SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: International Code of Zoological Nomenclature

197

Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented - Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.

Concepts: Biodiversity, Organism, Species, Taxonomy, Genus, Microorganism, International Code of Zoological Nomenclature, Nomenclature

170

Creation and use of the scientific names of animals are ruled by the International Code of Zoological Nomenclature. Until recently, publication of new names in a work produced with ink on paper was required for their availability. A long awaited amendment to the Code issued in September 2012 by the International Commission on Zoological Nomenclature now allows publication of new names in online-only works, provided that the latter are registered with ZooBank, the Official Register of Animal Names. With this amendment, the rules of zoological nomenclature have been aligned with the opportunities (and needs) of our digital era. However, possible causes for nomenclatural instability remain. These could be completely removed if the Code-compliant publication of new names will be identified with their online registration, under suitable technological and formal (legal) conditions. Future developments of the ZooBank may provide the tool required to make this definitive leap ahead in zoological nomenclature.

Concepts: Animal, Taxonomy, Noun, Binomial nomenclature, Name, International Code of Zoological Nomenclature, Nomenclature, International Code of Botanical Nomenclature

163

Tricholoma matsutake, an ectomycorrhizae that has mutual relationships with the rootlet of Pinus denisflora, forms a fruiting body that serves as a valuable food in Asia. However, the artificial culture of this fungus has not been successful. Soil fungi, including T. matsutake, coexist with many other microorganisms and plants; therefore, complex microbial communities have an influence on the fruiting body formation of T. matsutake. Here, we report on the structures of fungal communities associated with the fairy ring of T. matsutake through the pyrosequencing method. Soil samples were collected inside the fairy ring zone, in the fairy ring zone, and outside the fairy ring zone. A total of 37,125 sequencing reads were obtained and 728 to 1,962 Operational Taxonomic Units (OTUs) were observed in the sampling zones. The fairy ring zone had the lowest OTUs and the lowest fungal diversity of all sampling zones. The number of OTUs and fungal taxa inside and outside the fairy ring zone was, respectively, about two times and 1.5 times higher than the fairy ring. Taxonomic analysis showed that each sampling zone has different fungal communities. In particular, out of 209 genera total, six genera, in the fairy ring zone, such as genus Hemimycena, were uniquely present and 31 genera, such as genus Mycena, Boletopsis, and Repetophragma, were specifically absent. The results of metagenomic analysis based on the pyrosequencing indicate a decrease of fungal communities in the fairy ring zone and changes of fungal communities depending on the fairy ring growth of T. matsutake.

Concepts: Bacteria, Species, Fungus, Metagenomics, Kingdom, International Code of Zoological Nomenclature, Matsutake, Tricholoma

127

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.

Concepts: DNA, Genetics, Species, Germany, Eastern Europe, Central Europe, Snake, International Code of Zoological Nomenclature

107

The iconic primeval bird Archaeopteryx was so far mainly known from the Altmühltal Formation (early Tithonian) of Bavaria, southern Germany, with one specimen having been found in the overlying Mörnsheim Formation. A new specimen (the 12th skeletal specimen) from the earliest Tithonian Painten Formation of Schamhaupten (Bavaria) represents the so far oldest representative of the genus. The new specimen shows several interesting anatomical details, including the presence of a postorbital in contact with the jugal, the presence of a separate prefrontal and coronoid, and opisthocoelous mid-cervical vertebrae. Based on observations on the new specimen, we discuss several problematic issues concerning Archaeopteryx, including the monophyly and diagnosis of the genus, the absence/presence of the sternum, the position of the gastralia, and variation in morphometrics and dental morphology in that genus. Based on a new diagnosis for the genus Archaeopteryx, the Berlin, Eichstätt, Solnhofen, Munich, Daiting, Thermopolis, 11th, and 12th specimens can be referred to this genus with high certainty. The Maxberg specimen is very probably also an Archaeopteryx, based on overall similarity, although none of the diagnostic characters can be evaluated with certainty. The ninth specimen (‘chicken wing’) might be Archaeopteryx, but cannot be referred to the genus with any certainty. In comparison with other paravians, the presence of distally thickened anterior pectoral ribs indicates that a rather large cartilagenous sternum was present in this taxon. In contrast to non-opisthopubic theropods, opisthopubic taxa, such as Archaeopteryx and many other paravians, have the posterior end of the gastral basket preserved at about half-length of the pubis, which might reflect the post-mortem collapse of enlarged abdominal air sacs in these taxa. Specimens that can be referred to Archaeopteryx show a high amount of variation, both in the morphometrics of the limb bones as well as in the dentition. In respect to the latter aspect, variation is found in tooth number, spacing, orientation, and morphology, with no two specimens showing the exact same pattern. The significance of this variation is unclear, and possible explanations reach from high intraspecific (and possibly ontogenetic and/or sexual dimorphic) variation to the possibility that the known specimens represent a ‘species flock’ of Archaeopteryx, possibly due to island speciation after the initial dispersal of the genus into the Solnhofen Archipelago.

Concepts: Biology, Species, Bird, Teeth, Specimen, Archaeopteryx, Theropoda, International Code of Zoological Nomenclature

27

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine and basic research. This phylogenetically-guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for close to a century. Due to recent changes in the International Code of Nomenclature for algae, fungi and plants (16), this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we find unnecessary. Here we argue that our proposal will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.

Concepts: Biology, Species, Plant, Fungus, Binomial nomenclature, Genus, Kingdom, International Code of Zoological Nomenclature

26

Since the discovery of saponins in sea cucumbers, more than 150 triterpene glycosides have been described for the class Holothuroidea. The family Holothuriidae has been increasingly studied in search for these compounds. With many species awaiting recognition and formal description this family currently consists of five genera and the systematics at the species-level taxonomy is, however, not yet fully understood. We provide a bibliographic review of the triterpene glycosides that has been reported within the Holothuriidae and analyzed the relationship of certain compounds with the presence of Cuvierian tubules. We found 40 species belonging to four genera and 121 compounds. Holothurin A and B are the most common saponins for Actinopyga, Holothuria, and Pearsonothuria. The genus Bohadschia presents mainly bivittoside C and D. Actinopyga has only sulfated saponins mainly oxidized, Bohadschia non-sulfated ones mainly non-oxidized, Holothuria and Pearsonothuria contain both types of compounds, mainly oxidized. Within the genus Holothuria, the subgenus Panningothuria only has non-sulfated saponins. The presence of sulfated and non-sulfated compounds seemingly relates to the expellability or the absence of Cuvierian tubules and the temporal or permanent concealing habits of the species. Our study concludes that better insights into the systematic distribution of saponins in Holothuriidae will only be possible if the identifications of the investigated species are confirmed by a taxonomist, especially in this group wherein cryptic species and variation between life-history stages are common and yet poorly understood. Understanding of saponin distribution within the Holothuriidae would also benefit from a stabilization of triterpene glycoside nomenclature.

Concepts: Species, Taxonomy, Binomial nomenclature, Taxonomic rank, International Code of Zoological Nomenclature, Sea cucumber, Systematics, Holothuroidea

26

During our study of biodiversity of Rotifera in PR China, as model taxon of freshwater Micrometazoa, we came across several records that warrant revision regarding species of genus Mytilina Bory de St. Vincent, 1826 (Rotifera, Monogonta, Mytilinidae). In addition to this review we describe a new species encountered during examination of freshwater habitats of Inner Mongolia, P.R.China. This new species, Mytilina wangi n. sp., appears to belong to the Mytilina mucronata - ventralis complex but differs from the known taxa in the group by its domed lorica and relatively short toes. We provide an annotated checklist of the Chinese representatives of the genus and discuss the species of the M. mucronata-ventralis group. We suggest treating M. brevispina (Ehrenberg, 1830) and M. ventralis (Ehrenberg, 1830)(synonym: M. macracantha (Gosse, 1886)) as separate species-level taxa rather than as two infrasubspecific variants of the same species, and argue that Mytilina trigona var. bispinosa Wang, 1961 is a misidentified M. acanthophora Hauer, 1938 rather than an infrasubspecific variant of M. trigona (Gosse, 1851). 

Concepts: Species, China, People's Republic of China, Inner Mongolia, International Code of Zoological Nomenclature, Botanical nomenclature, Mongolia, Hui people

26

An updated list of Issidae known from Vietnam is provided. Two new species, one from the genus Darwallia Gnezdilov, 2010, and another one from a new genus are described from the Hòn Bà massif in Central Vietnam. A key to species of the genus Darwallia is provided. Gelastyrella hainanensis Ran et Liang, 2006 is placed in synonymy under Thabena litaoensis Yang, 1994. This last taxon and the genus Gergithoides Schumacher, 1915 are recorded for the first time for Vietnamese fauna. New records in Vietnam are given for Tetrica philo Fennah, 1978 and Gergithus iguchii Matsumura, 1916. 

Concepts: Class, Scientific classification, International Code of Zoological Nomenclature, Zoological nomenclature, Botanical nomenclature, Chresonym, March 10, March 14

25

Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov. and Singerocomus rubriflavus gen. and sp. nov. (Boletaceae, Boletales, Basidiomycota) are described from the Pakaraima Mountains and adjacent lowlands of Guyana. Xerocomus inundabilis, originally described from the central Brazilian Amazon and based solely on the type collection, is redescribed from numerous collections from Guyana and transferred into Singerocomus. These boletes occur in Neotropical forests dominated by ectomycorrhizal trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae) and Pakaraimaea (Dipterocarpaceae). Three of the species were repeatedly found in a multiyear sporocarp survey in Dicymbe corymbosa-monodominant forest. Macromorphological, micromorphological, habitat and multilocus DNA sequence data are provided for each species. A molecular phylogenetic analysis based on a large taxon set across the Boletaceae justifies erection of the new genera.

Concepts: Fungus, Faboideae, International Code of Zoological Nomenclature