Morphological and phylogenetic studies of Cytospora (Valsaceae,Diaporthales) isolates from Chinese scholar tree,with description of a new species

Cytospora species are the most serious and widespread pathogens associated with canker disease on multiple plants. In this study, three species, i.e., Cytospora sophoricola, C. chrysosperma, and C. sophorae, which were isolated from Sophora in China, are described and illustrated based on their morphological characteristics and phylogenetic analyses. Cytospora sophoricola was distinguished clearly by its larger disc, multiple ostioles, cystic and multiple locules, and specific cultural characteristics, i.e., protruding fruiting bodies. Maximum parsimony and maximum likelihood analysis showed that it did not cluster with any known species of Cytospora, so it is described as a new species. Cytospora sophorae is a previously reported species from Sophora, which is redescribed based on new isolates and additional observations. Another species was identified as C. chrysosperma, which is reported for the first time on Sophora, so Papilionaceae is shown to be a new host family for C. chrysosperma. The morphological affinities of these species with related taxa are discussed, while the phylogenetic relationships of these species with other fungus in the genus Cytospora were elucidated based on their internal transcribed spacer (ITS) rRNA region sequences.     

Aspergillus yunnanensis,a new and rare species in the Aspergillus section Jani

Aspergillus is a monophyletic genus comprising the subgenera Aspergillus, Circumdati, Cremei, Fumigati, Nidulantes and Polypaecilum. The subgenus Circumdati contains many economically important species and mycotoxin producers. Section Jani was recently introduced with morphological and molecular support. In the present study, two strains isolated from farmland soil were assigned in section Jani based on multi-locus phylogenetic analyses but showed low similarity with existing species. Further morphological observation found they had wider vesicles and conidia connections which were different from the known species. Based on phylogenetic and morphological data, Aspergillus yunnanensis was introduced as the third species in section Jani. Members in section Jani are rarely distributed, this is the first report of this section in China.     

Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora

The rare apothecial, cupulate fungus Geopora pellita (Pyronemataceae) is characterized by a uniquely bright yellow-orange excipulum. We here re-examine its affiliations by use of morphological, molecular phylogenetic and ultrastructural analyses. G. pellita appears as phylogenetically rather isolated, being the sister group of a clade comprising Phaeangium, Picoa, the majority of the Tricharina species, and the remaining Geopora species. Based on its phylogenetic position and its unique combination of morphological characters, we assign G. pellita to Hoffmannoscypha, gen. nov., as H. pellita, comb. nov. As in a previous study, analyses of both large subunit (LSU) and internal transcribed spacer (ITS) ribosomal DNA suggest that the remaining genus Geopora is paraphyletic, with the hypogeous, ptychothecial type species more closely related to Picoa and Phaeangium than to the greyish-brownish cupulate and apothecial Geopora spp., indicating that the latter should be reassigned to the genus Sepultaria. The current study also shows that ITS confirm LSU data regarding the polyphyly of Tricharina.     

An Expanded Combined Evidence Approach to the Gavialis Problem Using Geometric Morphometric Data from Crocodylian Braincases and Eustachian Systems

The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed - morphological characters place Gavialis as the sister to all other extant crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discrete morphological and molecular characters. The braincase data alone produced a clade that included crocodylids and Gavialis, whereas the Eustachian data resulted in Gavialis being considered a basally divergent lineage. When each morphometric dataset was used in a combined analysis with discrete morphological and molecular characters, it generated a tree that matched the topology of the molecular phylogeny of Crocodylia.     

Species delimitation in the European species of Clavulina (Cantharellales, Basidiomycota) inferred from phylogenetic analyses of ITS region and morphological data

The identification of the conventionally accepted species of Clavulina (Cantharellales, Basidiomycota) in Europe (Clavulina amethystina, Clavulina cinerea, Clavulina cristata, and Clavulina rugosa) is often difficult and many specimens are not straightforwardly assignable to any of those four species, which is why some authors have questioned their identity. In order to assess the status of those species, a morphological examination was combined with the molecular analysis of the ITS region. The same six major clades were obtained in the Bayesian and parsimony phylogenetic analyses, and all six clades were well-supported at least by one of the analyses. Morphological characters, such as the overall branching pattern, the presence and intensity of grey colour, the cristation of the apices, and basidiospore size and shape were to various extents correlated with the phylogenetic signal obtained from the ITS region. The congruence between the molecular analyses and morphology, rather than geographical origin, suggests the existence of several species that can be delimited using a combined phylogenetic and morphological species recognition. The analyses revealed that C. cristata and C. rugosa are well-delimited species. In contrast, more than one taxa could be subsumed under the names C. amethystina and C. cinerea, the taxonomical complexity of which is discussed. The ITS region is proved to be adequate to separate phylogenetic species of Clavulina.     

Molecular and morphological characterization of two aphid genera,Acyrthosiphon and Aulacorthum (Hemiptera: Aphididae)

The taxonomic histories of two genera, Acyrthosiphon and Aulacorthum, have been controversial because of the ambiguous morphology used as criteria to distinguish these genera. In this study, molecular and morphological characters were analyzed to determine whether the current classification of these genera is reasonable. Two phylogenetic trees based on five genes (COI, COII, srRNA, lrRNA, and EF1a) supported the distinctiveness of Acyrthosiphon and Aulacorthum, and a canonical discriminant analysis using 19 morphological characters showed that the two genera were separated by five morphological characters (HTB, C, Ant.III, HFM, and SIPH). Based on these results, we confirm that the current classification of Acyrthosiphon and Aulacorthum is supported by molecular and morphological characters.     

Phylogenetic relationships of five Oriental Apanteles species-groups (Hymenoptera: Braconidae: Microgastrinae) by concatenating four molecular markers

Genus Apanteles is a cosmopolitan and largest genus in Microgastrinae that can be set as chief example of the subfamily to be studied for. However, highly similar morphological characters intraspecifically lead to difficulty in identifying this genus. In this study, 25 individuals of Apanteles were identified morphologically and molecularly by using error rates approach of barcoding analysis. The phylogenetic of the Apanteles that consisted of five species-groups were studied together with their molecular time divergences by using four molecular markers i.e., COI, 16S, 28S and Cyt B. The species groups are mycetophilus, ultor, merula, merope and ater. The phylogenetic analyses show that each species groups were monophyletic with formation of sister clad for merula and merope-group. The phylogenetic analyses of Apanteles species-group were well resolved and supported by their morphological and taxonomical status. This study is a first record on the phylogenetic of five Oriental Apanteles species-group.     

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria

The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.     

Phylogenetic relationships of the enigmatic ornate shiner,Cyprinella ornata,a species endemic to Mexico (Teleostei: Cyprinidae)

The systematics and taxonomy of North Americancyprinid fishes has historically been said tobe in a chaotic state of affairs. Much of theconfusion as to relationships of species restsin the lack of explicit phylogenetic hypothesesof species and reliance upon degree ofdistinctiveness of taxa or their overallsimilarity for generic placement. Some specieshave had more turbulent or variable taxonomichistories than others. The ornate shiner, Cyprinella ornata, is one of those species,having been placed in the genera Notropis,Codoma, and Cyprinella within the last20 years and found in current texts in any ofthese three genera. Most of the confusionregarding placement of this species has beenrelated to lack of explicit phylogenetichypotheses to formulate its classification, butto a certain degree some researchers haveignored phylogenetic studies and preferred torely upon its morphological distinctiveness orreproductive behavioral traits of questionablehomology to place it in a monotypic genus andalign it with the genera Pimephales andOpsopoeodus.I present a phylogenetic analysis based oncomplete Cytochrome b sequences fromornate shiners, other species of Cyprinella, purported relatives, and severalother species of the Shiner Clade to determinethe phylogenetic affinities of this enigmaticspecies. Molecular analysis reveals the ornateshiner to be more closely related to species ofCyprinella than to a Pimephalesplus Opsopoeodus clade as previouslydiscussed in one morphological analysis, or asargued by Page and Johnston (1990), Johnstonand Page (1992) and Page and Ceas (1989) basedon observations of spawning behaviors andhypotheses of homology between crevice-spawningand egg-clumping behaviors. This molecularanalysis is more consistent with earliermorphological phylogenetic hypotheses of Mayden(1989) wherein these two clades are notconsidered to be closely related and the ornateshiner is a member of the genus Cyprinella.     

The correlation among molecular phylogenetics, morphological data, and growth temperature of the genus Emericella, and a new species

The species of the genus Emericella have been classified and identified on the basis of morphological features. However, the phylogenetic relationships in this genus have not been investigated. To clarify the relationships according to molecular phylogenetics, morphological characteristics, and growth temperature regimens in Emericella, multilocus sequencing analysis based on recent Aspergillus taxonomy was carried out. Various characteristic species formed individual clades, and maximum growth temperature reflected the phylogenetics. Emericella species exhibit various ascospore characteristics, although some species do not have distinct ascospore ornamentation. Species that have smooth-walled ascospores with two equatorial crests are polyphyletic. Here, Emericella pachycristata is described and illustrated as a new species. Its ascospores are similar to those of E. nidulans. These species produce smooth-walled ascospores, but the equatorial crests of E. pachycristata are thicker than those of E. nidulans. On the phylogenetic trees, E. pachycristata is closely related to E. rugulosa, which produces ascospores with ribbed convex surfaces. Thus, E. pachycristata is considered to be a new species both morphologically and phylogenetically.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Morphological and molecular identification of helminths of the greater bulldog bat Noctilio leporinus (Quiroptera: Noctilionidae) from Campeche,Mexico

Surveys on parasites of bats from the Americas have been conducted, but information on helminths is still scarce, especially in the Neotropical region. In Mexico, there are species of bats that lack of a record for helminth species, such as members of the family Noctilionidae. The present study describes for the first time the helminths of Noctilio leporinus in Campeche, Mexico. In 2017, six specimens of N. leporinus were studied for helminths. The species identification of helminths was based on morphological studies and molecular analysis of fragments of the 28S rDNA. All bat specimens were infected for at least one helminth species. Three helminth taxa were identified: the trematode Pygidiopsis macrostomum, and the nematodes Tricholeiperia cf. proencai, and Heligmonellidae gen. sp. The morphological identification of P. macrostomum was confirmed by sequence analysis of 28S rDNA gene. The phylogeny of P. macrostomum grouped our sequence with other sequences of the same species collected in Brazil. The phylogenetic tree of Heligmonellidae gen. sp. indicated that the helminth belongs to clade formed by the species Odilia bainae, Nippostrongylus magnus and Nippostrongylus brasiliensis of the family Heligmonellidae. The phylogenetic analysis of the 28S sequences of T. cf. proencai did not show any similarity or close affinity with nematodes from which that gene has been sequenced to date. The findings of the present study increase the number of helminth species parasitizing bats in Mexico.     

Evolutionary classification: A case study on the diverse plant genus Ranunculus L. (Ranunculaceae)

Evolutionary classification attempts to integrate information on shared ancestry, evolutionary process and phenetic information into the taxonomic concept. Here we exemplify this concept on the monophyletic, species-rich and cosmopolitan plant genus Ranunculus. Previous classifications have rendered almost all traditional sections as polyphyletic, and a modern revision based on phylogenetic principles was so far lacking. Maximum parsimony and Bayesian inference analysis of a combined nuclear (ITS of nrDNA) and plastid DNA dataset (matK/trnK, and psbJ–petA) provided a phylogenetic framework for the genus with nine well-supported subclades. Neighbor Net analysis revealed a reticulate data structure within two subclades with frequent polyploidy and/or hybridization. Character evolution was studied by McClade reconstructions of morphological data mapped on to the molecular tree topology. Morphological characters show a mosaic-like distribution, but express several shared states congruent to molecular clades. A total evidence approach (TE) based on the combined morphological and molecular dataset suggests a subdivision of Ranunculus into a paraphyletic, temperate to arctic group of five subclades (subg. Auricomus), and a temperate to subtropical clade with four subclades (subg. Ranunculus). Infrageneric classification of two subgenera and 17 sections is based on both monophyly s.l. as evident from TE and a minimum of shared morphological characters. Six subclades have shared morphological or karyological features (sects. Auricomus, Flammula, Oreophili, Polyanthemos, Ranunculus, Thora, and Trisecti). One subclade was subdivided into three smaller clades according to morphological data (sects. Epirotes, Leucoranunculus, Ranuncella, Aconitifolii). In the case of reticulate evolution and uncertain ancestry we accept well-supported genetic clusters with shared morphological features, as revealed by Neighbor Net analysis (sections Batrachium, Hecatonia, Pseudadonis). Character evolution connected to ecological shifts characterizes the paraphyletic section Ranunculastrum, the holophyletic section Euromontani (sect. nov.), and the monotypic sect. Echinella. The information content of our classification is compared to alternative concepts.     

Convoluted history and confusing morphology: Molecular phylogenetic analysis of dicrocoeliids reveals true systematic position of the Anenterotrematidae Yamaguti, 1958 (Platyhelminthes,Digenea)

The Dicrocoeliidae is a highly diverse family of digeneans parasitic in amniotic tetrapods. Detailed molecular phylogenetic analysis of dicrocoeliids is lacking and only a few dicrocoeliids from mammals have been included in previous studies. Sequence data were previously absent for the Anenterotrematidae that shares several morphological characteristics with dicrocoeliids. We examined phylogenetic affinities of several newly sequenced (nuclear 28S rDNA) taxa of dicrocoeliids and anenterotrematids collected from small mammals in Ecuador, Panama, Peru, USA and Vietnam. Our analyses demonstrated that the two anenterotrematid genera (Anenterotrema, Apharyngotrema) belong to the Dicrocoeliidae, placing the Anenterotrematidae into synonymy with the Dicrocoeliidae. Molecular data combined with morphological examination of type and new specimens provided evidence that Parametadelphis and Apharyngotrema are junior synonyms of Metadelphis, with all Metadelphis species lacking a digestive system. Phylogenetic analysis demonstrates that reduction of the alimentary tract in Lutztrema and its loss in Anenterotrema and Metadelphis represent at least two independent evolutionary events. Genera Brachylecithum, Brachydistomum, and Lyperosomum proved to be non-monophyletic, each likely representing more than a single genus. Furthermore, phylogenetic analysis did not support monophyly of the two largest subfamilies of the Dicrocoeliidae (Dicrocoeliinae and Leipertrematinae) with the other two subfamilies not included in this study. Therefore, we propose to abandon the current subfamily division of the Dicrocoeliidae. Analysis of host associations indicates multiple host-switching events throughout evolution of dicrocoeliids. Lastly, analysis of dicrocoeliid geographic distribution revealed that nearly all major clades included taxa from more than a single zoogeographic realm with the exception of the clade Anenterotrema?+?Metadelphis, found only in the Neotropics.     

Polycephalomyces lianzhouensis sp. nov., a new species,co-occurs with Ophiocordyceps crinalis

A new species from Guangdong Province in south China, Polycephalomyces lianzhouensis, is described and illustrated here; this species was found to co-occur with Ophiocordyceps crinalis. The phylogenetic position of this species was investigated according to morphological features and phylogenetic inferences based on the nrSSU, nrLSU, tef1, rpb1, and ITS gene sequences. Results demonstrated that P. lianzhouensis was highly associated with P. ramosopulvinatus but could be distinguished from the latter using the sequences of rpb1, nrLSU, and ITS gene and the features of much smaller stromata and perithecia and longer part-spores.     

Systematic position of the genus Metacanthocephalus Yamaguti, 1959 (Palaeacanthocephala: Echinorhynchida) inferred from molecular evidence,with a redescription of Metacanthocephalus ovicephalus (Zhukov, 1960)

The familial affiliation of the echinorhynchid palaeacanthocephalan genus Metacanthocephalus has been uncertain, with the three families Echinorhynchidae, Leptorhynchoididae, and Rhadinorhynchidae having been suggested as its parent taxon. In this study, adult individuals of Metacanthocephalus ovicephalus from the intestine of the cresthead flounder Pseudopleuronectes schrenki (new host) and the dark flounder Pseudopleuronectes obscurus in Hokkaido, Japan, were examined. Using three gene markers (mitochondrial cytochrome c oxidase subunit I; nuclear 18S and 28S rRNA genes) determined from two specimens of M. ovicephalus, a molecular phylogenetic analysis was performed along with relevant sequences available in public databases representing 26 species in eight families of the order Echinorhynchida, along with five species from Polymorphida and two from Eoacanthocephala. The resulting phylogram showed that M. ovicephalus was nested within a clade along with nine species in eight genera (Brentisentis yangtzensis, Dentitruncus truttae, Dollfusentis bravoae, Koronacantha mexicana, K. pectinaria, Leptorhynchoides thecatus, Neotegorhynchus cyprini, Pseudoleptorhynchoides lamothei, and Tegorhynchus [= Illiosentis] sp.). In this paper, we propose i) a set of morphological characters to circumscribe members represented by this clade as a Linnaean higher taxon, ii) to place this taxon at the rank of family, iii) to refer to it as Leptorhynchoididae, and iv) to regard Illiosentidae as a junior synonym of Leptorhynchoididae. Our morphological examination revealed a single vaginal sphincter in M. ovicephalus, a character that was not mentioned in any of the previous literature. By this character, along with geographical distribution and host fish, six congeners currently recognized in Metacanthocephalus can be divided into two groups.