Taxa Of Genus Research Articles

On the taxonomy of the genus Barsochrista Singh & Kirti, 2016 (Lepidoptera, Erebidae, Arctiinae)

The Asura / Miltochrista generic complex is one of the largest and taxonomically most difficult Lithosiini groups, including several hundreds of species, most of which occur in the Oriental Tropics. At present the complex includes about 25 valid genera as well as several generic taxa of unclear status, and some species groups not established taxonomically that probably represent distinct genera or subgenera (Holloway 2001; Kirti & Singh 2016; Volynkin 2016).

Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species.

The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.

Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions.

The Androgen-binding protein (Abp) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus (Mmd) and Mus musculus musculus (Mmm), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd, primarily representing the presence/absence of the final duplications described for the mouse genome. Clustering of Mmd individuals based on this variation did not reflect their geographical origin, suggesting no population divergence in the Abp gene cluster. However, copy number variation patterns differ substantially between Mmd and other mouse taxa. Large blocks of Abp genes are absent in Mmm, Mus musculus castaneus and an outgroup, Mus spretus, although with differences in variation and breakpoint locations. Our analysis calls into question the reliance on a reference genome for interpreting the detailed organization of genes in taxa more distant from the Mmd reference genome. The polymorphic nature of the gene family expansion in all four taxa suggests that the number of Abp genes, especially in the central gene region, is not critical to the survival and reproduction of the mouse. However, Abp haplotypes of variable length may serve as a source of raw genetic material for new signals influencing reproductive communication and thus speciation of mice.

Morphological characters, occurrence and distribution among members of the family Solanaceae in parts of the Niger Delta Ecological Zone

This study investigated a comparative micro-morphological features of 14 species in the family Solanaceae, using trichome and stomatal complements in delimitation of species and genera within the taxon, family. The genus Solanum L. is the largest among the genera in Solanaceae. Solanum aethiopicum Linn. Solanum macrocarpon Linn. Solanum torvum Swartz. Solanum anomalum Thonn. Solanum erianthum D. Don, are covered with stellate trichomes. While Solanum nigrum Linn., Solanum lycopersicum Linn., Solanum incanum Linn., Datura spp., Schwenckia spp., Capsicum spp., Physalis spp. have simple uniseriate trichomes. S. aethiopicum Linn. S. torvum Swartz. S. lycopersicum Linn, and Physalis micrantha Linn, revealed higher trichome indices. In most species, these trichomes are not visibly observed with the naked eyes. While in some others such as in S. torvum and S. lycopersicum the trichomes are observable on the plants. Glandular hairs are also present in Solanaceae. Stomata is amphistomatic, types commonly observed are: anisocytic and anomocytic, while paracytic and tetracytic stomata are sometimes revealed in stem epidermis in Solanaceae. The usefulness of trichome and stomatal complements in species and generic taxa are recommended as pertinent characters for classification in Solanaceae and their density may vary from one ecological zone to another.Keywords: Solanaceae, Solanum, Stomata, trichomes, Complements, Comparative

Molecular phylogeny and patterns of diversification in syngnathid fishes

The family Syngnathidae is a large and diverse clade of morphologically unique bony fishes, with 57 genera and 300 described species of seahorses, pipefishes, pipehorses, and seadragons. They primarily inhabit shallow coastal waters in temperate and tropical oceans, and are characterized by a fused jaw, male brooding, and extraordinary crypsis. Phylogenetic relationships within the Syngnathidae remain poorly resolved due to lack of generic taxon sampling, few diagnostic morphological characters, and limited molecular data. The phylogenetic placement of the threatened, commercially exploited seahorses remains a topic of intense interest, with conflicting topologies based on morphology and predominantly mitochondrial genetic data. In this study, we integrate eight nuclear and mitochondrial markers and 17 morphological characters to investigate the phylogenetic structure of the family Syngnathidae at the generic level. We include 91 syngnathid species representing 48 of the 57 recognized genera, all major ocean basins, and a broad array of temperate and tropical habitats including rocky and coral reefs, sand and silt, mangroves, seagrass beds, estuaries, and rivers. Maximum likelihood and Bayesian analyses of 5160bp from eight loci produced high congruence among alternate topologies, defining well-supported and sometimes novel clades. We present a hypothesis that confirms a deep phylogenetic split between lineages with trunk- or tail-brood pouch placement, and provides significant new insights into the morphological evolution and biogeography of this highly derived fish clade. Based on the fundamental division between lineages - the tail brooding “Urophori” and the trunk brooding “Gastrophori” - we propose a revision of Syngnathidae classification into only two subfamilies: the Nerophinae and the Syngnathinae. We find support for distinct principal clades within the trunk-brooders and tail-brooders, the latter of which include seahorses, seadragons, independent lineages of pipehorses, and clades that originated in southern Australia and the Western Atlantic. We suggest the seahorse genus Hippocampus is of Indo-Pacific origin and its sister clade is an unexpected grouping of several morphologically disparate Indo-Pacific genera, including the Pacific pygmy pipehorses. Taxonomic revision is required for multiple genera, particularly to reflect deep evolutionary splits in nominal lineages from the Atlantic versus the Indo-Pacific.

Phylogeny and circumscription of the genus Orinus (Poaceae: Eragrostideae): evidence from NRDNA its sequences

In this study, ITS sequences of the nuclear ribosomal DNA were conducted for six putative species of Orinus ( O . alticulmus , O . anomala , O . kokonorica , O . longiglumis , O . thoroldii and O . tibeticus ) with 572 individuals from 73 populations. The results found that the six species formed two monophyletic groups: the one ( O . anomala Keng ex Keng f. and L. Liou) with O . alticulmus , O . anomala and O . kokonorica , and another ( O . thoroldii (Stapfex Hemsl.) Bor) with O . longiglumis , O . thoroldii and O . tibeticus . The taxonomic data from ITS sequences were not congruent with those from morphological characteristics, likely resulting from rapid speciation trigged by the uplifts of the Qinghai-Tibetan Plateau and its adjacent regions and the extensive selection pressure under the alpine environments. The ITS data suggest that the classification of the six species within the genus Orinus should be reduced to two species. We include a complete taxonomic revision of the genus and a key to distinguish the two species. Therefore, it is very necessary to make the comprehensive revision and arrangement of these taxa, strictly regulate the taxa confusion of genus and species order, and do new reports on belonging to the genus taxa.

Where Do Fungi Fit? The Fungal Domain In Mixtepec Zapotec

We summarize results of two independent ethnobiological field studies in adjacent Zapotec towns in the Sierra de Miahuatlan, Oaxaca, Mexico. San Juan and San Pedro Mixtepec share a common language (with minor lexical variation) and occupy contiguous traditional municipal territories ranging from 1650 m to 3700 m elevation and practice a common subsistence agricultural tradition. In conjunction, our data provide a detailed account of how macro-fungi are classified, named, and used by residents of these two towns. We first consider “where fungi fit” in the local worldview as well as in the broader context of folk systematics, noting their relative neglect in ethnobiological studies to date. We document more than 30 distinct, named folk generic taxa of macro-fungi (known locally as mĕy), analyze the nomenclatural patterns characteristic of this life-form, and argue that it is best construed to be “an unaffiliated life-form” rather than an unaffiliated folk generic taxon or a kingdom on a par with that of plants or of animals. We briefly characterize the ecology and phenology of each recognized folk taxon and detail how 25 species are used as food. We note in particular how local harvesters distinguish confusingly similar toxic from edible species. We compare the Mixtepec Zapotec classification and nomenclature with that of two other Mexican Indigenous societies, the Purepecha of Michoacan, and the Tzeltal Maya of Chiapas, noting many similarities but also some intriguing contrasts.

On systematics of the subfamily Cybocephalinae (Coileoptera: Nitidulidae) with description of new species and generic taxa

This paper describes a new species, Hierronius madeiraensis sp. nov., from Madeira belonging to the wingless group of the family Nitidulidae, together with the description of new cybocephalin genera from Japan (Apastillus gen. nov., type species: Pastillus eminentithorax Sadatomo Hisamatsu, 2013), South America (Amedissia gen. nov., type species: Pycnocephalus argentines Brethes, 1922) and Micronesia (Pacicephalus gen. nov., type species: Cybocephalus gressitti Endrody-Younga, 1971). A key to all recent and fossil genera of the subfamily is provided. Theticephalus Kirejtshuk, 1988 is regarded as a separate genus (stat. nov.). The genera with species having partly or completely reduced hindwings (Apastillus gen. nov., Hierronius Endrody-Younga, 1968, Pastillodes Endrody-Younga, 1968, Pastillus Endrody-Younga, 1962, and probably the fossil Pastillocenicus Kirejtshuk et Nel, 2008), characterized by a short metaventrite, are considered as independent lineages. The systematics and phylogeny of the family are discussed in regards to recent publications affecting the position of the subfamily Cybocephalinae and proposing changes in the general system of the family Nitidulidae.

Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.

Sidama Agro-Pastoralism and Ethnobiological Classification of its Primary Plant, Enset (Ensete ventricosum)

Enset is an essential plant for the Ethiopian Sidama system of agropastoralism. Sidama agropastoralism and the folk taxonomy of enset is presented here in ethnographic context. One of several societies of Ethiopia’s enset complex, the highland Sidama are among the most wholly reliant on enset and maintain more enset varieties in their gardens than other groups. Sidama agro-pastoral systems revolve around human-enset-cattle interaction: Sidama eat low-protein parts of enset; cattle eat high-protein parts of enset; Sidama get protein from dairy; Sidama fertilize enset with cattle manure. In the Sidama language, enset offers an example of Hunn’s generic elevation within the framework of Berlinian perceptual-taxonomic theory. Weesho (enset) may serve both as a folk generic taxon and a life-form taxon depending on the frame of reference. Such expansion allows for an intermediate taxa translating to “male” or “female” ensets, followed by generic and specific taxa for kinds or “breeds” of enset. Generic elevation offers descriptive magnification of nomenclature for enset, a most salient species among Sidama people.

A plastid DNA phylogeny of tribe Miliuseae: Insights into relationships and character evolution in one of the most recalcitrant major clades of Annonaceae

Tribe Miliuseae (∼25 genera and ∼510 species) includes a substantial part of the species and generic diversity in the pantropical flowering-plant family Annonaceae (∼108 genera and ∼2400 species). Previous molecular phylogenetic analyses have failed to resolve the backbone phylogeny of the tribe, impeding biogeographical and evolutionary studies. We use a dense generic taxon sample (∼89% of generic diversity in Miliuseae) and plastid DNA sequence data (∼7 kb) to clarify the phylogenetic relationships of and within the tribe. Parsimony and Bayesian phylogenetic reconstructions and ancestral character-state reconstructions of several reproductive characters were performed. Dendrokingstoniae, Monocarpieae, and Miliuseae are recovered in a strongly supported clade, and each tribe is strongly supported as monophyletic. Miliuseae are characterized by a synapomorphic cryptoaperturate/disulculate pollen apertural system. Stenanona is shown to be nested within the paraphyletic genus Desmopsis. The only Neotropical clade (Sapranthus, Tridimeris, Desmopsis, and Stenanona) in the predominantly Asian Miliuseae is shown to be closely related to an undescribed genus from continental Southeast Asia and the Indo-Malayan and Austral-Pacific genus Meiogyne. Ancestral character-state reconstructions of several reproductive characters that are diagnostically important at the generic level indicate a considerable degree of homoplasy. The results improve our understanding of the relationships of and within Miliuseae, but parts of the backbone of the phylogeny remain poorly supported. Additional data from variable nuclear markers or reduced-genome-representation approaches seem to be required to further resolve relationships within this recalcitrant clade.

Biodiversity patterns in interstitial marine microturbellaria: a case study within the genus Parotoplana (Platyhelminthes: Rhabditophora) with the description of four new species

Four new species of Otoplanidae (Platyhelminthes: Rhabditophora: Proseriata) with ranges restricted to the central Mediterranean are described. These species are characterized by the presence of a tubular copulatory stylet and by a bursa lacking an open connection to the atrium. Both characters are novel for the family Otoplanidae. The four species differ mainly in details of the morphology of the sclerotized structures of the copulatory organ. Generic attribution of the new species has been problematic. Morphological characters shared with either Parotoplanina or Parotoplanella were detected. Molecular data (based on 18S rRNA and 28S D1-D6 rRNA genes) evidenced that the new species constitute a monophyletic group falling within species of Parotoplana, with a sister/taxon relationship with Parotoplana spathifera. The genus Parotoplana, however, appears to be paraphyletic, as Parotoplanella progermaria nests within Parotoplana species. The inadequate molecular sampling, combined with the lack of sequences from the type species of both Parotoplana and Parotoplanina, suggested a cautionary taxonomic approach, and the new species are therefore attributed to the earliest generic taxon available, Parotoplana.

DNA barcoding of life: a classification of uses according to function and scale after ten years of development

DNA barcoding technology provides molecular information, standard dataset platforms, and uni- versal technical regulations for modern biological research. We briefly review the history of DNA barcoding between 2003 and 2012, and classify DNA barcoding into three types of biological function: basic function (e.g., storing data, and identifying species), extending function (e.g., building phylogenies, serving specific subjects, and compiling biological atlas) and potential function (e.g., revealing cryptic species). We sort DNA barcoding studies at three levels: clade scale (e.g., familial and/or generic taxa), community scale (e.g., biotic communities in nature reserves and permanent forest dynamics plots), and regional scale (e.g., biodiversity hotpots). We further list ten major research programs proposed by the International Barcode of Life, which are related to DNA barcoding approaches from the prospective of systematics and taxonomy, biodiversity conservation, evolutionary ecology and phylogenetics, and the construction of digital platforms. We appreci- ate the huge capability of barcoding technology in the field of biological sciences, and also realize the chal- lenges of DNA barcoding utilizations in multidisciplinary studies and the essential to add more tests before

Mitochondrial DNA Corroborates Taxonomy of the South American Chelid Turtles of the GeneraPlatemysandAcanthochelys

Abstract A phylogenetic analysis of partial sequences of 2 mitochondrial genes, NADH dehydrogenase subunit 4 (ND4) and cytochrome b (cyt b), supports the generic distinction and sister taxon relationship of Platemys and a monophyletic Acanthochelys. Acanthochelys radiolata is the most distinct member of the genus Acanthochelys and is sister to a clade that includes A. spixii, A. pallidipectoris, and A. macrocephala. Parsimony and maximum likelihood analyses suggested A. spixii (A. pallidipectoris, A. macrocephala), but this was not strongly supported in bootstrap analysis parsimony and maximum likelihood analyses and low Bayesian posterior probabilities. Evidence of molecular diversity within morphologically defined species suggests that there may be additional cryptic species in this group.

A New Genus of Odontopygid Millipeds from Tanzania (Diplopoda: Spirostreptida: Odontopygidae)

The new generic taxon Calyptomastix is proposed to accommodate the type species Odontopyge kakandae Kraus, 1958, and, tentatively, Odontopyge dorsalis Carl, 1909, Haplothysanus leviceps Attems, 1909, and Spirostreptus pardalis Gerstäcker, 1873, all from Tanzania. This genus is defined by the broad basal separation of the male genitalia, the elongated basal whorl (torsion) of the gonopod telopodite, and the concealment of the solenomere within apical folds of the telopodite.

Of Mice and Rats: The Place of Murids in Nage Animal Classification and Symbolism

Abstract The folk zoological taxonomy of the Nage people of central Flores (Indonesia) classifies wild mammals into thirteen named folk generic taxa (sensu Berlin). Of these, nearly half denote murids (rats and mice). In addition, Nage employ dheke, a name that can specifically refer to large commensal rats, to further designate a folk intermediate taxon that subsumes other murid folk generics, thus resulting in a notably more elaborate classification of mice and rats than of other mammals. Murids also receive comparably distinctive treatment in other, special purpose forms of animal classification, and they occupy an especially prominent place in Nage symbolism. The paper considers how these several conceptual orders may be connected, including whether the ethnotaxonomic elaboration of murids may either reflect or be reflected in their symbolic value.

Oxynema, a New Genus Separated from the Genus Phormidium (Cyanophyta)

Taxonomic revision of the traditional polyphyletic cyanobacterial genus Phormidium is based on molecular sequencing combined with the definition of distinct, autapomorphic features. Several genera, clearly separated from each other (with genetic similarity lower than 95%), were already defined and separated from this widely conceived generic unit (Phormidesmis, Wilmottia and others). All of these new generic taxa are characterized by morphological markers also. We have studied another group of species (mainly the strains from salterns in Thailand), which was classified earlier in the genus Phormidium, but it represents an isolated cluster according to 16S rRNA gene sequencing and is characterized by specific uniform and morphological features. Because this whole group represents a phylogenetically and morphologically distinctly separated cluster (see Phormidium group I sensu Komárek & Anagnostidis 2005), we describe it as a special taxon Oxynema genus novum, in agreement with the Botanical Nomenclatoric Code (ICBN; McNeill & al. ed., 2007). The genetically most related clusters always have genetic similarity less than 93% and differ by distinct autapomorphic features. The filaments of members of Oxynema are cylindrical, narrowed and bent at the ends, commonly attenuated to a terminal elongated, more or less sharply pointed cells without calyptra. Thylakoids in cells are distinctly radially arranged, similarly as in the genera Microcoleus and “Phormidium autumnale”-type. The ecology of all members, which belong potentially to these types, is also similar: all species from this cluster were recorded from halophilic habitats, less frequently from thermal springs and soil biotopes with higher salt contents.

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

A new genus for a colorful spirostreptid milliped from East Africa (Diplopoda: Spirostreptida: Spirostreptidae)

The new generic taxon Sagmatostreptus is proposed for the type species Spirostreptus strongylopygus Attems, 1950, endemic to a limited area in northeastern Tanzania and adjacent Kenya.

A glimpse into the past of land plants and of their mycorrhizal affairs: from fossils to evo‐devo

A glimpse into the past of land plants and of their mycorrhizal affairs: from fossils to evo‐devo