Phylogenetic analyses of Cladophora vagabunda (L.) C. Hoek (Cladophorales, Chlorophyta) from Brazil based on SSU rDNA sequences

The complete SSU rDNA was sequenced for 10 individuals of Cladophora vagabunda collected along the coast of Brazil. For C. rupestris (L.) Kütz. a partial SSU rDNA sequence (1634 bp) was obtained. Phylogenetic trees indicate that Cladophora is paraphyletic, but the section Glomeratae sensu lato including C. vagabunda from Brazil, Japan and France, C. albida (Nees) Kütz., C. sericea (Hudson) Kütz., and C. glomerata (L.) Kütz. is monophyletic. Within this group C. vagabunda is paraphyletic. The sequence identity for the SSU rDNA varied from 98.9% to 100% for the Brazilian C. vagabunda, and from 98.3% to 99.7% comparing the Brazilian individuals to the ones from France and Japan. Sequence identity of the Brazilian C. vagabunda to C. albida and C. sericea vary from 98.0% to 98.6%. The SSU rDNA phylogeny support partially the morphological characteristics presented by Brazilian populations of C. vagabunda. On the other hand, C. rupestris from Brazil does not group with C. rupestris from France, both sequences presenting only 96.9% of identity. The inclusion of sequences of individuals from Brazil reinforces the need of taxonomical revision for the genus Cladophora and for the complex C. vagabunda.

Canine Distemper Virus in a Crab-eating Fox (Cerdocyon thous) in Brazil: Case Report and Phylogenetic Analyses

Although canine distemper is enzootic worldwide and has a wide host range, there are no reports of canine distemper virus there are no reports of canine distemper virus provide information on virus phylogeny and histopathologic lesions. The objective of this study is report and describe canine distemper in a crab-eating fox (C. thous), with a focus oil the phylogeny of the virus strain and the histopathologic lesions in the animal.

Phylogenetic Analyses of Eriotheca and Related Genera (Bombacoideae, Malvaceae)

Molecular and morphological data have shown that Bombacoideae and Malvoideae together form a well-supported Malvatheca clade. Phylogenetic relationships in Bombacoideae have been studied, but some genera in Bombax s. I. have not been adequately sampled for sufficiently variable molecular markers. The relationships of Eriotheca, for example, have yet to be resolved. Here, nuclear (ITS) and chloroplast (trnL-Fand matK) sequence data from 50 exemplars of Bombacoideae and seven additional taxa from other genera of Malvatheca were used to test monophyly of Eriotheca and its relationships with related genera of Bombax s. I. Parsimony and Bayesian analyses of individual and combined sequence data suggest that Eriotheca is not monophyletic as currently circumscribed but forms a paraphyletic grade containing Pachira s. 1. The newly discovered Eriotheca + Pachira clade has a probable synapomorphy of striate seeds. In addition, two other moderately supported clades emerged within the core Bombacoideae: Pseudobombax + Ceiba s. 1. and Bombax + Spirotheca + Pachira quinata. These three clades, and the African Rhodognaphalon together constitute the major clade of core Bombacoideae, whereas Adansonia appears to be more closely related to Catostemma, Scleronema, and Cavanillesia. The phylogenetic results imply three independent migrations from the New to Old World and homoplasy in staminal morphology.

Phylogenetic Analyses Based on Small Subunit rRNA and Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase Genes and Ultrastructural Characterization of Two Snake Trypanosomes: Trypanosoma serpentis n. sp from Pseudoboa nigra and Trypanosoma cascavelli from Crotalus durissus terrificus

We sequenced the small subunit (SSU) rRNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes of two trypanosomes isolated from the Brazilian snakes Pseudoboa nigra and Crotalus durissus terrificus. Trypanosomes were cultured and their morphometrical and ultrastructural features were characterized by light microscopy and scanning and transmission electron microscopy. Phylogenetic trees inferred using independent or combined SSU rRNA and gGAPDH data sets always clustered the snake trypanosomes together in a clade closest to lizard trypanosomes, forming a strongly supported monophyletic assemblage (i.e. lizard-snake clade). The positioning in the phylogenetic trees and the barcoding based on the variable V7-V8 region of the SSU rRNA, which showed high sequence divergences, allowed us to classify the isolates from distinct snake species as separate species. The isolate from P. nigra is described as a new species, Trypanosoma serpentis n. sp., whereas the isolate from C. d. terrificus is redescribed here as Trypanosoma cascavelli.

A new genotype of Trypanosoma cruzi associated with bats evidenced by phylogenetic analyses using SSU rDNA, cytochrome b and Histone H2B genes and genotyping based on ITS1 rDNA

We characterized 15 Trypanosoma cruzi isolates from bats captured in the Amazon, Central and Southeast Brazilian regions. Phylogenetic relationships among T. cruzi lineages using SSU rDNA, cytochrome b, and Histone H2B genes positioned all Amazonian isolates into T. cruzi I (TCI). However, bat isolates from the other regions, which had been genotyped as T. cruzi II (TC II) by the traditional genotyping method based on mini-exon gene employed in this study, Were not nested within any of the previously defined TCII sublineages, constituting a new genotype designated as TCbat. Phylogenetic analyses demonstrated that TCbat indeed belongs to T. cruzi and not to other closely related bat trypanosomes of the subgenus Schizotrypanum, and that although separated by large genetic distances TO-tat is closest to lineage TCI. A genotyping method targeting ITS1 rDNA distinguished TCbat from established T. cruzi lineages, and from other Schizotrypanum species. In experimentally infected mice, TCbat lacked virulence and yielded loss parasitaemias. Isolates of TCbat presented distinctive morphological features and behaviour in triatomines. To date, TCbat genotype wall found only in bats from anthropic environments of Central and Southeast Brazil. Our findings indicate that the complexity of T. cruzi is larger than currently known, and confirmed bats as important reservoirs and potential source of T. cruzi infections to humans.

Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

In this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports Clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that Circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDII sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

Background: Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction ( LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. Results: Analyses of a combined dataset of 18S and partial 28S sequences, and partial 28S alone, support the placement of Polypodium within Cnidaria. Removal of the long-branched myxozoans from the 18S dataset also results in Polypodium being nested within Cnidaria. These results suggest that previous reports showing that Polypodium and Myxozoa form a sister group to Bilateria were an artifact of long-branch attraction. Conclusion: By including 28S rDNA sequences and a comprehensive sampling of cnidarian taxa, we demonstrate that previously conflicting hypotheses concerning the phylogenetic placement of Polypodium can be reconciled. Specifically, the data presented provide evidence that Polypodium is indeed a cnidarian and is either the sister taxon to Hydrozoa, or part of the hydrozoan clade, Leptothecata. The former hypothesis is consistent with the traditional view that Polypodium should be placed in its own cnidarian class, Polypodiozoa.

DESCRIPTION OF ADULTS AND NYMPH, AND REDESCRIPTION OF THE LARVA, OF ORNITHODOROS MARINKELLEI (ACARI: ARGASIDAE), WITH DATA ON ITS PHYLOGENETIC POSITION

The argasid tick Ornithodoros marinkellei Kohls, Clifford, and Jones, 1969 was described 4 decades ago based on larval specimens collected from bats (Pteronotus spp.) in Colombia and Panama. Thereafter, larval O. marinkellei parasitizing bats were reported from Venezuela, Guyana, and Brazil. Herein, we describe the adults and nymph, and redescribe the larva of O. marinkellei based on specimens recently collected in the western Brazilian Amazon region. In contrast to all other known adult argasids, the idiosoma of both males and females of O. marinkellei is covered with sclerotized plaques. The idiosoma of the nymph of O. marinkellei is entirely micromamillated, and differs from the adults by the absence of plaques. The larva of O. marinkellei is morphologically similar to the larvae of the 2 other species belonging to the subgenus Subparmatus, i.e., Ornithodoros viguerasi Cooley and Kohls, 1941 and Ornithodoros mormoops Kohls, Clifford, and Jones, 1969. Because of the long and narrow dorsal plate, the larva of O. marinkellei is readily distinguished from O. viguerasi and O. mormoops. Comparison of our larvae from Brazil with O. marinkellei paratype specimens from Colombia confirmed their taxonomic identification. However, a few morphological differences, particularly in the size of the gnathosoma, were observed. Further studies are necessary to clarify whether O. marinkellei is a complex of different species, or a single species represented by morphologically polymorphic, and geographically distinct populations. Partial mitochondrial 16S rDNA gene sequences were generated for O. marinkellei specimens from Brazil, and compared with available homologous sequences in GenBank. Phylogenetic analyses revealed O. marinkellei to be distinct from the remaining argasid species available in GenBank, including other bat-associated tick species that are found in sympatry with O. marinkellei in the Neotropical region.

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

Marinussaurus curupira, a new genus and species of Gymnophthalmidae lizard is described from Iranduba, state of Amazonas, Brazil. The genus is characterized by an elongate body; short and stout pentadactyl limbs; all digits clawed; single frontonasal; two prefrontals; absence of frontoparietals; interparietal and parietals forming a straight posterior margin, with interparietal shorter than parietals; distinctive ear opening and eyelid; few temporals; three pairs of chin shields; nasal divided; a distinct collar; smooth, mainly hexagonal, dorsal scales; smooth quadrangular ventral scales; two precloacal and three femoral pores on each side in males; pores between three or four scales. Parsimony (PAR) and partitioned Bayesian (BA) phylogenetic analyses with morphological and molecular data recovered the new genus as a member of the Ecpleopodini radiation of the Cercosaurinae. A close relationship of the new genus with Arthrosaura is postulated.

Phylogenetic Analysis of Hepatitis B Virus Genotype F Complete Genome Sequences From Chilean Patients With Chronic Infection

Molecular epidemiological data concerning the hepatitis B virus (HBV) in Chile are not known completely. Since the HBV genotype F is the most prevalent in the country, the goal of this study was to obtain full HBV genome sequences from patients infected chronically in order to determine their subgenotypes and the occurrence of resistance-associated mutations. Twenty-one serum samples from antiviral drug-naive patients with chronic hepatitis B were subjected to full-length PCR amplification, and both strands of the whole genomes were fully sequenced. Phylogenetic analyses were performed along with reference sequences available from GenBank (n = 290). The sequences were aligned using Clustal X and edited in the SE-AL software. Bayesian phylogenetic analyses were conducted by Markov Chain Monte Carlo simulations (MCMC) for 10 million generations in order to obtain the substitution tree using BEAST. The sequences were also analyzed for the presence of primary drug resistance mutations using CodonCode Aligner Software. The phylogenetic analyses indicated that all sequences were found to be the HBV subgenotype F1b, clustered into four different groups, suggesting that diverse lineages of this subgenotype may be circulating within this population of Chilean patients. J. Med. Virol. 83: 1530-1536, 2011. (C) 2011 Wiley-Liss, Inc.

Taxonomic and Phylogenetic Relationships Between Species of the Genus Culex (Diptera: Culicidae) From Brazil Inferred From the Cytochrome c Oxidase I Mitochondrial Gene

Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.

Placement of Kuhlmanniodendron Fiaschi & Groppo in Lindackerieae (Achariaceae, Malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy

The phylogenetic placement of Kuhlmanniodendron Fiaschi & Groppo (Achariaceae) within Malpighiales was investigated with rbcL sequence data. This genus was recently created to accommodate Carpotroche apterocarpa Kuhlm., a poorly known species from the rainforests of Espirito Santo, Brazil. One rbcL sequence was obtained from Kuhlmanniodendron and analyzed with 73 additional sequences from Malpighiales, and 8 from two closer orders, Oxalidales and Celastrales, all of which were available at Genbank. Phylogenetic analyses were carried out with maximum parsimony and Bayesian inference; bootstrap analyses were used in maximum parsimony to evaluate branch support. The results confirmed the placement of Kuhlmanniodendron together with Camptostylus, Lindackeria, Xylotheca, and Caloncoba in a strongly supported clade (posterior probability = 0.99) that corresponds with the tribe Lindackerieae of Achariaceae (Malpighiales). Kuhlmanniodendron also does not appear to be closely related to Oncoba (Salicaceae), an African genus with similar floral and fruit morphology that has been traditionally placed among cyanogenic Flacourtiaceae (now Achariaceae). A picrosodic paper test was performed in herbarium dry leaves, and the presence of cyanogenic glycosides, a class of compounds usually found in Achariaceae, was detected. Pollen morphology and wood anatomy of Kuhlmanniodendron were also investigated, but both pollen (3-colporate and microreticulate) and wood, with solitary to multiple vessels, scalariform perforation plates and other features, do not seem to be useful to distinguish this genus from other members of the Achariaceae and are rather common among the eudicotyledons as a whole. However, perforated ray cells with scalariform plates, an uncommon wood character, present in Kuhlmanniodendron are similar to those found in Kiggelaria africana (Pangieae, Achariaceae), but the occurrence of such cells is not mapped among the angiosperms, and it is not clear how homoplastic this character could be.

Evidence for the conspecificity of Palisada papillosa with P. perforata (Ceramiales, Rhodophyta) from the western and eastern Atlantic Ocean on the basis of morphological and molecular analyses

Morphological and molecular studies were carried out on Palisada papillosa and P. perforata from the Canary Islands (type locality of P. perforata), Mexico and Brazil. The two species have been distinguished by features of their external morphology such as size and degree of compactness of the thalli, presence or absence of arcuate branches, branching pattern and basal system. A detailed morphological comparison between these taxa showed that none of the vegetative anatomical or reproductive characters was sufficient to separate these species. The presence or absence of cortical cells in a palisade-like arrangement, also previously used to. distinguish these species, is not applicable. The species present all characters typical of the genus, and both share production of the first pericentral cell underneath the basal cell of the trichoblast, production of two fertile pericentral cells (the second and the third additional, the first remaining sterile), spermatangial branches produced from one of two laterals on the suprabasal cell of trichoblasts, and the procarpbearing segment with four pericentral cells. Details of the procarp are described for the species for the first time. The phylogenetic position of these species was inferred by analysis of the chloroplast-encoded rbcL gene sequences from 39 taxa, using one other Rhodomelacean taxon and two Ceramiaceae as outgroups. Relationships within the clade formed by P. papillosa and P. perforata have not been resolved due to the low level of genetic variation in their rbcL sequences (0-0.4%). Considering this and the morphological similarities, we conclude that P. papillosa is a taxonomic synonym of P. perforata. The phylogenetic analyses also supported the nomenclatural transfer of two species of Chondrophycus to Palisada, namely, P. patentiramea (Montagne) Cassano, Senties, Gil-Rodriguez & M.T. Fujii comb. nov. and P. thuyoides (Kutzing) Cassano, Senties, Gil-Rodriguez & M.T. Fujii comb. nov.

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well-supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time-frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.

Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution

Evolutionary novelties in the skeleton are usually expressed as changes in the timing of growth of features intrinsically integrated at different hierarchical levels of development(1). As a consequence, most of the shape- traits observed across species do vary quantitatively rather than qualitatively(2), in a multivariate space(3) and in a modularized way(4,5). Because most phylogenetic analyses normally use discrete, hypothetically independent characters(6), previous attempts have disregarded the phylogenetic signals potentially enclosed in the shape of morphological structures. When analysing low taxonomic levels, where most variation is quantitative in nature, solving basic requirements like the choice of characters and the capacity of using continuous, integrated traits is of crucial importance in recovering wider phylogenetic information. This is particularly relevant when analysing extinct lineages, where available data are limited to fossilized structures. Here we show that when continuous, multivariant and modularized characters are treated as such, cladistic analysis successfully solves relationships among main Homo taxa. Our attempt is based on a combination of cladistics, evolutionary- development- derived selection of characters, and geometric morphometrics methods. In contrast with previous cladistic analyses of hominid phylogeny, our method accounts for the quantitative nature of the traits, and respects their morphological integration patterns. Because complex phenotypes are observable across different taxonomic groups and are potentially informative about phylogenetic relationships, future analyses should point strongly to the incorporation of these types of trait.