Tales of the flying earth: The effect of host flyways on the phylogeny of shorebird lice (Phthiraptera: Ischnocera)
05 Apr 2012-
About: The article was published on 2012-04-05 and is currently open access. It has received 10 citations till now. The article focuses on the topics: Ischnocera & Philopteridae.
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TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Abstract: The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/. (Algorithm; computer simulations; maximum likelihood; phylogeny; rbcL; RDPII project.) The size of homologous sequence data sets has in- creased dramatically in recent years, and many of these data sets now involve several hundreds of taxa. More- over, current probabilistic sequence evolution models (Swofford et al., 1996 ; Page and Holmes, 1998 ), notably those including rate variation among sites (Uzzell and Corbin, 1971 ; Jin and Nei, 1990 ; Yang, 1996 ), require an increasing number of calculations. Therefore, the speed of phylogeny reconstruction methods is becoming a sig- nificant requirement and good compromises between speed and accuracy must be found. The maximum likelihood (ML) approach is especially accurate for building molecular phylogenies. Felsenstein (1981) brought this framework to nucleotide-based phy- logenetic inference, and it was later also applied to amino acid sequences (Kishino et al., 1990). Several vari- ants were proposed, most notably the Bayesian meth- ods (Rannala and Yang 1996; and see below), and the discrete Fourier analysis of Hendy et al. (1994), for ex- ample. Numerous computer studies (Huelsenbeck and Hillis, 1993; Kuhner and Felsenstein, 1994; Huelsenbeck, 1995; Rosenberg and Kumar, 2001; Ranwez and Gascuel, 2002) have shown that ML programs can recover the cor- rect tree from simulated data sets more frequently than other methods can. Another important advantage of the ML approach is the ability to compare different trees and evolutionary models within a statistical framework (see Whelan et al., 2001, for a review). However, like all optimality criterion-based phylogenetic reconstruction approaches, ML is hampered by computational difficul- ties, making it impossible to obtain the optimal tree with certainty from even moderate data sets (Swofford et al., 1996). Therefore, all practical methods rely on heuristics that obtain near-optimal trees in reasonable computing time. Moreover, the computation problem is especially difficult with ML, because the tree likelihood not only depends on the tree topology but also on numerical pa- rameters, including branch lengths. Even computing the optimal values of these parameters on a single tree is not an easy task, particularly because of possible local optima (Chor et al., 2000). The usual heuristic method, implemented in the pop- ular PHYLIP (Felsenstein, 1993 ) and PAUP ∗ (Swofford, 1999 ) packages, is based on hill climbing. It combines stepwise insertion of taxa in a growing tree and topolog- ical rearrangement. For each possible insertion position and rearrangement, the branch lengths of the resulting tree are optimized and the tree likelihood is computed. When the rearrangement improves the current tree or when the position insertion is the best among all pos- sible positions, the corresponding tree becomes the new current tree. Simple rearrangements are used during tree growing, namely "nearest neighbor interchanges" (see below), while more intense rearrangements can be used once all taxa have been inserted. The procedure stops when no rearrangement improves the current best tree. Despite significant decreases in computing times, no- tably in fastDNAml (Olsen et al., 1994 ), this heuristic becomes impracticable with several hundreds of taxa. This is mainly due to the two-level strategy, which sepa- rates branch lengths and tree topology optimization. In- deed, most calculations are done to optimize the branch lengths and evaluate the likelihood of trees that are finally rejected. New methods have thus been proposed. Strimmer and von Haeseler (1996) and others have assembled four- taxon (quartet) trees inferred by ML, in order to recon- struct a complete tree. However, the results of this ap- proach have not been very satisfactory to date (Ranwez and Gascuel, 2001 ). Ota and Li (2000, 2001) described
16,261 citations
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
Abstract: PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
14,385 citations
TL;DR: Molecular processes are reviewed, the correction of genetic distances and the weighting of DNA data are discussed, and an assessment of the phylogenetic usefulness of specific mitochondrial genes is provided.
Abstract: DNA-sequence data from the mitochondrial genome are being used with increasing frequency to estimate phylogenetic relationships among animal taxa. The advantage to using DNA-sequence data is that many of the processes governing the evolution and inheritance of DNA are already understood. DNA data, however, do not guarantee the correct phylogenetic tree because of problems associated with shared ancestral polymorphisms and multiple substitutions at single nucleotide sites. Knowledge of evolutionary processes can be used to improve estimates of patterns of relationships and can help to assess the phylogenetic usefulness of individual genes and nucleotides. This article reviews molecular processes, discusses the correction of genetic distances and the weighting of DNA data, and provides an assessment of the phylogenetic usefulness of specific mitochondrial genes. The Appendix presents a compilation of conserved polymerase chain reaction primers that can be used to amplify virtually any gene in the mitochondrial genome. DNA data sets vary tremendously in degree of phylogenetic usefulness. Correction or weighting (or both) of DNA-sequence data based on level of variability can improve results in some cases. Gene choice is of critical importance. For studies of relationships among closely related species, the use of ribosomal genes can be problematic, whereas unconstrained sites in protein coding genes appear to have fewer problems. In addition, information from studies of amino acid substitutions in rapidly evolving genes may help to decipher close relationships. For intermediate levels of divergence where silent sites contain many multiple hits, amino acid changes can be useful for construction phylogenetic relationships. For deep levels of divergence, protein coding genes may be saturated at the amino acid level and highly conserved regions of ribosomal RNA and transfer RNA genes may be useful. Because of the arbitrariness of taxonomic categories, no sweeping generalizations can be made about the taxonomic rank at which particular genes are useful. As more DNA-sequence data accumulate, we will be able to gain an even better understanding of the way in which genes and species evolve.
5,623 citations
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..., 1994), 12SAI and 12SBI (12S; Simon et al., 1994), 16SAR and 16SBR (16S; Simon et al....
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TL;DR: This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods.
Abstract: Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.
1,833 citations
"Tales of the flying earth: The effe..." refers background in this paper
..., 2011), with no close living relatives (Hackett et al., 2008)....
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...Several large-scale phylogenies spanning the whole Charadriiformes are also available (Ericson et al., 2003; Paton et al., 2003; Thomas et al., 2004b; Paton and Baker, 2006; Baker et al., 2007; Fain and Houde, 2007; Hackett et al., 2008; Ödeen et al., 2010)....
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...However, despite their morphological and behavioural heterogeneity, the shorebirds form a monophyletic group of birds (Faine and Houde, 2004, 2007; Ericson et al, 2006; Hackett et al., 2008; Pásko et al., 2011), with no close living relatives (Hackett et al....
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TL;DR: In this article, the authors express the opinions of the individual evaluators regarding the strengths, weaknesses, and value of the books they review, as such the appraisals are subjective assessments and do not necessarily refl ect the opinion of the editors or any offi cial policy of the American Ornithologists' Union.
Abstract: Abstract The following critiques express the opinions of the individual evaluators regarding the strengths, weaknesses, and value of the books they review. As such, the appraisals are subjective assessments and do not necessarily refl ect the opinions of the editors or any offi cial policy of the American Ornithologists' Union.
760 citations
"Tales of the flying earth: The effe..." refers background in this paper
...In a few cases, these populations have been given subspecific status (Dickinson, 2003; Message and Taylor, 2005)....
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