoecology, taphonomy, physiology, tracks, eggs, histology, and extinction, among others. In some cases, several of these studies can be applied to a single taxon or locality to give us a fairly detailed understanding of the paleobiology of some species.

DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings

2016 ◽  
Vol 67 (3) ◽  
pp. 380 ◽  
Author(s):  
Michael Shackleton ◽  
Gavin N. Rees
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Sequence Data ◽  
Aquatic Environments ◽  
Molecular Approaches ◽  
Monitoring Programs ◽  
Online Databases ◽  
Murray Darling Basin ◽  
Freshwater Fauna ◽  
Australian Freshwater

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.

Cryptic diversity of the mangrove-associated alga Bostrychia (Rhodomelaceae, Rhodophyta) from Thailand

2016 ◽  
Vol 59 (5) ◽  
Author(s):  
Jantana Saengkaew ◽  
Narongrit Muangmai ◽  
Giuseppe C. Zuccarello
Keyword(s):  
Cryptic Species ◽  
Cryptic Diversity ◽  
Algal Diversity ◽  
Molecular Approaches

AbstractAlgal diversity has been extensively investigated using combinations of morphological and molecular approaches. These combined approaches are especially relevant for organisms where cryptic species are known to exist.

A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation

2011 ◽  
Vol 101 (5) ◽  
pp. 505-519 ◽  
Author(s):  
M.E. Carew ◽  
S.E. Marshall ◽  
A.A. Hoffmann
Keyword(s):  
Cryptic Species ◽  
Morphological Variation ◽  
Nuclear Gene ◽  
Pupal Stage ◽  
Mitochondrial Genes ◽  
Pollution Monitoring ◽  
Species Variation ◽  
Molecular Approaches ◽  
Difficult Genus ◽  
Morphological Criteria

AbstractMolecular approaches for identifying aquatic macroinvertebrate species are increasingly being used but there is ongoing debate about the number of DNA markers needed to differentiate species accurately. Here, we use two mitochondrial genes (cytochrome oxidase I, cytochrome b) and a nuclear gene (carbamoylphosphate synthetase) to differentiate species variation within the taxonomically challenging chironomid genus Procladius from southern Australia, a genus which is important for pollution monitoring. The mitochondrial genes indicated cryptic species that were subsequently linked to morphological variation at the larval and pupal stage. Two species previously described based on morphological criteria were linked to molecular markers, and there was evidence for additional cryptic species. Each genetic marker provided different information, highlighting the importance of considering multiple genes when dissecting taxonomically difficult groups, particularly those used in pollution monitoring.

scholarly journals Molecular Approaches to Identify Cryptic Species and Polymorphic Species within a Complex Community of Fig Wasps

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e15067 ◽  
Author(s):  
Jin-Hua Xiao ◽  
Ning-Xin Wang ◽  
Yan-Wei Li ◽  
Robert W. Murphy ◽  
Dong-Guang Wan ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Fig Wasps ◽  
Molecular Approaches ◽  
Polymorphic Species

scholarly journals Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

2021 ◽  
Vol 6 (3) ◽  
pp. 66391
Author(s):  
Katon Waskito Aji ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Distance ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Universal Primers ◽  
Molecular Approaches ◽  
Morphological Studies ◽  
The Family ◽  
Pcr Method

Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species. 

scholarly journals Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12515
Author(s):  
Andreu Santín ◽  
María-Jesús Uriz ◽  
Javier Cristobo ◽  
Joana R. Xavier ◽  
Pilar Ríos
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Deep Sea ◽  
Mediterranean Region ◽  
The Other ◽  
Species Differentiation ◽  
Okhotsk Sea ◽  
New Genera ◽  
Unique Type ◽  
Characteristic Features

Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.

Sampling and processing of freshwater nematodes with emphasis on molecular methods.

2021 ◽  
pp. 31-57
Author(s):  
Janina Schenk ◽  
Walter Traunspurger
Keyword(s):  
Cryptic Species ◽  
Species Identification ◽  
Molecular Species ◽  
Sampling Methods ◽  
Nematode Species ◽  
Molecular Methods ◽  
Specific Gene ◽  
Molecular Species Identification ◽  
Molecular Approaches ◽  
Freshwater Nematodes

Abstract This chapter provides an introduction to current methods of nematode sampling and processing, with the latter including molecular methods as well. It highlights that nematode sampling and processing for different habitats will require different sampling methods; nematode identification can be achieved with morphological or molecular approaches; the analysis of specific gene fragments can be used to delimitate nematode species; and molecular species identification can give further information about phylogenetic background and cryptic species.

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