Position of the genus Azygopterus (Stichaeidae,Perciformes) in the system of the suborder Zoarcoidei as inferred from sequence variation of mitochondrial and nuclear genes

Analysis of sequence variation in the mitochondrial and nuclear genes in Azygopterus corallinus showed that this species was genetically close to the group uniting the representatives of the families Zoarcidae, Neozoarcidae, and Anarhichadidae. The considerable genetic differences between A. corallinus and the members of the family Stichaedae, to which it was assigned earlier, are consistent with the divergence estimates between the other families of the suborder Zoarcoidei (Zaproridae, Ptilichthyidae, Pholidae, Cryptacanthodidae, Bathymasteridae).     

Position of neck banded blenny Leptostichaeus pumilus (Perciformes: Zoarcoidei) in the system of the suborder Zoarcoidei as inferred from molecular genetic data

Molecular genetic study of genetic variations within COI, cytochrome b, and 16S rRNA of mitochondrial DNA in neck banded blenny Leptostichaeus pumilus, which was earlier assigned to the family Stichaeidae, indicates that the species is most close to a group combining the families Zoarcidae, Neozoarcidae, and Anarhichadidae. Significant genetic differences between neck banded blenny and the family Stichaeidae correspond to the level of divergence between other families of the suborder Zoarcoidei (Zaproridae, Ptilichthyidae, Pholidae, Cryptacanthodidae, and Bathymasteridae).     

Aspects of the phylogeny of the marine Tubificidae

A tentative phylogeny of the oligochaete family Tubificidae, with emphasis on the marine representatives, is presented. The scheme is based on the morphology and arrangements of prostate glands and the setal patterns. The rhyacodriline, more or less diffuse prostates are regarded as a primitive stage in prostate evolution, preceded only by the aprostate condition assumed for the ancestor of the family. An early split of the subfamily Rhyacodrilinae supposedly led to (1) a marine branch, from which evolved the highly diverse, exclusively marine subfamilies Phallodrilinae and Limnodriloidinae, and (2) a freshwater branch, which later divided into the Telmatodrilinae, Tubificinae and Aulodrilinae. The marine subfamilies invariably lack hair setae, whereas about half of the species within the other, freshwater subfamilies possess such setae in their dorsal bundles. Some marine genera, such as Monopylephorus (Rhyacodrilinae), Tubificoides and Clitellio (both Tubificinae) are regarded as recent off-shoots from the main freshwater stock.The families Naididae and Opistocystidae are considered likely to have evolved from rhyacodriline Tubificidae, whereas Phreodrilidae, the fourth family within the suborder Tubificina, is regarded as a sister group to the Tubificidae.     

Position of the genera <Emphasis Type="Italic">Lycenchelys</Emphasis> Gill and <Emphasis Type="Italic">Lycodapus</Emphasis> Gilbert in the family zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis

Sequence variation of the mitochondrial COI, cytochrome b, and 16S RNA genes, as well as nuclear RNF213 gene was examined in the genera Lycenchelys and Lycodapus with the purpose of determination of their positions in the system of the family Zoarcidae. It was demonstrated that the genus Lycodapus was considerably closer to the generic group of Lycogramminae (Lycogrammoides, Bothrocara, Allolepis, Bothrocarhichthys) than the genus Lycenchelys. However, on the phylogenetic trees both of these genera were located in the clade of the subfamily Lycodinae. Genetic heterogeneity of the genus Lycenchelys, represented by two species groups differing in distribution patterns (northeastern Pacific and Antarctic) and showing more profound differences than the genera of subfamily Lycodinae, was demonstrated.     

Molecular phylogenetic study of several eelpout fishes (Perciformes,Zoarcoidei) from Far Eastern seas on the basis of the nucleotide sequences of the mitochondrial cytochrome oxidase 1 gene (<Emphasis Type="Italic">Co-1</Emphasis>)

A total of 95 nucleotide sequences of a Co-1 gene fragment of approximately 650 bp were analyzed for fishes of the orders Perciformes and Scorpaeniformes (outgroup). Gene trees based on four algorithms (BA, NJ, MP, and ML) were similar in topology of solved branches. An emphasis was placed on the species and generic levels, but a significant phylogenetic signal was obtained for higher taxonomic ranks as well. For instance, a monophyletic origin was confirmed for the family Zoarcidae and the subfamily Opisthocentrinae (Stichaeidae). The proportion of different nucleotides in the sequences compared (p-distances) significantly increased with increasing taxonomic rank. The p-distances were estimated for four hierarchic levels and were (1) 0.15 ± 0.06% for the within-species hierarchic level, (2) 6.33 ± 0.37% for the within-genus level, (3) 11.83 ± 0.06% for the within-family level, and (4) 15.22 ± 0.05% for the within-order level. The difference in the Co-1 gene fragments between levels (1) and (2) allows almost errorless species identification on the basis of this kind of a molecular bar code.     

Relationships among several species of the subfamily Gymnelinae (Zoarcidae) inferred from mitochondrial DNA sequence analysis

Nucleotide sequences of the mtDNA COI and cytochrome b genes were determined in Magadanichthys skopetsi, a member of the new monotypic genus Magadanichthys, endemic to the northern coast of the Sea of Okhotsk. Comparison of this species with other representatives of the subfamily Gymnelinae (family Zoarcidae) revealed high genetic similarity of M. skopetsi to Hadropareia middendorffii and considerable differences between these species and Gymnelopsis ochotensis.     

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.     

The origins of modern nonmarine ostracod faunas: evidence from the Late Cretaceous and Early Palaeogene of Mongolia

The Cretaceous and Tertiary development of Mongolian non-marine ostracod faunas is reviewed. During the Late Cretaceous and Early Palaeogene, representatives of the Cypridoidea were widespread and common, Cytheroidea less so and the Darwinuloidea comparatively rare. The evolutionary history of the subfamily Talicyprideinae is considered, with reference to the genera Talicypridea, Altanicypris, Khandiaand Bogdocypris. It is suggested that the extinct Talicyprideinae were related to the mid-Cretaceous to Recent subfamily Cypridinae (e.g. the genus Cypris), both belonging to the family Cyprididae. It is shown that early representatives of the Cyprididae, one of the most diverse non-marine cypridoidean families today, were present from Early Cretaceous onwards (e.g. Lycopterocypris, Mongolocypris), alongside the dominant Cretaceous cypridoideans, the Cyprideidae (e.g. Cypridea), which became extinct in the Palaeogene.     

Relationships and position of wrymouths of the family cryptacanthodidae in the system of the suborder Zoarcoidei (Pisces,Perciformes)

To determine the taxonomic position of wrymouths of the family Cryptacanthodidae in the system of the suborder Zoarcoidei, a study on molecular genetics and comparative morphology of Cryptacanthodes bergi from Peter the Great Bay (Sea of Japan) is conducted. Based on molecular genetic analysis using the genes of nuclear and mitochondrial DNA, Cryptacanthodes bergi is substantially similar to the representatives of the superfamily Stichaeoidae. Thus, the opinion of Makushok on a phylogenetically distinct position of wrymouths in relation to snake blennies and related families is not supported. The anatomical features of skull structure support the data of molecular genetics. The directions and time of distribution of wrymouths in the northwest Atlantic through the channel in the area of the Isthmus of Panama in approximately the late Miocene are discussed.     

Comparative osteology of <Emphasis Type="Italic">Bathylutichthys balushkini</Emphasis> and relationship of the family Bathylutichthyidae (Cottoidei)

The structure of skeleton of Bathylutichthys balushkini was studied and comparative analysis of it with representatives of other families of the suborder Cottoidei was performed. It was found that Bathylutichthyidae are characterized by the presence of a great number of original characters supporting its family status. They include: absence of mesethmoideum; bony canals of seismosensory system on frontale, pteroticum, and parietale and their strong reduction on infraorbitale; and absence of pterosphenoideum, intercalare, pharyngobranchiale 2, and basihyale. At the same time, Bathylutichthyidae retain a considerable number of generalized specific features: location of parietalia laterally to supraoccipitale and absence of their joint between themselves, presence of mesoptergoideum and basibranchialia 2 and 3. Cladistic analysis based on osteological characters and characters of the seismosensory system of 11 families of Cottoidei demonstrates that Bathylutichthyidae are combined into one group with families Rhamphocottidae, Agonidae, Psychrolutidae, Cyclopteridae, and Liparidae occupying an intermediate position between Psychrolutidae and the two last families. The cladogram obtained does not support the point of view of existence in the suborder Cottoidei of an independent superfamily Cyclopteroidea, including families Liparidae and Cyclopteridae.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

Diversity, Distribution, and Ancient Taxonomic Relationships Within the TIR and Non-TIR NBS-LRR Resistance Gene Subfamilies

Phylogenetic relationships among the NBS-LRR (nucleotide binding site–leucine-rich repeat) resistance gene homologues (RGHs) from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed, primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates (K _A/K _S values) in Arabidopsis thaliana. Lower K _A/K _S values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three of the five identified ancient clades appear to predate the angiosperm–gymnosperm radiation. Monocot sequences are absent from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately 150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide models for all major sequence types in other taxa. Received: 13 June 2001 / Accepted: 22 October 2001     

Relationships and position of the taxa of the subfamily Xiphisterinae in the system of the suborder Zoarcoidei (Perciformes)

Analysis of the nucleotide sequences of mitochondrial and nuclear DNA genes was used to examine the relationships and position of the subfamily Xiphisterinae in the system of the suborder Zoarcoidei. This study showed the genetic heterogeneity of Xiphisterinae and the propriety of its division into two subfamilies: Xiphisterinae with the genera Xiphister and Phytichthys and Cebidichthyinae with the genera Cebidichthys, Dictyosoma, Esselenichthys, and Nivchia. The genetic differences between the two subfamilies were not less, but in some cases even greater than the differences between families within the suborder; therefore, they should be raised to the rank of a family, Xiphisteridae and Cebidichthyidae, and classified not within the superfamily Stichaeoidae but rather as independent taxa of the suborder Zoarcoidei.     

Building the Coleoptera tree‐of‐life for >8000 species: composition of public DNA data and fit with Linnaean classification

The species representation of public databases is growing rapidly and permits increasingly detailed phylogenetic inferences. We present a supermatrix based on all gene sequences of Coleoptera available in Genbank for two nuclear (18S and 28S rRNA) and two mitochondrial (rrnL and cox1) genes. After filtering for unique species names and the addition of ?2000 unpublished sequences for cox1 and 18S rRNA, the resulting data matrix included 8441 species‐level terminals and 6600 aligned nucleotide positions. The concatenated matrix represents the equivalent of 2.17% of the 390 000 described species of Coleoptera and includes 152 beetle families. The remaining 29 families constitute small lineages with ?250 known species in total. Taxonomic coverage remains low for several major lineages, including Buprestidae (0.16% of described species), Staphylinidae (1.03%), Tenebrionidae (0.90%) and Cerambycidae (0.58%). The current taxon sampling was strongly biased towards the Northern Hemisphere. Phylogenetic trees obtained from the supermatrix were in very good agreement with the Linnaean classification, in particular at the family level, but lower for the subfamily and lowest for the genus level. The topology supports the basal split of Derodontidae and Scirtoidea from the remaining Polyphaga, and the broad paraphyly of Cucujoidea. The data extraction pipeline and detailed tree provide a framework for placement of any new sequences, including environmental samples, into a DNA‐based classification system of Coleoptera.     

A new family of diminutive zooxanthellate zoanthids (Hexacorallia: Zoantharia)

A new family, genus, and species of zooxanthellate macrocnemic zoanthid is described from Okinawa, Japan. The diminutive zoanthid N anozoanthus harenaceus sp. nov. occurs in sandy ‘pools’ upon hard substrates in coral reefs. The results of molecular phylogenetic analyses of mitochondrial 16S ribosomal DNA and cytochrome c oxidase subunit I suggests that Nanozoanthidae fam. nov. is genetically close to family Microzoanthidae and Isozoanthus sulcatus at the intrafamily–suborder level. The Nanozoanthidae fam. nov. –Microzoanthidae clade is clearly highly divergent from all other known zoanthid families and from the order Actiniaria at the suborder level or higher. These results demonstrate that much high‐level (e.g. above genus) diversity remains to be described within the order Zoantharia, and until such work is complete it will be difficult to completely understand their biodiversity. © 2013 The Linnean Society of London     

On the diploid state of the fish order Ostariophysi

Our previous study on the order Ostariophysi was limited to members of the family Cyprinidae, suborder Cyprinidea. It was shown that the carp and the goldfish with 104 chromosomes and a DNA value of 50% that of mammals are tetraploid, as the diploid species of this family has 50–52 chromosomes and a 25% DNA value. In order to obtain some idea as to how many changes in DNA values and chromosome complements have occurred among diploid members of Ostariophysi, the study was expanded to cover members of the families Cobitidae and Characinidae of the suborder Cyprinidea as well as members of the families Ictarulidae and Loricaridae of the suborder Siluroidea. Diploid chromosome numbers varied from 50 to 98 and DNA values from 27–51% that of mammals. Apparently, diploid members of Ostariophysi underwent extensive chromosomal rearrangements as well as steady increases in DNA contents by regional duplication of chromosomal segments.In Duarte, this work was supported by a grant CA-05138 from the Nationa Cancer Institute, U.S. Public Health Service, and in part by a research fund established in honor of General James H. Doolittle. Contribution No. 21-67, Department of Biology. In Northwood, this project was supported by the British Empire Cancer Campaign.Fellow of the Institute for Advanced Learning of the City of Hope Medical Center.     

On Nanognathia,a New Gnathostomulid Genus from the East Coast of the United States

In continuation of a series of papers describing new representatives of the phylum Gnathostomulida from the east coast of North America, the monotypic genus Nanognathia is presented. It is distinguished by small size, grouped epidermal inclusions on the ventral body surface, and flattened basket-type jaws with long teeth of which one is developed as a terminal tooth. Together with the structure of the reproductive system, these characteristics place Nanognathia within the suborder Scleroperalia, family Onychognathiidae.     

Phylogenetics and evolution of Capitata (Cnidaria: Hydrozoa), and the systematics of Corynidae

Nawrocki, A. M., Schuchert, P. & Cartwright, P. (2009). Phylogenetics and evolution of Capitata (Cnidaria: Hydrozoa), and the systematics of Corynidae.—Zoologica Scripta, 39, 290–304. Generic‐ and family level classifications in Hydrozoa have been historically problematic due to limited morphological characters for phylogenetic analyses and thus taxonomy, as well as disagreement over the relative importance of polyp vs. medusa characters. Within the recently redefined suborder Capitata (Cnidaria: Hydrozoa: Hydroidolina), which includes 15 families and almost 200 valid species, family level relationships based on morphology alone have proven elusive, and there exist numerous conflicting proposals for the relationships of component species. Relationships within the speciose capitate family Corynidae also remain uncertain, for similar reasons. Here, we combine mitochondrial 16S, and nuclear 18S and 28S sequences from capitate hydrozoans representing 12 of the 15 valid capitate families, to examine family level relationships within Capitata. We further sample densely within Corynidae to investigate the validity of several generic‐level classification schemes that rely heavily on the presence/absence of a medusa, a character that has been questioned for its utility in generic‐level classification. We recover largely congruent tree topologies from all three markers, with 28S and the combined dataset providing the most resolution. Our study confirms the monophyly of the redefined Capitata, and provides resolution for family level relationships of most sampled families within the suborder. These analyses reveal Corynidae as paraphyletic and suggest that the limits of the family have been underestimated. Our results contradict all available generic‐level classification schemes for Corynidae. As classification schemes for this family have been largely based on reproductive characters such as the presence/absence of a medusa, our results suggest that these are not valid generic‐level characters for the clade. We suggest a new taxonomic structure for the lineage that includes all members of the newly redefined Corynidae, based on molecular and morphological synapomorphies for recovered clades within the group.