verossimilhança no programa Mega 5.0. Os dados disponíveis no site Genomicus foram utilizados para a realização da sintenia e vizinhança. O padrão de evolução molecular foi estabelecido utilizando um conjunto de 23 espécies de mamíferos usando o pacote Paml 4.6. A fim de contribuir com o conhecimento da espécie Ovis aries analisou-se o gene OXTR, na raça Crioula Lanada (N=35) que apresenta um padrão distinto de seleção em comparação com as raças Ile de France (N=6) e Ideal (N=5) que são selecionadas para corte e lã. Nossos resultados indicam que OXTR, AVPR1a, AVPR1b, AVPR2 e o bloco sintênico desses receptores emergiram com o ancestral comum dos vertebrados no primeiro evento de duplicação do genoma. Primeiramente foram originados, o gene ancestral de AVPR1a e AVPR1b e o gene ancestral de OXTR e AVPR2. Os quatro receptores observados hoje se originaram após o segundo evento de duplicação do genoma ter ocorrido no ancestral comum dos vertebrados. Em termos de evolução molecular foram encontrados padrões distintos entre animais domesticados e selvagens nos receptores AVPR1a e AVPR1b. Isso indica que os animais domesticados estão sob seleção positiva para esses genes, clara marca molecular que pode estar ligada ao processo de seleção para docilidade, num contexto de evolução convergente. Para a espécie Ovis aries foi amplificado um total de 1644 pares de base (pb) obtidos do DNA das três raçasovinas estudadas. Embora tenha sido registrada variação entre as raças, não há uma quebra no padrão de evolução neutro com sinal de seleção purificadora. O que reforça a ideia que o sistema todo esteja evoluindo via os dois receptores de AVP,.

During the last 30 years, a number of alterations to the standard genetic code have been uncovered both in prokaryotes and eukaryotic nuclear and mitochondrial genomes. But, the study of the evolutionary pathways and molecular mechanisms of codon identity redefinition has been largely ignored due to the assumption that non-standard genetic codes can only evolve through neutral evolutionary mechanisms and that they have no functional significance. The recent discovery of a genetic code change in the genus Candida that evolved through an ambiguous messenger RNA decoding mechanism is bringing that naive assumption to an abrupt end by showing, in a rather dramatic way, that genetic code changes have profound physiological and evolutionary consequences for the species that redefine codon identity. In this paper, the recent data on the evolution of the Candida genetic code are reviewed and an experimental framework based on forced evolution, molecular genetics and comparative and functional genomics methodologies is put forward for the study of non-standard genetic codes and genetic code ambiguity in general. Additionally, the importance of using Saccharomyces cerevisiae as a model organism for elucidating the evolutionary pathway of the Candida and other genetic code changes is emphasised.

The molecular evolution of the clock gene period was studied in Phlebotomine sandflies (Diptera: Psychodidae). Comparison of the synonymous and nonsynonymous substitution rates between sandflies and Drosophila revealed a significantly higher evolutionary rate in the latter in three of the four regions analyzed. The differences in rate were higher in the sequences flanking the Thr-Gly repetitive domain, a region that has expanded in Drosophila but remained stable and short in sandflies, a result consistent with the coevolutionary scenario proposed for this region of the gene. An initial phylogenetic analysis including eight neotropical sandfly species and one from the Old World was also carried out. The results showed that only the subgenus Nyssomyia is well supported by distance (neighbor-joining) and maximum parsimony analysis. The grouping of the other species from the subgenus Lutzomyia and Migonei group shows very low bootstrap values and is not entirely consistent with classical morphological systematics of the genus Lutzomyia.

Background: Given the role of spA as a pivotal virulence factor decisive for Staphylococcus aureus ability to escape from innate and adaptive immune responses, one can consider it as an object subject to adaptive evolution and that variations in spA may uncover pathogenicity variations. Results: The population genetic structure was deduced from the extracellular domains of SpA gene sequence (domains A-E and the X-region) and compared to the MLST-analysis of 41 genetically diverse methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains. Incongruence between tree topologies was noticeable and in the inferred spA tree most MSSA isolates were clustered in a distinct group. Conversely, the distribution of strains according to their spA-type was not always congruent with the tree inferred from the complete spA gene foreseeing that spA is a mosaic gene composed of different segments exhibiting different evolutionary histories. Evidences of a network-like organization were identified through several conflicting phylogenetic signals and indeed several intragenic recombination events (within subdomains of the gene) were detected within and between CC’s of MRSA strains. The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a). Nevertheless, evidences of cluster specific structural arrangements were detected reflecting alterations on specific residues with potential impact on S. aureus pathogenicity. Conclusions: The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity. These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

Drosophila madeirensis is an endemic species of Madeira that inhabits the island Laurisilva forest. Nucleotide variation in D. madeirensis is analysed in six genomic regions and compared to that previously reported for the same regions in Drosophila subobscura, an abundant species in the Palearctic region that is closely related to D. madeirensis. The gene regions analysed are distributed along the O3 inversion. The O3 arrangement is monomorphic in D. madeirensis, and it was present in ancestral populations of D. subobscura but went extinct in this species after the origin of the derived OST and O3+4 arrangements. Levels of nucleotide polymorphism in D. madeirensis are similar to those present in the OST and O3+4 arrangements of D. subobscura, and the frequency spectrum is skewed towards rare variants. Purifying selection against deleterious nonsynonymous mutations is less effective in D. madeir ensis. Although D. madeirensis and D. subobscura coexist at present in Madeira, no clear evidence of introgression was detected in the studied regions.

Background Differently from HIV-1, HIV-2 disease progression usually takes decades without antiretroviral therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4+ T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected at birth. Results CD4+ T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4+ T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Conclusion Our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.

The carbonic anhydrase (CA; EC 4.2.1.1) superfamily is a class of ubiquitous metallo-enzymes that catalyse the reversible hydration of carbon dioxide. The ?-CA family, present in all metazoan clades, is a key enzyme involved in a wide range of physiological functions including pH regulation, respiration, photosynthesis, and biocalcification. This paper reviews the evolution of the ?-CA family, with an emphasis on metazoan ?-CA members involved in biocalcification. Phylogenetic analyses reveal a complex evolutionary history of ?-CAs, and suggest ?-CA was independently co-opted into a variety of skeleton forming roles (e.g. as a provider of HCO3? ions, a structural protein, a nucleation activator, etc.) in multiple metazoan lineages. This evolutionary history is most likely the result of multiple gene duplications coupled with the insertion of repetitive or non-repetitive low-complexity domains (RLCDs/LCDs). These domains, of largely unknown function, appear to be lineage-specific, and provide further support for the hypothesis of independent recruitment of ?-CAs to diverse metazoan biocalcification processes. An analysis of ?-CA sequences associated with biocalcification processes indicates that the domains involved in the activity and conformation of the active site are extremely conserved among metazoans.