Molecular Phylogenetics of Gadidae and Related Gadiformes Based on Mitochondrial DNA Sequences

Mitochondrial DNA sequences of selected regions of the small subunit and large subunit ribosomal RNAs and cytochrome b genes were analyzed for 10 gadid species, representing 8 genera within Gadidae, and 10 species representing 5 other gadiform families. Phylogenetic analyses revealed that Gadiculus is the most basal gadid genus, and that Trisopterus and Micromesistius constitute a relatively basal clade. Lotidae was identified as the family most closely related to Gadidae. Estimation of divergence times indicated that the most ancient Gadidae split between Gadiculus and the remaining gadid genera occurred about 20 million years ago. The clade including the most recent species (Gadus, Boreogadus, Merlangius, Melanogrammus, and Pollachius) diverged from the Trisopterus/Micromesistius clade approximately 12 million years ago.     

Morphology and molecular taxonomy of Evlachovaea-like fungi,and the status of this unusual conidial genus

The entomopathogenic anamorphic genus Evlachovaea was described to differ from other fungi in forming its conidia obliquely to the axis of the conidiogenous cell and with successive conidia having alternate orientations with a zipper- or chevron-like arrangement resulting in flat, ribbon-like chains. Morphological and molecular studies of six Evlachovaea-like isolates baited from Central Brazilian soils using Triatoma infestans (a vector of Chagas disease) and of other entomopathogens with Evlachovaea-like conidiogenesis led to a re-evaluation of the status of this little known fungal genus. The Brazilian isolates formed two distinct groups based on gene sequences for both the internal transcribed spacer (ITS) and translation elongation factor (EF-1α) genes, morphology, and growth patterns; both groups also differed from the type species, Evlachovaea kintrischica. More detailed studies of these fungi indicated that the alternatingly oblique orientations of forming conidia are neither a stable nor invariant character (even on single phialides). Furthermore, the molecular cladistic analysis unambiguously placed the Evlachovaea isolates firmly within the genus Isaria (Hypocreales: Cordycipitaceae). The ITS sequences of E. kintrischica were very similar or even identical to those of Isaria amoenerosea and Isaria cateniobliqua, thereby suggesting that E. kintrischica is a synonym of one of these species, and that the genus Evlachovaea must be treated as a later synonym of Isaria, which must now be recognized to include several highly divergent modes of conidiogenesis. These taxonomic findings are discussed in the context of dramatic changes recently imposed on the nomenclatural standards used to determine the correct names of all pleomorphic fungi.     

Is the mega-diverse genus Ocyptamus (Diptera, Syrphidae) monophyletic? Evidence from molecular characters including the secondary structure of 28S rRNA

Phylogenetic relationships between two New World Syrphinae taxa (Diptera, Syrphidae), i.e. the highly diverse genus Ocyptamus and the large genus Toxomerus, were analysed based on molecular characters. The monophyly of both taxa was tested and the taxonomic status of included subgenera and species groups was examined. Toxomerus constitutes the monogeneric tribe Toxomerini with more than 140 described species, while Ocyptamus (tribe Syrphini) is a very diverse genus (over 300 spp.) with multiple recognised subgenera and species groups. Sequence data from three gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The secondary structure of two expansion segments (D2, D3) of the ribosomal 28S RNA gene is presented for the family Syrphidae and used for the first time in a multiple sequence alignment. Molecular data were analysed using parsimony, maximum likelihood and Bayesian inference. Toxomerus was always recovered as monophyletic within Ocyptamus, and relationships to other New World taxa such as Salpingogaster (Eosalpingogaster) were well-supported. Only the subgenera and species groups of Ocyptamus were consistently recovered as monophyletic lineages, thus the apparent non-monophyly of Ocyptamus demands reclassification of this clade.     

The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often found to reflect the structure of phylogenies based on molecular data, many species remain of uncertain placement due to a lack of reliable data or conflicting morphological characters. A rigid, darkly pigmented stipe and the production of a Hirsutella-like anamorph in culture were taken as evidence for the transfer of the species Cordyceps cuboidea, Cordyceps prolifica, and Cordyceps ryogamiensis to the genus Ophiocordyceps. Data from ribosomal DNA supported these species as a single group, but were unable to infer deeper relationships in Hypocreales. Here, molecular data for ribosomal and protein coding DNA from specimens of Ophiocordyceps cuboidea, Ophiocordyceps ryogamiensis, Ophiocordyceps paracuboidea, Ophiocordyceps prolifica, Cordyceps ramosopulvinata, Cordyceps nipponica, and isolates of Polycephalomyces were combined with a broadly sampled dataset of Hypocreales. Phylogenetic analyses of these data revealed that these species represent a clade distinct from the other clavicipitoid genera. Applying the recently adopted single system of nomenclature, new taxonomic combinations are proposed for these species in the genus Polycephalomyces, which has been historically reserved for asexual or anamorphic taxa.     

Two newly recognized species of Hemidactylus (Squamata,Gekkonidae) from the Arabian Peninsula?and Sinai,Egypt

A recent molecular phylogeny of the Arid clade of the genus Hemidactylus revealed that the recently described H. saba and two unnamed Hemidactylus species from Sinai, Saudi Arabia and Yemen form a well-supported monophyletic group within the Arabian radiation of the genus. The name ‘Hemidactylus saba species group’ is suggested for this clade. According to the results of morphological comparisons and the molecular analyses using two mitochondrial (12S and cytb) and four nuclear (cmos, mc1r, rag1, rag2) genes, the name Hemidactylus granosus Heyden, 1827 is resurrected from the synonymy of H. turcicus for the Sinai and Saudi Arabian species. The third species of this group from Yemen is described formally as a new species H. ulii sp. n. The phylogenetic relationships of the members of ‘Hemidactylus saba species group’ are evaluated and the distribution and ecology of individual species are discussed.     

Are unusual plasmodesmata in the embryo-suspensor restricted to species from the genus Sedum among Crassulaceae?

The Crassulaceae family comprises mainly herbaceous leaf succulents, some of which have an ornamental value. During embryogenesis, they produce a suspensor with a giant polyploid basal cell. It has recently been shown that in Sedum acre and S. hispanicum this cell has compound plasmodesmata with an unusual dome of electron-dense material associated on the cell's side. These compound plasmodesmata differ from the typical ones occurring in other angiosperms. In this study, the hypothesis was tested that the unusual plasmodesmata in the embryo-suspensor are a feature not only restricted to species from the genus Sedum, but are also found in other Crassulaceae genera. Suspensors of example species from the genera Sempervivum and Jovibarba, which have vegetative morphologies quite different from Sedum and which are placed in the traditional classification into another subfamily, were first examined using an electron microscope. It was found that the unusual compound plasmodesmata in the suspensor are not only restricted to species from the genus Sedum but are also found in species from other Crassulaceae genera (Sempervivum arachnoideum and Jovibarba sobolifera). It should be noted that some ultrastructural features of compound plasmodesmata in the analyzed genera (e.g. the character of the wall with plasmodesmata, plasmodesmata diameter or occurrence of the electron-dense material) are different from the suspensor plasmodesmata recorded in species from the Sedum genus. We found that in Sempervivum arachnoideum the size of the plasmodesmata diameter varies according to the micropylar-chalazal axis of the embryo. This is the first report of variation in the diameter of the plasmodesmata within the embryo of angiosperms. Further study will be needed to show whether compound plasmodesmata occur in other Crassulaceae clades, whether they are a stable feature at the genus level in this family, and also whether they have evolved several times or only once in Crassulaceae.     

Species delimitation in downy mildews: the case of Hyaloperonospora in the light of nuclear ribosomal ITS and LSU sequences

Species definitions for plant pathogens have considerable practical impact for measures such as plant protection or biological control, and are also important for comparative studies involving model organisms. However, in many groups, the delimitation of species is a notoriously difficult taxonomic problem. This is particularly evident in the obligate biotrophic downy mildew genera (Peronosporaceae, Peronosporales, Oomycetes), which display a considerable diversity with respect to genetic distances and host plants, but are, for the most part, morphologically rather uniform. The recently established genus Hyaloperonospora is of particular biological interest because it shows an impressive radiation on virtually a single host family, Brassicaceae, and it contains the downy mildew parasite, Arabidopsis thaliana, of importance as a model organism. Based on the most comprehensive molecular sampling of specimens from a downy mildew genus to date, including various collections from different host species and geographic locations, we investigate the phylogenetic relationships of Hyaloperonospora by molecular analysis of the nuclear ribosomal ITS and LSU sequences. Phylogenetic trees were inferred with ML and MP from the combined dataset; partitioned Bremer support (PBrS) was used to assess potential conflict between data partitions. As in other downy mildew groups, the molecular data clearly corroborate earlier results that supported the use of narrow species delimitations and host ranges as taxonomic markers. With few exceptions, suggested species boundaries are supported without conflict between different data partitions. The results indicate that a combination of molecular and host features is a reliable means to discriminate downy mildew species for which morphological differences are unknown.     

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Euonymeae (∼230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.     

Phylogenetic evaluation of Geomyces and allies reveals no close relatives of Pseudogymnoascus destructans, comb. nov., in bat hibernacula of eastern North America

White-nose syndrome (WNS)  of bats, caused by the fungus previously known as Geomyces destructans, has decimated populations of insectivorous bats in eastern North America. Recent work on fungi associated with bat hibernacula uncovered a large number of species of Geomyces and allies, far exceeding the number of described species. Communication about these species has been hindered by the lack of a modern taxonomic evaluation, and a phylogenetic framework of the group is needed to understand the origin of G. destructans and to target closely related species and their genomes for the purposes of understanding mechanisms of pathogenicity. We addressed these issues by generating DNA sequence data for the internal transcribed spacer (ITS) region, nuclear large subunit (LSU) rDNA, MCM7, RPB2, and TEF1 from a diverse array of Geomyces and allies that included isolates recovered from bat hibernacula as well as those that represent important type species. Phylogenetic analyses indicate Geomyces and allies should be classified in the family Pseudeurotiaceae, and the genera Geomyces, Gymnostellatospora, and Pseudogymnoascus should be recognized as distinct. True Geomyces are restricted to a basal lineage based on phylogenetic placement of the type species, Geomyces auratus. Thus, G. destructans is placed in genus Pseudogymnoascus. The closest relatives of Pseudogymnoascus destructans are members of the Pseudogymnoascus roseus species complex, however, the isolated and long branch of P. destructans indicates that none of the species included in this study are closely related, thus providing further support to the hypothesis that this pathogen is non-native and invasive in eastern North America. Several conidia-producing isolates from bat hibernacula previously identified as members of Pseudeurotium are determined to belong to the genus Leuconeurospora, which is widespread, especially in colder regions. Teberdinia hygrophila is transferred to Pseudeurotium as Pseudeurotium hygrophilum, comb. nov., in accordance with the one name per fungus system of classification, and two additional combinations are made in Pseudogymnoascus including Pseudogymnoascus carnis and Pseudogymnoascus pannorum. Additional sampling from other regions of the world is needed to better understand the evolution and biogeography of this important and diverse group of fungi.     

Phylogenetic position of Octosporea muscaedomesticae (Microsporidia) and its relationship to Octosporea bayeri based on small subunit rDNA analysis

Comparative phylogenetic analysis of the small subunit rDNA sequence of Octosporea muscaedomesticae (Flu, 1911) (type species) (Microsporidia) isolated from the blowfly Phormia regina (Diptera:Calliphoridae) is presented. Neighbor Joining bootstrap, Maximum Parsimony and Maximum Likelihood analyses with 38 microsporidian taxa representing five major clades of Microsporidia placed O. muscaedomesticae on a separate branch within a clade containing parasites of freshwater hosts. O. muscaedomesticae differed from Octosporea bayeri, a parasite of the microcrustacean, Daphnia magna (Cladocera:Daphniidae) by 29% demonstrating that the latter microsporidium is not closely related to the type species at the generic level, and should not be placed within the genus Octosporea, a conclusion that is further supported by morphological and developmental differences. Considering the number of disparately related hosts from which Octosporea species have been previously described based mostly on developmental and morphological characters it is likely that many will not fit the current definition of the genus, and it is possible that molecular analysis of these species will show that this genus as defined represents a polyphyletic grouping of unrelated taxa.     

Two new species of yellow-shouldered bats,genus Sturnira Gray, 1842 (Chiroptera,Phyllostomidae) from Costa Rica,Panama and western Ecuador

Two new species of yellow-shouldered bats Sturnira Gray, 1842 (Chiroptera, Phyllostomidae) from Central America and western South America are described using molecular and morphological data. The two new species, which occur in Costa Rica and Panama and in western Ecuador, were previously confused with S. ludovici, and S. lilium and S. luisi, respectively. Sturnira now includes 22 described species, making it the most speciose genus in the Neotropical family Phyllostomidae.     

Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae)

We reconstructed the matrilineal phylogeny of Asian algae-eating fishes of the genus Capoeta based on complete mitochondrial gene for cytochrome b sequences obtained from 20 species sampled from the majority of the range and 44 species of closely related barbs of the genera Barbus s. str. and Luciobarbus. The results of this study show that Capoeta forms a strongly supported monophyletic subclade nested within the Luciobarbus clade, suggesting that specialized scraping morphology appeared once in the evolutionary history of the genus. We detected three main groups of Capoeta: the Mesopotamian group, which includes three species from the Tigris-Euphrates system and adjacent water bodies, the Anatolian-Iranian group, which has the most diversified structure and encompasses many species distributed throughout Anatolian and Iranian inland waters, and the Aralo-Caspian group, which consists of species distributed in basins of the Caspian and Aral Seas, including many dead-end rivers in Central Asia and Northern Iran. The most probable origination pathway of the genus Capoeta is hypothesized to occur as a result of allopolyploidization. The origin of Capoeta was found around the Langhian-Serravallian boundary according to our molecular clock. The diversification within the genus occurred along Middle Miocene-Late Pliocene periods.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

Hebeloma species associated with Cistus

The genus Hebeloma has a number of species highly specific to Cistus and others that occur with several host genera. This paper discusses the species of Hebeloma that appear to be ectomycorrhizal with Cistus, judging from their occurrence when Cistus is the only available host. The previously unknown species H. plesiocistum spec. nov. is described. We also provide a key to the known Hebeloma associates of Cistus. Molecular analyses based on ITS sequence data further illustrate the distinctness of the newly described species and difficulties in the species delimitation with view to H. erumpens. Specific associations with Cistus may have evolved more than once within the genus Hebeloma.     

A new genus of soft coral (Cnidaria,Octocorallia) from the Republic of Congo (Pointe-Noire Region)

A new genus of soft coral from the Republic of Congo is described, Complexum gen. n. Nine West African octocoral species previously described in the genus Alcyonium by Tixier-Durivault (1955) are referred to this new genus, and a new species is described and figured, Complexum pusillum sp. n. The new species is characterized by having encrusting growth form and abundant spiny clubs in the surface of the polyparium. It colonizes shallow calcareous rocky banks (5 to 20 m depth) existing in coastal water of the region of Pointe-Noire. Based on molecular phylogeny this new genus is well separated from Alcyonium species.     

Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha

A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18 % of the genera and ca 3 % of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.     

Molecular phylogeny and biogeography of the narrow endemic Coelonema and affinitive Draba (Brassicaceae) based on two DNA regions

To clarify the relationship between two genera, Draba and the narrow genus Coelonema, endemic to the QilianMountains of the northeastern Qinghai-Tibet Plateau, phylogenetic analyses were conducted using nuclear ribosomal DNA ITS, and the chloroplast DNA trnL, from Coelonema draboides and 30 species of Draba representing eight sections, including 25 species of Chinese Draba, seven of which were endemic to the study region. The results unambiguously support several previously published proposals to unite Coelonema with Draba and accommodate C. draboides in the latter genus on the basis of morphological re-examination. Our molecular data presented here also provide evidence that these two genera should be combined as a monophyletic group with high support. In addition, it is estimated that Draba may have originated about 1.36–2.71 Mya, with C. draboides diverging from Draba about 0.15–0.31 Mya, based on the molecular calibration of ITS datasets. The assumed speciation and rapid expansion of these two genera is likely to have occurred in the eastern edge of the QilianMountains area according to molecular phylogeny and estimated divergence times, which correspond well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau.