Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

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Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / O presente trabalho foi conduzido no perÃodo de abril de 2006 a marÃo de 2008, nos departamentos de Zootecnia e de Biologia, da Universidade Federal do CearÃ. O objetivo desta pesquisa foi investigar, atravÃs de dados moleculares, as relaÃÃes filogenÃticas de algumas abelhas indÃgenas sem ferrÃo do tÃxon Melipona Illiger, 1806, nativas do Brasil. Procurou-se fornecer subsÃdios para facilitar uma futura revisÃo taxonÃmica sobre essas abelhas, e desse modo gerar informaÃÃes para o desenvolvimento de um criatÃrio racional, adequado Ãs diferentes espÃcies deste tÃxon, dessa forma contribuindo para o melhor aproveitamento comercial e conservaÃÃo dessas abelhas. As amostras de abelhas foram coletadas em vÃrios estados das regiÃes Norte, Nordeste e Sudeste do Brasil. Por meio da extraÃÃo, amplificaÃÃo e seqÃenciamento parcial da regiÃo ITS1 do DNA ribossÃmico nuclear dessas amostras, somadas Ãs seqÃÃncias parciais da regiÃo ITS1 de outras abelhas do mesmo tÃxon retiradas do GenBank, pÃde-se verificar os seguintes aspectos: alinhamento mÃltiplo, composiÃÃo nucleotÃdica, matriz de distÃncia genÃtica e reconstruÃÃo filogenÃtica entre as mesmas. Os resultados mostraram que o alinhamento mÃltiplo produziu uma interseÃÃo central com o comprimento de apenas 141 pb e a mÃdia da distÃncia genÃtica entre todas as seqÃÃncias estudadas do tÃxon Melipona foi de 7,6%. As Ãrvores construÃdas usando algoritmos baseados nos mÃtodos de agrupamento do vizinho mais prÃximo (NJ), mÃxima parcimÃnia (MP) e mÃxima verossimilhanÃa (MV) para as seqÃÃncias parciais da regiÃo pesquisada mostraram essencialmente a mesma topologia, sendo esta bem definida em trÃs grandes clados: Clado 1- contendo as sequÃncias de M. subnitida, M. quadrifasciata e M. mandacaia (todas pertencendo ao subgÃnero Melipona); Clado 2 â abrangendo as seqÃÃncias de M. quinquefasciata e M. fasciculata (ambas pertencendo ao subgÃnero Melikerria); Clado 3 â tendo como representantes no presente trabalho, as seqÃÃncias de M. mondury, M. flavolineata e M. scutellaris (todas pertencentes ao subgÃnero Michmelia). Todas as trÃs Ãrvores filogenÃticas foram capazes de recuperar a monofilia tanto do gÃnero Melipona como tambÃm a dos trÃs clados, que apareceram como grupos monofilÃticos / The present work was carried out from April 2006 to March 2008, in the departments of Biology and Animal Science in the Universidade Federal do CearÃ. The aim of this research was to investigate, through molecular data, the phylogenetic relationships among some Brazilian stingless bee species belonging to the taxon Melipona Illiger, 1806. It was attempted to obtain information that could facilitate a taxonomic revision of this bee group in the future and to generate information useful to the development of rational rearing adequate to the distinct species of this taxon, contributing to a better commercial exploitation and conservation of these bee species. Bee samples were collected in various states of the North, Northeast and Southeast regions of Brazil. Through the extraction, amplification and partial DNA sequencing of the ITS1 region of nuclear ribosomal DNA of those samples and the partial sequences of the ITS1 region of other bees of the same taxon searched in the GenBank, it was possible to observe the following parameters: multiple alignment, nucleotide composition, matrixes of genetic distances and phylogenetic reconstruction. Results showed that multiple alignment resulted produced a central intersection of only 141 bp long and the average of the genetic distance among all the studied sequences of the taxon Melipona was of 7,6%. The phylogenetic trees built using algorithms based on the methods of the Neighbor-Joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) for the partial sequences showed essentially the same topology, which was clearly distinct in three great clados: Clado 1 - contained the sequences of M. subnitida, M. quadrifasciata and M. mandacaia (all belonging to the subgenus Melipona); Clado 2 - included the sequences of M. quinquefasciata and M. fasciculata (both belonging to the subgenus Melikerria); and Clado 3 â represented in this work by the sequences of M. mondury, M. flavolineata and M. scutellaris (all belonging to the subgenus Michmelia). The three phylogenetic trees were capable to recover the monophyly of the genus Melipona as well as of the three clados, that appeared as monophyletic groups

MicroRNAs represent a special class of small (~21–25 nucleotides) non-coding RNA molecules which exert powerful post-transcriptional control over gene expression in eukaryotes. Indeed microRNAs likely represent the most abundant class of regulators in animal gene regulatory networks. This study describes the recovery and network analyses of a suite of homologous microRNA targets recovered through two different prediction methods for whole gene regions across twelve Drosophila species. Phylogenetic criteria under an accepted tree topology were used as a reference frame to 1) make inference into microRNA-target predictions, 2) study mathematical properties of microRNA-gene regulatory networks, 3) and conduct novel phylogenetic analyses using character data derived from weighted edges of the microRNA-target networks. This study investigates the evidences of natural selection and phylogenetic signatures inherent within the microRNA regulatory networks and quantifies time and mutation necessary to rewire a microRNA regulatory network. Selective factors that appear to operate upon seed aptamers include cooperativity (redundancy) of interactions and transcript length. Topological analyses of microRNA regulatory networks recovered significant enrichment for a motif possessing a redundant link in all twelve species sampled. This would suggest that optimization of the whole interactome topology itself has been historically subject to natural selection where resilience to attack have offered selective advantage. It seems that only a modest number of microRNA–mRNA interactions exhibit conservation over Drosophila cladogenesis. The decrease in conserved microRNA-target interactions with increasing phylogenetic distance exhibited a cure typical of a saturation phenomena. Scale free properties of a network intersection of microRNA target predictions methods were found to transect taxonomic hierarchy.

Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.

Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.