Phylogeny of the genus Stephomyia Tavares, 1916 (Diptera: Cecidomyiidae) / Filogenia do gênero Stephomyia Tavares, 1916 (Diptera: Cecidomyiidae)

Abstract Stephomyia Tavares, 1916 comprises seven species, all Neotropical: S. clavata (Tavares, 1920); S. epeugeniae Gagné, 1994; S. espiralis Maia, 1993; S. mina Maia, 1993; S. rotundifoliorum Maia, 1993; S. tetralobae Maia, 1993; and S. eugeniae (Felt, 1913). In the present study, a cladistic analysis based upon adult, pupa, larva and gall morphological characters as well as host plant data is carried out in order to discuss the monophyly of the genus and the relationships among the known species. The Stephomyia monophyly was supported by eight synapomorphies: five homoplastic characters and three non-homoplastic characters. Analyzes showed S. clavata with great instability within the genus, probably due to lack of larva, pupa and female data, so S. clavata was deactivated in analyze. The topology found was (S. mina ((S. eugeniae + S. epeugeniae) (S. tetralobae (S. rotundifoliorum + S. espiralis)))).

Resumo Stephomyia Tavares, 1916 compreende sete espécies, todas neotropicais: S. clavata (Tavares, 1920); S. epeugeniae Gagné, 1994; S. espiralis Maia, 1993; S. mina Maia, 1993; S. rotundifoliorum Maia, 1993; S. tetralobae Maia, 1993 e S. eugeniae (Felt, 1913). Neste estudo, uma análise cladística baseada em caracteres morfológicos dos adultos, pupa, larva e galha, bem como na informação das plantas hospedeiras é realizada e a monofilia do gênero e as relações entre as espécies conhecidas são discutidas. A monofilia de Stephomyia foi suportada por oito sinapomorfias: cinco caracteres homoplásticos e três não homoplásticos. Análises mostraram uma grande instabilidade de S. clavata dentro do gênero, provavelmente devido à falta de informações sobre a larva, a pupa e a fêmea, o que resultou em desativação na análise. A topologia encontrada foi (S. mina ((S. eugeniae + S. epeugeniae) (S. tetralobae (S. rotundifoliorum + S. espiralis)))).

Phylogeny of the genus Stephomyia Tavares, 1916 (Diptera: Cecidomyiidae)

Abstract Stephomyia Tavares, 1916 comprises seven species, all Neotropical: S. clavata (Tavares, 1920); S. epeugeniae Gagné, 1994; S. espiralis Maia, 1993; S. mina Maia, 1993; S. rotundifoliorum Maia, 1993; S. tetralobae Maia, 1993; and S. eugeniae (Felt, 1913). In the present study, a cladistic analysis based upon adult, pupa, larva and gall morphological characters as well as host plant data is carried out in order to discuss the monophyly of the genus and the relationships among the known species. The Stephomyia monophyly was supported by eight synapomorphies: five homoplastic characters and three non-homoplastic characters. Analyzes showed S. clavata with great instability within the genus, probably due to lack of larva, pupa and female data, so S. clavata was deactivated in analyze. The topology found was (S. mina ((S. eugeniae + S. epeugeniae) (S. tetralobae (S. rotundifoliorum + S. espiralis)))).

Resumo Stephomyia Tavares, 1916 compreende sete espécies, todas neotropicais: S. clavata (Tavares, 1920); S. epeugeniae Gagné, 1994; S. espiralis Maia, 1993; S. mina Maia, 1993; S. rotundifoliorum Maia, 1993; S. tetralobae Maia, 1993 e S. eugeniae (Felt, 1913). Neste estudo, uma análise cladística baseada em caracteres morfológicos dos adultos, pupa, larva e galha, bem como na informação das plantas hospedeiras é realizada e a monofilia do gênero e as relações entre as espécies conhecidas são discutidas. A monofilia de Stephomyia foi suportada por oito sinapomorfias: cinco caracteres homoplásticos e três não homoplásticos. Análises mostraram uma grande instabilidade de S. clavata dentro do gênero, provavelmente devido à falta de informações sobre a larva, a pupa e a fêmea, o que resultou em desativação na análise. A topologia encontrada foi (S. mina ((S. eugeniae + S. epeugeniae) (S. tetralobae (S. rotundifoliorum + S. espiralis)))).

The dawn of phylogenetic research on Neotropical fishes: a commentary and introduction to Baskin (1973), with an overview of past progress on trichomycterid phylogenetics

A review is made of the impact of the landmark Ph. D. Thesis of Jonathan N. Baskin from 1973 on the development of the phylogenetics of catfishes and some of its main subgroups and on neotropical ichthyology in general. Baskin's work is the first to propose a hypothesis of relationships for loricarioid catfishes and for the family Trichomycteridae on the basis of explicit Hennigian principles. It is arguably also the first application of phylogenetic methods to any group of neotropical fishes. The hypotheses presented by Baskin covered the monophyly of Siluriformes, the monophyly and relationships of loricarioid families and the relationships of Trichomycteridae (including the monophyly of the family and the relationships among its constituent genera). His discoveries are analyzed in view of the subsequent 40-odd years of progress on the understanding of the phylogeny of the respective groups. The ideas proposed in 1973 have resisted the test of time remarkably well, and a majority of them have been corroborated by additional characters and taxa (including molecular data and several taxa newly discovered in the meantime), as well as by modern quantitative analysis.

Um ensaio é realizado sobre o impacto da tese de doutorado pioneira de 1973 de Jonathan N. Baskin no desenvolvimento do conhecimento filogenético de Siluriformes e alguns dos seus principais subgrupos e na ictiologia neotropical em geral. O trabalho de Baskin é o primeiro a propor uma hipótese de relações para os bagres loricarioides e para a família Trichomycteridae com base em princípios Hennigianos explícitos. Provavelmente é também a primeira implementação de métodos filogenéticos em qualquer grupo de peixes de água doce neotropicais. As hipóteses apresentadas por Baskin cobrem o monofiletismo de Siluriformes, o monofiletismo e as relações filogenéticas das famílias de Loricarioidea, e as relações filogenéticas de Trichomycteridae (incluindo o monofiletismo da família e as relações entre seus gêneros constituintes). Suas descobertas são analisadas à luz dos mais de 40 anos de progresso no entendimento da filogenia dos respectivos grupos. As ideias propostas em 1973 resistiram ao teste do tempo bastante bem e a maioria delas foi corroborada por caracteres ou táxons adicionais (incluindo dados moleculares e muitos táxons descobertos no interim), assim como por análises quantitativas mais modernas.

Romance of the three domains: how cladistics transformed the classification of cellular organisms

Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig's 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960-1980. In 1977-1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.

The phylogeny of Simulium (Chirostilbia) (Diptera: Simuliidae) and perspectives on the systematics of the genus in the Neotropical Region

Recently, knowledge of Neotropical Simuliidae has been accumulating quickly. However, information about supra-specific relationships is scarce and diagnoses of Simulium subgenera are unsatisfactory. To investigate the relationships among Simulium (Chirostilbia) species and test the subgenus monophyly, we performed a cladistic analysis. The ingroup included all species of this subgenus and the outgroup included representatives of the 17 species groups of Neotropical Simulium and three Holarctic species. The study was based on a data matrix with 31 terminal taxa and 45 morphological characteristics of adult, pupa and larva. The phylogenetic analysis under equal weights resulted in eight most-parsimonious trees (length = 178, consistency index = 34, retention index = 67). The monophyly of the S. (Chirostilbia) was not supported in our analysis. The Simulium subpallidum species group was closer to Simulium (Psilopelmia) and Simulium (Ectemnaspis) than to the Simulium pertinax species group. Additionally, we describe the three-dimensional shape of the terminalia of male and female of Simulium (Chirostilbia) for the first time and provide comments about the taxonomic problems involving some species of the subgenus: Simulium acarayense, Simulium papaveroi, S. pertinax, Simulium serranum, Simulium striginotum and S. subpallidum.

New morphological aspects and phylogenetic considerations of Cicindis Bruch (Coleoptera: Carabidae: Cicindini)

Cicindis Bruch is a monospecific genus of carabid beetles endemic to Argentina. In this contribution, Cicindis horni Bruch is re-described, with addition of new morphological features of male internal sac, female genital tract and elytral closure. New information on the species' habitat and distribution is also provided. The phylogenetic placement and relationships of Cicindis within the family Carabidae are discussed on the basis of a cladistic analysis. Terminal taxa included representatives of all subfamilies of Carabidae and supertribes of Carabinae, with a major sampling of those taxa considered to be closely related to Cicindini by previous authors. The phylogenetic analysis shows the basal position of Cicindis in a clade that includes Ozaeninae, Omophronini, Scaritinae and Conjuncta. A close relationship of Cicindis with Ozaenini + Metriini is supported by the particular closure of the procoxa and the ventral position of the oviduct with respect to the spermatheca.

Invalidación de autapomorfías putativas mediante análisis de filogenia molecular en Anopheles subgénero Nyssorhynchus / Invalidation of putative autapomorphic characters using molecular phylogenetic analyses in Anopheles subgenus Nyssorhynchus

Colectas e identificaciones realizadas en un área de transmisión malárica en el estado Sucre, Venezuela, mostraron mediante el uso de las claves ad hoc, la posible presencia en simpatría de poblaciones de Anopheles aquasalis Curry y An. benarrochi Gabaldón, Cova-García & López. Adicionalmente, se detectaron poblaciones de individuos que mostraron mezcla de los caracteres diagnósticos señalados en las claves. Debido a la importancia epidemiológica que representan ambas especies en dicha zona malárica, este estudio se orientó hacia la determinación de las tres entidades señaladas, mediante filogenia molecular con las secuencias de ADN mitocondrial (region Citocromo Oxidasa 1). En este sentido, el concepto de especie filogenética fue evaluada utilizando análisis de parsimonia máxima que mostraron politomías (nodos no resueltos) fuertemente apoyadas entre las secuencias inclusive la del haplotipo proveniente de un macho identificado como aquasalis, mostrando hipótesis (árboles) totales sin resolución ni apoyo de grupos internos con los tres morfotipos como un grupo natural único. Las distancias genéticas (Kimura-2P) mostraron que la variablidad inter-morfotipos están dentro de la varianza intra sugiriendo que los haplotipos problema son una única entidad polimórfica y con plasticidad fenotípica. Se concluye que An. aquasalis es la entidad única de las poblaciones estudiadas y que los caracteres morfológicos como: 1) vena Medial con escamas negras y 2) palpos maxilares con superficie ventral cubierta de escamas blancas, que son propuestas en la mayoría de las claves no son caracteres válidos para la identificación de hembras de An. benarrochi y que tales caracteres forman parte de la variación intraespecífica en An. aquasalis. Esta conclusión apoya la revisión de Faran (1980), quién no propone caracteres diferenciales para hembras de ambas especies, siendo indistinguibles por medio de los caracteres morfológicos tradicionalmente utilizados.

Collected specimens from a malaric area in Sucre State, Venezuela, using the ad hoc Keys, were identified as Anopheles aquasalis Curry and An. benarrochi Gabaldón, Cova-García & López populations. Additionally, other individuals have shown a mixture of diagnostic characters of both species. As a consequence of the epidemiological importance that both species represent in this malaric area and its correct identification for vector control aims, we addressed the research to the determination of both entities by mean of phylogenetic methods using mitochondrial DNA (Cytochrome Oxidase 1) from these three entities. In order to evaluate the phylogenetic species concept, the Maximum Parsimony analyses showed strong supported politomies (unresolved nodes), yielded solutions with no supported groups correlated with two or three morphological entities including the male haplotype identified as An. aquasalis. The genetic distances (K-2P) showed that the variability inter-morphotype is in the variance intra, suggesting that the haplotypes belong to the three morphotypes and represent a unique polymorphic species with phenotypic plasticity. We conclude that An. aquasalis is a unique taxonomic entity in the populations studied and also that the morphological characters such as: 1) medial vein with black scales and 2) maxillary palpus with ventral surface covered with white scales, proposed in most of the keys used are not valid characters to distinguish females of An. benarrochi from An. aquasalis as these characters belong to the intra-specific variation of An. aquasalis. This conclusion supports the Faran (1980) key, which did not report any morphological characters, showing undistinguished females under classical characters used

A molecular method for a qualitative analysis of potentially coding sequences of DNA

Total sequence phylogenies have low information content. Ordinary misconceptions are that character quality can be ignored and that relying on computer algorithms is enough. Despite widespread preference for a posteriori methods of character evaluation, a priori methods are necessary to produce transformation series that are independent of tree topologies. We propose a stepwise qualitative method for analyzing protein sequences. Informative codons are selected, alternative amino acid transformation series are analyzed, and most parsimonious transformations are hypothesized. We conduct four phylogenetic analyses of philodryanine snakes. The tree based on all nucleotides produces least resolution. Trees based on the exclusion of third positions, on an asymmetric step matrix, and on our protocol, produce similar results. Our method eliminates noise by hypothesizing explicit transformation series for each informative protein-coding amino acid. This approaches qualitative methods for morphological data, in which only characters successfully interpreted in a phylogenetic context are used in cladistic analyses. The method allows utilizing character information contained in the original sequence alignment and, therefore, has higher resolution in inferring a phylogenetic tree than some traditional methods (such as distance methods).

Filogenias baseadas em seqüências totais têm baixo conteúdo informativo. Erros comuns são acreditar que a qualidade dos caracteres pode ser ignorada e que é suficiente confiar nos algoritmos computacionais. Apesar de ampla preferência por métodos a posteriori para a avaliação de caracteres, métodos a priori tornam-se necessários para produzir séries de transformação independentes das topologias das árvores. Propomos um método qualitativo passo a passo para analisar seqüências de proteínas. Codons informativos são selecionados, séries de transformação alternativas de aminoácidos são analisadas e as transformações mais parcimoniosas são hipotetizadas. Conduzimos quatro análises filogenéticas em cobras Phylodrininae. A árvore baseada em todos os nucleotídeos produz a menor resolução. Árvores baseadas na exclusão das terceiras posições, numa matriz de passos assimétrica, e em nosso protocolo de análise produzem resultados similares. Nosso método elimina ruído ao hipotetizar séries de transformação explícitas para cada aminoácido informativo para a codificação de proteínas. Essa abordagem se aproxima de métodos qualitativos para dados morfológicos, nos quais apenas caracteres interpretados com sucesso num contexto filogenético são usados em análises cladísticas. O método permite utilizar informação de caracteres contidos no alinhamento original da seqüência e, portanto, tem maior poder de resolução para inferir árvores filogenéticas que alguns métodos tradicionais (como métodos de distância).

Triatominae (Hemiptera: Reduviidae): Systematic questions and some others / Triatominae (Hemiptera: Reduviidae): Questões sistemáticas e algumas outras

The Neotropical Chagas' disease vectors are classified as members of the reduviid subfamily Triatominae. However, this classification has been suggested to be incorrect, and the suggestion has been treated as fact by some authors; the suggestion is that some (all?) groups in Triatominae had different nontriatomine reduviid ancestors. In this article I raise this question explicitly and ask other questions ancillary to it. I do not answer these questions. Of particular interest is the systematic position of Linshcosteus, the only genus of Triatominae all of whose species occur outside the New World (in India). Related to this question is that of the origin(s) of the several species and populations probably derived from the tropicopolitan Triatoma rubrofasciata (De Geer). Answering these questions is of more than academic interest, for if triatomines had more than one nontriatomine ancestor, and therefore are not phylogenetically close, it is impossible to generalize what is known about one group to others, and this inability may hinder control of these disease vectors. It is therefore vital (literally!) to determine if Triatominae is a holophyletic group and, if not, to determine which groups now classified as triatomines are related to which others. This determination may best be accomplished with a cladistic analysis of the genera now included in Triatominae. Some comments on cladistics are presented in an Appendix.

Os vetores da doença de Chagas são classificados como membros dos reduviídeos da sub-família Triatominae. Entretanto, essa classificação tem sido referida como incorreta por alguns autores, que consideram que alguns (ou todos?) os grupos de Triatominae têm diferentes ancestrais não-triatomíneos. Neste artigo essa questão é discutida amplamente e outras questões relacionadas ao tema são também levantadas, em particular a posição sistemática de Linshcosteus, o único gênero de Triatominae que ocorre fora do Novo Mundo (na índia). Outro exemplo é o fato de diversas espécies e populações terem derivado da espécie tropical Triatoma rubrofasciata (De Geer). A resposta a essas questões - se os triatomíneos têm mais de um ancestral não-triatomíneo e, portanto, seriam filogeneticamente distantes - não tem apenas interesse acadêmico. É impossível generalizar para todos os grupos o que é conhecido apenas para um grupo, e isso pode prevenir o controle desses vetores de doenças. Portanto, é literalmente vital determinar se Triatominae é um grupo holofilético e, se não, quais grupos classificados como triatomíneos são relacionados entre si. Essa determinação poderá ser feita através da análise cladística dos generos atualmente incluídos em Triatominae. Alguns comentários sobre cladística são apresentados em um Apêndice.