Relationships of osmerid fishes (Osmeridae) of Russia: divergence of nucleotide sequences of mitochondrial and nuclear genes

Relationships of seven species of smelts (family Osmeridae) inhabiting Russian waters were analyzed on the basis of nucleotide sequence divergence of cytb, COI and intron 1 of rpS7 genes. Nuclear sequence divergence between the species within of the genera Osmerus, Mallotus and Hypomesus was 1.6–2.6, 2.9 and 6.6–11.8 %, respectively, and mitochondrial sequence divergence was 8.9–9.7, 3.9 and 15.1–18.3 %, respectively. The mtDNA divergence was 20.4 % between the genera Hypomesus and Mallotus, 18.47 % between Hypomesus and Osmerus, and 17.62 % between Mallotus and Osmerus. Nuclear DNA divergence was 11.58, 11.19, and 11.37 %, respectively. MP, ML and Bayesian analyses coupled with inclusion in analyses of GenBank-derived sequences of osmerid species that do not inhabit this region suggest that the lineage of the genus Mallotus was the first to separate from the common hypothetic ancestor of the smelts and is sister to the Osmerus–Hypomesus clade. The position of Hypomesus olidus is not resolved and points to the need for further research.     

Evolutionary and biogeographical patterns within the smelt genus Hypomesus in the North Pacific Ocean

Aim We address questions about trans‐Pacific distributions of marine organisms and the North Pacific Ocean as a centre of marine biodiversity through a phylogenetic and biogeographical study of a pan‐Pacific genus of Northern Hemisphere smelts (Hypomesus, Pisces: Osmeridae). Location North Pacific Ocean. Methods Relationships of the five species of Hypomesus from throughout the North Pacific were reconstructed through maximum likelihood and Bayesian phylogenetic analyses of sequence data from two mitochondrial (cytb, 16S) and three nuclear (ITS2, S71, RAG1) gene regions of five to 25 individuals per species, totalling 3588 characters. The resulting phylogenies were used to test hypotheses of species relationships and geographical origins using both dispersal‐based and maximum likelihood methods for inferring ancestral areas (lagrange ). Cytb sequence divergence and a Bayesian approach (beast ) were used to estimate the timeframe of Hypomesus evolution, which was compared with work on similarly distributed taxa. Results Hypothesized trans‐Pacific Ocean relationships based on lateral line scale counts were not supported by the phylogeny, suggesting parallel evolution of this phenotype, although we found one such relationship between the western H. japonicus and the two eastern Pacific species (H. pretiosus and H. transpacificus). Dispersalist approaches rejected an early proposal of a double‐compression vicariant mechanism as well as an eastern Pacific origin. Results from the lagrange analysis suggested a more widespread ancestor, although also supporting a role for the western Pacific. Divergence estimates suggested that most splits between species occurred in the mid‐Miocene, and the most recent speciation event, between the eastern Pacific species, occurred in the Pliocene to early Pleistocene. Main conclusions Our molecular data indicate that the character historically used to define relationships within Hypomesus, lateral line scale count, does not reflect ancestry within the genus. Biogeographical reconstructions suggest an important role for the western North Pacific in the diversification of Hypomesus. While uncertainty remains over the date of origin for this genus, estimates place the divergences during periods of climatic cooling that have been important in generating diversity in a number of similarly distributed organisms. Additional comparative data will provide further insight into the relative importance of the western region in generating diversity in the North Pacific Ocean.     

Mallotus species from Vietnamese mountainous areas: phytochemistry and pharmacological activities

The genus Mallotus belongs to Malphighiales order and Euphorbiaceae family. Mallotus, commonly known as “Ba bet” in Vietnam, is one of the most diverse and richest genera of the Euphorbiaceae family in Vietnam, where about 40 Mallotus species may be found. Some Mallotus species are used in traditional medicine in Vietnam for different indications. They are concentrated in mountainous areas with an altitude below 1,000 m, but some species can grow at an altitude of 2,000 m, such as Mallotus oreophilus Müll. Arg. Some Mallotus species are known to contain different natural compounds, mainly diterpenoids, triterpenoids, steroids, flavonoids, coumarinolignoids, phloroglucinol derivatives or benzopyrans, and to exhibit interesting biological activities such as antimicrobial, antioxidant, antiviral, or cytototoxic ones. Some of these properties may be explained by their chemical composition as, for example, benzopyrans accounting for the cytotoxicity of Mallotus apelta extracts. However, although these species seem to have a great medicinal potential, the existing knowledge about most Mallotus species is still in most cases very limited. This review underlines the interest to continue the study of this genus of the Euphorbiaceae.     

Morphology and systematics in mesopsammic nemerteans of the genus Ototyphlonemertes (Nemertea,Hoplonemertea, Ototyphlonemertidae)

Interstitial nemerteans of the genus Ototyphlonemertes are difficult to organize into traditional morphospecies. They occur in a multitude of slightly different local varieties that form a seemingly continuous morphological cline. In this paper, we summarize most published morphological data on the group, plus 73 new records of geographic varieties from the Mediterranean Sea in the East to the Sea of Japan in the West. We summarize morphological variation, partition traits into character and character states, propose a standardized protocol for examination of live specimens and discuss the phylogenetic structure of the group. The phylogenetic discussion leads to a hypothesis that partitions all varieties (including the established species) into six groups. These are the smallest morphologically homogenous sets of varieties (corresponding to traditional morphospecies) we can diagnose on phylogenetically reliable traits. Variation within the groups appears to be unreliable phylogenetic markers that may distinguish ecological forms rather than relatedness. However, we distinguish four of the groups by combinations of two traits, one apomorphy for a more inclusive group and one plesiomorphy, and the remaining two by one trait each that may be either a unique plesiomorphy or an apomorphy depending on the rooting, and most of them may thus join paraphyletic groups of cryptic monophyletic units. We call this kind of group phylomorph and name them the Duplex-, Pallida-, Cirrula-, Fila-, Lactea- and Macintoshi-morph (referring to the first established species within each group, i.e. Ototyphlonemertes duplex, O. pallida, O. cirrula, O. fila, O. lactea and O. macintoshi respectively). The phylogenetic scheme provides a simple tool to allocate geographical varieties to a group of possible `species' and a phylogenetic null-hypothesis for further tests with genetic data.     

Morphological analysis and taxonomical status of four fish species of the genera <Emphasis Type="Italic">Opisthocentrus</Emphasis> and <Emphasis Type="Italic">Pholidapus</Emphasis> (Perciformes: Stichaeidae)

No common opinion on the systematics position of species of the fishes of the subfamily Opisthocentrinae, Stichaeidae family has been formed up to the present. Therefore, a morphological analysis of fishes belonging to taxa Opisthocentrus ocellatus, O. tenuis, O. zonope, and Pholidapus dybowskii was undertaken. The obtained data treated by various methods of statistics implied the species independence of these taxa, which sympatrically occurred in the coastal areas of the northwest of the Sea of Japan. All the four studied species were similar in some attributes and distinct by other. Minor differences in the structure of the seismosensory system of Ph. dybowskii and Opisthocentrus species gave no basis on which to distinguish the independent genus Pholidapus. It would be correct to consider this as a subgenus of the Opisthocentrus genus, which includes three other species.     

Phylogenetic Position of Cryothecomonas Inferred from Nuclear-Encoded Small Subunit Ribosomal RNA

The systematic position of the genus Cryothecomonas has been determined from an analysis of the nuclear-encoded small subunit ribosomal RNA gene of Cryothecomonas longipes and two strains of Cryothecomonas aestivalis. Our phylogenetic trees inferred from maximum likelihood, distance and maximum parsimony methods robustly show that the genus Cryothecomonas clusters within the phylum Cercozoa, and is related to the sarcomonad flagellate Heteromita globosa. Morphological data supporting the taxonomic placement of Cryothecomonas near the sarcomonad flagellates has been compiled from the literature. The high number of nucleotide substitutions found between two morphologically indistinguishable strains of Cryothecomonas aestivalis suggests the possibility of cryptic species within Cryothecomonas aestivalis.     

Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. in situ hybridization experiments showed dispersed organization of the sequences over all chromosomes of H. vulgare and the wild barley species H. bulbosum, H. marinum and H. murinum. Southern blot hybridization revealed different levels of polymorphism among barley species and the RFLP data were used to generate a phylogenetic tree for the genus Hordeum. Our data are in a good agreement with the classification system which suggests the division of the genus into four major groups, containing the genomes I, X, Y, and H. However, our investigation also supports previous molecular studies of barley species where the unique position of H. bulbosum has been pointed out. In our experiments, H. bulbosum generally had hybridization patterns different from those of H. vulgare, although both carry the I genome. Based on our results we present a hypothesis concerning the possible origin and phylogeny of the polyploid barley species H. secalinum, H. depressum and the H. brachyantherum complex.     

Isolation and characterization of novel bacterial taxa from extreme alkali-saline soil

In northeast China there are large areas of nearly bare soda saline-alkali soil, in which plant survival is exteremely difficult because the land has a pH greater than 10.5. In order to obtain resistant microbial resources able to grow in such conditions, we analyzed environmental microbial samples from this extreme saline-alkali soil region. Through selective culture conditions, 8 bacterial strains were isolated from medium with no less than 1.5 M NaCl, 12 were isolated in the medium with a pH value of no less than 11.0, and 8 were isolated in the medium with of no less than 200 mM Na₂CO₃. Based on 16S rRNA gene sequence analysis 20 novel strains of bacteria were identified and classified into four groups: 8 group I strains belong to the genus Bacillus; three group II belong to genus Nesterenkonia (2 strains) and genus Zhihengliuella (1 strain); eight group III strains belong to the genera Halomonas (6), Stenotrophomonas (1) and Alkalimonas (1); one group IV strain belongs to genus Litoribacter. These four groups belong to the phylum Firmicutes, phylum Actinobacteria, phylum Gamma-Proteobacteria and phylum Bacteroidetes, respectively. The sequence homology of 16S rRNA in strains ANESC-S, H.sp.C4 and H.sp.C6 with that of known strains was 93.2, 96.5 and 96.5%, respectively. Based on the 97.0% identity cutoff commonly used to discriminate bacterial species, our data suggest that H. sp.C4 and H.sp.C6 may be new species, and ANESC-S may be belong to a new genus of classified into order Cytophagales. The morphological characteristics by scanning electron microscopy (SEM) showed that, in addition to the coccal N.sp.N3, the majority (19) of the isolates are bacilli of various lengths. In culture the colonies appeared red, orange, yellow, light yellow, and milk-white, with milk-white being predominant. Based on the resistance to NaCl and pH, the 20 novel strains were classified into obligate alkaliphilic and halophilic bacteria, obligate alkaliphilic halotolerant bacteria, and facultative alkalophilic salt-tolerant bacteria. This is the first study reporting the isolation and characterization of bacterial resources from extreme saline-alkali soils from northeast China.     

Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae)

Ainscough, B.J., Breinholt, J.W., Robison, H.W. & Crandall, K.A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). —Zoologica Scripta, 42, 306–316. The crayfish genus Fallicambarus contains 19 species of primary burrowing freshwater crayfish divided into two distinct subgenera. We test current hypotheses of the phylogenetic relationships among species within the genus as well as the monophyly of the genus. Our study samples all 19 species for five gene regions (both nuclear and mitochondrial) to estimate a robust phylogenetic hypothesis for the genus. We show that the genus is not a monophyletic group. The subgenus Creaserinus does fall out as a monophyletic group, but distinct from the subgenus Fallicambarus. The subgenus Fallicambarus appears to be monophyletic with the exception of the species Procambarus (Tenuicambarus) tenuis, which falls in the midst of this subgenus suggesting that it might be better classified as a Fallicambarus species. We also show that the species Fallicambarus fodiens is a species complex with distinct evolutionary lineages that are regionalized to different geographic areas.     

Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data

 Chloroplast DNA (cpDNA) restriction site data were used to analyze phylogenetic relationships within Helianthus. Data from new samples were consistent with previous results and showed the genus to be a well-defined (11 site changes) lineage within subtribe Helianthinae. The affinities of 2 species, Viguiera similis and V. phenax (V. ludens) that have sometimes been included in Helianthus were shown to lie outside the genus. The two species of Phoebanthus, however, formed a phylogenetic ingroup to the perennial Helianthus. Within the genus, cpDNA data indicated that there are four distinct phylogenetic lineages. Two of the lineages each contained a single, annual species (H. agrestis and H. porteri, respectively). The remaining annual species collectively formed a third lineage (sect. Helianthus). The fourth lineage contained all of the perennial species, including those of Phoebanthus. Within the perennial lineage, there was little variation in restriction site characters. The 3 species of series Pumili formed a paraphyletic group at the base of the perennial lineage, and the 3 species of series Ciliares formed a group that was supported by a single restriction site character. Received: 2 September 1996 / Accepted: 25 October 1996     

Species delimitation in the Andean grasshopper genus Orotettix Ronderos & Carbonell (Orthoptera: Melanoplinae): an integrative approach combining morphological,molecular and biogeographical data

The reciprocal illumination nature of integrative taxonomy through hypothesis testing, corroboration and revision is a powerful tool for species delimitation as more than one source has to support the hypothesis of a new species. In this study, we applied an integrative taxonomy approach combining molecular and morphological data sets with distributional patterns to examine the level of differentiation between and within the grasshopper Orotettix species. Orotettix was described based on five valid species distributed in the Andes of Peru. In our study, initially a molecular‐based hypothesis was postulated and tested against morphological data and geographical patterns of distribution. Results from molecular and morphological analyses showed agreement among the species delimitation in Orotettix, and were also consistent with the geographical distribution. The analyses allowed us to delimit five new species for the genus ( O. lunatus sp. nov. , O . astreptos sp. nov. , O. colcaensis sp. nov. , O . paucartambensis sp. nov. and O . dichrous sp. nov. ) from the Eastern and Western Cordilleras of Peru. We also provide critical knowledge on the phylogenetic relationships and distribution of the genus and conduct a revision of Orotettix. © 2015 The Linnean Society of London     

Re‐evaluation of the taxonomic status of Hackelochloa (Poaceae) based on anatomical and phenetic analyses

Hackelochloa is a pantropical genus of plant in the Poaceae, in which only two species have been included, H. granularis and H. porifera. Despite several morphological differences, notably the more prominent sculpturing of the lower glume and the larger dimensions of several quantitative traits, H. porifera has been reduced to the synonymy of H. granularis. Moreover, the status of the genus itself has been questioned, with a regional revision of the genus proposing inclusion of its members in the genus Mnesithea. In the present study, we investigated a range of morphological and anatomical attributes to assess critically the generic delimitation between Hackelochloa and Mnesithea. In clustering analysis, H. granularis, H. porifera and Mnesithea species were clearly resolved as three distinct groups with an R‐value of 0.98114. Likewise, three clusters representing these taxonomic units were revealed using principal component analysis (PCA), with the first two principal components highlighting key qualitative and quantitative characters. Scanning electron microscopy was used to reveal different patterns of sculpturing on the lower glumes in the two putative species and the ecological significance of these differences is inferred. The outline of leaf transverse sections, presence of parenchymatous tissue in the midrib region, number of adjacent bundles and number of chlorenchyma layers in the culm were also found to be diagnostic anatomical characters. This study supports the recognition of H. porifera as distinct from H. granularis and provides evidence that the genus Hackelochloa should be maintained.     

Taxonomic proposal for a deep branching bacterial phylogenetic lineage: transfer of the family Thermodesulfobiaceae to Thermodesulfobiales ord. nov., Thermodesulfobiia classis nov. and Thermodesulfobiota phyl. nov

The family Thermodesulfobiaceae, comprising one genus Thermodesulfobium with two validly published species, is currently assigned to order Thermoanaerobacterales within the class Clostridia of the phylum Bacillota. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between Thermodesulfobium and other members of the phylum Bacillota. Subsequent studies of new Thermodesulfobium representatives supported deep phylogenetic branching of this lineage within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that Thermodesulfobium represents a distinct phylum-level lineage. Thus, we propose the transfer of the family Thermodesulfobiaceae to the new order Thermodesulfobiales within the new class Thermodesulfobiia and the new phylum Thermodesulfobiota.     

Phylogenetic Analysis of the Gut Bacterial Microflora of the Fungus-Growing Termite Odontotermes formosanus

We constructed a bacterial 16S rRNA gene clone library from the gut microbial community of O. formosanus and phylogenetically analyzed it in order to contribute to the evolutional study of digestive symbiosis and method development for termite control. After screening by restriction fragment length polymorphism (RFLP) analysis, 56 out of 280 clones with unique RFLP patterns were sequenced and phylogenetically analyzed. The representative phylotypes were affiliated to four phylogenetic groups, Firmicutes, the Bacteroidetes/Chlorobi group, Proteobacteria, and Actinobacteria of the domain Bacteira. No one clone affiliated with the phylum Spirochaetes was identified, in contrast to the case of wood-feeding termites. The phylogenetic analysis revealed that nearly half of the representative clones (25 phylotypes) formed monophyletic clusters with clones obtained from other termite species, especially with the sequences retrieved from fungus-growing termites. These results indicate that the presence of termite-specific bacterial lineages implies a coevolutional relationship of gut microbes and host termites.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

On species composition of northern pacific genera <Emphasis Type="Italic">Eurycope</Emphasis> and <Emphasis Type="Italic">Baeonectes</Emphasis> and Redescription of <Emphasis Type="Italic">E. ochotensis</Emphasis> Kussakin, 1979 (Crustacea,Isopoda)

Two northwestern Pacific species of the munnopsid subfamily Eurycopinae, Eurycope pavlenkoi Gurjanova, 1933 and E. ochotensis Kussakin, 1979 are transferred to the other genus of the subfamily, Baeonectes Wilson, 1982, on the basis of the following characteristics: short truncated epipod of maxilliped, broad rostrum without distinct margins, absence of a distomedial lobe of the article 1 of antenna 1, mandible with broad, rounded molar and long condyle and pereonites 5–7 fused dorsomedially. Based on the mentioned characters E. pygmaea G.O. Sars, 1870, which was put into the genus Tytthocope Wilson & Hessler, 1981 is also suggested to be transferred into the genus Baeonectes. After the clarification of the taxonomical position of the species, the geographical range of the genus Baeonectes expanded. In the Sea of Japan the genus was registered for the first time.     

A skeleton‐less sponge of Caribbean mangroves: invasive or undescribed?

Recent surveys of sponges occurring on Caribbean mangrove roots demonstrated the presence of a skeleton‐less sponge of the genus Halisarca, very similar in its morphology to the temperate H. dujardinii. This study evaluated the possibility that the mangrove sponge was actually H. dujardinii that had been introduced into the Caribbean mangroves. Detailed histology revealed differences between the mangrove sponge and H. dujardinii in cuticle thickness, and in characteristics of the choanocytes, spherulous, and granular cells. Also, phylogenetic reconstruction and genetic distance estimates based on cytochrome oxidase I gene sequences clearly differentiated the mangrove Halisarca sp. from H. dujardinii. Therefore, we rejected the hypothesis of the invasion of H. dujardinii, recognizing instead the mangrove Halisarca sp. as a new species and naming it H. restingaensis sp. nov. Estimated levels of genetic variation in the ribosomal internal transcribed spacers indicated that populations of H. restingaensis sp. nov. are highly differentiated between Venezuela and Panama (F_st=0.71). This level of population differentiation is consistent with the short larval competence period that is common in members of the genus Halisarca.