Phylogenetic relations in the family pholidae (Perciformes: Zoarcoidei) based on genetic and morphological data

Molecular-genetic study of Pholidae of the suborder Zoarcoidei was first performed. Analysis of variation of genes of COI, cytochrome b, and 16S rRNA of mitochondrial DNA indicates different phylogenetic isolation of the family taxa. The groundlessness of separating subgenera (or genera) Enedrias and Allopholis and the rightfulness of including them in the composition of the genus Pholis are shown. Genetic close relation of the genera Pholis and Rhodymenichthys and their differences from the genus Apodichthys are established. The obtained results agree with the data of Makushok (1958) who separated in the composition of the family two subfamilies—Pholinae (with genera Pholis and Rhodymenichthys) and Apodichthyinae (with the genera Apodichthys, Xererpes, and Ulvicola). A key to species, genera, and subfamilies of gunnels of the northern part of the Pacific Ocean is provided.     

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).     

Transition to viviparity in the order Scorpaeniformes: Brief review

Among teleost percoid fishes (Percomorpha), the subordes Scorpaenoidei (Scorpaeniformes) and Zoarcoidei (Perciformes) are of particular interest due to the presence of intermediate stages between oviparity and viviparity in several species. We analyze the features of reproductive biology in the fishes of the suborder Scorpaenoidei, including morphology of the urogenital system, gametogenesis, gamete ultrastructure, and embryonic development. The new materials are represented for three tropical coral reef fish species with external insemination from the family Scorpaenidae (Scorpaenopsis possi, Sebastapistes cyanostigma, and Dendrochirus zebra). In particular, a hypertrophied urinary bladder used for storage of mature sperm for insemination of pelagic egg clutch is described in the males. Evolutionary transition to viviparity within the family Sebastidae is discussed. Alternative reproductive strategies are registered in viviparous fishes from the suborders Scorpaenoidei and Zoarcoidei. They are connected with the production of a large number of morphologically weakly developed larvae and a small number of individuals at the juvenile state, respectively.     

Molecular evidence for the origins of Antarctic fishes: paraphyly of the Bovichtidae and no indication for the monophyly of the Notothenioidei (Teleostei)

The notothenioids are an Antarctic suborder of perciform fishes to which increasing interest is being devoted. To investigate their origin, one must address two questions. First, are Bovichtidae (Bovichtus, Cottoperca, Pseudaphritis), the sister-group of the rest of the suborder, monophyletic ? Secondly, what is the sister-group of the Notothenioidei ? These questions were addressed by determining the complete nucleotide sequence of the D2 and D8 domains of 28S rDNA (759 sites, among which 158 informative for parsimony), for 6 notothenioids and a collection of 6 outgroup taxa including the Trachinoidei and Zoarcoidei. Different outgroups (or combinations of outgroups) and different weighting schemes support the inference that Pseudaphritis is closer to the rest of the Notothenioidei than Cottoperca and Bovichtus are. Relationships of Cottoperca and Bovichtus remain unclear with respect to outgroups. Our molecular data therefore clearly show that the Bovichtidae are paraphyletic, but their relationships are not those suggested by Balushkin in 1992. Our data provide no indication of the monophyly of the Notothenioidei in its classical sense. Most of the homoplasy is due to outgroup sequences and interrelationships of outgroups are unresolved. Some morphological synapomorphies shared by Pseudaphritis and the rest of the non-bovichtid Notothenioidei are proposed, including some that were identified by Voskoboynikova in 1993.     

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).     

Analysis of the taxonomic structure of the crane fly family Limoniidae (Diptera) based on the larval characters

A morphological study of the larval characters in the genera Elephantomyia, Helius, Microlimonia, Lipsothrix, and Teucholabis was conducted. Significant differences between Elephantomyia and Helius were discovered; Elephantomyia should be placed in the subfamily Hexatominae, while Helius cannot be assigned to any known subfamily. The genus Microlimonia has nothing in common with other representatives of the tribe Limoniini, and the genera Lipsothrix and Teucholabis, with those of Gonomyini; these genera cannot be included in any of the existing tribes. The presently accepted subdivision of the Limoniidae into 4 subfamilies does not reflect its actual diversity.     

First song descriptions of some Anatolian species of Tettigoniidae Krauss, 1902 (Orthoptera,Ensifera)

Fourteen endemic and two sub-endemic species belonging to three subfamilies of Tettigoniidae (Tettigoniinae, Bradyporinae and Saginae) were sampled during field trips throughout the different ranges of Anatolia between the years of 2004 and 2013. Acoustic parameters of these 16 species affiliated to 8 genera (Anterastes, Apholidoptera, Gampsocleis, Parapholidoptera, Pezodrymadusa, Psorodonotus, Bradyporus and Saga) have been described for the first time in this study. Acoustical analysis showed that song characters are species-specific in the genera Saga and Psorodonotus. On the other hand, we could not find big differences among species of the genus Pezodrymadusa and Parapholidoptera castaneoviridis species-group.     

External thoracic scent efferent system of Scutelleridae (Hemiptera: Heteroptera)

The metathoracic scent glands in the Heteroptera produce defence secretions which are spread outside the body through and by using the thoracic external scent efferent system. That complex system was studied in 18 species from 11 genera of four subfamilies, Elvisurinae, Eurygastrinae, Hoteinae and Scutellerinae of the family Scutelleridae (Pentatomoidea). The results have been compared with published data. The pattern of that system is more consistent at the level of genus, mostly very similar in the congeneric species, but mostly variable within higher taxonomic levels, tribes and subfamilies. Five types of the external scent efferent system are recognized within the family Scutelleridae, basic two of them in studied species: (i) peritreme well developed, covering large part of metapleuron, evaporatorium small, developed only on metapleuron, (ii) evaporatorium large, more conspicuous than moderate-sized to small peritreme, extending to mesopleuron as large structure. The results do not support a hypothesis that the system of structures associated externally with metathoracic scent glands is in correlation with type of a habitat. However, these structures are well usable as diagnostic characters for scutellerid genera (e.g. Cantao, Hyperonchus, Scutellera and Solenosthedium).     

Genetic divergence in the tribe Electronini (Myctophidae)

To reveal evolutionary relationships and the rate of divergence of lanternfishes in the tribe Electronini (Myctophidae), analysis of sequence of cox 1 mtDNA fragment in three genera (12 species) of the tribe and in a closely related genus Myctophum (9 species) was performed. The results support the tribe monophyly; however, the divergence within it appeared to be not profound: genetic distances between genera and subgenera are smaller than between species within Myctophum and other genera of myctophids. In subgenera of Protomyctophum, species formation has obviously not completed since interspecies distances in them (0.5–4.7%) are comparable to estimates of intraspecific variation in other lanternfishes. Minimal genetic differences were found between species P. (Hierops) arcticum and P. (H.) subparallelum, whose ranges at the present time are isolated in the northern and southern hemispheres. After calibration of the molecular clock, the time of isolation of these two species can be dated to the Middle Pleistocene. Weak tribe diversification indicates its evolutionary youth, which can be related to the absence of efficient hydrographic barriers for isolation. The data obtained do not permit to consider tribe members as the most primitive in the family Myctophidae.     

Anatomy and affinities of pseudococculinid limpets (Mollusca, Archaeogastropoda)

The anatomy of 12 pseudococculinid species, representing the two subfamilies and 10 (of 11 known) genera, is described in detail. Three new genera are erected, Yaquinabyssia, Copulabyssia and Amphiplica. Subfamilial and generic systematics are reconsidered and additionally based on anatomical characters. Characters defining subfamilies and genera (Pseudoeoeculininae: Pseudococculina, Notocrater, Tentaoculus, Mcsopelex, Bandabyssia, Kurilabyssia; Caymanabyssiinae: Caymanabyssia, Colotrachelus, Yuquinabyssia, Copulabyssia, Amphiplica) are the modifications in shell and radula, the number and arrangement of gill-leaflets, the size of the pedal gland, the degree of eye-reduction and the modifications of the seminal groove and of the copulatory organ. Separation of the Pseudococculinidae Hiekman, 1983 from the Cocculinidae Dall, 1882 at the superfamilial level is confirmed by great differences in their anatomy. Whereas the Cocculinidae are closely related to the Bathysciadiidae (Cocculinoidea). the Lepctcllidae, Pyropeltidae, Pseudococculinidae,? Bathyphytophilidae, Osteopeltidae, Cocculinellidae, Addisoniidae and Choristellidae form a clearly separated supcrfamily (Lepetelloidea). Both superfamilies compose the Cocculiniformia. a primitive but highly specialized arehaeogastropod suborder.     

Phylogeny and classification of Rosaceae

Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear (18S, gbssi1, gbssi2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions, separately and in various combinations, with parsimony and likelihood-based Bayesian approaches. The results were used to examine evolution of non-molecular characters and to develop a new phylogenetically based infrafamilial classification. As in previous molecular phylogenetic analyses of the family, we found strong support for monophyly of groups corresponding closely to many previously recognized tribes and subfamilies, but no previous classification was entirely supported, and relationships among the strongly supported clades were weakly resolved and/or conflicted between some data sets. We recognize three subfamilies in Rosaceae: Rosoideae, including Filipendula, Rubus, Rosa, and three tribes; Dryadoideae, comprising the four actinorhizal genera; and Spiraeoideae, comprising Lyonothamnus and seven tribes. All genera previously assigned to Amygdaloideae and Maloideae are included in Spiraeoideae. Three supertribes, one in Rosoideae and two in Spiraeoideae, are recognized.     

Differential spreading of HinfI satellite DNA variants during radiation in Centaureinae

Background and Aims

Subtribe Centaureinae appears to be an excellent model group in which to analyse satellite DNA and assess the influence that the biology and/or the evolution of different lineages have had on the evolution of this class of repetitive DNA. Phylogenetic analyses of Centaureinae support two main phases of radiation, leading to two major groups of genera of different ages. Furthermore, different modes of evolution are observed in different lineages, reflected by morphology and DNA sequences.

Methods

The sequences of 502 repeat units of the HinfI satellite DNA family from 38 species belonging to ten genera of Centaureinae were isolated and compared. A phylogenetic reconstruction was carried out by maximum likelihood and Bayesian inference.

Key Results

Up to eight different HinfI subfamilies were found, based on the presence of a set of diagnostic positions given by a specific mutation shared by all the sequences of one group. Subfamilies V–VIII were mostly found in older genera (first phase of radiation in the subtribe, late Oligocene–Miocene), although some copies of these types of repeats were also found in some species of the derived genera. Subfamilies I–IV spread mostly in species of the derived clade (second phase of radiation, Pliocene to Pleistocene), although repeats of these subfamilies exist in older species. Phylogenetic trees did not group the repeats by taxonomic affinity, but sequences were grouped by subfamily provenance. Concerted evolution was observed in HinfI subfamilies spread in older genera, whereas no genetic differentiation was found between species, and several subfamilies even coexist within the same species, in recently radiated groups or in groups with a history of recurrent hybridization of lineages.

Conclusions

The results suggest that the eight HinfI subfamilies were present in the common ancestor of Centaureinae and that each spread differentially in different genera during the two main phases of radiation following the library model of satellite DNA evolution. Additionally, differential speciation pathways gave rise to differential patterns of sequence evolution in different lineages. Thus, the evolutionary history of each group of Centaureinae is reflected in HinfI satellite DNA evolution. The data reinforce the value of satellite DNA sequences as markers of evolutionary processes.     

Restriction fragment variation of the mitochondrial gene of cytochrome b in some taxa of the Eelpout Family (Pisces, Perciformes, Zoarcidae) from the northern Sea of Okhotsk

The first analysis of restriction fragment length polymorphism (RFLP) of the mitochondrial gene of cytochrome b of fish from the Eelpout Family (Zoarcidae) from the northern Sea of Okhotsk has been performed. The mean genetic distances between the subfamilies Zoarcinae and Lycodinae, subfamilies Lycodinae and Gymnelinae, and subfamilies Zoarcinae and Gymnelinae are 11.14, 13.87, and 14.00%, respectively. Species of the genus Lycodes (Lycodinae) are characterized by a mtDNA small divergence (on average, 2.04%) and are divided into two groups on the basis of lateral line morphology. Magadania skopetsi, an endemic of Tauiskaya Bay of the Sea of Okhotsk, is genetically close to Hadropareia middendorffii from the same subfamily (Gymnelinae). The mtDNA sequences of species from the genus Lycogrammoides (Lycodinae) differ by 3.83%. The genetic differences between the eelpout Zoarces elongatus Zoarces sp. (d = 4.54%) suggest that the latter is a separate species.     

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.     

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809 bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group + Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated “new subfamily”); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter + rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.     

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter

The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.     

Shape and size variations in the cranium of elephant-shrews: a morphometric contribution to a phylogenetic debate

A geometric morphometric analysis was carried out on the crania of 13 species of elephant-shrews (Macroscelidea), a group of African mammals whose phylogeny is still debated. The material examined consisted of 313 crania and included all the genera of Macroscelididae, the unique family recognized by taxonomists. The results obtained from the analysis of the cranium shape and size, either from dorsal or lateral view, were very similar. The first one appeared more reliable because of the higher number of intersection points fixed between the cranial sutures. All the cranial features that distinguished the genus Rhynchocyon were a consequence of the extreme enlargement of frontal bones. Instead, within the subfamily Macroscelidinae, the differences between genera were based on modification involving other bones, mainly mastoids and nasals, as shown by the deformation grids. A cluster analysis confirmed the traditional subdivision in two subfamilies (Rhynchocyoninae and Macroscelidinae) but suggested a different relationship among the recognized genera belonging to Macroscelidinae. Our results are congruent with data obtained from previous biochemical research and support the traditional subdivision in two subfamilies, the monophily of the genus Elephantulus and its closeness with Petrodromus, relating to their similar cranium shapes. The latter presumably is a case of gigantism as adaptation to forest habitats. Further studies on all the species of Elephantulus could provide new evidence for assessing the relationships within this clade, including Macroscelides that by the present analysis appeared as a well-distinguished taxonomic entity.     

Thysanoptera of Bulgaria

The present checklist includes data on the species composition, geographic distribution and feeding preferences of thrips species in Bulgaria. In total, 155 species in 48 genera are listed. Of these, 125 species belong to suborder Terebrantia and include 103 species of 33 genera in family Thripidae, 14 species of two genera in Aeolothripidae, seven species of two genera in Melanthripidae and one species in Fauriellidae. In suborder Tubulifera, 30 species of 10 genera in the single family Phlaeothripidae are listed. Of the 155 Bulgarian thrips species, 87.7% are phytophagous, 4.5% are obligate predators, 5.8% are mycophagous and 1.9% are with unknown feeding preferences. Fourteen pest species are listed for Bulgaria, of which Frankliniella occidentalis, Thrips tabaci and Haplothrips tritici are of economic importance. The list provides detailed information on the horizontal and vertical distribution of Thysanoptera in 5 regions and 45 subregions of Bulgaria. The present paper also includes an evaluation of the biodiversity of Thysanoptera and the extent to which each region of the country has been studied.     

Phylogeny and taxonomy of casebearer moths (Lepidoptera,Coleophoridae) based on morphological and molecular genetic data. 1. Reconstruction of phylogeny of coleophoridae using analysis of <Emphasis Type="Italic">COI</Emphasis> gene variability

A phylogenetic study of representatives of the family Coleophoridae was conducted using a comprehensive approach, including methods of morphological and molecular genetic analyses. The existent data on the family system were compared with the results of phylogenetic analysis of the COI mitochondrial gene sequences. Four of the five studied subfamilies (Coleophorinae, Ischnophaninae, Augasminae, and Tolleophorinae) corresponded to their location on the phylogram; representatives of Metriotinae were part of Coleophorinae. According to the aggregate data from molecular phylogeny and morphology, the most numerous subfamily of casebearers, Coleophorinae, is polyphyletic within its current boundaries. The results of our analysis of COI molecular divergence does not refute the monophyly of the tribes Casignetellini, Carpochenini, Klinzigedini, Goniodomini, Casasini, and Atractulini from the subfamily Coleophorinae. The allocation of the tribes Aporipturini and Sistrophoecini within the subfamily does not correspond to the molecular data. Monophyly of the genera Ecebalia, Perygra, and Casignetella was confirmed. These genera are well isolated, which reflects the evolutionary significance of the morphological characters chosen for their taxonomic division. The boundaries of the cluster containing these genera correspond to those of the tribe Casignetellini, justifying the allocation of this tribe within the subfamily. The existence of monophyletic tribes Goniodomini (genus Goniodoma) and Carpochenini (genera Ionescumia, Carpochena, and Falkmisa) was also supported. The exceptions were the genera Kasyfia, Tollsia, and Agapalsa, whose monophyly was not confirmed by our results. The distribution of the sequences of species of these genera indicated a paraphyletic origin of Kasyfia and Tollsia and a polyphyletic origin of Agapalsa.