Behaviour, Setal Inversion and Phylogeny of Sabellida (Polychaeta)

The path taken by the faecal groove, following two right angle bends, appears inefficient in Sabellidae. It fits well with the thoracic folds of serpulids and follows a gentle spiral in caobangiids, but only in spirorbids is it of obvious adaptive value, being suited to life in a coiled tube. The associated setal inversion is not necessary for locomotion, which does not depend wholly on setal leverage, except in the smaller Fabriciinae where long-shafted uncini also thrust actively against the elastic tube wall. The collar setae of spirorbids and some serpulids thrust anteriorly, giving some backward movement, but such motion is mainly by body contraction. Short uncini are virtually passive, engaged by opposing setae acting as distance pieces. Some broad bladed setae have a hollow structure around a central core. Pick-axe setae of Sabellinae may have developed to counteract the thrust of respiratory peristalsis. This is not seen in spirorbids and serpulids, the thoracic folds of which are a sufficient respiratory supplement to the tentacles. — Numbers of thoracic segments in Sabellidae range from 1 to 16, and the abdomen becomes vestigial in some Fabriciinae. Abdominal inversion is important to spirorbids but not to sabellids, which are more varied. It seems that the former are archaic and the latter had a coiled ancestry. Sabellariids also show abdominal inversion suggesting a distant relationship with Sabellida.     

On the unique isotropic aragonitic tube microstructure of some serpulids (Polychaeta,Annelida)

A Scanning electron microscopy study of peculiar serpulid tube microstructures was carried out to determine whether this structure is unique to serpulids and to understand its formation and evolution. The isotropic aragonitic tube microstructure of some serpulids, termed spherulitic irregularly oriented prismatic structure (SIOP), is unknown in other animal skeletons. After nucleation, initial spherulitic prismatic aragonite crystals presumably grow in length and width at one end, collide with the surrounding growing crystal fans, and then continue intertwined growth until the secreted carbonate‐charged mucus is completely crystallized. Spherulitic irregularly oriented prismati structure presumably evolved either from the IOP or homogeneous rounded crystal microstructures. J. Morphol., 2013. © 2012 Wiley Periodicals, Inc.     

ON THE TUBE ULTRASTRUCTURE AND ORIGIN OF CALCIFICATION IN SABELLIDS (ANNELIDA, POLYCHAETA)

Abstract:  Tube ultrastructure of Jurassic and Cretaceous Glomerula is very similar to that of Recent Calcisabella , supporting the synonymy of these genera and the early Mesozoic origin of calcification in sabellids. Tube structure of serpulids differs from that of Glomerula ; calcareous tubes probably evolved convergently within Sabellida. The tube wall in Recent Glomerula piloseta is composed of subparallel lamellae of aragonitic, irregular spherulitic prisms in the inner layer, and spherulites in the outer layer. Calcified lamellae are separated by organic films of different thickness. The structure of the internal tube layer in Glomerula piloseta , and the structure of entire wall in fossil Glomerula , are similar to the tube structure of Dodecaceria (Polychaeta, Cirratulidae). The irregular spherulitic prisms of Glomerula are similar to those found in the external layer of Hydroides dianthus and the internal layer of Spiraserpula caribensis .     

Serpula aggregates and their role in deep-sea coral communities in the southern Adriatic Sea

We document a remarkable abundance of the tubeworm Serpula vermicularis Linnaeus, 1767, in bathyal coral habitats from the Bari Canyon System in the southern Adriatic Sea. Here, the specimens of S. vermicularis grow from muddy substrate either as isolated individuals or as localized clusters of multiple individuals. Peculiar tube aggregations are also associated with Madrepora oculata build-ups and other stony corals including Desmophyllum dianthus. Three types of coral-serpulid (C–S) frameworks have been recognized based upon size and shape. The abundance of S. vermicularis increases with the size of C–S frameworks, which results from superimposition, overgrowth, and/or intergrowth of scleractinians and serpulids. Several generations of S. vermicularis contribute to the C–S frameworks, each most probably accounting for more than 8 years and presumably existing in the area for the last hundreds of years. At a meso-scale, the distribution pattern of serpulids seems to be mainly governed by currents and siltation. A further constraint is the co-occurring solitary coral D. dianthus within frameworks. The successful sea-bottom colonization by S. vermicularis and associated C–S frameworks is possibly related to a high oxygen content and food supply derived from the North Adriatic Dense Water (NAdDW). The flourishing populations of S. vermicularis as well as the peculiarity of C–S frameworks suggest that deep-sea canyons provide important benthic habitats in bathyal environments.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Petrosal and Bony Labyrinth Morphology Supports Paraphyly of Elephantulus Within Macroscelididae (Mammalia,Afrotheria)

Interest in the phylogeny of Macroscelididae (sengis or elephant shrews) has been prompted by molecular studies indicating that Elephantulus rozeti is best placed as the sister group of Petrodromus tetradactylus (this clade being in turn the sister taxon to Macroscelides proboscideus) than among other species of the genus Elephantulus. Until now, no discrete morphological characters have been proposed to support the grouping of E. rozeti, Petrodromus, and Macroscelides into this single so-called ‘Panelephantulus’ clade. Here, we employed μCT scanning in order to investigate the petrosal and bony labyrinth (bony capsule of the inner ear) morphology of most species of extant Macroscelididae. We performed a cladistic analysis on ear traits and found that despite some convergences (e.g., concerning the bony arterial canals in Macroscelides and Rhynchocyon) the middle and inner ear morphology furnishes significant support for the ‘Panelephantulus’ clade. In our analysis, this clade is unambigously supported by the presence of a fully ossified stapediofacial tube. Two additional characters (the presence of a bony septum at the mouth of the fenestra cochleae dividing the D3 sinus into two distinct cavities and the absence of an accessory lateral pneumatic fossa) could also support ‘Panelephantulus.’ These newly discovered morphological characters support the molecular phylogenies published and highlight the importance of coding hitherto difficult to sample morphologies within cladistic analyses using micro-CT techniques. Taxonomic implications are briefly discussed.     

Tempestitic shell beds formed by a new serpulid polychaete from the Bajocian (Middle Jurassic) of the Central High Atlas (Morocco)

Serpulid-dominated shell beds from the Lower Bajocian (Middle Jurassic) of the Central High Atlas (Morocco) are primarily formed by quadrangular tubes of the serpulid polychaete Nogrobs moroccensis sp. nov. The transverse tube ornament consisting predominately of wrinkles, the lack of narrow spirals and the shortness or absence of attached posterior tube portion represent the diagnostic features of this new species. Tubes of Nogrobs moroccensis co-occur with gastropods and oyster–crinoidal debris. We suggest that these serpulids were free-lying in their adult stage and formed benthic meadows on soft-bottom habitats. They frequently show parallel alignment in plane views in both graded and non-graded, few-cm-thick shell beds, corresponding to distal tempestites deposited close to and below storm wave base in an outer-ramp environment. The excellent preservation of serpulids implies short residence time on the seafloor, and the lack of compositional mixing with other communities and their restriction to outer-ramp habitats indicate that they represent parautochthonous assemblages. Analyses of serpulid orientation on the bottom bedding planes of shell beds revealed weak unidirectional arrangement of tubes, whereas orientation on the top bedding planes revealed strong unidirectional arrangement of tubes, with significantly different orientation relative to the bottom planes. This change could suggest a shift from predominantly a current component of the combined storm flow (with uneven seafloor surface and adhesion of skeletal grains to muddy substrate) to significant oscillatory component of the waning storm, as also suggested by bidirectional orientation of gastropods.     

The Trichoderma brevicompactum clade: a separate lineage with new species, new peptaibiotics, and mycotoxins

The Brevicompactum clade is recognized as a separate lineage in Trichoderma/Hypocrea. This includes T. brevicompactum and the new species T. arundinaceum, T. turrialbense, T. protrudens and Hypocrea rodmanii. The closest relative of the Brevicompactum clade is the Lutea clade. With the exception of H. rodmanii, all members of this clade produce the simple trichothecene-type toxins harzianum A or trichodermin. All members of the clade produce peptaibiotics, including alamethicins. Strains previously reported as T. harzianum (ATCC 90237), T. viride (NRRL 3199) or Hypocrea sp. (F000527, CBS 113214) to produce trichothecenes are reidentified as T. arundinaceum. The Brevicompactum clade is not closely related to species that have biological application.     

The molecular phylogeny of aquatic hyphomycetes with affinity to the Leotiomycetes

Aquatic hyphomycetes play a key role in decomposition of submerged organic matter and stream ecosystem functioning. We examined the phylogenetic relationships among various genera of aquatic hyphomycetes belonging to the Leotiomycetes (Ascomycota) using sequences of internal transcribed spacer (ITS) and large subunit (LSU) regions of rDNA generated from 42 pure cultures including 19 ex-types. These new sequence data were analyzed together with additional sequences from 36 aquatic hyphomycetes and 60 related fungi obtained from GenBank. Aquatic hyphomycetes, characterized by their tetraradiate or sigmoid conidia, were scattered in nine supported clades within the Helotiales (Leotiomycetes). Tricladium, Lemonniera, Articulospora, Anguillospora, Varicosporium, Filosporella, and Flagellospora are not monophyletic, with species from the same genus distributed among several major clades. The Gyoerffyella clade and the Hymenoscyphus clade accommodated species from eight and six different genera, respectively. Thirteen aquatic hyphomycete taxa were grouped in the Leotia-Bulgaria clade while twelve species clustered within the Hymenoscyphus clade along with several amphibious ascomycetes. Species of Filosporella and some species from four other aquatic genera were placed in the Ascocoryne-Hydrocina clade. It is evident that many aquatic hyphomycetes have relatives of terrestrial origin. Adaptation to colonize the aquatic environment has evolved independently in multiple phylogenetic lineages within the Leotiomycetes.     

Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A,B and C

We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses.     

Allodaposuchus palustris sp. nov. from the Upper Cretaceous of Fumanya (South-Eastern Pyrenees,Iberian Peninsula): Systematics,Palaeoecology and Palaeobiogeography of the Enigmatic Allodaposuchian Crocodylians

The controversial European genus Allodaposuchus is currently composed of two species (A. precedens, A. subjuniperus) and it has been traditionally considered a basal eusuchian clade of crocodylomorphs. In the present work, the new species A. palustris is erected on the base of cranial and postcranial remains from the lower Maastrichtian of the southern Pyrenees. Phylogenetic analyses here including both cranial and postcranial data support the hypothesis that Allodaposuchus is included within Crocodylia. The studied specimen suggests little change in postcranial skeleton along the evolutionary history of crocodylians, except for some bone elements such as the axis, the first caudal vertebra and the ilium. The specimen was found in an organic mudstone corresponding to a coastal wetland environment. Thus, A. palustris from Fumanya is the first Allodaposuchus reported in lacustrine-palustrine settings that expand the ecological range for this genus. The S-DIVA palaeobiogeographic reconstruction of ancestral area suggests that early members of Crocodylia rapidly widespread for the Northern Hemisphere landmasses no later than the Campanian, leading the apparition of endemic groups. In that way “Allodaposuchia” represents an endemic European clade probably originated in the Ibero-Armorican domain in the late Campanian and dispersed by the Southern European archipelago prior to the early Maastrichtian.     

Forming nacreous layer of the shells of the bivalves Atrina rigida and Pinctada margaritifera: an environmental- and cryo-scanning electron microscopy study

A key to understanding control over mineral formation in mollusk shells is the microenvironment inside the pre-formed 3-dimensional organic matrix framework where mineral forms. Much of what is known about nacre formation is from observations of the mature tissue. Although these studies have elucidated several important aspects of this process, the structure of the organic matrix and the microenvironment where the crystal nucleates and grows are very difficult to infer from observations of the mature nacre. Here, we use environmental- and cryo-scanning electron microscopy to investigate the organic matrix structure at the onset of mineralization in the nacre of two mollusk species: the bivalves Atrina rigida and Pinctada margaritifera. These two techniques allow the visualization of hydrated biological materials coupled with the preservation of the organic matrix close to physiological conditions. We identified a hydrated gel-like protein phase filling the space between two interlamellar sheets prior to mineral formation. The results are consistent with this phase being the silk-like proteins, and show that mineral formation does not occur in an aqueous solution, but in a hydrated gel-like medium. As the tablets grow, the silk-fibroin is pushed aside and becomes sandwiched between the mineral and the chitin layer.     

Eridites undulatum壳体微细构造

利用偏光显微镜及扫描电子显微镜观察了假直角石类Ｅｒｉｄｉｔｅｓｕｎｄｕｌａｔｕｍ的体管沉积及气室沉积微细构造特征,体管沉积内部有机质层及矿物晶体层形态及厚度较稳定。气室沉积中有机质层及矿物晶体层形态及厚度变化大,晶体层内部具有柱状晶体。基于内部微细构造特征,推测体管沉积由软体上皮细胞直接分泌而成,气室沉积由体液渗透连接环在气室内表面上形成矿化基质后通过有机质层及矿物晶体层不断加积而成。另外,通过与石炭纪其它假直角石类内部沉积微细构造特征的比较,认为假直角石类内部沉积的微细构造特征不具有分类学意义。     

Cladistic relationships of extant and fossil hominoids

There is general agreement that the hominoid primates form a monophyletic group, that the extant great apes and humans form a second clade within that group with the gibbons as the sister group, and that the African apes and humans form a third clade. Although it has recently been proposed that humans and orang utans are sister taxa and also that the great apes form a clade to the exclusion of humans, our analysis, particularly of the molecular evidence, supports the existence of an African ape and human clade. The major problem in hominoid phylogeny at present is the relationships of the species within this clade: morphological data generally support the existence of an African ape clade which is the sister group to humans; some molecular data also support this conclusion, but most molecular evidence indicates the existence of a chimpanzee/human clade. We have cladistically re-analysed the DNA and protein sequence data for which apomorphic character states can be assessed. It is clear that there is a high degree of homoplasy whichever branching pattern is produced, with some characters supporting the existence of a chimpanzee/human clade and others supporting an African ape clade. When the cladistic analyses of morphological and molecular data are combined we believe that the most parsimonious interpretation of the data is that the African apes form a clade which is the sister taxon of the human (i.e., Australopithecus, Homo and Paranthropus) clade.This paper is not intended as a survey of all hominoid fossils but as a study of branching points in hominoid evolution and fossils are included which are relevant to this branching pattern. The analysis of fossil taxa in this study leads us to conclude that Proconsul is the sister taxon to the later Hominoidea. A number of middle Miocene forms such as Dryopithecus, Kenyapithecus, Heliopithecus and Afropithecus are shown to share derived characters with great apes and humans and provide evidence for the divergence of that clade from the gibbon lineage prior to 18 Ma. The position that Sivapithecus represents the sister group of the orang utan clade is supported here and shows that the orang utan lineage had diverged from the African ape and human lineage prior to 11·5 Ma. There is unfortunately no definitive fossil cvidence on branching sequences within the African ape and human clade, although a new specimen from Samburu, Kenya may be related to the gorilla.     

Biosynthesis of UDP-GlcNAc,UndPP-GlcNAc and UDP-GlcNAcA Involves Three Easily Distinguished 4-Epimerase Enzymes,Gne, Gnu and GnaB

We have undertaken an extensive survey of a group of epimerases originally named Gne, that were thought to be responsible for inter-conversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc). The analysis builds on recent work clarifying the specificity of some of these epimerases. We find three well defined clades responsible for inter-conversion of the gluco- and galacto-configuration at C4 of different N-acetylhexosamines. Their major biological roles are the formation of UDP-GalNAc, UDP-N-acetylgalactosaminuronic acid (UDP-GalNAcA) and undecaprenyl pyrophosphate-N-acetylgalactosamine (UndPP-GalNAc) from the corresponding glucose forms. We propose that the clade of UDP-GlcNAcA epimerase genes be named gnaB and the clade of UndPP-GlcNAc epimerase genes be named gnu, while the UDP-GlcNAc epimerase genes retain the name gne. The Gne epimerases, as now defined after exclusion of those to be named GnaB or Gnu, are in the same clade as the GalE 4-epimerases for inter-conversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal). This work brings clarity to an area that had become quite confusing. The identification of distinct enzymes for epimerisation of UDP-GlcNAc, UDP-GlcNAcA and UndPP-GlcNAc will greatly facilitate allocation of gene function in polysaccharide gene clusters, including those found in bacterial genome sequences. A table of the accession numbers for the 295 proteins used in the analysis is provided to enable the major tree to be regenerated with the inclusion of additional proteins of interest. This and other suggestions for annotation of 4-epimerase genes will facilitate annotation.     

Native ecosystem engineer facilitates recruitment of invasive crab and native invertebrates

Native ecosystem engineers that add physical structure to ecosystems can facilitate invasive species. In this study we determined the effects of the native tube-forming serpulid worm, Galeolaria caespitose on the recruitment of the invasive New Zealand porcelain crab, Petrolisthes elongatus, and whether invasive crab recruitment was related to the recruitment of native species. P. elongatus is abundant beneath intertidal rocks around Tasmania, southern Australia, and the underside of these rocks is usually covered with a calcareous matrix formed by the serpulid. We used an experimental approach to investigate whether rocks, serpulids on the underside of rocks and adult P. elongatus influenced the recruitment P. elongatus and native communities. P. elongatus and native invertebrates only recruited in the presence of rocks indicating the importance of rock as primary recruitment habitat. Moreover, the presence of serpulids on the underside of rocks significantly increased the recruitment of P. elongatus and native invertebrates compared to rocks without serpulids. Rocks with higher densities of adult P. elongatus at the end of the experiment also had higher densities of P. elongatus recruits. The density of P. elongatus recruits did not influence native species richness and abundance although there was some evidence that high P. elongatus recruitment was correlated with shifts in native community structure. We have shown that a native ecosystem engineer facilitates recruitment of an invasive crab but this does not appear to influence the recruitment of native species.     

Cyanophages from a less virulent clade dominate over their sister clade in global oceans

Environmental virus communities are highly diverse. However, the infection physiology underlying the evolution of diverse phage lineages and their ecological consequences are largely unknown. T7-like cyanophages are abundant in nature and infect the marine unicellular cyanobacteria, Synechococcus and Prochlorococcus, important primary producers in the oceans. Viruses belonging to this genus are divided into two distinct phylogenetic clades: clade A and clade B. These viruses have narrow host-ranges with clade A phages primarily infecting Synechococcus genotypes, while clade B phages are more diverse and can infect either Synechococcus or Prochlorococcus genotypes. Here we investigated infection properties (life history traits) and environmental abundances of these two clades of T7-like cyanophages. We show that clade A cyanophages have more rapid infection dynamics, larger burst sizes and greater virulence than clade B cyanophages. However, clade B cyanophages were at least 10-fold more abundant in all seasons, and infected more cyanobacteria, than clade A cyanophages in the Red Sea. Models predicted that steady-state cyanophage abundances, infection frequency, and virus-induced mortality, peak at intermediate virulence values. Our findings indicate that differences in infection properties are reflected in virus phylogeny at the clade level. They further indicate that infection properties, together with differences in subclade diversity and host repertoire, have important ecological consequences with the less aggressive, more diverse virus clade having greater ecological impacts.Subject terms: Microbial ecology, Molecular ecology, Bacteriophages, Population dynamics, Microbial biooceanography     

Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria

A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.