Flagellar apparatus structure of choanocyte in Sycon sp. and its significance for phylogeny of Porifera

The problem of the origin of Metazoa has been one of the most discussed for nearly the last one and a half centuries. Some 20 years ago, morphological approaches were replaced with molecules, but the problem then became more complex. At the same time, morphological data were incomplete, and therefore, this approach can still help in comparison with choanoflagellates and sponges—two sister groups having uniflagellated cells with a collar. The structure of the flagellar apparatus has phylogenetic significance, but sponge choanocytes are poorly studied in this respect, and we still do not know what the ancestral kinetid of Porifera looks like. The kinetid structure of choanocytes in Sycon sp. is investigated here for the first time, and a 3D reconstruction of the kinetid provided. It is composed of a flagellar kinetosome with a nuclear fibrillar root and a basal foot with a few microtubules; the accessory centriole lies orthogonal to and just below the foot of the kinetosome, and a dictyosome is near the centriole. This kinetid is similar to that of the choanocyte of Corticium candelabrum (Homoscleromorpha) and is considered to be the ancestral type for the whole branch Calcarea + Homoscleromorpha.     

Kinetid structure in Choanocytes of Sponges (Heteroscleromorpha): Toward the ancestral Kinetid of Demospongiae

Every large clade of Eukarya has its own pattern of kinetid (flagellar apparatus) structure, which is stable and specific within the group, thereby being a good phylogenetic marker. The kinetid structure of sponge choanocytes might be a candidate for such marker for the phylogeny of Porifera. Kinetids of two heteroscleromorphs, Halichondria sp. (Suberitida) and Crellomima imparidens (Poecilosclerida), have been investigated here for the first time, and a reconstruction of the kinetid for each species is provided. The kinetids of both species comprise a flagellar kinetosome with a nuclear fibrillar root, a basal foot and satellite producing microtubules; a centriole is absent. Good resolution images reveal a new thin structure, the axial granule, in the flagellar transition zone which might be present in other sponges. The comparison of kinetids in investigated sponges revealed three types of kinetid in Demospongiae, and their distribution in the taxon has been shown on a molecular phylogenetic tree. Kinetid characters of the common ancestor of Demospongiae are discussed. J. Morphol. 277:925–934, 2016. © 2016 Wiley Periodicals, Inc.     

Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges

Sponges are an important source of secondary metabolites showing a great diversity of structures and biological activities. Secondary metabolites can display specificity on different taxonomic levels, from species to phylum, which can make them good taxonomic biomarkers. However, the knowledge available on the metabolome of non-model organisms is often poor. In this study, we demonstrate that sponge chemical diversity may be useful for fundamental issues in systematics or evolutionary biology, by using metabolic fingerprints as indicators of metabolomic diversity in order to assess interspecific relationships. The sponge clade Homoscleromorpha is particularly challenging because its chemistry has been little studied and its phylogeny is still debated. Identification at species level is often troublesome, especially for the highly diversified Oscarella genus which lacks the fundamental characters of sponge taxonomy. An HPLC–DAD–ELSD–MS metabolic fingerprinting approach was developed and applied to 10 Mediterranean Homoscleromorpha species as a rapid assessment of their chemical diversity. A first validation of our approach was to measure intraspecific variability, which was found significantly lower than interspecific variability obtained between two Oscarella sister-species. Interspecific relationships among Homoscleromorpha species were then inferred from the alignment of their metabolic fingerprints. The resulting classification is congruent with phylogenetic trees obtained for a DNA marker (mitochondrial COI) and demonstrates the existence of two distinct groups within Homoscleromorpha. Metabolic fingerprinting proves a useful complementary tool in sponge systematics. Our case study calls for a revision of Homoscleromorpha with further phylogenetic studies and identification of additional chemical synapomorphic characters.     

Phylogenetic and morphometric analyses reveal ecophenotypic plasticity in freshwater mussels Obovaria jacksoniana and Villosa arkansasensis (Bivalvia: Unionidae)

Freshwater mollusk shell morphology exhibits clinal variation along a stream continuum that has been termed the Law of Stream Distribution. We analyzed phylogenetic relationships and morphological similarity of two freshwater mussels (Bivalvia: Unionidae), Obovaria jacksoniana and Villosa arkansasensis, throughout their ranges. The objectives were to investigate phylogenetic structure and evolutionary divergence of O. jacksoniana and V. arkansasensis and morphological similarity between the two species. Our analyses were the first explicit tests of phenotypic plasticity in shell morphologies using a combination of genetics and morphometrics. We conducted phylogenetic analyses of mitochondrial DNA (1416 bp; two genes) and morphometric analyses for 135 individuals of O. jacksoniana and V. arkansasensis from 12 streams. We examined correlations among genetic, morphological, and spatial distances using Mantel tests. Molecular phylogenetic analyses revealed a monophyletic relationship between O. jacksoniana and V. arkansasensis. Within this O. jacksoniana/V. arkansasensis complex, five distinct clades corresponding to drainage patterns showed high genetic divergence. Morphometric analysis revealed relative differences in shell morphologies between the two currently recognized species. We conclude that morphological differences between the two species are caused by ecophenotypic plasticity. A series of Mantel tests showed regional and local genetic isolation by distance. We observed clear positive correlations between morphological and geographic distances within a single drainage. We did not observe correlations between genetic and morphological distances. Phylogenetic analyses suggest O. jacksoniana and V. arkansasensis are synonomous and most closely related to a clade composed of O. retusa, O. subrotunda, and O. unicolor. Therefore, the synonomous O. jacksoniana and V. arkansasensis should be recognized as Obovaria arkansasensis (Lea 1862) n. comb. Phylogenetic analyses also showed relative genetic isolation among drainages, suggesting no current gene flow. Further investigation of in‐progress speciation and/or cryptic species within O. arkansasensis is warranted followed by appropriate revision of conservation management designations.     

Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: The case of genus Guibourtia Benn.

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The Kinetid Structures of the Choreotrichous Ciliate Strobilidium velox and an Assessment of Its Evolutionary Lineage1

The ciliary (kinetid) structures of the ciliate Strobilidium velox have been examined with scanning and transmission electron microscopes. Somatic kineties consist of a linear row of kinetosomes (monokinetids) and short cilia lying partially beneath a thin fold of cytoplasm. The only fibrillar kinetid structure extending from the kinetosomes is a transverse ribbon of microtubules. The paroral membrane is a single-file polykinetid possessing a possible transverse ribbon of microtubules and a nematodesma. The oral polykinetids or membranelles are complex, with microtubules extending from both anterior and posterior rows of cilia. While the kinetid structures do not satisfy the criteria for the order Choreotrichida, they are similar to the tintinnids in several other relevant ways. Strobilidium velox is proposed to be an unusual ciliate that is an exception to the concept that somatic kinetids are conservative and reliable phylogenetic indicator structures.     

A Somatic Kinetid Study of the Pycnotrichid Ciliate Vestibulongum corlissi N. G., N. Sp. (Class: Litostomatea), Symbiont in the Intestines of the Surgeonfish,Acanthurus xanthopterus1

ABSTRACT The ciliate Vestibulongum corlissi n. g., n. sp. was collected from the intestines of surgeonfish, Acanthurus xanthopterus, in the summer of 1986. In has been examined in the light microscope after protargol staining and by scanning and transmission electron microscopy. Its form is distinct from that of other pycnotrichid ciliates at the generic level. Somatic kinetids were examined; these demonstrate that its cytostome is posterior and that the kinetid structures and the presence of a second transverse microtubular ribbon confirm its placement in the class Litostomatea.     

The Ultrastructure of Sanchytrium tribonematis (Sanchytriaceae,Fungi incertae sedis) Confirms its Close Relationship to Amoeboradix

Fungi encompass, in addition to classically well‐studied lineages, an ever‐expanding diversity of poorly known lineages that include, among others, zoosporic chytrid‐like parasites. According to recent phylogenetic analysis based on 18S + 28S rRNA concatenated genes two unusual chytrid‐like fungi Amoeboradix gromovi and Sanchytrium tribonematis form a monophyletic group, the family Sanchytriaceae, which represents a new divergent taxon that remains incertae sedis within Fungi. Zoospores of Amoeboradix gromovi contain one of the longest kinetosomes known in eukaryotic cells, which are composed of microtubular singlets or doublets. However, the ultrastructure of S. tribonematis, the type species of the genus had not been yet studied. Here, we provide the results of TEM investigations of zoospores and sporangia from two strains of S. tribonematis. The two strains are endowed with unusual features. Like in A. gromovi, amoeboid zoospores of S. tribonematis contain a long kinetosome composed of microtubular singlets, and the two orthogonal centrioles in their sporangia have nine microtubular singlets with an internal ring. The morphological and ultrastructural features of S. tribonematis are now included in the improved taxonomic diagnosis for this species.     

Structure of the choanocyte kinetid in the sponge <Emphasis Type="Italic">Haliclona</Emphasis> sp. (Demospongiae: Haplosclerida) and its implication for taxonomy and phylogeny of Demospongiae

Sponges are a group of primitive animals that are of particular interest in terms of evolutionary theory. Molecular and phylogenic studies have revealed the common origin of sponges and Metazoa and the relationship of Metazoa to Choanoflagellata. Comparative studies of the morphology have allowed reconstruction of the structure of ancestors common to Metazoa and Choanoflagellata, as well as for Porifera and other Metazoa. For this purpose, a comparative analysis of phylogenically informative structures, such as the kinetid, is needed. This article presents data on the structure of the choanocyte kinetid in Haliclona sp., which was investigated for the first time. The reconstruction of the kinetid based on ultrathin serial sections shows that it lacks an accessory centriole; it has fibrillar roots despite the basal position of the nucleus; two-to-three triplets of the kinetosome are longer than the others; bundles of lateral microtubules arise from fibrillar roots and reach the cytoplasmic membrane in the region of intercellular contact. The studies of the kinetid in the few representatives of Demospongiae investigated showed the compatibility of the data on the ultrastructure and molecular phylogeny.     

THE ORGANIZATION AND EVOLUTION OF MICROTUBULAR ORGANELLES IN CILIATED PROTOZOA

(1) Ciliated protozoa are viewed as unicellular organisms structured in a hierarchy of organizational levels that include the macromolecular, suborganellar, unit organellar, organellar complex, and organellar system. (2) The ciliate cortex is divided into two major functional regions, the somatic region and the oral region. The fundamental component of the cortex is an organellar complex, the kinetid, whose organizing centre is the kinetosome with which are associated three fibrillar associates diagnostic of ciliates. These three fibrillar associates are the periodically striated kinetodesmal fibril and two microtubular ribbons, the transverse and postciliary ribbons. (3) Somatic and oral kinetids are found to be of three major types: monokinetids are composed of one kinetosome and its fibrillar associates; dikinetids are composed of two kinetosomes and their fibrillar associates; polykinetids are composed of more than two kinetosomes and their fibrillar associptes. (4) The mechanisms underlying kinetid function and development remain largely unexplored. Research into the molecular biology and ultrastructure, especially of mutant forms, should provide basic insights in the near future. (5) The conservation of kinetid structure across major phyla of organisms suggests that this subcellular structure should be useful in phylogenetic analysis despite the concepts of ‘chemical identity’ and ‘organic design’. (6) The evolutionary rate of change of oral features is greater than that of somatic features, probably due to developmental and ecological factors. Nevertheless both cortical regions are constrained by the phenomenon of structural conservatism; that is, the conservation of structure through time is inversely related to the level of biological organization. (7) Eight major groupings of ciliate species are recognized, based on ultrastruc-tural features of the cortex. Several examples of differences between these eight groups and the groups presently recognized are discussed.     

Oscarella lobularis (Homoscleromorpha,Porifera) Regeneration: Epithelial Morphogenesis and Metaplasia

Sponges are known to possess remarkable reconstitutive and regenerative abilities ranging from common wounding or body part regeneration to more impressive re-building of a functional body from dissociated cells. Among the four sponge classes, Homoscleromorpha is notably the only sponge group to possess morphologically distinct basement membrane and specialized cell-junctions, and is therefore considered to possess true epithelia. The consequence of this peculiar organization is the predominance of epithelial morphogenesis during ontogenesis of these sponges. In this work we reveal the underlying cellular mechanisms used during morphogenesis accompanying ectosome regeneration in the homoscleromorph sponge model: Oscarella lobularis. We identified three main sources of novel exopinacoderm during the processes of its regeneration and the restoration of functional peripheral parts of the aquiferous system in O. lobularis: (1) intact exopinacoderm surrounding the wound surface, (2) the endopinacoderm from peripheral exhalant and inhalant canals, and (3) the intact choanoderm found on the wound surface. The basic morphogenetic processes during regeneration are the spreading and fusion of epithelial sheets that merge into one continuous epithelium. Transdifferentiation of choanocytes into exopinacocytes is also present. Epithelial-mesenchymal transition is absent during regeneration. Moreover, we cannot reveal any other morphologically distinct pluripotent cells. In Oscarella, neither blastema formation nor local dedifferentiation and proliferation have been detected, which is probably due to the high morphogenetic plasticity of the tissue. Regeneration in O. lobularis goes through cell transdifferentiation and through the processes, when lost body parts are replaced by the remodeling of the remaining tissue. Morphogenesis during ectosome regeneration in O. lobularis is correlated with its true epithelial organization. Knowledge of the morphological basis of morphogenesis during Oscarella regeneration could have important implications for our understanding of the diversity and evolution of regeneration mechanisms in metazoans, and is a strong basis for future investigations with molecular-biological approaches.     

Somatic Infraciliature in the Haptorid Ciliate Homalozoon vermiculare (Kinetophragminophora, Gymnostomata) Ditransversalia N. Subcl. and Phylogenetic Implications

The ultrastructure of the cortex of Homalozoon vermiculare is described. The ventral side bears 13–15 iongitudinal kineties composed of monokinetids. On the dorsal surface, there are 3 kineties, 2 of which are composed of dikinetids in the anteriormost part of the cell. Consequently there exist 3 different kinds of kinetids within the somatic cortex: 1) The monokinetids on the ventral side are associated with a kinctodesmal fibril, 2 transverse microtubular ribbons and 7 postciliary microtubules in a double-row configuration; 2) The monokinetids on the dorsal side are very similar but they are associated with just 3 very 'short postciliary microtubules; 3) The posterior kinetosome of the dorsal dikinetids bears the same fibrillar associates as the dorsal monokinetid, but it lacks the second transverse ribbon. The anterior kinetosome of each pair is associated with a single postciliary' microtubule. The kinetid organization of Homalozoon is compared to that of other members of the Haptorida. Their phylogeny is discussed. A monophyleiic taxon within the litostomate ciliates is characterized by data on the somatic kinetids, and the new subclass Ditransversalia n. subcl. is constituted. The new subclass comprises the genera Balantidium, Bryophyllum, Enchelydium, Homalozoon, Isotricha, Lacrymaria, Lepidolrachelophyllum, Spathidium and Vestibulongum .     

Five chemically rich species of tropical marine cyanobacteria of the genus Okeania gen. nov. (Oscillatoriales,Cyanoprokaryota)

An adverse consequence of applying morphology‐based taxonomic systems to catalog cyanobacteria, which generally are limited in the number of available morphological characters, is a fundamental underestimation of natural biodiversity. In this study, we further dissect the polyphyletic cyanobacterial genus Lyngbya and delineate the new genus Okeania gen. nov. Okeania is a tropical and subtropical, globally distributed marine group abundant in the shallow‐water benthos. Members of Okeania are of considerable ecological and biomedical importance because specimens within this group biosynthesize biologically active secondary metabolites and are known to form blooms in coastal benthic environments. Herein, we describe five species of the genus Okeania: O. hirsuta (type species of the genus), O. plumata, O. lorea, O. erythroflocculosa, and O. comitata, under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants. All five Okeania species were morphologically, phylogenetically, and chemically distinct. This investigation provides a classification system that is able to identify Okeania spp. and predict their production of bioactive secondary metabolites.     

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.     

Molecular phylogeny,analysis of character evolution,and submersible collections enable a new classification of a diverse group of gobies (Teleostei: Gobiidae: Nes subgroup), including nine new species and four new genera

The Nes subgroup of the Gobiosomatini (Teleostei: Gobiiformes: Gobiidae) is an ecologically diverse clade of fishes endemic to the tropical western Atlantic and eastern Pacific oceans. It has been suggested that morphological characters in gobies tend to evolve via reduction and loss associated with miniaturization, and this, coupled with the parallel evolution of adaptations to similar microhabitats, may lead to homoplasy and ultimately obscure our ability to discern phylogenetic relationships using morphological characters alone. This may be particularly true for the Nes subgroup of gobies, where several genera that are diagnosed by ‘reductive characters’ have been shown to be polyphyletic. Here we present the most comprehensive phylogeny to date of the Nes subgroup using mitochondrial and nuclear sequence data. We then evaluate the congruence between the distribution of morphological characters and our molecular tree using maximum‐likelihood ancestral state reconstruction, and test for phylogenetic signal in characters using Pagel's λ tree transformations (Nature, 401 , 1999 and 877). Our results indicate that all of the characters previously used to diagnose genera of the Nes subgroup display some degree of homoplasy with respect to our molecular tree; however, many characters display considerable phylogenetic signal and thus may be useful in diagnosing genera when used in combination with other characters. We present a new classification for the group in which all genera are monophyletic and in most cases diagnosed by combinations of morphological characters. The new classification includes four new genera and nine new species described here, many of which were collected from rarely sampled deep Caribbean reefs using manned submersibles. The group now contains 38 species in the genera Carrigobius gen. nov., Chriolepis, Eleotrica, Gobulus, Gymneleotris, Nes, Paedovaricus gen. nov., Pinnichthys gen. nov., Psilotris, and Varicus. Lastly, we provide a key to all named species of the Nes subgroup along with photographs and illustrations to aid in identification.     

Systematics of spiny‐backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Spiny‐backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly of Osteocephalus with respect to Tepuihyla, (ii) the placement of ‘Hyla’ warreni as sister to Tepuihyla, (iii) the non‐monophyly of several currently recognized species within Osteocephalus and (iv) the presence of low (<1%) and overlapping genetic distances among phenotypically well‐characterized nominal species (e.g. O. taurinus and O. oophagus) for the 16S gene fragment used in amphibian DNA barcoding. We propose a new taxonomy, securing the monophyly of Osteocephalus and Tepuihyla by rearranging and redefining the content of both genera and also erect a new genus for the sister group of Osteocephalus. The colouration of newly metamorphosed individuals is proposed as a morphological synapomorphy for Osteocephalus. We recognize and define five monophyletic species groups within Osteocephalus, synonymize three species of Osteocephalus (O. germani, O. phasmatus and O. vilmae) and three species of Tepuihyla (T. celsae, T. galani and T. talbergae) and reallocate three species (Hyla helenae to Osteocephalus, O. exophthalmus to Tepuihyla and O. pearsoni to Dryaderces gen. n.). Furthermore, we flag nine putative new species (an increase to 138% of the current diversity). We conclude that species numbers are largely underestimated, with most hidden diversity centred on widespread and polymorphic nominal species. The evolutionary origin of breeding strategies within Osteocephalus is discussed in the light of this new phylogenetic hypothesis, and a novel type of amplexus (gular amplexus) is described.