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At least 19 recordsLinked to original sources

PubMed2005

Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.

Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining (NJ) algorithm have been proposed, as well as a number of methods to estimate protein distances. We here present a large-scale assessment of performance in reconstructing the correct tree topology for the most popular algorithms. The programs BIONJ, FastME, Weighbor, and standard NJ were run using 12 distance estimators, producing 48 tree-building/distance estimation method combinations. These were evaluated on a test set based on real trees taken from 100 Pfam families. Each tree was used to generate multiple sequence alignments with the ROSE program using three evolutionary models. The accuracy of each method was analyzed as a function of both sequence divergence and location in the tree. We found that BIONJ produced the overall best results, although the average accuracy differed little between the tree-building methods (normally less than 1%). A noticeable trend was that FastME performed poorer than the rest on long branches. Weighbor was several orders of magnitude slower than the other programs. Larger differences were observed when using different distance estimators. Protein-adapted Jukes-Cantor and Kimura distance correction produced clearly poorer results than the other methods, even worse than uncorrected distances. We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods.

Base Sequence↗

PubMed1996

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.

The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.

Algorithms↗

PubMed2001

Efficiencies of genes and accuracy of tree-building methods in recovering a known Drosophila genealogy.

Phylogenetic hypotheses generated from seven Drosophila mitochondrial genomes support a well-corroborated genealogy with a single evolutionary history. These mitochondrial data form a model system for investigating the efficiency of genes and accuracy of different tree-building methods in recovering a well-supported genealogy. We consider 15 genes (13 protein-coding and 2 rRNAs) and 83 tree-building methods (27 distance, 4 parsimony, 50 maximum likelihood, and 2 Bayesian). Among the 15 genes examined, ND4 recovered the true genealogy most efficiently (82 out of 83 methods). Generally, maximum likelihood models enforcing a clock most accurately reclaim the true genealogy. Surprisingly, however, this method fails to recover the well-supported topology for more than half of the genes. Additional studies are required to test the generality of the results presented here.

Animals↗

PubMed2006

SDM: a fast distance-based approach for (super) tree building in phylogenomics.

Phylogenomic studies aim to build phylogenies from large sets of homologous genes. Such "genome-sized" data require fast methods, because of the typically large numbers of taxa examined. In this framework, distance-based methods are useful for exploratory studies and building a starting tree to be refined by a more powerful maximum likelihood (ML) approach. However, estimating evolutionary distances directly from concatenated genes gives poor topological signal as genes evolve at different rates. We propose a novel method, named super distance matrix (SDM), which follows the same line as average consensus supertree (ACS; Lapointe and Cucumel, 1997) and combines the evolutionary distances obtained from each gene into a single distance supermatrix to be analyzed using a standard distance-based algorithm. SDM deforms the source matrices, without modifying their topological message, to bring them as close as possible to each other; these deformed matrices are then averaged to obtain the distance supermatrix. We show that this problem is equivalent to the minimization of a least-squares criterion subject to linear constraints. This problem has a unique solution which is obtained by resolving a linear system. As this system is sparse, its practical resolution requires O(naka) time, where n is the number of taxa, k the number of matrices, and a < 2, which allows the distance supermatrix to be quickly obtained. Several uses of SDM are proposed, from fast exploratory studies to more accurate approaches requiring heavier computing time. Using simulations, we show that SDM is a relevant alternative to the standard matrix representation with parsimony (MRP) method, notably when the taxa sets of the different genes have low overlap. We also show that SDM can be used to build an excellent starting tree for an ML approach, which both reduces the computing time and increases the topogical accuracy. We use SDM to analyze the data set of Gatesy et al. (2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions.

Algorithms↗

PubMed2005

Heterotachy and tree building: a case study with plastids and eubacteria.

The nature of heterotachy at the center of recent controversy over the relative performance of tree-building methods is different from the form of heterotachy that has been inferred in empirical studies. The latter have suggested that proportions of variable sites (p(var)) vary among orthologues and among paralogues. However, the strength of this inference, describing what may be one of the most important evolutionary properties of sequence data, has remained weak. Consequently, other models of sequence evolution have been proposed to explain some long-branch attraction (LBA) problems that could be attributed to differences in p(var). For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm using capture-recapture estimates and simulations that p(var) can differ among orthologues in anciently diverged evolutionary lineages. We find that parsimony and a least squares distance method that implements an overly simple model of sequence evolution are susceptible to LBA induced by this form of heterotachy. Although homogeneous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so.

Bacteria↗

PubMed1996

Phylogenetic tree-building.

Cladistic analysis is an approach to phylogeny reconstruction that groups taxa in such a way that those with historically more-recent ancestors form groups nested within groups of taxa with more-distant ancestors. This nested set of taxa can be represented as a branching diagram or tree (a cladogram), which is an hypothesis of the evolutionary history of the taxa. The analysis is performed by searching for nested groups of shared derived character states. These shared derived character states define monophyletic groups of taxa (clades), which include all of the descendants of the most recent common ancestor. If all of the characters for a set of taxa are congruent, then reconstructing the phylogenetic tree is unproblematic. However, most real data sets contain incongruent characters, and consequently a wide range of tree-building methods has been developed. These methods differ in a variety of characteristics, and they may produce topologically distinct trees for a single data set. None of the currently-available methods are simultaneously efficient, powerful, consistent and robust, and thus there is no single ideal method. However, many of them appear to perform well under a wide range of conditions, with the exception of the UPGMA method and the Invariants method.

Algorithms↗

PubMedDate not supplied

Primer on medical decision analysis: Part 2--Building a tree.

This part of a five-part series covering practical issues in the performance of decision analysis outlines the basic strategies for building decision trees. The authors offer six recommendations for building and programming decision trees. Following these six recommendations will facilitate performance of the sensitivity analyses required to achieve two goals. The first is to find modeling or programming errors, a process known as "debugging" the tree. The second is to determine the robustness of the qualitative conclusions drawn from the analysis.

Decision Making, Computer-Assisted↗

PubMed2002

QuickTree: building huge Neighbour-Joining trees of protein sequences.

We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods.

Algorithms↗

PubMed2002

Shade trees reduce building energy use and CO2 emissions from power plants.

Urban shade trees offer significant benefits in reducing building air-conditioning demand and improving urban air quality by reducing smog. The savings associated with these benefits vary by climate region and can be up to $200 per tree. The cost of planting trees and maintaining them can vary from $10 to $500 per tree. Tree-planting programs can be designed to have lower costs so that they offer potential savings to communities that plant trees. Our calculations suggest that urban trees play a major role in sequestering CO2 and thereby delay global warming. We estimate that a tree planted in Los Angeles avoids the combustion of 18 kg of carbon annually, even though it sequesters only 4.5-11 kg (as it would if growing in a forest). In this sense, one shade tree in Los Angeles is equivalent to three to five forest trees. In a recent analysis for Baton Rouge, Sacramento, and Salt Lake City, we estimated that planting an average of four shade trees per house (each with a top view cross section of 50 m2) would lead to an annual reduction in carbon emissions from power plants of 16,000, 41,000, and 9000 t, respectively (the per-tree reduction in carbon emissions is about 10-11 kg per year). These reductions only account for the direct reduction in the net cooling- and heating-energy use of buildings. Once the impact of the community cooling is included, these savings are increased by at least 25%.

Air Conditioning↗

PubMed2005

Towards building the tree of life: a simulation study for all angiosperm genera.

Comprehensive phylogenetic trees are essential tools to better understand evolutionary processes. For many groups of organisms or projects aiming to build the Tree of Life, comprehensive phylogenetic analysis implies sampling hundreds to thousands of taxa. For the tree of all life this task rises to a highly conservative 13 million. Here, we assessed the performances of methods to reconstruct large trees using Monte Carlo simulations with parameters inferred from four large angiosperm DNA matrices, containing between 141 and 567 taxa. For each data set, parameters of the HKY85+G model were estimated and used to simulate 20 new matrices for sequence lengths from 100 to 10,000 base pairs. Maximum parsimony and neighbor joining were used to analyze each simulated matrix. In our simulations, accuracy was measured by counting the number of nodes in the model tree that were correctly inferred. The accuracy of the two methods increased very quickly with the addition of characters before reaching a plateau around 1000 nucleotides for any sizes of trees simulated. An increase in the number of taxa from 141 to 567 did not significantly decrease the accuracy of the methods used, despite the increase in the complexity of tree space. Moreover, the distribution of branch lengths rather than the rate of evolution was found to be the most important factor for accurately inferring these large trees. Finally, a tree containing 13,000 taxa was created to represent a hypothetical tree of all angiosperm genera and the efficiency of phylogenetic reconstructions was tested with simulated matrices containing an increasing number of nucleotides up to a maximum of 30,000. Even with such a large tree, our simulations suggested that simple heuristic searches were able to infer up to 80% of the nodes correctly.

Base Sequence↗

PubMed2004

DPRml: distributed phylogeny reconstruction by maximum likelihood.

MOTIVATION: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood-based phylogenetic analysis. RESULTS: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses an already proven maximum likelihood-based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near-linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a 'free' ML supercomputer.

Algorithms↗

PubMed2000

The art of building decision trees.

Decision support systems that help physicians are becoming a very important part of medical decision making. They are based on different models and the best of them are providing an explanation together with an accurate, reliable, and quick response. One of the most viable among models are decision trees, already successfully used for many medical decision-making purposes. Although effective and reliable, the traditional decision tree construction approach still contains several deficiencies. Therefore we decided to develop and compare several decision support models using four different approaches. We took statistical analysis, a MtDeciT, in our laboratory developed tool for building decision trees with a classical method, the well-known C5.0 tool and a self-adapting evolutionary decision support model that uses evolutionary principles for the induction of decision trees. Several solutions were evolved for the classification of metabolic and respiratory acidosis (MRA). A comparison between developed models and obtained results has shown that our approach can be considered as a good choice for different kinds of real-world medical decision making.

Acidosis, Respiratory↗

PubMed2001

The phylogenetic analysis of variable-length sequence data: elongation factor-1alpha introns in European populations of the parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae).

Elongation factor-1alpha (EF-1alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using congruence as a criterion for assessing a range of methods for aligning such variable-length EF-1alpha intron sequences. These methods included distance- and parsimony-based multiple-alignment programs (CLUSTAL W and MALIGN), direct optimization (POY), and two "by eye" alignment strategies. Furthermore, with one method (CLUSTAL W) we explored in detail the robustness of results to changes in the gap cost parameters. Phenetic-based alignments ("by eye" and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more demanding, methods. In general, all of our alignment and tree-building strategies recovered the same basic topological structure, which means that an underlying phylogenetic signal remained regardless of the strategy chosen. However, several relationships between clades were sensitive both to alignment and to tree-building protocol. Further alignments, considering only sequences belonging to the same group, allowed us to infer a range of phylogenetic relationships that were highly robust to tree-building protocol. By comparing these topologies with those obtained by varying the CLUSTAL parameters, we generated the distribution area of congruence and taxonomic compatibility. Finally, we present the first robust estimate of the European Pauesia phylogeny by using two EF-1alpha introns and 38 taxa (plus 3 outgroups). This estimate conflicts markedly with the traditional subgeneric classification. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.

Animals↗

PubMedDate not supplied

A novel method for building regression tree models for QSAR based on artificial ant colony systems.

Among the multitude of learning algorithms that can be employed for deriving quantitative structure-activity relationships, regression trees have the advantage of being able to handle large data sets, dynamically perform the key feature selection, and yield readily interpretable models. A conventional method of building a regression tree model is recursive partitioning, a fast greedy algorithm that works well in many, but not all, cases. This work introduces a novel method of data partitioning based on artificial ants. This method is shown to perform better than recursive partitioning on three well-studied data sets.

Algorithms↗

PubMed2006

Phylogenetic analyses of parasites in the new millennium.

Phylogenetic analysis has changed greatly in the last decade, and the most important themes in that change are reviewed here. Sequence data have become the most common source of phylogenetic information. This means that explicit models for evolutionary processes have been developed in a likelihood context, which allow more realistic data analyses. These models are becoming increasingly complex, both for nucleotides and for amino acid sequences, and so all such models need to be quantitatively assessed for each data set, to find the most appropriate one for use in any particular tree-building analysis. Bayesian analysis has been developed for tree-building and is greatly increasing in popularity. This is because a good heuristic strategy exists, which allows large data sets to be analyzed with complex evolutionary models in a practical time. Perhaps the most disappointing aspect of tree interpretation is the ongoing confusion between rooted and unrooted trees, while the effect of taxon and character sampling is often overlooked when constructing a phylogeny (especially in parasitology). The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted in the review.

Animals↗

PubMed1999

Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia).

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter: supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources. Beyond providing a 'consensus' estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Animals↗

PubMed2001

An algorithm for constructing local regions in a phylogenetic network.

The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a tree-building program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the tree-building program as "The Tree." This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example.

Algorithms↗

PubMed2004

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.

Animals↗