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

A simulation study comparing supertree and combined analysis methods using SMIDGen

<p>Abstract</p> <p>Background</p> <p>Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.</p> <p>Results</p> <p>In this paper, we describe an extensive simulation study we performed comparing two supertree methods, MRP and weighted MRP, to combined analysis methods on large model trees. A key contribution of this study is our novel simulation methodology (Super-Method Input Data Generator, or <it>SMIDGen</it>) that better reflects biological processes and the practices of systematists than earlier simulations. We show that combined analysis based upon maximum likelihood outperforms MRP and weighted MRP, giving especially big improvements when the largest subtree does not contain most of the taxa.</p> <p>Conclusions</p> <p>This study demonstrates that MRP and weighted MRP produce distinctly less accurate trees than combined analyses for a given base method (maximum parsimony or maximum likelihood). Since there are situations in which combined analyses are not feasible, there is a clear need for better supertree methods. The source tree and combined datasets used in this study can be used to test other supertree and combined analysis methods.</p

Inferring the Tree of Life: chopping a phylogenomic problem down to size?

The combination of molecular sequence data and bioinformatics has revolutionized phylogenetic inference over the past decade, vastly increasing the scope of the evolutionary trees that we are able to infer. A recent paper in BMC Biology describing a new phylogenomic pipeline to help automate the inference of evolutionary trees from public sequence databases provides another important tool in our efforts to derive the Tree of Life

Colony size predicts division of labour in Attine ants

Division of labour is central to the ecological success of eusocial insects, yet the evolutionary factors driving increases in complexity in division of labour are little known. The size–complexity hypothesis proposes that, as larger colonies evolve, both non-reproductive and reproductive division of labour become more complex as workers and queens act to maximize inclusive fitness. Using a statistically robust phylogenetic comparative analysis of social and environmental traits of species within the ant tribe Attini, we show that colony size is positively related to both non-reproductive (worker size variation) and reproductive (queen–worker dimorphism) division of labour. The results also suggested that colony size acts on non-reproductive and reproductive division of labour in different ways. Environmental factors, including measures of variation in temperature and precipitation, had no significant effects on any division of labour measure or colony size. Overall, these results support the size–complexity hypothesis for the evolution of social complexity and division of labour in eusocial insects. Determining the evolutionary drivers of colony size may help contribute to our understanding of the evolution of social complexity

Colony size predicts division of labour in Attine ants

Division of labour is central to the ecological success of eusocial insects, yet the evolutionary factors driving increases in complexity in division of labour are little known. The size–complexity hypothesis proposes that, as larger colonies evolve, both non-reproductive and reproductive division of labour become more complex as workers and queens act to maximize inclusive fitness. Using a statistically robust phylogenetic comparative analysis of social and environmental traits of species within the ant tribe Attini, we show that colony size is positively related to both non-reproductive (worker size variation) and reproductive (queen–worker dimorphism) division of labour. The results also suggested that colony size acts on non-reproductive and reproductive division of labour in different ways. Environmental factors, including measures of variation in temperature and precipitation, had no significant effects on any division of labour measure or colony size. Overall, these results support the size–complexity hypothesis for the evolution of social complexity and division of labour in eusocial insects. Determining the evolutionary drivers of colony size may help contribute to our understanding of the evolution of social complexity

Do we still need supertrees?

The up-dated species level phylogeny for the carnivores using a supertree approach provides new insights into the evolutionary origin and relationships of carnivores. While the gain in biological knowledge is substantial, the supertree approach is not undisputed. I discuss the principles of supertree methods and the competitor supermatrix approaches. I argue that both methods are important to infer phylogenetic relationships

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

An experimental study of Quartets MaxCut and other supertree methods

<p>Abstract</p> <p>Background</p> <p>Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algorithmic supertree method.</p> <p>Results</p> <p>We evaluated the performance of several supertree methods based upon the Quartets MaxCut (QMC) method of Snir and Rao and showed that two of these methods usually outperform MRP and five other supertree methods that we studied, under many realistic model conditions. However, the QMC-based methods have scalability issues that may limit their utility on large datasets. We also observed that taxon sampling impacted supertree accuracy, with poor results obtained when all of the source trees were only sparsely sampled. Finally, we showed that the popular optimality criterion of minimizing the total topological distance of the supertree to the source trees is only weakly correlated with supertree topological accuracy. Therefore evaluating supertree methods on biological datasets is problematic.</p> <p>Conclusions</p> <p>Our results show that supertree methods that improve upon MRP are possible, and that an effort should be made to produce scalable and robust implementations of the most accurate supertree methods. Also, because topological accuracy depends upon taxon sampling strategies, attempts to construct very large phylogenetic trees using supertree methods should consider the selection of source tree datasets, as well as supertree methods. Finally, since supertree topological error is only weakly correlated with the supertree's topological distance to its source trees, development and testing of supertree methods presents methodological challenges.</p

Global cooling as a driver of diversification in a major marine clade

Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems