Morphology and phylogeny of a new woodruffiid ciliate,Etoschophrya inornata sp. n. (Ciliophora,Colpodea, Platyophryida), with an account on evolution of platyophryids

Bourland, W. A., Hampikian, G. & V?a?ný, P. (2012). Morphology and phylogeny of a new woodruffiid ciliate, Etoschophrya inornata sp. n. (Ciliophora, Colpodea, Platyophryida), with an account on evolution of platyophryids. —Zoologica Scripta, 41, 400–416. We studied the morphology, morphometry, resting cysts and molecular phylogeny of a new woodruffiid ciliate, Etoschophrya inornata, from ephemeral puddles and two lacustrine habitats in Idaho, North‐west USA. Up to now, the genus Etoschophrya has included a single species, Etoschophrya oscillatoriophaga, from which our new form is distinguished by (i) the absence of interkinetal cortical granules and, consequently, the absence of extrusible red material in methyl green‐pyronin stains, (ii) usually ≥5 adoral membranelles vs. usually four, (iii) greater length and length/width ratio, (iv) prominent cortical furrows vs. inconspicuous and (v) adaptation to non‐saline semi‐terrestrial and lacustrine habitats in the Nearctic vs. highly saline alkaline Afrotropic soil habitats. Resting cysts have two distinct membranes and a thick hyaline mucous pericyst layer. However, only one membrane persists in older cysts. Like its congener, Etoschophrya inornata feeds exclusively on filamentous cyanobacteria. The 18S rRNA gene sequence places this species in a strongly supported clade with Kuklikophrya ougandae basal to the other platyophryids. We include a morphologic cladistic analysis of platyophryid ciliates and present a hypothetical scenario for the evolution of the platyophryid oral structures.     

Intraclass Evolution and Classification of the Colpodea (Ciliophora)

ABSTRACT. Using nine new taxa and statistical inferences based on morphological and molecular data, we analyze the evolution within the class Colpodea. The molecular and cladistic analyses show four well‐supported clades: platyophryids, bursariomorphids, cyrtolophosidids, and colpodids. There is a widespread occurrence of homoplasies, affecting even conspicuous morphological characteristics, e.g. the inclusion of the micronucleus in the perinuclear space of the macronucleus. The most distinct changes in the morphological classification are the lack of a basal divergence into two subclasses and the split of the cyrtolophosidids into two main clades, differing mainly by the presence vs. absence of an oral cavity. The most complex clade is that of the colpodids. We partially reconcile the morphological and molecular data using evolutionary systematics, providing a scenario in which the colpodids evolved from a Bardeliella‐like ancestor and the genus Colpoda performed an intense adaptive radiation, giving rise to three main clades: Colpodina n. subord., Grossglockneriina, and Bryophryina. Three new taxa are established: Colpodina n. subord., Tillinidae n. fam., and Ottowphryidae n. fam. Colpodean evolution and classification are far from being understood because sequences are lacking for most species and half of their diversity is possibly undescribed.     

Re-analysis of the 18S rRNA gene phylogeny of the ciliate class Colpodea

We critically re-analyzed the 18S rRNA gene phylogeny of the ciliate class Colpodea where four main lineages have been recognized: (1) Bursariomorphida including bryometopids, (2) Platyophryida including sorogenids, (3) Cyrtolophosidida, and (4) Colpodida including bryophryids and grossglockneriids. The Platyophryida branched off first and the Cyrtolophosidida and Colpodida were classified as sister groups. On basis of multiple statistical tests, we unraveled three problematic issues in colpodean phylogenies: the positions of the Bursariomorphida and Platyophryida are unstable and depend on alignment masking; a sister relationship of the Platyophryida and Cyrtolophosidida cannot be excluded by any statistical tree topology test; and clustering of bryophryids and grossglockneriids outside the Colpodida are also statistically valid possibilities. Natural classification of the highly diverse order Colpodida remains puzzling, possibly due to the lack of a phylogenetic signal and morphostasis of the oral ciliature in several Colpoda-like lineages. According to the “Ur-Colpoda” hypothesis, Colpoda represents the stem lineage from which both Colpoda-like and morphologically more derived taxa might have branched off. This evolutionary concept preserves not only information on morphology, ecology, and evolutionary processes of colpodid ciliates, but also aids practicability because the connection to the traditional literature is optimally maintained.     

Molecular Phylogeny of Asian Meconopsis Based on Nuclear Ribosomal and Chloroplast DNA Sequence Data

The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species of Asian Meconopsis did not constitute a monophyletic clade, but formed two solid clades (I and V) separated in the phylogenetic tree by three clades (II, III and IV) of Papaver and its allies. Clade V includes only four Asian Meconopsis species, with the remaining 90 percent of Asian species included in clade I. In this core Asian Meconopsis clade, five subclades (Ia–Ie) were recognized in the nrDNA ITS tree. Three species (Meconopsis discigera, M. pinnatifolia, and M. torquata) of subgenus Discogyne were imbedded in subclade Ia, indicating that the present definition of subgenera in Meconopsis should be rejected. These subclades are inconsistent with any series or sections of the present classifications, suggesting that classifications of the genus should be completely revised. Finally, proposals for further revision of the genus Meconopsis were put forward based on molecular, morphological, and biogeographical evidences.     

Contributions of molecular phylogenetics to foraminiferal taxonomy: General overview and example of Pseudoeponides falsobeccarii

Molecular phylogenetics gives new insights into the taxonomy of foraminifera, independent of their morphology. After a survey of the present knowledge on how molecular phylogeny can contribute to foraminiferal taxonomy, we present an applied example. The comparison of ribosomal DNA (rDNA) sequences belonging to the SSU (Small Subunit) and LSU (Large Subunit) genes of Pseudoeponides falsobeccarii with other similar sequences of rotaliids available in GenBank shows that this species actually belongs to the genus Ammonia, because it groups inside the other Ammonia sequences instead of forming a distinct clade. Moreover, Ammonia falsobeccarii forms a clade well separated from other Ammonia phylotypes, meaning that it can be considered as a distinct species, and not as an ecophenotype of one of the other Ammonia species.     

Six new species of Pythiogeton in Taiwan,with an account of the molecular phylogeny of this genus

Pythiogeton is a little-studied genus of pythialean Oomycete. The genus is characterized by producing its zoospores outside of the sporangium within an apparently naked protoplasmic mass, which formed from a discharge tube-vesicle complex. A total of nine morphologically distinct Pythiogeton species were identified, of which six were new species (Pythiogeton abundans, Pythiogeton microzoosporum, Pythiogeton oblongilobum, Pythiogeton paucisporum, Pythiogeton proliferatum, and Pythiogeton puliensis). A phylogenetic analysis based on internal transcribed spacer sequences revealed that all isolates of Pythiogeton formed a highly supported clade, nested within the wider clade of Pythium species. Each newly recognized Pythiogeton species that was established on the basis of morphological characters was found to occur in a well-supported subgroup within the Pythiogeton clade, confirming their assignment to new species. Pythiogeton shares a common ancestor with the monophyletic group of Pythium species that have predominantly filamentous sporangia rather than with the separate clade of Pythium species that have predominantly globose or ovoid sporangia. This study confirms that Pythium is an extremely heterogenous and polyphyletic genus containing a number of distinct clades of species, including Pythiogeton, which possess morphologically distinguishable characters. A synoptic key to all the described Pythiogeton species is provided.     

Favolaschia in remnants of the Atlantic Forest,Brazil

The examination of recent collections of Favolaschia from remnants of the Atlantic Forest, Brazil, resulted in the identification of F. aurantiaca, F. cinnabarina and F. luteoaurantiaca sp. nov. Internal transcribed spacer (ITS) sequences obtained from these collections were introduced into the previously published phylogenetic tree of the genus to assess the position of these species within the Favolaschia clade. A maximum likelihood analysis generated a phylogenetic tree with a better resolution, especially for the clade that contains species belonging to section Favolaschia subsection Auriscalpium, where the three specimens collected in Brazil also were clustered in.     

Genetic diversity among different species of the genus Leiurus (Scorpiones: Buthidae) in Saudi Arabia and the Middle East

The molecular phylogenetic relationship among two species of genus Leiurus, from Saudi Arabia with additional comparative sequence data available from Egypt, Oman and Turkey is presented. The molecular phylogeny was performed using maximum parsimony, neighbor joining and bayesian inference. Our results indicate a clear deep splitting between the Western clade, which represented by L. quinuestriatus sequences from Egypt and those from the Eastern clade which encompassing different Leiurus species from Saudi Arabia, Oman and Turkey was shown. Also, the phylogenetic relationship represents additional support for the taxonomic status of Arabian Leiurus species.     

Morphology and morphogenesis of Apoholosticha sinica n. g., n. sp. (Ciliophora,Hypotrichia), with consideration of its systematic position among urostylids

This paper investigates the morphology, morphogenesis and SSU rRNA gene-based phylogeny of Apoholosticha sinica n. g., n. sp., isolated from mangrove wetland in Shenzhen, southern China. The new genus Apoholosticha is characterized by its bipartite adoral zone, clearly differentiated frontal cirri arranged in a bicorona, midventral complex composed of midventral pairs only, one marginal cirral row on each side, presence of frontoterminal and transverse cirri, and the lack of a buccal cirrus and caudal cirri. The type species, Apoholosticha sinica n. sp. is diagnosed by the elongated body shape and two kinds of cortical granules. Its main morphogenetic features are similar to that of Pseudokeronopsis except for (1) no buccal cirrus is formed and (2) its macronuclear nodules fuse into a single mass during cell division. Phylogenetic analyses for the new taxon indicate that Apoholosticha n. g. is most closely related to Nothoholosticha and Heterokeronopsis, and falls into the family Pseudokeronopsidae within the core Urostylida clade. In addition, a species that had been misidentified in previous literature is here recognized and assigned to the new genus as Apoholosticha sepetibensis (Wanick and Silva-Neto, 2004) n. comb. (basionym: Pseudokeronopsis sepetibensis Wanick and Silva-Neto, 2004).     

Le genre Postepithyris makridin (térébratulidés,brachiopodes) dans l'oxfordien et le kimméridgien Français

The questions relating to the type-species of genus PostepithyrisMakridin and to its systematic position within Terebratulids are discussed.The French species are described: besides the type-species P. cincta (Cotteau) from Upper Oxfordian, two species from Inferior Kimmeridgian can be included in this genus: P. minor (Douvillé) and P. dubisensis nov. sp.A new subspecies P. cincta mosensis nov., recently discovered in Oxfordian from East of the Paris Basin, can also be assigned to the genus.Postepithyris did not evolve through a single special facies: the species could supported different environmental conditions.     

Fukuyoa paulensis gen. et sp. nov., a New Genus for the Globular Species of the Dinoflagellate Gambierdiscus (Dinophyceae)

The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi / G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2'' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1'' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov.     

A New Species of the Genus <Emphasis Type="Italic">Placoblatta</Emphasis> Bey-Bienko (Dictyoptera,Blaberidae, Epilamprinae) from Southern Vietnam

A new species of the genus Placoblatta, P. minorsp. n., is described from Southern Vietnam. The similarity between representatives of the genus Placoblatta and larvae of the subfamily Epilamprinae is briefly discussed. It is suggested that the origin of the genus Placoblatta has a paedomorph nature.     

Molecular phylogenetic status of the Bulgarian marbled polecat (Vormela peregusna,Mustelidae, Carnivora), revealed by Y chromosomal genes and mitochondrial DNA sequences

In this study, we investigated molecular phylogenetic status of the marbled polecat (Vormela peregusna) from Bulgaria, using sequences of two Y-chromosomal genes (SRY and ZFY). The phylogenetic tree inferred using combined sequences of both genes indicated that the marbled polecat was split from genera Lutra, Neovison and Mustela after genus Martes was diverged in family Mustelidae. In addition, we analyzed molecular phylogeography of the Bulgarian population of the marbled polecat, using cytochrome b and control region sequences of mitochondrial DNA (mtDNA). The phylogenetic tree of cytochrome b indicated that the haplotypes of the Bulgarian population comprised two haplogroups, which were the most ancestral clades. Additionally, the control region phylogeny showed that the haplotypes of Bulgaria formed two haplogroups: one was the most ancestral clade, and the other was the derivative clade. One individual with the most ancestral cytochrome b clade had a control region haplotype of the derivative clade. Thus, this study revealed that the most ancestral lineages of the marbled polecat are included in the population of Bulgaria. The Bulgarian population could be a remnant lineage from a basal for the species, which in Pleistocene occupied a relatively large area related to the Balkan-Caucasian.     

Molecular Evidence for a Deep Clade of Dunnarts (Marsupialia: Dasyuridae: Sminthopsis)

Sminthopsis is the most speciose genus of living dasyurid marsupials and, along with its close relatives Antechinomys and Ningaui, constitutes the clade Sminthopsini. Phylogenetic relationships among the 23 species in this clade have been the subject of much morphological and molecular investigation, including a recent integration of penis morphology (in Sminthopsis) with molecular systematics. Several phylogenetic issues remain open, however, including the monophyly of Sminthopsis and branching order among early sminthopsin lineages. In this study, we revisit sminthopsin systematics with an expanded molecular data set, including new DNA sequences from mitochondrial (valine transfer-RNA and 16S ribosomal RNA) and nuclear (interphotoreceptor retinoid binding protein and beta-fibrinogen) loci, along with previously published sequences of cytochrome b, 12S ribosomal RNA, control region, and protamine P1. Our results again fail to establish the monophyly of Sminthopsis, but do provide a clearer resolution of early sminthopsin branching. Specifically, our phylogeny suggests three major groups of Sminthopsis species: S. longicaudata (perhaps the sister of Antechinomys); the Macroura species group of previous authors (S. crassicaudata, S. macroura, S. virginiae, S. douglasi, and S. bindi); and the remaining 13 species allied with the Murina species group. Our results depart from previous molecular findings by reuniting S. ooldea with the Murina group, while resolving S. psammophila as sister to the hairy-footed dunnarts (S. hirtipes and S. youngsoni). We suggest that this conflict traces to anomalous phylogenetic signal in previously published cytochrome b sequences. Penis morphology maps reasonably well onto our phylogeny, requiring parallel origination of only one of the ten morphotypes described for Sminthopsis.     

The More We Search,the More We Find: Discovery of a New Lineage and a New Species Complex in the Genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.     

Species of Gonostomum and Paragonostomum (Ciliophora, Hypotrichida, Oxytrichidae) from the Valley of Flowers, India, with descriptions of Gonostomum singhii sp nov, Paragonostomum ghangriai sp nov and Paragonostomum minuta sp nov

Soil samples taken from the Valley of Flowers, a component of the Nanda Devi Biosphere Reserve in the Himalayan regions of India showed the presence of twenty two free living species of ciliates. There is a preponderance of species which exhibit oral ciliature and ontogenesis in the Gonostomum pattern. Of the four species of the genus Gonostomum, three viz., G affine, G gonostomoida and G kuehnelti are similar to described species; Gonostomum singhii is new. The two species of genus Paragonostomum viz., P minuta and P ghangriai are new. The three new species are described in the present paper. All these species show prominent hypertrophied ciliary structures. Their paroral membranes reveal characteristic differences with respect to their position, number of constituent cilia and the distance between adjacent cilia. It is proposed that such species specific features of the paroral membrane have a bearing in exercising different food organism preferences as they co-exist at many sites. This single factor has possibly played an important role in species diversification of this group of hypotrichs in this isolated habitat.     

Molecular phylogenetic evaluation of Antrodiella and morphologically allied genera in China

Three new wood-decaying polypores from China, Antrodiella lactea, A. nanospora and Frantisekia abieticola, are described and illustrated using morphological characteristics and rDNA internal transcribed spacer (ITS) and large subunit (LSU) sequences. Phylogenetic analyses of the generated sequences, along with those retrieved from GenBank, confirmed the polyphyly of the genus Antrodiella. The Antrodiella s.s. clade includes A. citrinella, A. faginea, A. hoehnelii, A. ichnusana, A. lactea, A. micra, A. nanospora, A. onychoides, A. pallasii, A. pallescens, A. parasitica, A. romellii, A. semisupina and A. stipitata. Antrodiella albocinnamomea and A. zonata grouped with Cerrena unicolour in the Cerrena clade, and they are transferred to Cerrena, as C. albocinnamomea and C. zonata were proposed. The main morphological characters of the genus Antrodiella s.s., and discriminating characters of the new species and the closely related species are discussed.