Phylogenetic analysis of 16S mitochondrial DNA data in sloths and anteaters

We sequenced part of the 16S rRNA mitochondrial gene in 17 extant taxa of Pilosa (sloths and anteaters) and used these sequences along with GenBank sequences of both extant and extinct sloths to perform phylogenetic analysis based on parsimony, maximum-likelihood and Bayesian methods. By increasing the taxa density for anteaters and sloths we were able to clarify some points of the Pilosa phylogenetic tree. Our mitochondrial 16S results show Bradypodidae as a monophyletic and robustly supported clade in all the analysis. However, the Pleistocene fossil Mylodon darwinii does not group significantly to either Bradypodidae or Megalonychidae which indicates that trichotomy best represents the relationship between the families Mylodontidae, Bradypodidae and Megalonychidae. Divergence times also allowed us to discuss the taxonomic status of Cyclopes and the three species of three-toed sloths, Bradypus tridactylus, Bradypus variegatus and Bradypus torquatus. In the Bradypodidae the split between Bradypus torquatus and the proto-Bradypus tridactylus / B. variegatus was estimated as about 7.7 million years ago (MYA), while in the Myrmecophagidae the first offshoot was Cyclopes at about 31.8 MYA followed by the split between Myrmecophaga and Tamandua at 12.9 MYA. We estimate the split between sloths and anteaters to have occurred at about 37 MYA.

A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia

A phylogenetic analysis based on nuclear ITS and plastid trnK intron sequences confirms that Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia are members of the Cryptocarya group, as expected from morphology. Dahlgrenodendron from South Africa is sister to Aspidostemon from Madagascar. Triadodaphne inaequitepala is nested within Endiandra (both from Australasia), and Yasunia from South America is nested among South American Beilschmiedia species. Sinopora is a member of the Beilschmiedia clade, but its precise position is still uncertain. Among large genera of the group, Cryptocarya is clearly monophyletic, and Endiandra appears to be as well, if T. inaequitepala is included. Beilschmiedia is paraphyletic with respect to (at least) Potameia and Yasunia. Most well-supported clades within genera are geographically homogeneous, except a clade including the Chilean Cryptocarya alba and two New Caledonian species. Both Beilschmiedia and Cryptocarya have reached the Americas more than once. Four-locular anthers are plesiomorphic in the Cryptocarya group; two-locular anthers have arisen by fusion of the two pollen sacs of a theca. In the plesiomorphic fruit type, the ovary is completely enclosed in receptacular tissue; a superior fruit, seated free on its pedicel, is a synapomorphy of the Beilschmiedia clade.

Entoepidemiology of Chagas disease in northwest Sao Paulo and cytogenetic analysis of its main vector, Triatoma sordida (Hemiptera: Triatominae)

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

Molecular detection and phylogenetic analysis of bovine astrovirus in Brazil

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

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)

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 analysis of rubella virus strains during an outbreak in Sao Paulo, 2007-2008

Rubella virus (RV) is an important human pathogen that causes rubella, an acute contagious disease. It also causes severe birth defects collectively known as congenital rubella syndrome when infection occurs during the first trimester of pregnancy. Here, we present the phylogenetic analysis of RV that circulated in Sao Paulo during the 20072008 outbreak. Samples collected from patients diagnosed with rubella were isolated in cell culture and sequenced. RV RNA was obtained from samples or RV-infected cell cultures and amplified by reverse transcriptase-polymerase chain reaction. Sequences were assigned to genotypes by phylogenetic analysis using RV reference sequences. Seventeen sequences were analyzed, and three genotypes were identified: 1a, 1G, and 2B. Genotypes 1a and 1G, which were isolated in 2007, were responsible for sporadic rubella cases in Sao Paulo. Thereafter, in late 2007, the epidemiological conditions changed, resulting in a large RV outbreak with the clear dominance of genotype 2B. The results of this study provide new approaches for monitoring the progress of elimination of rubella from Sao Paulo, Brazil. J. Med. Virol. 84:16661671, 2012. (c) 2012 Wiley Periodicals, Inc.

Phylogenetic analysis of Codium species from Brazil, with the description of the new species C. pernambucensis (Bryopsidales, Chlorophyta)

The genus Codium comprises c. 125 species widely distributed in marine coastal environments throughout the world. Due to morphological plasticity, the taxonomic delimitation of Codium species can be difficult. Sequences of the first exon of the large subunit of RUBISCO (rbcL) have been used in the molecular delimitation of species and for phylogenetic purposes. In the present study, we complement previous morphological work on Brazilian Codium species with molecular systematics. Based on the partial rbcL sequences, seven species are recognized along the Brazilian coast: C. decorticatum, C. intertextum, C. isthmocladum, C. profundum, C. spongiosum, C. taylorii and the new species Codium pernambucensis. Ten unique sequences were obtained among the samples examined, which we used in combination with previously published sequences to infer molecular phylogenies using various methods. The resulting trees showed three principal monophyletic groupings: Clade A with species having a prostrate habit, not branched, and mostly with small, grouped utricles; Clade B primarily consisting of upright species with cylindrical branches and large individual utricles; and Clade C composed of upright species with cylindrical branches that are slightly flattened, and have intermediate-sized individual utricles. The Brazilian species grouped with morphologically similar taxa from other geographic localities, and are present in all three main clades. A new sprawling species, Codium pernambucensis is described based on morphology and molecular analyses.

Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.

Molecular characterization and phylogenetic analysis of small ruminant lentiviruses isolated from Canadian sheep and goats

Background: Small Ruminant Lentiviruses (SRLV) are widespread in Canadian sheep and goats and represent an important health issue in these animals. There is however no data about the genetic diversity of Caprine Arthritis Encephalitis Virus (CAEV) or Maedi Visna Virus (MVV) in this country. Findings: We performed a molecular and phylogenetic analysis of sheep and goat lentiviruses from a small geographic area in Canada using long sequences from the gag region of 30 infected sheep and 36 infected goats originating from 14 different flocks. Pairwise DNA distance and phylogenetic analyses revealed that all SRLV sequences obtained from sheep clustered tightly with prototypical Maedi visna sequences from America. Similarly, all SRLV strains obtained from goats clustered tightly with prototypical US CAEV-Cork strain. Conclusions: The data reported in this study suggests that Canadian and US SRLV strains share common origins. In addition, the molecular data failed to bring to light any evidence of past cross species transmission between sheep and goats, which is consistent with the type of farming practiced in this part of the country where single species flocks predominate and where opportunities of cross species transmissions are proportionately low.

Phylogenetic analysis of "Candidatus Mycoplasma turicensis" isolates from pet cats in the United Kingdom, Australia, and South Africa, with analysis of risk factors for infection

Two hemotropic mycoplasmas have been recognized in cats, Mycoplasma haemofelis and "Candidatus Mycoplasma haemominutum." We recently described a third feline hemoplasma species, designated "Candidatus Mycoplasma turicensis," in a Swiss cat with hemolytic anemia. This isolate induced anemia after experimental transmission to two specific-pathogen-free cats and analysis of the 16S rRNA gene revealed its close relationship to rodent hemotropic mycoplasmas. The agent was recently shown to be prevalent in Swiss pet cats. We sought to investigate the presence and clinical importance of "Candidatus Mycoplasma turicensis" infection in pet cats outside of Switzerland and to perform the molecular characterization of isolates from different countries. A "Candidatus Mycoplasma turicensis"-specific real-time PCR assay was applied to blood samples from 426 United Kingdom (UK), 147 Australian, and 69 South African pet cats. The 16S rRNA genes of isolates from different countries were sequenced and signalment and laboratory data for the cats were evaluated for associations with "Candidatus Mycoplasma turicensis" infection. Infections were detected in samples from UK, Australian, and South African pet cats. Infection was associated with the male gender, and "Candidatus Mycoplasma haemominutum" and M. haemofelis coinfection. Coinfected cats exhibited significantly lower packed cell volume (PCV) values than uninfected cats. Phylogenetic analyses revealed that some Australian and South African "Candidatus Mycoplasma turicensis" isolates branched away from the remaining isolates. In summary, "Candidatus Mycoplasma turicensis" infection in pet cats exists over a wide geographical area and significantly decreased PCV values are observed in cats coinfected with other feline hemoplasmas.