The Supertree Tool Kit

<p>Abstract</p> <p>Background</p> <p>Large phylogenies are crucial for many areas of biological research. One method of creating such large phylogenies is the supertree method, but creating supertrees containing thousands of taxa, and hence providing a comprehensive phylogeny, requires hundred or even thousands of source input trees. Managing and processing these data in a systematic and error-free manner is challenging and will become even more so as supertrees contain ever increasing numbers of taxa. Protocols for processing input source phylogenies have been proposed to ensure data quality, but no robust software implementations of these protocols as yet exist.</p> <p>Findings</p> <p>The aim of the Supertree Tool Kit (STK) is to aid in the collection, storage and processing of input source trees for use in supertree analysis. It is therefore invaluable when creating supertrees containing thousands of taxa and hundreds of source trees. The STK is a Perl module with executable scripts to carry out various steps in the processing protocols. In order to aid processing we have added meta-data, via XML, to each tree which contains information such as the bibliographic source information for the tree and how the data were derived, for instance the character data used to carry out the original analysis. These data are essential parts of previously proposed protocols.</p> <p>Conclusions</p> <p>The STK is a bioinformatics tool designed to make it easier to process source phylogenies for inclusion in supertree analysis from hundreds or thousands of input source trees, whilst reducing potential errors and enabling easy sharing of such datasets. It has been successfully used to create the largest known supertree to date containing over 5000 taxa from over 700 source phylogenies.</p

The diversity of Class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome

DNA transposons make up three percent of the human genome, roughly the same percentage as genes. However, due to their inactivity, they are often ignored in favour of the more abundant, active, retroelements. Despite this relative ignominy, there are a number of interesting questions to be asked of these transposon families. One particular question relates to the timing of proliferation and inactivation of elements in a family. Does an ongoing process of turnover occur, or is the process more akin to a life cycle for the family, with elements proliferating rapidly before deactivation at a later date? We answer this question by tracing back to the most recent common ancestor of each modern transposon family, using two different methods. The first method identifies the most recent common ancestor of the species in which a family of transposon fossils can still be found, which we assume will have existed soon after the true origin date of the transposon family. The second method uses molecular dating techniques to predict the age of the most recent common ancestor element from which all elements found in a modern genome are descended. Independent data from five pairs of species are used in the molecular dating analysis: Human- Chimpanzee, Human-Orangutan, Dog-Panda, Dog-Cat and Cow-Pig. Orthologous pairs of elements from host species pairs are included, and the divergence dates of these species are used to constrain the analysis. We discover that, in general, the times to element common ancestry, for a given family, are the same for the different species pairs, suggesting that there has been no order-specific process of turnover. Furthermore, for most families, the ages of the common ancestor of the host species and of that of the elements are similar, suggesting a life cycle model for the proliferation of transposons. Where these two ages differ, in families found only in Primates and Rodentia, for example, we find that the host species date is later than that of the common ancestor of the elements, implying that there may be large deletions of elements from host species, examples of which were found in their ancestors

SuperTriplets: a triplet-based supertree approach to phylogenomics

Motivation: Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes and taxa. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. This task is generally conducted by a two-step approach whereby a binary representation of the initial trees is first inferred and then a maximum parsimony (MP) analysis is performed on it. This binary representation uses a decomposition of all source trees that is usually based on clades, but that can also be based on triplets or quartets. The relative performances of these representations have been discussed but are difficult to assess since both are limited to relatively small datasets

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection is an important driver of many of the most spectacular morphological traits that we find in the animal kingdom (for example see Andersson, 1994). As such, sexual selection is most often emphasized as

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies

Expression and function of human hemokinin-1 in human and guinea pig airways

<p>Abstract</p> <p>Background</p> <p>Human hemokinin-1 (hHK-1) and endokinins are peptides of the tachykinin family encoded by the <it>TAC4 </it>gene. <it>TAC4 </it>and hHK-1 expression as well as effects of hHK-1 in the lung and airways remain however unknown and were explored in this study.</p> <p>Methods</p> <p>RT-PCR analysis was performed on human bronchi to assess expression of tachykinin and tachykinin receptors genes. Enzyme immunoassay was used to quantify hHK-1, and effects of hHK-1 and endokinins on contraction of human and guinea pig airways were then evaluated, as well as the role of hHK-1 on cytokines production by human lung parenchyma or bronchi explants and by lung macrophages.</p> <p>Results</p> <p>In human bronchi, expression of the genes that encode for hHK-1, tachykinin NK₁-and NK₂-receptors was demonstrated. hHK-1 protein was found in supernatants from explants of human bronchi, lung parenchyma and lung macrophages. Exogenous hHK-1 caused a contractile response in human bronchi mainly through the activation of NK₂-receptors, which blockade unmasked a NK₁-receptor involvement, subject to a rapid desensitization. In the guinea pig trachea, hHK-1 caused a concentration-dependant contraction mainly mediated through the activation of NK₁-receptors. Endokinin A/B exerted similar effects to hHK-1 on both human bronchi and guinea pig trachea, whereas endokinins C and D were inactive. hHK-1 had no impact on the production of cytokines by explants of human bronchi or lung parenchyma, or by human lung macrophages.</p> <p>Conclusions</p> <p>We demonstrate endogenous expression of <it>TAC4 </it>in human bronchi, the encoded peptide hHK-1 being expressed and involved in contraction of human and guinea pig airways.</p

A quantitative description of the transition between intuitive altruism and rational deliberation in iterated Prisoner's Dilemma experiments

What is intuitive: pro-social or anti-social behaviour? To answer this fundamental question, recent studies analyse decision times in game theory experiments under the assumption that intuitive decisions are fast and that deliberation is slow. These analyses keep track of the average time taken to make decisions under different conditions. Lacking any knowledge of the underlying dynamics, such simplistic approach might however lead to erroneous interpretations. Here we model the cognitive basis of strategic cooperative decision making using the Drift Diffusion Model to discern between deliberation and intuition and describe the evolution of the decision making in iterated Prisoner's Dilemma experiments. We find that, although initially people's intuitive decision is to cooperate, rational deliberation quickly becomes dominant over an initial intuitive bias towards cooperation, which is fostered by positive interactions as much as frustrated by a negative one. However, this initial pro-social tendency is resilient, as after a pause it resets to the same initial value. These results illustrate the new insight that can be achieved thanks to a quantitative modelling of human behavior

Towards a supertree of Arthropoda:a species-level supertree of the spiny, slipper and coral lobsters (Decapoda: Achelata)

While supertrees have been built for many vertebrate groups (notably birds, mammals and dinosaurs), invertebrates have attracted relatively little attention. The paucity of supertrees of arthropods is particularly surprising given their economic and ecological importance, as well as their overwhelming contribution to biodiversity. The absence of comprehensive archives of machine-readable source trees, coupled with the need for software implementing repeatable protocols for managing them, has undoubtedly impeded progress. Here we present a supertree of Achelata (spiny, slipper and coral lobsters) as a proof of concept, constructed using new supertree specific software (the Supertree Toolkit; STK) and following a published protocol. We also introduce a new resource for archiving and managing published source trees. Our supertree of Achelata is synthesised from morphological and molecular source trees, and represents the most complete species-level tree of the group to date. Our findings are consistent with recent taxonomic treatments, confirming the validity of just two families: Palinuridae and Scyllaridae; Synaxidae were resolved within Palinuridae. Monophyletic Silentes and Stridentes lineages are recovered within Palinuridae, and all sub-families within Scyllaridae are found to be monophyletic with the exception of Ibacinae. We demonstrate the feasibility of building larger supertrees of arthropods, with the ultimate objective of building a complete species-level phylogeny for the entire phylum using a divide and conquer strategy