Phylogenetics and the origin of species

A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive ties are related aspects of phylogeny and jointly illuminate biotic discontinuity.

Variação geográfica, zonas de intergradação e especiação no complexo Icterus Cayanensis-Chrysocephalus (Aves : Icteridae)

O complexo Icterus cayanensis-chtysocephalus apresenta um intrincado padrão de variação em plumagem e tamanho corpóreo. São reconhecidos, tradicionalmente, para o grupo seis táxons: Icterus chtysocephalus, I. cayanensis cayanensís. I. cayanensis tibialis, I. cayanensis tibialis, I. cayanensis valenciobuenoi, I. cayanensis periporphyrus e I. cayanensis pyrrhopterus, que se substituem geograficamente ao longo de grande parte da América do Sul. Neste estudo foi feita a descrição dos padrões de variação geográfica. Foram diagnosticadas quatro espécies, à luz do conceito filogenético de espécie: Icterus cayanensis (Amazônia Meridional), Icterus chrysocephalus (Amazônia Setentrional), Icterus tibialis (Caatinga) e Icterus pyrrhopterus (Chaco); os táxons I. cayanensis valenciobuenoi e I. cayanensis periporphyrus foram sinonimizados. Entre as formas amazonicas (chrysocephalus e cayanensis) foi detectada a presença de uma zona híbrida mais extensa do que aquela reportada na literatura. No Brasil Central foi diagnosticada a maior zona de intergradação conhecida para aves, com aproximadamente 2.300 km de extensão, produto do intercruzamento entre Icterus tibialis e Icterus pyrrhopterus, formas distribuídas pela Caatinga e Chaco, respectivamente. Postula-se que as zonas de intergradação diagnosticadas neste estudo são produto do intercruzamento de populações previamente diferenciadas em isolamento geográfico.

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.

Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.

Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

Epitypification and phylogeny of Colletotrichum acutatum J.H. Simmonds

Simmonds introduced Colletotrichum acutatum in 1965, validated in 1968, with a broad concept, as demonstrated by the selection of several type specimens from a range of hosts. This has created some confusion in the species concept and identification of C. acutatum. There are no viable ex-type cultures of C. acutatum and furthermore there are no existing cultures of C. acutatum on Carica papaya from the type locality in south-east Queensland. The application of molecular phylogenetic studies to isolates of C. acutatum is only meaningful if the taxonomy is stable and species are properly named. In order to clarify the species concept of C. acutatum, an isolate of Colletotrichum acutatum from Carica papaya from Yandina in Southeast Queensland (Australia) is designated as an epitype. A detailed morphological description is provided. Phylogenies based on a combined ITS and beta-tubulin gene analysis indicate that C. acutatum bears close phylogenetic affinities to C. gloeosporioides and C. capsici. Results also indicate that C. acutatum is monophyletic and there is a close relationship between the epitype and other Australian C. acutatum isolates from Carica papaya. Molecular data, however did not provide further evidence to properly elucidate the taxonomie affinities of C. acutatum especially the holotype and epitype. Our studies indicate that given the complexity of the genus Colletotrichum, there is a need to check previously described type specimens and redesign neotypes where necessary in order to clarify taxonomie uncertainties.

Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Are there species smaller than 1 mm?

The rapid advance in genetic sequencing technologies has provided an unprecedented amount of data on the biodiversity of meiofauna. It was hoped that these data would allow the identification and counting of species, distinguished as tight clusters of similar genomes. Surprisingly, this appears not to be the case. Here, we begin a theoretical discussion of this phenomenon, drawing on an individual-based ecological model to inform our arguments. The determining factor in the emergence (or not) of distinguishable genetic clusters in the model is the product of population size with mutation rate—a measure of the adaptability of the population as a whole. This result suggests that indeed one should not expect to observe clearly distinguishable species groupings in data gathered from ultrasequencing of meiofauna.

Phylogenetic analysis reveals a high level of speciation in the Paracoccidioides genus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

DNA barcoding reveals hidden diversity in the Neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Parana Basin of Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Taxonomic status of the genus Sotalia: Species level ranking for tucuxi (Sotalia fluviatilis) and costero (Sotalia guianensis) dolphins

Dolphins of the genus Sotalia are found along the Caribbean and Atlantic coasts of Central and South America and in the Amazon River and most of its tributaries. At present, the taxonomy of these dolphins remains unresolved. Although five species were described in the late 1800s, only one species is recognized currently (Sotalia fluviatilis) with two ecotypes or subspecies, the coastal subspecies (Sotalia fluviatilis guianensis) and the riverine subspecies (Sotalia fluviatilis fluviatilis). Recent morphometric analyses, as well as mitochondrial DNA analysis, suggested recognition of each subspecies as separate species. Here we review the history of the classification of this genus and present new genetic evidence from ten nuclear and three mitochondrial genes supporting the elevation of each subspecies to the species level under the Genealogical/Lineage Concordance Species Concept and the criterion of irreversible divergence. We also review additional evidence for this taxonomic revision from previously published and unpublished genetic, morphological, and ecological studies. We propose the common name costero for the coastal species, Sotalia guianensis (Van Beneden 1864), and accept the previously proposed tucuxi dolphin, Sotalia fluviatilis (Gervais, 1853), for the riverine species.

Revisão sistemática e biogeografia da espécie politípica campylorhamphus procurvoides

A última revisão do gênero Campylorhamphus (realizada por Zimmer em 1934), definiu a espécie politípica C. procurvoides como constituída pelos seguintes táxons de diagnose tradicionalmente difícil, feita principalmente com base em caracteres de plumagem: C. p. procurvoides, C. p multostriatus, C. p. probatus, C. p. sanus e C. p. successor. O objetivo do presente estudo foi revisar a sistemática desta espécie politípica através da descrição da variação geográfica e análise crítica da validade dos táxons atualmente reconhecidos, utilizando-se caracteres morfológicos e moleculares. A análise molecular indicou com forte apoio estatístico que a espécie politípica de C. procurvoides é polifilética, uma vez que os táxons nela agrupados se encontram distribuídos em três clados distintos e não proximamente relacionado dentro do gênero Campylorhamphus. Uma análise combinada dos caracteres morfológicos e genéticos possibilitou a diagnose objetiva dos táxons procurvoides, ultostriatus, probatus e sanus, mas não de successor, que foi sinonimizada com um táxon agrupado numa outra espécie politípica (C. t. notabilis); esta mesma análise indicou a existência de dois táxons distintos previamente não reconhecidos e que aqui são diagnosticados e referidos como taxon novum 1 e táxon novum 2. Com base nas suas relações fologenéticas e diagnose consistente, os táxons considerados válidos nesta revisão e tradicionalmente tratados como subespécies de C. procurvoides, são aqui elevados ao nível de espécie com base no Conceito Filético Geral de Espécie.

Variação morfológica, vocal e genética na espécie politípica Lepidocolaptes albolineatus (Aves – Dendrocolaptidae)

Lepidocolaptes albolineatus (Aves: Dendrocolaptidae) é uma espécie biológica politípica, constituída pelos seguintes táxons: L. a. albolineatus, que ocorre na Área de Endemismo (AE) Guiana, L. a. duidae (AE Imeri), L .a. fuscicapillus (AE Rondônia), L. a. madeirae (AE Rondônia) e L. a .layardi (AEs Tapajós, Xingu e Belém). Os objetivos deste trabalho foram: (1) revisar a validade e a diagnosabilidade dos táxons atualmente agrupados em L. albolineatus com base em caracteres morfológicos, vocais e moleculares e (2) reavaliar os limites interespecíficos entre estes táxons. Foram mensurados 150 espécimes depositados em 8 museus do Brasil e EUA. Para a análise molecular, foram seqüenciados um total de 940 pb do gene mitocondrial ND2 para 35 indivíduos de todos os táxons de L. albolineatus. As análises filogenéticas foram realizadas nos programa PAUP 4.0 b 10 e MrBayes 3.1 utilizando-se os métodos de parcimônia (MP), máxima verossimilhança (MV) e inferência Bayesiana. A combinação de dados morfológicos e moleculares revelou a existência de 5 clados fortemente apoiados estatisticamente: clado 1 (agrupando indivíduos da AE Rondônia), clado 2 (agrupando espécimes das AE Belém, Xingu e Tapajós), clado 3 (incluindo espécimes da AE Inambari), clado 4 (incluindo indivíduos da AE Imeri) e clado 5 (agrupando indivíduos da AE Guiana). Todos os clados corresponderam a táxons já nomeados, exceto o clado 3 para o qual nenhum nome válido se encontra disponível, já que o nome fuscicapillus na verdade se aplica ao clado 1 e, portanto, deve ser considerado sinônimo sênior de madeirae. A principal separação genética e morfológica em L. albolineatus acontece entre o táxon nominal e os demais, embora cada um dos 5 clados possa ser considerado uma espécie distinta (com base no Conceito Filético Geral de Espécie) através de uma combinação única de caracteres morfológicos, vocais e moleculares diagnósticos.