Gymnoxanthella radiolariae gen. et sp. nov. (Dinophyceae), a dinoflagellate symbiont from solitary polycystine radiolarians

The symbiotic dinoflagellate Gymnoxanthella radiolariae T. Yuasa et T. Horiguchi gen. et sp. nov. isolated from polycystine radiolarians is described herein based on light, scanning and transmission electron microscopy as well as molecular phylogenetic analyses of SSU and LSU rDNA sequences. Motile cells of G. radiolariae were obtained in culture, and appeared to be unarmored. The cells were 9.1–11.4 μm long and 5.7–9.4 μm wide, and oval to elongate oval in the ventral view. They possessed an counterclockwise horseshoe‐shaped apical groove, a nuclear envelope with vesicular chambers, cingulum displacement with one cingulum width, and the nuclear fibrous connective; all of these are characteristics of Gymnodinium sensu stricto (Gymnodinium s.s.). Molecular phylogenetic analyses also indicated that G. radiolariae belongs to the clade of Gymnodinium s.s. However, in our molecular phylogenetic trees, G. radiolariae was distantly related to Gymnodinium fuscum, the type species of Gymnodinium. Based on the consistent morphological, genetic, and ecological divergence of our species with the other genera and species of Gymnodinium s.s., we considered it justified to erect a new, separate genus and species G. radiolariae gen. et sp. nov. As for the peridinioid symbiont of radiolarians, Brandtodinium has been erected as a new genus instead of Zooxanthella, but the name Zooxanthella is still valid. Brandtodinium is a junior synonym of Zooxanthella. Our results suggest that at least two dinoflagellate symbiont species, peridinioid Zooxanthella nutricula and gymnodinioid G. radiolariae, exist in radiolarians, and that they may have been mixed and reported as “Z. nutricula” since the 19th century.     

MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND‐DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM1

The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition of this genus ～100 species remain now of uncertain or unknown generic affiliation. In an effort to improve our taxonomic and phylogenetic understanding of one of these species, namely Amphidinium semilunatum, we re‐investigated organisms from several distant sites around the world using light and scanning electron microscopy and molecular phylogenetic methods. Our results enabled us to describe this species within a new heterotrophic genus, Ankistrodinium. Cells of A. semilunatum were strongly laterally flattened, rounded‐quadrangular to oval in lateral view, and possessed a small asymmetrical epicone. The sulcus was wide and characteristically deeply incised on the hypocone running around the antapex and reaching the dorsal side. The straight acrobase with hook‐shaped end started at the sulcal extension and continued onto the epicone. The molecular phylogenetic results clearly showed that A. semilunatum is a distinct taxon and is only distantly related to species within the genus Amphidinium sensu stricto. The nearest sister group to Ankistrodinium could not be reliably determined.     

Phylogeography and phylogeny of the genus Acanthonyx (Decapoda,Epialtidae) in the north‐east Atlantic and Mediterranean

The genus Acanthonyx Latreille, 1828 (Majoidea, Epialtidae) contains 17 or 18 known species, depending on competing taxonomic views, that are widely distributed across the world. Morphologically, most species look superficially alike, and therefore, similar taxonomic concepts have been described under different names. Consequently, there is today a considerable list of synonyms, which further complicates the taxonomy of the genus Acanthonyx. In this study, we conducted a phylogeographical and phylogenetic analysis of populations of the genus Acanthonyx in the NE Atlantic, Mediterranean and Macaronesia using the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear 28S rRNA loci. Our phylogenetic and phylogeographical results revealed that Acanthonyx lunulatus sensu lato is a complex of three distinct lineages: one corresponding to the previously described Acanthonyx brevifrons, another to A. lunulatus sensu stricto and a third to a yet undescribed group. Whereas our results confirms that A. brevifrons deserves the status of a species, as it can be easily distinguishable from A. lunulatus by a few morphological traits, we could not find any such traits suitable for the discrimination between A. lunulatus sensu stricto and the third lineage. Furthermore, the degree of COI divergence between this lineage and A. lunulatus is below average levels for Decapoda species. Yet, no shared haplotypes have been detected between them. The differences found in the nuclear gene (indels), together with the sympatric occurrence of the two forms, prompt for a more detailed analysis of this group. Overall, the results show that significant genetic differentiation between specimens with similar morphology occurs in the Epialtidae, thus reinforcing the importance of combining morphological and genetic tools to fully resolve the taxonomy of these decapods.     

Morphology,phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes,Viperidae)

Carrasco, P.A., Mattoni, C.I., Leynaud, G.C. & Scrocchi, G.J. (2012). Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae). —Zoologica Scripta, 41, 109–124. South American bothropoids comprise a monophyletic and greatly diverse group of pitvipers that were initially included in the genus Bothrops and later assigned to five genera. Until recently, most phylogenetic analyses of bothropoids used exclusively mitochondrial DNA sequences, whereas few of them have included morphological traits. Moreover, the systematic affinities of some species remain unclear. In this study, we performed a parsimony analysis of morphological data obtained from the examination of 111 characters related to lepidosis, colour pattern, osteology, and hemipenial morphology of 35 of the 48 species that compose the bothropoid group. The morphological data analysed contain novel information about several species, including the incertae sedis. Morphology was analysed separately and combined with 2393 molecular characters obtained from published sequences of four mitochondrial genes. Five characters of the ecology were also included. A sensitivity analysis was performed using different weighting criteria for the characters. The congruence among different sources of evidence was evaluated through partitioned and total evidence analyses, the analyses of reduced datasets and the use of incongruence length difference test. With few exceptions, results showed groups of species similar to those obtained in previous studies; however, incongruences between morphological and molecular characters, and within the molecular partition, were revealed. This conflict affects the relationship between particular groups of species, leading to alternative phylogenetic hypotheses for bothropoids: hierarchical radiation or two major lineages within the group. The results also showed that Bothrops sensu stricto is paraphyletic. We discuss previous taxonomic approaches and, considering both phylogenetic hypotheses, we propose an arrangement that rectifies the paraphyly of Bothrops: maintaining Bothrocophias, assigning Bothrops andianus to this genus; and recognising the sister clade as Bothrops, synonymising Bothriopsis, Bothropoides and Rhinocerophis.     

Molecular phylogeny of the New World gecko genus Homonota (Squamata: Phyllodactylidae)

The genus Homonota was described by Gray (1845) and currently includes 10 species: Homonota andicola, H. borellii, H. darwinii, H. fasciata, H. rupicola, H. taragui, H. underwoodi, H. uruguayensis, H. williamsii & H. whitii and one subspecies of H. darwinii (H. darwinii macrocephala). It is distributed from 15° latitude south in southern Brazil, through much of Bolivia, Paraguay, Uruguay and Argentina to 54° south in Patagonia and across multiple different habitats. Several morphological taxonomic studies on a subset of these species have been published, but no molecular phylogenetic hypotheses are available for the genus. The objective of this study is to present a molecular phylogenetic hypothesis for all the described species in the genus. We sequenced two mitochondrial genes (cyt‐b & 12S: 1745 bp), seven nuclear protein coding (RBMX, DMLX, NKTR, PLRL, SINCAIP, MXRA5, ACA4: 5804 bp) and two anonymous nuclear loci (30Hb, 19Hb: 1306 bp) and implemented traditional concatenated analyses (MP, ML, BI) as well as species‐tree (*beast ) approaches. All methods recovered almost the same topology. We recovered the genus Homonota as monophyletic with strong statistical support. Within Homonota, there are three strongly supported clades (whitii, borellii and fasciata), which differ from those previously proposed based on scale shape, osteology, myology and quantitative characters. Detailed morphological analyses based on this highly resolved and well‐supported phylogeny will provide a framework for understanding morphological evolution and historical biogeography of this phenotypically conservative genus. We hypothesize that extensive marine transgressions during Middle and Late Miocene most probably isolated the ancestors of the three main clades in eastern Uruguay (borellii group), north‐western Argentina‐southern Bolivia (fasciata group), and central‐western Argentina (whitii group). Phylogeographic and morphological/morphometric analyses coupled with paleo‐niche modelling are needed to better understand its biogeographical history.     

Taxonomic revision of the Agaraceae with a description of Neoagarum gen. nov. and reinstatement of Thalassiophyllum

We confirmed the monophyly of the Agaraceae based on phylogenetic analyses of six mitochondrial and six chloroplast gene sequences from Agarum, Costaria, Dictyoneurum, and Thalassiophyllum species, as well as representative species from other laminarialean families. However, the genus Agarum was paraphyletic, comprising two independent clades, A. clathratum/A. turneri and A. fimbriatum/A. oharaense. The latter clade was genetically most closely related to Dictyoneurum spp., and morphologically, the species shared a flattened stipe bearing fimbriae (potential secondary haptera) in the mid‐ to upper portion. The phylogenetic position of Thalassiophyllum differed between the two datasets: in the chloroplast gene phylogeny, Thalassiophyllum was included in the A. clathratum/A. turneri clade, but in the mitochondrial gene phylogeny, it formed an independent clade at the base of the Agaraceae, the same position it took in the phylogeny when the data from both genomes were combined despite a larger number of bp being contributed by the chloroplast gene sequences. Considering the remarkable morphological differences between Thalassiophyllum and other Agaraceae, and the molecular support, we conclude that Thalassiophyllum should be reinstated as an independent genus. Dictyoneurum reticulatum was morphologically distinguishable from D. californicum due to its midrib, but because of their close genetic relationship, further investigations are needed to clarify species‐level taxonomy. In summary, we propose the establishment of a new genus Neoagarum to accommodate A. fimbriatum and A. oharanese and the reinstatement of the genus Thalassiophyllum.     

Integrative taxonomy of the Rhinolophus macrotis complex (Chiroptera,Rhinolophidae) in Vietnam and nearby regions

The taxonomic status of Rhinolophus macrotis sensu lato (s.l.) in Vietnam and adjacent territories remains problematic. To address this issue, we performed an integrated study of morphological, acoustic, and genetic characters of R. macrotis s.l. specimens and compared these with sympatric species within the philippinensis group (R. marshalli, R. paradoxolophus, and R. rex). Our results reveal that in addition to a cryptic species of R. macrotis previously found in Jiangxi and Jingmen, China, R. macrotis s.l. in continental Asia includes three further species, namely R. cf. siamensis, R. cf. macrotis, and R. cf. macrotis “Phia Oac.” These four taxa are distinguished from genuine R. macrotis in Nepal and R. siamensis in Thailand by their morphological and/or genetic features. Further taxonomic evaluation of the subspecies of R. macrotis s.l. is needed to determine their affinities with recently recognized cryptic species and to possibly describe new taxa. Our results also show that interspecific divergences in mitochondrial DNA sequences (Cytb and COI genes) among taxa within the philippinensis group (particularly between R. cf. siamensis/R. cf. macrotis and R. rex/R. paradoxolophus) are significantly lower than those of other morphological groups in the genus. These phylogenetic patterns might be explained by recent allopatric speciation or ancient introgression events among ancestors of the taxa during the Pleistocene. However, further investigations including genetic analyses of nuclear genes are needed to test the latter hypothesis.     

Comparative Genome Analysis Reveals Cyanidiococcus gen. nov., A New Extremophilic Red Algal Genus Sister to Cyanidioschyzon (Cyanidioschyzonaceae,Rhodophyta)

The taxonomic placement of strains belonging to the extremophilic red alga Galdieria maxima has been controversial due to the inconsistent phylogenetic position inferred from molecular phylogenetic analyses. Galdieria maxima nom. inval. was classified in this genus based on morphology and molecular data in the early work, but some subsequent molecular phylogenetic analyses have inferred strains of G. maxima to be closely related to the genus Cyanidioschyzon. To address this controversy, an isolated strain identified as G. maxima using the rbcL gene sequence as the genetic barcode was examined using a comprehensive analysis across morphological, physiological, and genomic traits. Herein are reported the chloroplast-, mitochondrion-, and chromosome-level nuclear genome assemblies. Comparative analysis of orthologous gene clusters and genome arrangements suggested that the genome structure of this strain was more similar to that of the generitype of Cyanidioschyzon, C. merolae than to the generitype of Galdieria, G. sulphuraria. While the ability to uptake various forms of organic carbon for growth is an important physiological trait of Galdieria, this strain was identified as an ecologically obligate photoautotroph (i.e., the inability to utilize the natural concentrations of organic carbons) and lacked various gene models predicted as sugar transporters. Based on the genomic, morphological, and physiological traits, we propose this strain to be a new genus and species, Cyanidiococcus yangmingshanensis. Re-evaluation of the 18S rRNA and rbcL gene sequences of the authentic strain of G. maxima, IPPAS-P507, with those of C. yangmingshanensis suggests that the rbcL sequences of “G. maxima” deposited in GenBank correspond to misidentified isolates.     

The embryology of <Emphasis Type="Italic">Xanthoceras</Emphasis> and its phylogenetic implications

Recent molecular analyses found the Chinese monotypic genus Xanthoceras to be either a sister genus to the rest of a broadly defined Sapindaceae sensu lato (s.l.) including Aceraceae and Hippocastanaceae or the only genus of the Xanthoceraceae. Here we investigate for the first time the embryology of Xanthoceras and compare the embryological data with related taxa to aid in understanding the phylogenetic relationships of this genus. The results indicate that Xanthoceras shares many embryological features with Sapindaceae sensu stricto (s.s.), Aceraceae, and Hippocastanaceae, including a glandular tapetum, simultaneous microsporogenesis, three-colporate pollen grains, a bitegmic and crassinucellate ovule, Polygonum type of embryo sac development, endosperm formation of the nuclear type, and exalbuminous mature seeds. The wide range of similarities in embryological features suggests that Xanthoceras is closely related to other members of Sapindaceae s.l. However, Xanthoceras differs from other Sapindaceae in several morphological characteristics, for instance, five to eight ovules in each locule in Xanthoceras versus one to two ovules in each locule in other Sapindaceae s.l., and five golden horn-like appendages present on both staminate and hermaphrodite flowers of Xanthoceras versus absent on the flowers of other Sapindaceae s.l. We propose that Xanthoceras merits recognition at the subfamily level as Xanthoceroideae, rather than at the family level as Xanthoceraceae. The present study also reveals that late-acting ovarian self-incompatibility (OSI) occurs in X. sorbifolium and that postzygotic OSI contributes to the self-sterility of the species.     

The higher‐level phylogenetic relationships of the Eumeninae (Insecta,Hymenoptera, Vespidae), with emphasis on Eumenes sensu lato

Cladistic analyses were carried out to infer the phylogenetic relationships among taxa that were originally part of the large genus Eumenes. Terminals belonging to other eumenine lineages were also included, as well as terminals from other vespid subfamilies. Analyses under equal weights and implied weights were carried out, and better results were obtained with the latter. The results corroborated the monophyly of Eumeninae, and recovered Zethini sensu lato as the sister‐lineage to the remaining eumenines. Eumenes sensu lato as originally recognized is paraphyletic relative to Odynerus sensu lato. A natural classification at the tribal level congruent with the phylogenetic results may be proposed, and the names Zethini, Odynerini, and Eumenini are already available. This is the most comprehensive phylogeny of the Eumeninae to date. A new generic synonymy is Alfieria Giordani Soika, 1934 = Delta de Saussure, 1855.     

Morphological and molecular characterization within 26 strains of the genus Cylindrospermum (Nostocaceae,Cyanobacteria), with descriptions of three new species

Twenty‐six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S rRNA gene and the 16S‐23S internal transcribed spacer (ITS) region. Phylogenetic analysis of the 16S rRNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto contained all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these taxa, three species new to science in this clade were described: C. badium, C. moravicum, and C. pellucidum. Our evidence indicated that Cronbergia is a later synonym of Cylindrospermum. The phylogenetic position of Cylindrospermum within the Nostocaceae was not clearly resolved in our analyses. Cylindrospermum is unusual among cyanobacterial genera in that the morphological diversity appears to be more evident than sequence divergence. Taxa were clearly separable using morphology, but had very high percent similarity among ribosomal sequences. Given the high diversity we noted in this study, we conclude that there is likely much more diversity remaining to be described in this genus.     

Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales,Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.

Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400–600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy—in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria—and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup “Pleiochloris,” was included in the genus Ixipapillifera as I. deasonii comb. nov.     

Three new species of <Emphasis Type="Italic">Disterigma</Emphasis> (Ericaceae: Vaccinieae) from Western Colombia,with comments on morphological terminology

Three new endemic species are described and illustrated from the floristically diverse western mountain ranges of Colombia. Disterigma appendiculatum, D. hiatum, and D. verruculatum have interesting floral characters that are unique in the genus and in the Vaccinieae. These new morphological characters and the terminology adopted for bracteoles and staminal appendages are briefly discussed.     

Molecular phylogeny and taxonomy of the genus Chaetophora (Chlorophyceae,Chlorophyta), including descriptions of Chaetophoropsis aershanensis gen. et sp. nov.

The broadly defined genus Chaetophora consisted of species with minute, uniseriate branching filaments enveloped in soft or firm mucilage forming macroscopic growths that are spherical, hemispherical, and tubercular or arbuscular, growing epiphytically on freshwater aquatic plants and other submerged surfaces in standing or fast‐flowing water. Recent molecular analyses clearly showed that this genus was polyphyletic. In this study, eight strains of Chaetophora and three strains of Stigeoclonium were identified and successfully cultured. In combination with the morphological data, a concatenated data set of four markers (18S + 5.8S + ITS2+ partial 28S rDNA) was also used to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved the broadly defined Chaetophora to at least two genera. Species with a globose thallus of genus Chaetophora formed a separate monophyletic clade, which clearly separated from, a type of lobe‐form Chaetophora species. Therefore, we propose to erect a new genus, Chaetophoropsis, which includes all globose species of the Chaetophora. Chaetophoropsis aershanensis was determined to be a new species, based on its special characteristic of profuse long rhizoids. Stigeoclonium polyrhizum, as the closest relative to Chaetophoropsis, revealed its distant relationships to other species of Stigeoclonium. A globose thallus with a thick, soft mucilage matrix, and special rhizoidal branches lent further support to the placement of S. polyrhizum in the genus Chaetophoropsis and had the closest relationship to C. aershanensis. Taxonomic diversity was proven by distinctive morphological differences and by phylogenetic divergence in the broadly defined Chaetophora identified herein.     

Phylogeny and biogeography of the genus Cephalenchus (Tylenchomorpha,Nematoda)

The phylogenetic position of Cephalenchus is enigmatic with respect to other tylench nematodes. In this study, Cephalenchus populations representing 11 nominal species were sampled worldwide for molecular and morphological characterization. Species identification was based on light microscopy (LM) and scanning electron microscopy (SEM). Molecular analyses were based on the genes (i.e. 18S, 28S, 5.8S) and internal transcribed spacers (ITS‐1 and ITS‐2) of the ribosomal RNA (rRNA). Phylogenetic analyses (i.e. full and reduced alignments) of either concatenated or single genes always supported the monophyly of Cephalenchus. A sister relationship between Cephalenchus and Eutylenchus excretorius was recovered by most analyses, although branch support varies depending on the dataset used. The position of Cephalenchus + E. excretorius within Tylenchomorpha nevertheless remains ambiguous, thus highlighting the importance of sampling additional genes as well as taxa. Placement of Cephalenchus + E. excretorius as sister of Tylenchinae or Boleodorinae could not be rejected on the basis of 18S and 28S rRNA genes. Within Cephalenchus, amphidial opening morphology shows congruence with molecular‐based phylogenetic relationships, whereas the number of lines in the lateral field is likely to be a convergent trait. Morphometric analyses clearly distinguished short tail from medium–long tail species, and SEM observations seem to suggest a relation between tail length and amphidial opening. In addition, molecular phylogenies support the non‐monophyly of Cephalenchus cephalodiscus, Cephalenchus cylindricus, Cephalenchus daisuce and Cephalenchus leptus. The known extent of Cephalenchus diversity is increased with the inclusion of two new species, and the biogeography of the genus is discussed.     

Laboulbeniales hyperparasites (Fungi,Ascomycota) of bat flies: Independent origins and host associations

The aim of this study was to explore the diversity of ectoparasitic fungi (Ascomycota, Laboulbeniales) that use bat flies (Diptera, Hippoboscoidea) as hosts. Bat flies themselves live as ectoparasites on the fur and wing membranes of bats (Mammalia, Chiroptera); hence this is a tripartite parasite system. Here, we collected bats, bat flies, and Laboulbeniales, and conducted phylogenetic analyses of Laboulbeniales to contrast morphology with ribosomal sequence data. Parasitism of bat flies by Laboulbeniales arose at least three times independently, once in the Eastern Hemisphere (Arthrorhynchus) and twice in the Western Hemisphere (Gloeandromyces, Nycteromyces). We hypothesize that the genera Arthrorhynchus and Nycteromyces evolved independently from lineages of ectoparasites of true bugs (Hemiptera). We assessed phylogenetic diversity of the genus Gloeandromyces by considering the LSU rDNA region. Phenotypic plasticity and position‐induced morphological adaptations go hand in hand. Different morphotypes belong to the same phylogenetic species. Two species, G. pageanus and G. streblae, show divergence by host utilization. In our assessment of coevolution, we only observe congruence between the Old World clades of bat flies and Laboulbeniales. The other associations are the result of the roosting ecology of the bat hosts. This study has considerably increased our knowledge about bats and their associated ectoparasites and shown the necessity of including molecular data in Laboulbeniales taxonomy.