Performance of flip supertree construction with a heuristic algorithm

Supertree methods are used to assemble separate phylogenetic trees with shared taxa into larger trees (supertrees) in an effort to construct more comprehensive phylogenetic hypotheses. In spite of much recent interest in supertrees, there are still few methods for supertree construction. The flip supertree problem is an error correction approach that seeks to find a minimum number of changes (flips) to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees. We developed a heuristic algorithm for the flip supertree problem suitable for much larger input trees. We used a series of 48- and 96-taxon simulations to compare supertrees constructed with the flip supertree heuristic algorithm with supertrees constructed using other approaches, including MinCut (MC), modified MC (MMC), and matrix representation with parsimony (MRP). Flip supertrees are generally far more accurate than supertrees constructed using MC or MMC algorithms and are at least as accurate as supertrees built with MRP. The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large.     

Clann: investigating phylogenetic information through supertree analyses

SUMMARY: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. AVAILABILITY: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request.     

Problems with supertrees based on the subtree prune‐and‐regraft distance,with comments on majority rule supertrees

This paper examines a recent proposal to calculate supertrees by minimizing the sum of subtree prune‐and‐regraft distances to the input trees. The supertrees thus calculated may display groups present in a minority of the input trees but contradicted by the majority, or groups that are not supported by any input tree or combination of input trees. The proponents of the method themselves stated that these are serious problems of “matrix representation with parsimony”, but they can in fact occur in their own method. The majority rule supertrees, being explicitly clade‐based, cannot have these problems, and seem much more suited to retrieving common clades from a set of trees with different taxon sets. However, it is dubious that so‐called majority rule supertrees can always be interpreted as displaying those clades present (or compatible with) with a majority of the trees. The majority rule consensus is always a median tree, in terms of the Robinson–Foulds distances (i.e. it minimizes the sum of Robinson–Foulds distances to the input trees). In contrast, majority rule supertrees may not be median—different, contradictory trees may minimize Robinson–Foulds distances, while their strict consensus does not. If being “majority” results from being median in Robinson–Foulds distances, this means that in the supertree setting a “majority” is ambiguously defined, sometimes achievable only by mutually contradictory trees.     

PhySIC_IST: cleaning source trees to infer more informative supertrees

Background  

Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees.     

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.     

Fast local search for unrooted Robinson-Foulds supertrees

A Robinson-Foulds (RF) supertree for a collection of input trees is a tree containing all the species in the input trees that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing RF supertrees for rooted and unrooted data is NP-hard. Nevertheless, effective local search heuristics have been developed for the restricted case where the input trees and the supertree are rooted. We describe new heuristics, based on the Edge Contract and Refine (ECR) operation, that remove this restriction, thereby expanding the utility of RF supertrees. Our experimental results on simulated and empirical data sets show that our unrooted local search algorithms yield better supertrees than those obtained from MRP and rooted RF heuristics in terms of total RF distance to the input trees and, for simulated data, in terms of RF distance to the true tree.     

Semi-strict supertrees

A method to calculate semi‐strict supertrees is proposed. The semi‐strict supertrees are calculated by creating the matrix that represents all the groups in the source trees (as done in already existing techniques), and then finding the trees determined by the ultra‐clique. The ultra‐clique is defined as the set of characters where each possible subset is compatible with each possible subset from the entire matrix. Finding the ultra‐clique is computationally complex (since in most cases many of the characters have missing entries), but a heuristic method yields reliable results. When the trees have no conflict, or when there are only two trees, the method produces the exact result for any ordering of the input trees and any ordering of the groups within them; when there are more than two trees and they have conflict, a single ordering or sequence can create some spurious groups, but doing multiple sequences eliminates the spurious groups. The method uses only state set operations, and is thus easily implemented in computer programs. Unlike any existing type of supertree, semi‐strict supertrees display all the groups, and only those groups, that are implied by at least some combination of the input trees and contradicted by none. The idea that supertrees should take into account the number of occurences of a given group, so as to retain some groups even in the case of conflict, is discussed; it is argued that a conceptual equivalent of the majority rule consensus is not possible when the sets of taxa differ among trees. Also, when pruning taxa from a set of trees, the supertree can display groups that contradict the consensus for the entire trees, suggesting that supertrees for matrices with very dissimilar sets of taxa should be interpreted with caution. If (for any valid reason) the data cannot be combined in a single matrix, it is advisable that the taxon sets in the matrices be as similar as possible.     

Robinson-Foulds Supertrees

Background  

Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods based on the well established Robinson-Foulds (RF) distance have the potential to build supertrees that retain much information from the input trees. Specifically, the RF supertree problem seeks a binary supertree that minimizes the sum of the RF distances from the supertree to the input trees. Thus, an RF supertree is a supertree that is consistent with the largest number of clusters (or clades) from the input trees.     

Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees

Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study, I investigated the frequency of unsupported clades in both simulated and empirical MRP supertrees. Here, I propose a new index, QS, to quantify the qualitative support for a supertree and its clades among the set of source trees. Results show that unsupported clades are very rare in MRP supertrees, occurring most often when there are few source trees that all possess the same set of taxa. However, even under these conditions the frequency of unsupported clades was <0.2%. Unsupported clades were absent from both the Carnivora and Lagomorpha supertrees, reflecting the use of large numbers of source trees for both. The proposed QS indices are correlated broadly with another measure of quantitative clade support (bootstrap frequencies, as derived from resampling of the MRP matrix) but appear to be more sensitive. More importantly, they sample at the level of the source trees and thus, unlike the bootstrap, are suitable for summarizing the support of MRP supertree clades.     

Phylogenetic diversity,structure and diversification patterns of endemic plants along the elevational gradient in the Eastern Himalaya

ABSTRACT

Background: Several studies have documented the variation in species diversity patterns along elevational gradients in the Himalaya, but few have reported the evolutionary and biogeographic processes behind these patterns.

Aims: To understand whether evolutionary history and phylogeny have any role in structuring plant species communities along an elevational gradient in the Sikkim Himalaya.

Methods: We used data on endemic plant species occurrence from primary and secondary sources to construct family-level phylogenetic supertrees for different growth forms with the help of Phylomatic tool of Phylocom. These phylogenetic supertrees were used as a base for testing phylogenetic diversity (PD), niche conservatism, diversification time patterns and phylogenetic structure of various plant growth forms along an elevational gradient.

Results: PD was the highest at mid-elevations for all growth forms and PD had a significant positive correlation with endemic species richness. Species at mid-elevations were dominated by the ancestral/primitive taxa. There was phylogenetic clustering at higher elevations and phylogenetic overdispersion at lower and mid-elevations for the majority of the growth forms.

Conclusions: Time-for-speciation effect and niche conservatism along elevation (retention of niche-related ancestral elevational distribution over evolutionary time scale by species) together determine plant species diversity patterns in the Himalaya.     

A supertree of temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods

As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus including minority components shows slightly greater resolution than other supertrees, and its shape matches well several currently accepted hypotheses of higher-level phylogeny for temnospondyls as a whole. Also, its node support is higher than those of other supertrees (except the combined standard plus Purvis MRP supertree). We explore the distribution of significant as well as informative changes (shifts) in branch splitting employing the standard MRP supertree as a reference, and discuss the temporal distribution of changes in time-sliced, pruned trees derived from this supertree. Also, we analyse those shifts that are most relevant to the end-Permian mass extinction. For the Palaeozoic, shifts occur almost invariably along branches that connect major Palaeozoic groups. By contrast, shifts in the Mesozoic occur predominantly within major groups. Numerous shifts bracket narrowly the end-Permian extinction, indicating not only rapid recovery and extensive diversification of temnospondyls over a short time period after the extinction event (possibly less than half a million years), but also the role of intense cladogenesis in the late part of the Permian (although this was counteracted by numerous 'background' extinctions).     

Phylogenetic supertrees: Assembling the trees of life

Systematists and comparative biologists commonly want to make statements about relationships among taxa that have never been collectively included in any single phylogenetic analysis. Construction of phylogenetic 'supertrees' provides one solution. Supertrees are estimates of phylogeny assembled from sets of smaller estimates (source trees) sharing some but not necessarily all their taxa in common. If certain conditions are met, supertrees can retain all or most of the information from the source trees and also make novel statements about relationships of taxa that do not co-occur on any one source tree. Supertrees have commonly been constructed using subjective and informal approaches, but several explicit approaches have recently been proposed.     

Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study

For the last 2 decades, supertree reconstruction has been an active field of research and has seen the development of a large number of major algorithms. Because of the growing popularity of the supertree methods, it has become necessary to evaluate the performance of these algorithms to determine which are the best options (especially with regard to the supermatrix approach that is widely used). In this study, seven of the most commonly used supertree methods are investigated by using a large empirical data set (in terms of number of taxa and molecular markers) from the worldwide flowering plant family Sapindaceae. Supertree methods were evaluated using several criteria: similarity of the supertrees with the input trees, similarity between the supertrees and the total evidence tree, level of resolution of the supertree and computational time required by the algorithm. Additional analyses were also conducted on a reduced data set to test if the performance levels were affected by the heuristic searches rather than the algorithms themselves. Based on our results, two main groups of supertree methods were identified: on one hand, the matrix representation with parsimony (MRP), MinFlip, and MinCut methods performed well according to our criteria, whereas the average consensus, split fit, and most similar supertree methods showed a poorer performance or at least did not behave the same way as the total evidence tree. Results for the super distance matrix, that is, the most recent approach tested here, were promising with at least one derived method performing as well as MRP, MinFlip, and MinCut. The output of each method was only slightly improved when applied to the reduced data set, suggesting a correct behavior of the heuristic searches and a relatively low sensitivity of the algorithms to data set sizes and missing data. Results also showed that the MRP analyses could reach a high level of quality even when using a simple heuristic search strategy, with the exception of MRP with Purvis coding scheme and reversible parsimony. The future of supertrees lies in the implementation of a standardized heuristic search for all methods and the increase in computing power to handle large data sets. The latter would prove to be particularly useful for promising approaches such as the maximum quartet fit method that yet requires substantial computing power.     

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

Many traits have been linked to extinction risk among modern vertebrates, including mode of life and body size. However, previous work has indicated there is little evidence that body size, or any other trait, was selective during past mass extinctions. Here, we investigate the impact of the Triassic–Jurassic mass extinction on early Archosauromorpha (basal dinosaurs, crocodylomorphs and their relatives) by focusing on body size and other life history traits. We built several new archosauromorph maximum‐likelihood supertrees, incorporating uncertainty in phylogenetic relationships. These supertrees were then employed as a framework to test whether extinction had a phylogenetic signal during the Triassic–Jurassic mass extinction, and whether species with certain traits were more or less likely to go extinct. We find evidence for phylogenetic signal in extinction, in that taxa were more likely to become extinct if a close relative also did. However, there is no correlation between extinction and body size, or any other tested trait. These conclusions add to previous findings that body size, and other traits, were not subject to selection during mass extinctions in closely‐related clades, although the phylogenetic signal in extinction indicates that selection may have acted on traits not investigated here.     

New Territories for Anthropologists

Genetic Nature/Culture: Anthropology and Science beyond the Two-Culture Divide . Alan H. Goodman, Deborah Heath, M. Susan Lindee, eds. Berkeley: University of California Press, 2003. 328 pp.
Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People . Joan Roughgarden. Berkeley: University of California Press, 2004. 474 pp.     

Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping

The estimation of ever larger phylogenies requires consideration of alternative inference strategies, including divide-and-conquer approaches that decompose the global inference problem to a set of smaller, more manageable component problems. A prominent locus of research in this area is the development of supertree methods, which estimate a composite tree by combining a set of partially overlapping component topologies. Although promising, the use of component tree topologies as the primary data dissociates supertrees from complexities within the underling character data and complicates the evaluation of phylogenetic uncertainty. We address these issues by exploring three approaches that variously incorporate nonparametric bootstrapping into a common supertree estimation algorithm (matrix representation with parsimony, although any algorithm might be used), including bootstrap-weighting, source-tree bootstrapping, and hierarchical bootstrapping. We illustrate these procedures by means of hypothetical and empirical examples. Our preliminary experiments suggest that these methods have the potential to improve the correspondence of supertree estimates to those derived from simultaneous analysis of the combined data and to allow uncertainty in supertree topologies to be quantified. The ability to increase the transparency of supertrees to the underlying character data has several practical implications and sheds new light on an old debate. These methods have been implemented in the freely available program, tREeBOOT.     

Molecular cloning of an IL-8-like CXC chemokine and tissue factor in rainbow trout (Oncorhynchus mykiss) by use of suppression subtractive hybridization

Suppression subtractive hybridization (SSH) was performed to construct a Rainbow trout cDNA library enriched in sequences up-regulated in head kidney leukocytes after lipopolysaccharide (LPS) and tumour necrosis factor alpha (TNFalpha) stimulation. Random sequencing of fifty clones allowed the identification of a Rainbow trout interleukin 8 (IL-8)-related CXC chemokine, as well as the Rainbow trout tissue factor (TF) precursor. Expression of both the IL-8-like chemokine and TF is induced after LPS and TNFalpha stimulation, indicating that they are associated with inflammatory responses in fish, as has been suggested in mammals. These results confirm the potential of SSH to identify cytokines and immuno-regulatory genes in fish.     

A Rainbow of Gangs: Street Cultures of the Mega-City

A Rainbow of Gangs: Street Cultures of the Mega-City . James Diego Vigil. Austin: University of Texas Press, 2002. 213 pp.     

Adding time-calibrated branch lengths to the Asteraceae supertree

New inference techniques,such as supertrees,have improved the construction of large phylogenies,helping to reveal the tree of life.In addition,these large phylogenies have enhanced the study of other evolutionary questions,such as whether traits have evolved in a neutral or adaptive way,or what factors have influenced diversification.However,supertrees usually lack branch lengths,which are necessary for all these issues to be investigated.Here,divergence times within the largest family of flowering plants,namely the Asteraceae,are reviewed to estimate time-calibrated branch lengths in the supertree of this lineage.An inconsistency between estimated dates of basal branching events and the earliest asteraceous fossil pollen record was detected.In addition,the impact of different methods of branch length assignment on the total number of transitions between states in the reconstruction of sexual system evolution in Asteraceae was investigated.At least for this dataset,different branch length assignation approaches influenced maximum likelihood(ML)reconstructions only and not Bayesian ones.Therefore,the selection of different branch length information is not arbitrary and should be carefully assessed,at least when ML approaches are being used.The reviewed divergence times and the estimated time-calibrated branch lengths provide a useful tool for future phylogenetic comparative and macroevolutionary studies of Asteraceae.