French Polynesian Scytosiphonaceae (Ectocarpales,Phaeophyceae): A combined molecular and morphological approach to their diversity and systematics

This study revisited the taxonomy and diversity of brown macroalgae within the Scytosiphonaceae family in French Polynesia, which had previously been recognized as encompassing only six species. Using the chloroplast and mitochondrial genes rbcL, psbA, and cox3 as molecular markers in conjunction with morpho-anatomical observations, we unveiled the presence of 11 species spanning six genera: Chnoospora minima, Colpomenia claytoniae, Co. sinuosa [groups IIIa and IIIb], Hydroclathrus rapanuii, H. tenuis, H. tilesii, Manzaea minuta, Pseudochnoospora implexa, Rosenvingea australis, and the newly described species R. polynesiensis sp. nov. and R. tahitiensis sp. nov. This encompasses the recognition of two previously unreported genera in this region: Manzaea and Pseudochnoospora. Sequences were successfully acquired for four taxa that had been documented previously, while the absence of sequences for H. clathratus and H. tumulis in French Polynesia raises queries about their presence in this region. With these additions, the total species count now stands at 13 (including H. clathratus and H. tumulis), one being an endemic species. The molecular-assisted alpha taxonomic approach used here allowed for a critical revision of the Scytosiphonaceae species checklist for French Polynesia. The diversity revealed in this region accounts for a substantial 20% of the family's global diversity. Additionally, our study presents an updated species-level phylogeny for the Scytosiphonaceae.     

Antiviral polysaccharides isolated from Hong Kong brown seaweed <Emphasis Type="Italic">Hydroclathrus clathratus</Emphasis>

Two relatively pure polysaccharides H3-a1 and H3-b1 had been isolated from the brown seaweed Hydroclathrus clathratus. They were characterized by HPLC, ultraviolet scanning, gas chromatography, infrared spectroscopy and elemental analysis, and shown to be two different sulfated polysaccharides with different monosaccharide content, but both with high relative molecular mass. They contained some proteins and uronic acid respectively. The sulfate content and bioactivity of these polysaccharides varied during purification. The fractions derived from the hot water extract also exhibited low anticoagulant effect. This is the first time that the antiherpetic and anticoagulant activities were evaluated for the polysaccharides from the Hong Kong brown seaweed Hydroclathrus clathratus.     

Life histories of Colpomenia sinuosa and Hydroclathrus clathratus (Scytosiphonaceae, Phaeophyceae) in culture

Life-history studies in culture were carried out on Colpomenia sinuosa (Mertens ex Roth) Derbès et Solier and Hydroclathrus clathratus (C. Agardh) Howe (Scytosiphonales, Phaeophyceae) from Japan. These species showed a heteromorphic life-history pattern with an alternation between erect thalli bearing plurilocular zoidangia and prostrate thalli bearing ectocarpoid plurilocular and unilocular zoidangia. Plurizoids released from erect and prostrate thalli developed into prostrate thalli. Unizoids, however, developed into erect thalli. Prostrate thalli produced plurilocular zoidangia in long-day conditions and unilocular zoidangia in short-day conditions at 10-20°C. Prostrate thalli of C. sinuosa formed ascocysts. Germlings of both species did not grow at 5°C.     

Natural feeding habits of two nudibranchs: Kalinga ornata and Plocamopherus tilesii (Nudibranchia: Doridacea: Polyceridae)

Stomach contents of Kalinga ornata and Plocamopherus tilesii (Nudibranchia: Doridacea: Polyceridae) were investigated using a light microscope to reveal their natural diets. Ossicles of ophiuroids were found in the stomachs of four out of 29 specimens of K. ornata. In contrast, both zooecia of Bryozoa and ossicles of ophiuroids were found in the stomachs of P. tilesii specimens. This is only the second record of a nudibranch species feeding on ophiuroids.     

Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis

Ciona intestinalis is considered a widespread and easily recognizable tunicate, the sister group of vertebrates. In recent years, molecular studies suggested that C. intestinalis includes at least two cryptic species, named ‘type A’ and ‘type B’, morphologically indistinguishable. It is dramatic to certify that two different species may be hidden under the name of a species widely used as a model species in biological researches. This raised the problem of identifying diagnostic morphological characters capable of distinguishing these types. We compared the morphology of specimens belonging to the two types and found that only type A specimens possess tunic tubercular prominences, allowing unambiguous discrimination. Remarkably, these structures were already described as distinctive of the Japanese species Ciona robusta, Hoshino and Tokioka, 1967; later synonymized under C. intestinalis (sensu Millar, 1953). In this study, we have confirmed that C. intestinalis type A corresponds to C. robusta. Based on the geographic distribution of C. intestinalis type B, and considering that the original C. intestinalis species was described from North European waters, we determined that C. intestinalis type B corresponds to C. intestinalis as described by Millar in 1953 and possibly to Linnaeus' Ascidia intestinalis L., 1767 for which we have deposited a neotype (from Roscoff, France) and for which we retain the name Ciona intestinalis (Linnaeus, 1767).     

Isolation and Molecular Characterization of Entamoeba nuttalli Strains Showing Novel Isoenzyme Patterns from Wild Toque Macaques in Sri Lanka

We have proposed the revival of the name Entamoeba nuttalli for a virulent ameba strain, P19‐061405, from a rhesus macaque and located it phylogenetically between E. histolytica and E. dispar. As E. nuttalli was originally described for an ameba found in a toque macaque in Sri Lanka, the prevalence and characteristics of Entamoeba species in wild toque macaques were examined. PCR analysis of 227 stool samples from six locations showed positive rates for E. nuttalli, E. dispar, and E. histolytica of 18.5%, 0.4%, and 0%, respectively. Fifteen E. nuttalli strains were cultured successfully from five locations. The 18S ribosomal RNA gene showed only three nucleotide differences in comparison with P19‐061405 strain. In isoenzyme analysis, the pattern of hexokinase in Sri Lankan strains was different from that of P19‐061405 strains and the difference was confirmed by analysis of the genes. Hepatic inoculation of one of the Sri Lankan E. nuttalli strains in hamsters resulted in amebic abscess formation and body weight loss. These results demonstrate that E. nuttalli is prevalent in wild toque macaques and that several characteristics of the strains are unique. We conclude that use of the name E. nuttalli is appropriate for the new Entamoeba species found in nonhuman primates.     

Taxonomic Characterization and Experimental Host Ranges of Four Newly Recorded Species of Alternaria from Japan

Alternaria fungi are important plant pathogens. Here, we identified three species new to the Japanese mycoflora: Alternaria celosiae, Alternaria crassa and Alternaria petroselini. We proposed a new name for A. celosiae (E.G. Simmons & Holcomb) Lawrence, Park & Pryor, a later homonym of A. celosiae (Tassi) O. S?vul. To characterize these and a fourth morphological taxon, Alternaria alstroemeriae, which was recently added to Japan's mycoflora, an integrated species concept was tested. We determined the host range of each isolate using inoculation tests and analysed its phylogenetic position using sequences of the internal transcribed spacer rDNA. The pathogenicity of our A. alstroemeriae isolate was strictly limited to Alstroemeria sp. (Alstroemeriaceae), but the species was phylogenetically indistinguishable from other small‐spored Alternaria. Alternaria celosiae on Celosia argentea var. plumosa (Amaranthaceae) was also pathogenic to Amaranthus tricolor, to Alternanthera paronychioides and weakly to Gomphrena globosa (all Amaranthaceae) and formed a clade with the former Nimbya celosiae. Alternaria crassa on Datura stramonium (Solanaceae) was also pathogenic to Brugmansia × candida and Capsicum annuum in Solanaceae, but not to other confamilial plants; phylogenetically it belonged to a clade of large‐spored species with filamentous beaks. Morphological similarity, phylogenetic relationship and experimental host range suggested that A. crassa, Alternaria capsici and Alternaria daturicola were conspecific. Alternaria petroselini on Petroselinum crispum (Apiaceae) was pathogenic to five species in the tribe Apieae as well as representatives of Bupleureae, Coriandreae, Seliaeae and Scandiceae in Apiaceae. Both phylogeny and morphology suggested conspecificity between A. petroselini and Alternaria selini.     

Cyanomargarita gen. nov. (Nostocales,Cyanobacteria): convergent evolution resulting in a cryptic genus

Two populations of Rivularia‐like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase‐Escalante National Monument, a desert park‐land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae.     

The ‘Oxycythereis’ problem: taxonomy and palaeobiogeography of deep‐sea ostracod genera Pennyella and Rugocythereis

Systematic revision of the globally distributed deep‐sea ostracod genera Pennyella Neale, 1974 and Rugocythereis Dingle, Lord and Boomer, 1990, which have been considered to correspond, at least partially, to nomen nudum but widely used genus name ‘Oxycythereis,’ was conducted to reduce taxonomic uncertainty of these important components of the Modern and fossil deep‐sea ostracod community. Approximately 100 specimens from 18 species were examined, ranging in age from the Cretaceous to the present day. Nine new species are described: Pennyella rexi, Pennyella sanfordae, Pennyella liowae, Pennyella schellenbergi, Pennyella majorani, Pennyella iani, Pennyella ayressi, Rugocythereis melonis and Rugocythereis zarikiani. Emended generic concepts of Pennyella and Rugocythereis are proposed, and the palaeobiogeographical distributions of these two genera are discussed.     

Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians

Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free‐living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free‐living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine‐symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free‐living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA‐based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.     

Identification and Molecular Characterization of a New Geminivirus Betasatellite Infecting Malvastrum coromandelianum in China

The complete nucleotide sequence of a satellite molecule associated with Malvastrum leaf curl Guangdong virus (MLCuGdV) infecting M. coromandelianum plants exhibiting leaf curl symptoms in a suburb of Guangzhou, Guangdong Province of China, is described and analysed. The molecule has typical features of betasatellites, containing a single ORF in the complementary‐sense strand, an A‐rich region, the satellite‐conserved region and a stem–loop structure. Compared with the geminivirus betasatellites in GenBank database, this molecule shows the highest nucleotide sequence identity of 71.9% with Tomato leaf curl Philippine betasatellite isolate Laguna1 (ToLCPB, AB307732). Phylogenetic analysis indicates that it is more related to isolate Laguna 1 and Laguna 2 of ToLCPB. According to the proposed species demarcation threshold of betasatellites (78% nucleotide identity), it is a novel betasatellite species, for which we propose the name Malvastrum leaf curl Guangdong betasatellite (MLCuGdB).     

Identification of a distinct strain of Cotton leaf curl Gezira virus infecting tomato in Oman

Tomato (Solanum lycopersicum) plants exhibiting yellowing, curling and stunting symptoms were identified in fields of the Tawoos Agricultural Systems, in Al‐Batinah in Oman. Cloning and sequencing of restriction endonuclease digested rolling circle amplified viral DNA identified a cotton begomovirus (family Geminiviridae) associated with the symptomatic tomato plants. Detailed analysis of complete sequences showed the virus to be a previously unknown strain of Cotton leaf curl Gezira virus (CLCuGeV) in association with the betasatellite Tomato leaf curl betasatellite (ToLCB). The new CLCuGeV strain, for which the name “Al Batinah” strain is suggested, has the greatest levels of sequence identity (91.9%) to an isolate of CLCuGeV recently reported from the neighbouring United Arab Emirates. Additionally, CLCuGeV‐Al Batinah was shown to have a recombinant origin with sequences donated by an African cassava mosaic virus‐like parent. This is the first identification of this Malvaceae‐adapted begomovirus in tomato. Although ToLCB is common in Oman, being one of only two betasatellites identified there so far, this is the first identification of this betasatellite with CLCuGeV. The significance of these findings is discussed.     

Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Comparative phylogeographies of six species of hinged terrapins (Pelusios spp.) reveal discordant patterns and unexpected differentiation in the P. castaneus/P. chapini complex and P. rhodesianus

Using up to 2117 bp of mitochondrial DNA and up to 2012 bp of nuclear DNA, we analysed phylogeographic differentiation of six widely distributed species of African hinged terrapins (Pelusios spp.) representing different habitat types. Two taxa each live in savannahs or in forests and mesic savannahs, respectively, and the remaining two species occur in intermediate habitats. The species living in forests and mesic savannahs do not enter dry savannahs, whereas the savannah species may occur in dry and wet savannahs and even in semi‐arid steppe regions. We found no obvious correlation between habitat type and phylogeographic pattern: one savannah species (P. rhodesianus) shows phylogeographic structure, i.e. pronounced genetic differences among geographically distinct populations, and the other (P. nanus) not. One species inhabiting forests and mesic savannahs (P. carinatus) has phylogeographic structure, the other (P. gabonensis) not. The same pattern is true for the two ecologically intermediate species, with phylogeographic structure present in P. castaneus and absent in P. chapini. Nuclear evidence suggests that the latter two taxa with abutting and partially overlapping ranges are distinct, while mtDNA is only weakly differentiated. Pelusios castaneus shows pronounced phylogeographic structure, which could reflect Pleistocene range interruptions correlated with the fluctuating forest cover in West and Central Africa. Our results do not support the recognition of an extinct subspecies of P. castaneus for the Seychelles. Pelusios carinatus contains two well supported clades, which are separated by the Congo River. This species is closely related to P. rhodesianus, a taxon consisting of two deeply divergent mitochondrial clades. One of these clades is paraphyletic with respect to P. carinatus, but the two clades of P. rhodesianus are not differentiated in the studied nuclear markers and, again, paraphyletic with respect to P. carinatus. Using mtDNA sequences from the type material of P. rhodesianus, we were able to allocate this name to one of the two clades. However, owing to the confusing relationships of P. rhodesianus and P. carinatus, we refrain from taxonomic decisions.     

Welcome back Janolidae and Antiopella: Improving the understanding of Janolidae and Madrellidae (Cladobranchia,Heterobranchia) with description of four new species

Proctonotidae and Madrellidae are families that belong to the suborder Cladobranchia. Historically, both have been the subjects of taxonomic confusion. Thus, Proctonotidae Gray, 1853, was subsequently named as Zephyrinidae Iredale and O'Donoghue, 1923 and Janolidae Pruvot‐Fol, 1933, but currently both are considered as synonyms of Proctonotidae. On the other hand, Alder and Hancock (1864) erected the genus Madrella in Proctonotidae. Here, we completed a detailed morphological and molecular study of four apparently undescribed species of Madrellidae and Proctonotidae from the Indo‐Pacific. We performed a maximum likelihood and Bayesian inference phylogenetic analyses using two mitochondrial and one nuclear genes to improve the understanding of the families. Prompted by our results, Janolidae is removed from synonymy with Proctonotidae. Within Janolidae, there are two well‐supported clades. One includes species with smooth cerata that are found in the Atlantic and eastern Pacific Oceans. The taxa in this clade include the type species of Antiopella and several other species. We resurrect Antiopella as the valid name for this clade. The sister clade to Antiopella includes a variety of taxa with species that have been traditionally included in Janolus Bergh, 1884 and Bonisa Gosliner, 1981. Further systematic revision requires more comprehensive taxon sampling. The new species discovered have clear morphological differences and strong molecular support. They include Madrella amphora Pola and Gosliner sp. nov. , Janolus tricellariodes Pola and Gosliner sp. nov. , Janolus flavoanulatus Pola and Gosliner sp. nov., and Janolus incrustans Pola and Gosliner sp. nov.     

Two closely related species of Nipponaphis (Hemiptera: Aphididae) that migrate between Distylium racemosum and Machilus trees in Japan

Nipponaphis loochooensis Sorin, 1996 and N. machilicola (Shinji, 1941) form fig‐shaped or globular galls on Distylium racemosum in southern Japan. Nipponaphis machilicola migrates to the lauraceous evergreen Machilus thunbergii. Nipponaphis loochooensis has also been supposed to migrate to M. thunbergii, but its secondary‐host generation has not been found in the field to date. Through sampling Nipponaphis aphids from trees of M. japonica in addition to M. thunbergii, and sequencing their mitochondrial DNA, we found that the two species form colonies on twigs of both Machilus species, and that the two at times colonize on the same trees and even form mixed colonies. Only N. loochooensis forms colonies on leaves of M. japonica, but neither species colonizes on leaves of M. thunbergii. The secondary‐host generations of the two species could be clearly discriminated from each other, based on morphology. It was confirmed by examining the type specimens of Nipponaphis amamiana Takahashi, 1962 that the name is a junior synonym of N. machilicola.     

AUXIN RESPONSE FACTOR 3 integrates the functions of AGAMOUS and APETALA2 in floral meristem determinacy

In Arabidopsis, AUXIN RESPONSE FACTOR 3 (ARF3) belongs to the auxin response factor (ARF) family that regulates the expression of auxin‐responsive genes. ARF3 is known to function in leaf polarity specification and gynoecium patterning. In this study, we discovered a previously unknown role for ARF3 in floral meristem (FM) determinacy through the isolation and characterization of a mutant of ARF3 that enhanced the FM determinacy defects of agamous (ag)‐10, a weak ag allele. Central players in FM determinacy include WUSCHEL (WUS), a gene critical for FM maintenance, and AG and APETALA2 (AP2), which regulate FM determinacy by repression and promotion of WUS expression, respectively. We showed that ARF3 confers FM determinacy through repression of WUS expression, and associates with the WUS locus in part in an AG‐dependent manner. We demonstrated that ARF3 is a direct target of AP2 and partially mediates AP2's function in FM determinacy. ARF3 exhibits dynamic and complex expression patterns in floral organ primordia; altering the patterns spatially compromised FM determinacy. This study uncovered a role for ARF3 in FM determinacy and revealed relationships among genes in the genetic network governing FM determinacy.