Comparative neurocranial morphology of angelsharks from the south-western Atlantic Ocean (Chondrichthyes, Elasmobranchii, Squatinidae): implications for taxonomy and phylogeny

Neurocrania of three species of angelsharks from the south-western Atlantic Ocean, occurring off south-eastern and southern Brazil, are described. A detailed morphological description is provided of the neurocranium of Squatina guggenheim and compared with S. argentina and S. occulta. Despite being generally conservative, the neurocranium of Squatina presents significant differences among these species which aid in their identification, which is otherwise problematical. The main distinctions were found in rostral projections, anterior fontanellae, supraorbital crests, upper and lower postorbital processes, otic capsules, suborbital crests, and pterotic processes. Squatina guggenheim and S. occulta share more neurocranial characters when compared to S. argentina. No basal angle was found, but we confirm the presence of a very much reduced and barely noticeable basioccipital fovea in Squatina; systematic implications within elasmobranchs of these and other features are discussed.

Taxonomy, Hemipenial Morphology, and Natural History of Two Poorly Known Species of Anadia (Gymnophthalmidae) from Northern South America

Anadia pariaensis Rivas, La Marca, and Oliveros, 1999, and Anadia steyeri Nieden, 1914, are two particularly rare and poorly known lizards described from single specimens. In the case of A. pariaensis, it remains known from the holotype, whereas A. steyeri is known from three additional specimens reported in the literature after the original description of the species. A single new specimen of A. pariaensis and five of A. steyeri, including the first adult males recorded for both species, make possible a more representative description of both species, including descriptions of the hemipenes. Despite both species presenting some similar morphological characteristics, the examination of the hemipenial morphology revealed very different organs. The hemipenis of A. steyeri presents some characteristics that resemble the organs of two species from the Santa Marta Mountain Range in the "bitaeniata-group" (Anadia pulchella and Anadia altaserrania). On the other hand, the hemipenes of A. pariaensis are unique morphologically and cannot be associated with the hemipenes known from other species in the genus. We describe variation within both species, and we comment on possible sexual dimorphism (number and arrangement of the femoral pores), natural history, and the known geographic distribution of the species. We also comment on Anadia bumanguesa Rueda-Almonacid and Caicedo 2004 based on a new specimen, the second known. This species may be a synonym of A. steyeri.

New species of Pseudanos Winterbottom, 1980 (Characiformes: Anostomidae), with notes on the taxonomy of P. gracilis and P. trimaculatus

A new species of Pseudanos (Characiformes, Anostomidae) is described from the Rio Negro in Brazil, and the Rio Casiquiare and Rio Atabapo, in Venezuela. Specimens of the new species were previously mistakenly identified as Pseudanos gracilis. The new species is diagnosed by having three branchiostegal rays (vs. four in P. gracilis and most specimens of P. winterbottomi), dark transversal bars on dorsum absent (vs. present in P. trimaculatus), dark spots present on the center of each body scale, forming conspicuous, straight dark lines (vs. dark spots absent in P. gracilis and in some specimens of P. trimaculatus), four midlateral dark blotches on body (vs. usually two, sometimes three or four in P. trimaculatus, or body lacking midlateral blotches and presenting instead a broad midlateral stripe in P. winterbottomi), angle of dorsal and ventralmost radii of body scales between 40 degrees and 90 degrees (vs. angle between 110 degrees and 180 degrees in P. gracilis and P. trimaculatus), and cranial fontanel opened along its entire length (vs. cranial fontanel partially closed in P. trimaculatus). Type specimens and extensive additional material of Pseudanos gracilis and P. trimaculatus were examined and comments on the taxonomy of both species are provided. Pseudanos irinae is herein considered a junior synonym of P. trimaculatus. In addition, an updated key to identification of valid species of Pseudanos is presented.

Microfossils in micrites from Serra da Bodoquena (MS), Brazil: taxonomy and paleoenvironmental implications

Microfossils present in Quaternary micrites from Serra da Bodoquena, Mato Grosso do Sul State, Brazil, are here described for the first time. The studied taxa are: a) ostracods: Candona sp., Candonopsis sp., Cyclocypris sp., Cypria sp., Cypridopsis sp., Notodromas sp., Ilyocypris sp., Cyprideis sp., Wolburgiopsis cf. chinamuertensis (Musacchio 1970), Darwinula sp. and 5 morphotypes; b) microgastropod Acrobis sp., and c) Characeae remains and gyrogonites Chara sp.. The presence of these microfossils suggests clear-water shallow lacustrine paleoenvironments and the presence of aquatic vegetation. Similarities between microfossils and the living taxa suggest possible Holocene ages for these deposits, which is in accordance with previous C14 dates.

Molecular phylogeny, morphology and their implications for the taxonomy of Eriocaulaceae

The pantropical family Eriocaulaceae includes ten genera and c. 1,400 species, with diversity concentrated in the New World. The last complete revision of the family was published more than 100 years ago, and until recently the generic and infrageneric relationships were poorly resolved. However, a multi-disciplinary approach over the last 30 years, using morphological and anatomical characters, has been supplemented with additional data from palynology, chemistry, embryology, population genetics, cytology and, more recently, molecular phylogenetic studies. This led to a reassessment of phylogenetic relationships within the family. In this paper we present new data for the ITS and trnL-F regions, analysed separately and in combination, using maximum parsimony and Bayesian inference. The data confirm previous results, and show that many characters traditionally used for differentiating and circumscribing the genera within the family are homoplasious. A new generic key with characters from various sources and reflecting the current taxonomic changes is presented.

Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

A new genus, Cradoscrupocellaria n. gen., is erected for Scrupocellaria bertholletii Audouin, 1826), reported as widespread in tropical and subtropical waters. Here we select a neotype of this species in order to establish its identity and distinguish it from morphologically similar species. We include redescriptions and figures of additional species now assigned to this new genus: Cradoscrupocellaria curacaoensis (Fransen, 1986) n. comb., Cradoscrupocellaria hirsuta (Jullien & Calvet, 1903) n. comb., and Cradoscrupocellaria macrorhyncha (Gautier, 1962) n. comb. Five additional species are assigned to the genus: Cradoscrupocellaria ellisi (Vieira & Spencer Jones, 2012) n. comb., Cradoscrupocellaria nanshaensis (Liu, 1991) n. comb., Cradoscrupocellaria reptans (Linnaeus, 1758) n. comb., Cradoscrupocellaria serrata (Waters, 1909) n. comb., and Cradoscrupocellaria tenuirostris (Osburn, 1950) n. comb. Eighteen new species are described: Cradoscrupocellaria aegyptiana n. sp., Cradoscrupocellaria arisaigensis n. sp., Cradoscrupocellaria atlantica n. sp., Cradoscrupocellaria calypso n. sp., Cradoscrupocellaria floridana n. sp., Cradoscrupocellaria galapagensis n. sp., Cradoscrupocellaria gautieri n. sp., Cradoscrupocellaria gorgonensis n. sp., Cradoscrupocellaria hastingsae n. sp., Cradoscrupocellaria insularis n. sp., Cradoscrupocellaria jamaicensis n. sp., Cradoscrupocellaria lagaaiji n. sp., Cradoscrupocellaria macrorhynchoides n. sp., Cradoscrupocellaria makua n. sp., Cradoscrupocellaria marcusorum n. sp., Cradoscrupocellaria normani n. sp., Cradoscrupocellaria odonoghuei n. sp., and Cradoscrupocellaria osburni n. sp.

DNA barcoding taxonomy and diversity of the Mediterranean sharks and rays

Elasmobranchs are an important by-catch of commercial fisheries targeting bony fishes. Fisheries targeting sharks are rare, but usually almost all specimen bycatched are marketed. They risk extinction if current fishing pressure continues (Ferretti et al., 2008). Accurate species identification is critical for the design of sustainable fisheries and appropriate management plans, especially since not all species are equally sensitive to fishing pressure (Walker & Hislop 1998). The identification of species constitutes the first basic step for biodiversity monitoring and conservation (Dayrat B et al., 2005). More recently, mtDNA sequencing has also been used for species identification and its use has become widespread under the DNA Barcode initiative (e.g. Hebert et al. 2003a, 2003b; Ward et al. 2005, 2008a; Moura et al 2008; Steinke et al. 2009). The aims of this work were: 1) identify sharks and skates species using DNA barcode; 2) compare species of different provenance; 3) use DNA barcode for misidentified species. Using DNA barcode 15 species of sharks (Alopias vulpinus, Centrophorus granulosus, Cetorhinus maximus, Dalatias licha, Etmopterus spinax, Galeorhinus galeus, Galeus melastomus, Heptranchias perlo, Hexanchus griseus, Mustelus mustelus, Mustelus punctulatus, Oxynotus centrina, Scyliorhinus canicula Squalus acanthias, Squalus blainville), 1 species of chimaera (Chimaera monstrosa) and 21 species of rays/skayes (Dasyatis centroura, Dasyatis pastinaca, Dasyatis sp., Dipturus nidarosiensis, Dipturus oxyrinchus, Leucoraja circularis, Leucoraja melitensis, Myliobatis aquila, Pteromylaeus bovinus, Pteroplatytrygon violacea, Raja asterias, Raja brachyura, Raja clavata, Raja miraletus, Raja montagui, Raja radula, Raja polystigma, Raja undulata, Rostroraja alba, Torpedo marmorata, Torpedo nobiliana, Torpedo torpedo) was identified.

Morphological-molecular taxonomy and population genetic structure of common and Egyptian soles of the Adriatic Sea

A total of 352 specimens were analyzed to achieve the different aims of this thesis. 255 central-northern Adriatic specimens of S. solea and S. aegyptiaca were molecularly analysed using microsatellite locus Sos(AC)40 and 205 also morphologically due to evaluate the abundance and the distribution of the cryptic species S. aegyptiaca and to confirm morphologic analyses. Morphological and molecular analyses comparated show a correspondence of 96%. A combined morphologic approach could be proposed to apply multiple criteria on the analyzed external morphological keys. The Adriatic Egyptian soles may lives in shallow waters (up 30 m) and in brackish lagoon. 127 samples of Adriatic common sole added to 326 samples of previous studies showed, using mitochondrial marker (CytB), that the Adriatic Sea as contact zone between Tyrrhenian and Aegean Sea, the divergence within the Adriatic Sea is low but significant between central-north and south, with a longitudinal strong gene flow in central-northern side. It’s also showed as in the Adriatic Sea two near-panmictic populations of common sole exist.

Taxonomy, phylogeny and reproductive ecology of Gentiana lutea L.

This research focuses on taxonomy, phylogeny and reproductive ecology of Gentiana lutea. L.. Taxonomic analysis is a critical step in botanical studies, as it is necessary to recognize taxonomical unit. Herbarium specimens were observed to assess the reliability of several subspecies-diagnostic characters. The analysis of G. lutea genetic variability and the comparison with that of the other species of sect. Gentiana were performed to elucidate phylogenetic relationships among G. lutea subspecies and to propose a phylogenetic hypothesis for the evolution and the colonization dynamics of the section. Appropriate scientific information is critical for the assessment of species conservation status and for effective management plans. I carried out field work on five natural populations and performed laboratory analyses on specific critical aspects, with special regard to G. lutea breeding system and type and efficiency of plant-pollinator system. Bracts length is a reliable character to identify subsp. vardjanii, however it is not exclusive, hence to clearly identify subsp. vardjanii, other traits have to be considered. The phylogenetic hypotheses obtained from nuclear and chloroplast data are not congruent. Nuclear markers show a monophyly of sect. Gentiana, a strongly species identity of G. lutea and clear genetic identity of subsp. vardjanii. The little information emerging from plastid markers indicate a weak signal of hybridization and incomplete sorting of ancestral lineages. G. lutea shows a striking variation in intra-floral dichogamy probably evolved to reduce pollen-stigma interference. Although the species is partially self-compatible, pollen vectors are necessary for a successful reproduction, and moreover it shows a strong inbreeding depression. G. lutea is a generalist species: within its spectrum of visitors is possible to recognize "nectar thieves" and pollinators with sedentary or dynamic behaviour. Pollen limitation is frequent and it could be mainly explained by poor pollen quality.

Genus Bifidobacterium: taxonomy studies and gene expression analysis on folate pathway

Folates (vitamin B9) are essential water soluble vitamins, whose deficiency in humans may contribute to the onset of several diseases, such as anaemia, cancer, cardiovascular diseases, neurological problems as well as defects in embryonic development. Human and other mammals are unable to synthesize ex novo folate obtaining it from exogenous sources, via intestinal absorption. Recently the gut microbiota has been identified as an important source of folates and the selection and use of folate producing microorganisms represents an innovative strategy to increase human folate levels. The aim of this thesis was to gain a fundamental understanding of folate metabolism in Bifidobacterium adolescentis. The work was subdivided in three main phases, also aimed to solve different problems encountered working with Bifidobacterium strains. First, a new identification method (based on PCR-RFLP of hsp60 gene) was specifically developed to identify Bifidobacterium strains. Secondly, Bifidobacterium adolescentis biodiversity was explored in order to recognize representing strains of this species to be screened for their folate production ability. Results showed that this species is characterized by a wide variability and support the idea that a possible new taxonomic re-organization would be required. Finally B. adolescentis folate metabolism was studied using a double approach. A quantitative analysis of folate content was complemented by the examination of expression levels of genes involved in folate related pathways. For the normalization process, required to increase the robustness of the qRT-PCR analysis, an appropriate set of reference genes was tested using two different algorithms. Results demonstrate that B.adolescentis strains may represent an endogenous source of natural folate and they could be used to fortify fermented dairy products. This bio-fortification strategy presents many advantages for the consumer, providing native folate forms more bio-available, and not implicated in the discussed controversy concerning the safety of high intake of synthetic folic acid.

Bacillus anthracis: Molecular taxonomy, population genetics, phylogeny and patho-evolution

Bacillus anthracis, the etiological agent of anthrax, manifests a particular bimodal lifestyle. This bacterial species alternates between short replication phases of 20-40 generations that strictly require infection of the host, normally causing death, interrupted by relatively long, mostly dormant phases as spores in the environment. Hence, the B. anthracis genome is highly homogeneous. This feature and the fact that strains from nearly all parts of the world have been analysed for canonical single nucleotide polymorphisms (canSNPs) and variable number tandem repeats (VNTRs) has allowed the development of molecular epidemiological and molecular clock models to estimate the age of major diversifications in the evolution of B. anthracis and to trace the global spread of this pathogen, which was mostly promoted by movement of domestic cattle with settlers and by international trade of contaminated animal products. From a taxonomic and phylogenetic point of view, B. anthracis is a member of the Bacillus cereus group. The differentiation of B. anthracis from B. cereus sensu strict, solely based on chromosomal markers, is difficult. However, differences in pathogenicity clearly differentiate B. anthracis from B. cereus and are marked by the strict presence of virulence genes located on the two virulence plasmids pXO1 and pXO2, which both are required by the bacterium to cause anthrax. Conversely, anthrax-like symptoms can also be caused by organisms with chromosomal features that are more closely related to B. cereus, but which carry these virulence genes on two plasmids that largely resemble the B. anthracis virulence plasmids. (C) 2011 Elsevier B.V. All rights reserved.

Etiology in a taxonomy of illnesses

According to what Robert Koch termed the etiological standpoint, illnesses are best understood and controlled by focusing on their causes, including in their definitions and, thus, in the construction of their taxonomies. In some ways flawed, this standpoint has been misunderstood and misapplied. A taxonomy based solely on etiology was an unrealistic dream in the context of 'the bacteriological revolution', and it also is unrealistic in the present context of 'the genetic revolution.' We argue that the illnesses in a taxonomy of them are in some cases best defined directly in terms of their respective somatic anomalies, in some others indirectly by the unique and universal etiology of that anomaly (left unspecified) in a 'deeper' somatic anomaly, and in yet others as a combination of these; and when the somatic anomaly for direct definition remains unknown, it is to be defined indirectly by the clinical syndrome that is its patient-relevant manifestation, possibly in conjunction with a somatic cause. We note, also, that these taxonomic issues have no material bearing on epidemiologists' etiologic research for the knowledge base of community-level preventive medicine.