Molecular detection and phylogenetic analysis of bovine astrovirus in Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Big, bad, and beautiful: phylogenetic relationships of the horned frogs (Anura: Ceratophryidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Spatial patterns of species richness and phylogenetic diversity of woody plants in the neotropical savannas of Brazil

Savanna woody plant communities are widespread in Brazil, where this vegetation type can be divided into core-central and marginal areas within its range of distribution. The study of diversity patterns of plant communities can provide insights into the distribution, biogeography, and diversity of plant species in widespread biomes. The objectives of this study were to measure standard and phylogenetic indices of diversity in woody plant communities of the savanna vegetation of Brazil (Cerrado) throughout its extensive range. Based on a metaanalysis, the diversity indexes were compared using traditional statistical methods, a phylogenetic approach, and by mapping. Similar patterns were found for phylogenetic and traditional indexes of diversity in core and marginal areas, suggesting that both lower and higher diversity sites can occur within the Cerrado geographical area. The only difference was found in low diversity, disjunct savanna sites within the Amazon basin, which are isolated by the Amazon River from the more continuous central-southern Cerrado area.

A phylogenetic analysis of Brycon and Henochilus (Characiformes, Characidae, Bryconinae) based on the mitochondrial gene 16S rRNA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cytogenetic and molecular data demonstrate that the bryconinae (ostariophysi, bryconidae) species from southeastern Brazil form a phylogenetic and phylogeographic unit

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Karyologic diversification and phylogenetic relationships of the genus Thalpomys (Rodentia, Sigmodontinae)

We describe the karyotype of Thalpomys species, from different Brazilian localities of the Cerrado. Thalpomys cerradensis Herskovitz, 1990 showed 2n = 36, FN = 34 and T. lasiotis Thomas, 1916 2n = 38, FN = 38. Comparisons of G-band karyotypes showed evident inter-specific homologies indicating that their chromosome complements could be derived from one another by two presumed rearrangements. Both species showed pericentromeric C-band regions in almost all chromosomes but a comparison with CMA3/DA/DAPI staining indicated that the molecular content of heterochromatic regions was different. T. lasiotis specimens from two different localities differed in the morphology of the X chromosome due to the presence of a short heterochromatic arm. These chromosome types are apparently fixed in each population rather than maintained as a polymorphic variation. Phylogenetic analyses supported the monophyly of the genus Thalpomys but was not capable of elucidating its phylogenetic relationship to other Akodontini rodents. These analyses also showed inter-individual variation in T. lasiotis, even within a given population. Phylogenetic analyses placed T. lasiotis specimens with different karyotypes in different monophyletic branches. Molecular and karyologic data confirmed the identity of the genus Thalpomys.

The Phylogenetic Relationships and Biogeography of True Porpoises (Mammalia: Phocoenidae) Based On Morphological Data

Prior studies of phylogenetic relationships among phocoenids based on morphology and molecular sequence data conflict and yield unresolved relationships among species. This study evaluates a comprehensive set of cranial, postcranial, and soft anatomical characters to infer interrelationships among extant species and several well-known fossil phocoenids, using two different methods to analyze polymorphic data: polymorphic coding and frequency step matrix. Our phylogenetic results confirmed phocoenid monophyly. The division of Phocoenidae into two subfamilies previously proposed was rejected, as well as the alliance of the two extinct genera Salumiphocaena and Piscolithax with Phocoena dioptrica and Phocoenoides dalli. Extinct phocoenids are basal to all extant species. We also examined the origin and distribution of porpoises within the context of this phylogenetic framework. Phocoenid phylogeny together with available geologic evidence suggests that the early history of phocoenids was centered in the North Pacific during the middle Miocene, with subsequent dispersal into the southern hemisphere in the middle Pliocene. A cooling period in the Pleistocene allowed dispersal of the southern ancestor of Phocoena sinusinto the North Pacific (Gulf of California).

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith-Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high-resolution X-ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard-like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister-taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem-taxa to the crown-clade Macrostomata. The hypothesis of a sister-group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis.

Reproductive apparatus of the male giant hermit crab Petrochirus diogenes (Anomura, Diogenidae): morphology and phylogenetic implications

We describe the male reproductive apparatus of the giant hermit crab Petrochirus diogenes, with morphological and biometric analyses of the spermatophore, the gonopore and the ultrastructure of the spermatozoa. Specimens were collected from the southern coast of Sao Paulo, Brazil. Morphological analyses were done using stereoscopic, light, transmission and scanning electron microscopy. The reproductive system of this hermit crab is composed of elongate and lobular testes followed by vasa deferentia that connect to the exterior via gonopores. The gonopores are ovoid and surrounded by setae, and each gonopore is composed of a membranous operculum that forms a depression constituting the gonopore opening. The gonopore constitutes a unique structure among the Diogenidae due to its number of setae. The spermatophores are tripartite, composed of a sperm-containing ampulla, a peduncle and a proximal foot. The spermatozoon has 3 main regions (acrosomal vesicle, nucleus and cytoplasm). The structure of the spermatophore indicates that this species can be considered an exception within Diogenidae with regard to spermatophore morphology and can therefore be used for phylogenetic inferences.

Postispinatus youngi n. gen., n. sp (Apseudomorpha; Tanaidacea; Crustacea): phylogenetic analysis and taxonomic remarks about kalliapseudids

The presence of setae or a sensorial structure on the dactylus of pereopod 1 as one of the defining features of the family Kalliapseudidae is re-evaluated. A new genus, Postispinatus, including the new species P. youngi n. gen., n. sp., is described and thought to belong to the Kalliapseudidae based on phylogenetic analysis. The diagnostic features of new genus-and species by monotypy -are: basal article of uropod with two curved spiniform processes; exopods on the fourth and fifth pereopods of the manca stage; absence of a maxillule palp.

Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia

The rock-wallaby genus Petrogale comprises a group of habitat-specialist macropodids endemic to Australia. Their restriction to rocky outcrops, with infrequent interpopulation dispersal, has been suggested as the cause of their recent and rapid diversification. Molecular phylogenetic relationships within and among species of Petrogale were analysed using mitochondrial (cytochrome oxidase c subunit 1, cytochrome b. NADH dehydrogenase subunit 2) and nuclear (omega-globin intron, breast and ovarian cancer susceptibility gene) sequence data with representatives that encompassed the morphological and chromosomal variation within the genus, including for the first time both Petrogale concinna and Petrogale purpureicollis. Four distinct lineages were identified, (1) the brachyotis group, (2) Petrogale persephone, (3) Petrogale xanthopus and (4) the lateralis-penicillata group. Three of these lineages include taxa with the ancestral karyotype (2n = 22). Paraphyletic relationships within the brachyotis group indicate the need for a focused phylogeographic study. There was support for P. purpureicollis being reinstated as a full species and P. concinna being placed within Petrogale rather than in the monotypic genus Peradorcas. Bayesian analyses of divergence times suggest that episodes of diversification commenced in the late Miocene-Pliocene and continued throughout the Pleistocene. Ancestral state reconstructions suggest that Petrogale originated in a mesic environment and dispersed into more arid environments, events that correlate with the timing of radiations in other arid zone vertebrate taxa across Australia. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Revisiting the Acanthamoeba species that form star-shaped cysts (genotypes T7, T8, T9, and T17): characterization of seven new Brazilian environmental isolates and phylogenetic inferences

Free-living amoebae of the genus Acanthamoeba are the agents of both opportunistic and non-opportunistic infections and are frequently isolated from the environment. Of the 17 genotypes (T1-T17) identified thus far, 4 (T7, T8, T9, and T17) accommodate the rarely investigated species of morphological group I, those that form large, star-shaped cysts. We report the isolation and characterization of 7 new Brazilian environmental Acanthamoeba isolates, all assigned to group I. Phylogenetic analyses based on partial (similar to 1200 bp) SSU rRNA gene sequences placed the new isolates in the robustly supported clade composed of the species of morphological group I. One of the Brazilian isolates is closely related to A. comandoni (genotype T9), while the other 6, together with 2 isolates recently assigned to genotype T17, form a homogeneous, well-supported group (2-0% sequence divergence) that likely represents a new Acanthamoeba species. Thermotolerance, osmotolerance, and cytophatic effects, features often associated with pathogenic potential, were also examined. The results indicated that all 7 Brazilian isolates grow at temperatures up to 40 degrees C, and resist under hvperosmotic conditions. Additionally, media conditioned by each of the new Acanthamoeba isolates induced the disruption of SIRC and HeLa cell monolayers.

Molecular and phylogenetic analysis of bovine coronavirus based on the spike glycoprotein gene

Bovine coronavirus has been associated with diarrhoea in newborn calves, winter dysentery in adult cattle and respiratory tract infections in calves and feedlot cattle. In Cuba, the presence of BCoV was first reported in 2006. Since then, sporadic outbreaks have continued to occur. This study was aimed at deepening the knowledge of the evolution, molecular markers of virulence and epidemiology of BCoV in Cuba. A total of 30 samples collected between 2009 and 2011 were used for PCR amplification and direct sequencing of partial or full S gene. Sequence comparison and phylogenetic studies were conducted using partial or complete S gene sequences as phylogenetic markers. All Cuban bovine coronavirus sequences were located in a single cluster supported by 100% bootstrap and 1.00 posterior probability values. The Cuban bovine coronavirus sequences were also clustered with the USA BCoV strains corresponding to the GenBank accession numbers EF424621 and EF424623, suggesting a common origin for these viruses. This phylogenetic cluster was also the only group of sequences in which no recombination events were detected. Of the 45 amino acid changes found in the Cuban strains, four were unique. (C) 2012 Elsevier B.V. All rights reserved.

Variable patterns of Y chromosome homology in Akodontini rodents (Sigmodontinae): a phylogenetic signal revealed by chromosome painting

The Akodontini is the second most speciose tribe of sigmodontine rodents, one of the most diverse groups of neotropical mammals. Molecular phylogenetic analyses are discordant regarding the interrelationships of genera, with low support for some clades. However, two clades are concordant, one (clade A) with Akodon sensu strictu (excluding Akodon serrensis), "Akodon" serrensis, Bibimys, Deltamys, Juscelinomys, Necromys, Oxymycterus, Podoxymys, Thalpomys and Thaptomys, and another (clade B) with Blarinomys, Brucepattersonius, Kunsia, Lenoxus and Scapteromys. Here, we present chromosome painting using Akodon paranaensis (APA) Y paint, after suppression of simple repetitive sequences, on ten Akodontini genera. Partial Y chromosome homology, in addition to the homology already reported on the Akodon genus, was detected on the Y chromosomes of "A." serrensis, Thaptomys, Deltamys, Necromys and Thalpomys and on Y and X chromosomes in Oxymycterus. In Blarinomys, Brucepattersonius, Scapteromys and Kunsia, no APA Y signal was observed using different hybridization conditions; APA X paint gave positive signals only on the X chromosome in all genera. The Y chromosome homology was variable in size and positioning among the species studied as follow: (1) whole acrocentric Y chromosome in Akodon and "A." serrensis, (2) Yp and pericentromeric region in submetacentric Y of Necromys and Thaptomys, (3) pericentromeric region in acrocentric Y of Deltamys, (4) distal Yq in the acrocentric Y chromosome of Thalpomys and (5) proximal Yq in the acrocentric Y and Xp in the basal clade A genus Oxymycterus. The results suggest that the homology involves pairing (pseudoautosomal) and additional regions that have undergone rearrangement during divergence. The widespread Y homology represents a phylogenetic signal in Akodontini that provides additional evidence supporting the monophyly of clade A. The findings also raise questions about the evolution of the pseudoautosomal region observed in Oxymycterus. The Y chromosomes of these closely related species seem to have undergone dynamic rearrangements, including restructuring and reduction of homologous segments. Furthermore, the changes observed may indicate progressive attrition of the Y chromosome in more distantly related species.

Phylogenetic and host-parasite relationship analysis of Henneguya multiplasmodialis n. sp infecting Pseudoplatystoma spp. in Brazilian Pantanal wetland

A new species of the genus Henneguya (Henneguya multiplasmodialis n. sp.) was found infecting the gills of three of 89 specimens (3.3%) of Pseudoplatystoma corruscans and two of 79 specimens (2.6%) of Pseudoplatystoma reticulatum from rivers in the Pantanal wetland, Brazil. Partial sequencing of the 18S rDNA gene of the spores obtained from one plasmodium from the gills of P. corruscans and other one from the gills of P. reticulatum, respectively, resulted in a total of 1560 and 1147 base pairs. As the spores of H. multiplasmodialis n. sp. resemble those of Henneguya corruscans, which is also a parasite of P. corruscans, sequencing of the 18S rDNA gene of the spores of H. corruscans found on P. corruscans caught in the Brazilian Pantanal wetland was also provided to avoid any taxonomic pendency between these two species, resulting in 1913 base pairs. The sequences of H. multiplasmodialis n. sp. parasite of P. corruscans and P. reticulatum and H. corruscans did not match any of the Myxozoa available in the GenBank. The similarity of H. multiplasmodialis n. sp. obtained from P. corruscans to that from P. reticulatum was of 99.7%. Phylogeny revealed a strong tendency among Henneguya species to form clades based on the order and/or family of the host fish. H. multiplasmodialis n. sp. clustered in a clade with Henneguya eirasi and H. corruscans, which are also parasites of siluriforms of the family Pimelodidae and, together with the clade composed of Henneguya spp. parasites of siluriforms of the family Ictaluridae, formed a monophyletic clade of parasites of siluriform hosts. The histological study revealed that the wall of the plasmodia of H. multiplasmodialis n. sp. were covered with a stratified epithelium rich in club cells and supported by a layer of connective tissue. The interior of the plasmodia had a network of septa that divided the plasmodia into numerous compartments. The septa were composed of connective tissue also covered on both sides with a stratified epithelium rich in club cells. Inflammatory infiltrate was found in the tissue surrounding the plasmodia as well as in the septa. (C) 2011 Elsevier B.V. All rights reserved.