New parasite identified in Blennius sanguinolentus Pallas, 1811: Schikhobalotrema longivesiculatum sp. n (Haplosplanchnidae Poche, 1925)]

Schikhobalotrema longivesiculatum sp.n from Blennius sanguinolentus Pallas, 1811 at Gulf of Gaeta (Italy) is described, figured and compared with other species of the genus Schikhobalotrema Skrjabin et Guschanskaja, 1955. Schikhobalotrema longivesiculatum differs from Schikhobalotrema obtusa (Linton, 1916) Skrjabin et Guschanskaja, 1955, especially for sucker ratio, lobed ovary, seminal vesicle coiled and in larger size of eggs; from Schikhobalotrema pomacentri (Manter, 1937) Skrjabin et Guschanskaja, 1955 for lobed ovary, elongated seminal receptacle, smaller vitelline follicles and coiled seminal vesicle; from Schikhobalotrema sparisomae (Manter, 1937) Skrjabin et Guschanskaja, 1955 for elongated seminal receptacle, coiled seminal vesicle and extent of escretory vesicle.     

Tyrrhenia blennii g.n. sp. n. (Hemiurata : Halipegidae Poche, 1925) parasite of Blennius gattorugine and Blennius sanguinolentus]

Trematodes recovered from Blennius gattorugine and Blennius sanguinolentus from the Gulf of Gaeta, Italy, are described and figured as Tyrrhenia blennii g.n. sp.n. The new genus differs from other members of the Arnolinae Skrjabin and Guschanskaja, 1958 (Halipegidae Poche, 1925) chiefly in having acetabulum equatorial, receptaculum seminis uterinum present and eggs without filaments. The diagnosis of the new genus Tyrrhenia and a key to genera of Arnolinae are given.     

Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions

Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.     

Revision of the superfamily Rhynchoporoidae Muir-Wood, 1955

The revision of punctate rhynchonellids of the superfamily Rhynchoporoidea revealed that the superfamily is composite. Based on the detail study of shell interior, the punctate rhynchonellids of the genus Rhynchopora King, 1865, subfamily Rhynchoporinae Muir-Wood, 1955 are placed into the family Trigonirhynchiidae Schmidt, 1965, superfamily Rhynchotrematoidea Schuchert, 1913. The genera Greira Erlanger, 1993, Tchanakhtchirostrum Sartenaer et Plodowski, 2003, Sharovaella Pakhnevich, 2012, Zaigunrostrum Sartenaer et Plodowski, 2003 are also referred to this family within the subfamily Greirinae Erlanger, 1993. The only genus of the subfamily Tretorhynchinae Savage, 2002, Tretorhynchia Brunton, 1971, is moved to the family Leiorhynchidae Stainbrook, 1945, superfamily Camarotoechioidea Schuchert, 1929. Araratella Abrahamian, Plodowski, et Sartenaer, 1975 within the subfamily Araratellinae Erlanger, 1986 is referred to the family Septalariidae Havlicek, 1960 of the same superfamily. The position of Rariella Zhang, 1981, Yingtangella Bai et Ying, 1977, Momarhynchus Baranov et Sartenaer, 1996 in the order Rhynchonellida remains controversial. The punctation and exopunctation is found to arise parallel in different rhynchonellid evolutionary branches after the Frasnian-Famennian mass extinction.     

Chromosomal-level assembly of the Leptodermis oblonga (Rubiaceae) genome and its phylogenetic implications

Rubiaceae is the fourth largest and a taxonomically complex family of angiosperms. Many species in this family harbor low reproductive isolation and frequently exhibit inconsistent phenotypic characteristics. Therefore, taxonomic classification and their phylogenetic relationships in the Rubiaceae family is challenging, especially in the genus Leptodermis. Considering the low taxonomic confusion and wide distribution, Leptodermis oblonga is selected as a representative Leptodermis for genome sequencing. The assemblies resulted in 497 Mbp nuclear and 155,100 bp chloroplast genomes, respectively. Using the nuclear genome as a reference, SNPs were called from 37 Leptodermis species or varieties. The phylogenetic tree based on SNPs exhibited high resolution for species delimitation of the complex and well-resolved phylogenetic relationships in the genus. Moreover, 28,987 genes were predicted in the nuclear genome and used for comparative genomics study. As the first chromosomal-level genome of the subfamily Rubioideae in Rubiaceae, it will provide fruitfully evolutionary understanding in the family.     

Experimental studies on the taxonomic relationships in the subfamily Typhlocoelinae (Digenea: Cyclocoelidae)

Summary Two morphologically distinct digeneans of the subfamily Typhlocoelinae, family Cyclocoelidae, were subjected to a detailed morphological examination in which the variability of 20 numerical and nine character variables within and among various duck host species was assessed. By means of experimental cross infections in a variety of duck species, it was demonstrated that the two parasites are not separate species and that the morphological differences are not host-induced. It was concluded that the two forms are subspecies of a single species. Typhlocoelum cucumerinum sisowi (Skrjabin, 1913) has small, round or oval testes and occurs almost exclusively in ducks of the genus Anas, whereas T. cucumerinum cucumerinum (Rudolphi, 1809) has large, deeply-lobed testes and occurs almost exclusively in ducks of the genus Aythya. T. americanum Manter & Williams, 1928, T. indicum Fotedar, 1964 and T. sisowi acirratus Jain, 1966 are considered synonyms of T. c. sisowi. ac]19810129     

57 Systematics of hydropuntia montagne (gracilariaceae,gracilariales, rhodophyta) based on comparative morphology and rbcL sequence analysis

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbcL DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbcL sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo‐Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

Phylogenetic relationship among East Asian species of the Stegana genus group (Diptera,Drosophilidae)

The phylogenetic relationship among 27 East Asian species of the Stegana genus group was reconstructed using DNA sequences of mitochondrial (COI and ND2) and nuclear (28S) genes. The results lent support to the current generic/subgeneric taxonomic classification in the genus group with the exceptions of the paraphyly of the genus Parastegana and the subgenus Oxyphortica in the genus Stegana. The ancestral areas and divergence times in the genus group were reconstructed/estimated, and accordingly, the biogeographical history of this important clade was discussed. It was proposed that, the evolution of the plant family Fagaceae, especially Quercus, may have played a certain role in facilitating the diversification of the Stegana genus group.     

Phylogenetic Systematics of Peccaries (Tayassuidae: Artiodactyla) and a Classification of South American Tayassuids

Tayassuidae is a family of pig-like Artiodactyla restricted to the New World. Despite its rich fossil history, they have received less attention from a taxonomic and phylogenetic perspective when compared to the Old World pigs, Suidae. In this study, we performed a computer assisted phylogenetic analysis using morphological and molecular data including fossil and extant Tayassuidae, using parsimony and Bayesian approaches. We recovered the monophyly of the family Tayassuidae, confirming previous proposals, as well as the monophyly of the subfamilies Hesperhyinae and Tayassuinae, and the genus Platygonus, which we placed in a new taxon of tribe level. The three living peccaries and a number of fossil species belong to a new, tribe level, monophyletic group. The genus Catagonus comes out as paraphyletic, leading us to propose to restrict the generic name to the type species, C. metropolitanus, and a new taxonomic arrangement for the remaining species previously included in it, revalidating the genera Brasiliochoerus and Parachoerus, and describing a new genus, Protherohyus, gen. nov.     

A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic,phylogenetic, and phenotypic criteria

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA–DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G + C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of “aerotolerant campylobacters” as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].     

Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny,Genomics-Based Taxonomy,Pathogenicity, and Diagnostics

The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.     

Phylogenetic reassessment of Hyaloscyphaceae sensu lato (Helotiales, Leotiomycetes) based on multigene analyses

Hyaloscyphaceae is the largest family in Helotiales, Leotiomycetes. It is mainly characterized by minute apothecia with well-differentiated hairs, but its taxonomic delimitation and infrafamilial classification remain ambiguous. This study performed molecular phylogenetic analyses using multiple genes including the ITS-5.8S rDNA, the D1–D2 region of large subunit of rDNA, RNA polymerase II subunit 2, and the mitochondrial small subunit. The primary objective was to evaluate the phylogenetic utility of morphological characters traditionally used in the taxonomy of Hyaloscyphaceae through reassessment of the monophyly of this family and its genera. The phylogenetic analyses inferred Hyaloscyphaceae as being a heterogeneous assemblage of a diverse group of fungi and not supported as monophyletic. Among the three tribes of Hyaloscyphaceae only Lachneae formed a monophyletic lineage. The presence of hairs is rejected as a synapomorphy, since morphologically diversified hairs have originated independently during the evolution of Helotiales. The true- and false-subiculum in Arachnopezizeae are hypothesized to have evolved through different evolutionary processes; the true-subiculum is likely the product of a single evolutionary origin, while the false-subiculum is hypothesized to have originated multiple times. Since Hyaloscyphaceae sensu lato was not resolved as monophyletic, Hyaloscyphaceae sensu stricto is redefined and only applied to the genus Hyaloscypha.     

A new genus and species of arboreal toad with phytotelmonous larvae,from the Andaman Islands,India (Lissamphibia,Anura, Bufonidae)

A new bufonid amphibian, belonging to a new monotypic genus, is described from the Andaman Islands, in the Bay of Bengal, Republic of India, based on unique external morphological and skeletal characters which are compared with those of known Oriental and other relevant bufonid genera. Blythophryne gen. n. is distinguished from other bufonid genera by its small adult size (mean SVL 24.02 mm), the presence of six presacral vertebrae, an absence of coccygeal expansions, presence of an elongated pair of parotoid glands, expanded discs at digit tips and phytotelmonous tadpoles that lack oral denticles. The taxonomic and phylogenetic position of the new taxon (that we named as Blythophryne beryet gen. et sp. n.) was ascertained by comparing its 12S and 16S partial genes with those of Oriental and other relevant bufonid lineages. Resulting molecular phylogeny supports the erection of a novel monotypic genus for this lineage from the Andaman Islands of India.     

The Genus Lactobacillus: A Taxonomic Update

Lactic Acid Bacteria (LAB) are a functional group of microorganisms comprising Gram-positive, catalase negative bacteria that produce lactic acid as the major metabolic end-product of carbohydrate fermentation. Among LAB, Lactobacillus is the genus including a high number of GRAS species (Generally Recognized As Safe) and many strains are among the most important bacteria in food microbiology and human nutrition, due to their contribution to fermented food production or their use as probiotics. From a taxonomic point of view, the genus Lactobacillus includes at present (October 2012), 152 validly described species, and it belongs to the family Lactobacillaceae together with genus Pediococcus, with whom it is phylogenetically intermixed. The updated phylogenetic analysis based on 16S rRNA gene sequence revealed that the family is divided into 15 groups of three or more species, 4 couples and 10 single lines of descents. In addition, other taxonomically relevant information for Lactobacillus species was collected. This study aims at updating the taxonomy of the genus Lactobacillus, presenting the phylogenetic structure of the Lactobacillaceae and discussing the clusters as possible nuclei of genera to be described in the future. It is expected that scientists and producers in the field of probiotics could benefit from information reported here about the correct identification procedures and nomenclature of beneficial strains of lactobacilli.     

Genome-based taxonomy of genera Halomicrobium and Halosiccatus,and description of Halomicrobium salinisoli sp. nov

The genera Halosiccatus and Halomicrobium are the most closely related genera within the family Haloarculaceae (class Halobacteria). All species of these two genera are closely related to each other in phylogenetic analyses based on their 16S rRNA gene sequences, and also using the sequences of four housekeeping genes. The genus Halosiccatus was proposed based on inferred phylogeny using only one of the three distinct 16S rRNA genes detected in strain DC8^T, while Halomicrobium zhouii, one of three species of Halomicrobium, was omitted from the reference species used in these analyses. The related 16S rRNA gene sequence similarities of type strains of Halomicrobium katesii and Halomicrobium mukohataei were as high as 99.5%–99.7%, much higher than the threshold values proposed as species boundaries. These issues could have resulted in taxonomic inaccuracies in the genera Halosiccatus and Halomicrobium, and a thorough study was undertaken to clarify the status of all species in both genera. Based on phylogenetic and phylogenomic analyses, the current four species of the two genera form a single clade with high bootstrap confidence, indicating that the genus Halosiccatus should be merged with Halomicrobium. Halomicrobium katesii Kharroub et al. 2008 is proposed as a later heterotypic synonym of Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002. An additional species is also described (strains LT50^T and TH30), and was isolated from different Gobi saline soil samples of Tarim Basin, Xinjiang, China. Phenotypic, chemotaxonomic, genomic and phylogenetic properties indicated that strains LT50^T (=CGMCC 1.15187^T = JCM 30837^T) and TH30 (=CGMCC 1.15189 = JCM 30839) represent a novel species of the genus Halomicrobium, for which the name Halomicrobium salinisoli sp. nov. is proposed.     

Phylogeny of the Permian family Metalegoceratidae (Goniatitida,Ammonoidea)

The paper discusses the evolution of the Permian ammonoid family Metalegoceratidae, and a new phylogenetic reconstruction is proposed. Three subfamilies are recognized in this family: Metalegoceratinae Plummer et Scott, 1937; Pericycloceratinae Zhao et Zheng, 1977; and Eothinitinae Ruzhencev, 1956. The genus Metalegoceras Schindewolf, 1931 is subdivided into three subgenera: Metalegoceras s. str., Mesometalegoceras subgen. nov., and Artimetalegoceras subgen. nov. Five species of the endemic South Chinese metalegoceratids are described: Pseudometalegoceras shangraoense (Zhao et Zheng, 1977), P. liratum (Zhao et Zheng, 1977), P. platyventrum (Zhao et Zheng, 1977), P. spirale (Zhao et Zheng, 1977), and Pericycloceras costatum (Zhao et Zheng, 1977).     

The Opecoelidae (Digenea) of sparid fishes of the western Mediterranean. I. Pachycreadium Manter, 1954

Problems of the systematics of the Opecoelidae in the Mediterranean region are discussed. The genus Pachycreadium Manter, 1954 is redefined and its validity commented upon. Pachycreadium carnosum (Rud., 1819) is described from Sparus pagrus and Pagellus erythrinus off Corsica (Scandola) and compared with P. gastrocotylum (Manter, 1940) and P. lerneri Sogandares-Bernal, 1959.

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Résumé Les problèmes concernant la systématique des Opécoelidés de la région méditerranéenne sont abordés. Les auteurs redéfinissent et discutent la validité du genre Pachycreadium Manter, 1954. Pachycreadium carnosum (Rudolphi, 1819) est décrit à partlr d'exemplaires parasites de Sparus pagrus et de Pagellus erythrinus des côtes de Corse (Scandola), puis comparé à P. gastrocotylum (Manter, 1940) et à P. lerneri Sogandares-Bernal, 1959.

     

Morphogenesis,origin, and paleoecology of the bryozoans of the family Medvedkellidae fam. nov. (Upper Carboniferous,East European Platform)

A new family of the order Rhabdomesida, Medvedkellidae fam. nov., is described. This family consists of a new genus, Medvedkella gen. nov., comprising three species transferred from the genus Rhombopora Meek, 1872: the type species M. riasanensis (Schulga-Nesterenko, 1955), M. diaphragmata (Schulga-Nesterenko, 1955), and M. mariae (Dunaeva, 1961). The morphogenesis of the first two species is studied. For the first time axial zooecia are revealed in the suborder Golgdfussitrypina, which existed in parallel with the suborder Rhabdomesina of the order Rhabdomesida. A hypothesis that the new family evolved from the subfamily Nicklesoporinae Gorjunova, 1985 of the family Goldfussitrypidae, 1985 is proposed. Some questions of the ecological adaptation of these bryozoans in the Late Carboniferous marine basin of the East European Platform are discussed.