共查询到20条相似文献,搜索用时 9 毫秒
1.
Taxonomic names and phylogenetic trees 总被引:2,自引:0,他引:2
Mikael Härlin 《Zoologica scripta》1998,27(4):381-390
This paper addresses the issue of philosophy of names within the context of biological taxonomy, more specifically how names refer. By contrasting two philosophies of names, one that is based on the idea that names can be defined and one that they cannot be defined, I point out some advantages of the latter within phylogenetic systematics. Due to the changing nature of phylogenetic hypotheses, the former approach tends to rob taxonomy from its unique communicative value since a name that is defined refers to whatever fits the definition. This is particularly troublesome should the hypothesis of phylogenetic relationship change. I argue that, should we decide to accept a new phylogenetic hypothesis, it is also likely that our view of what to name may change. A system where names only refer acknowledge this, and accordingly leaves it open whether to keep a name (and accept the way it refers in the new hypothesis) or discard a name and introduce new names for the parts of the tree that we find scientifically interesting. One of the main differences between a phylogenetic system of definition (PSD) and a phylogenetic system of reference (PSR) is that the former is governed by laws of language while the latter by communicative needs of taxonomists. Thus, a PSR tends to give primacy to phylogenetic trees rather than phylogenetic definitions of names should our views of which phylogenetic hypothesis to accept change. © 1998 The Norwegian Academy of Sciences and Letters 相似文献
2.
Holmes S 《Theoretical population biology》2003,63(1):17-32
This paper poses the problem of estimating and validating phylogenetic trees in statistical terms. The problem is hard enough to warrant several tacks: we reason by analogy to rounding real numbers, and dealing with ranking data. These are both cases where, as in phylogeny the parameters of interest are not real numbers. Then we pose the problem in geometrical terms, using distances and measures on a natural space of trees. We do not solve the problems of inference on tree space, but suggest some coherent ways of tackling them. 相似文献
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MOTIVATION: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain. RESULTS: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces. 相似文献
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Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html 相似文献
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Pinelis I 《Proceedings. Biological sciences / The Royal Society》2003,270(1522):1425-1431
The most widely used evolutionary model for phylogenetic trees is the equal-rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional-to-distinguishable-arrangements (PDA) model. Here, a continuous multi-rate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from 'completely balanced' to 'completely unbalanced' models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi-stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance. 相似文献
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Background
Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to better understand the evolutionary history of genomes.Results
Here we describe PhylDiag, a software that identifies statistically significant synteny blocks in pairwise comparisons of eukaryote genomes. Compared to previous methods, PhylDiag uses gene trees to define gene homologies, thus allowing gene deletions to be considered as events that may break the synteny. PhylDiag also accounts for gene orientations, blocks of tandem duplicates and lineage specific de novo gene births. Starting from two genomes and the corresponding gene trees, PhylDiag returns synteny blocks with gaps less than or equal to the maximum gap parameter gapmax. This parameter is theoretically estimated, and together with a utility to graphically display results, contributes to making PhylDiag a user friendly method. In addition, putative synteny blocks are subject to a statistical validation to verify that they are unlikely to be due to a random combination of genes.Conclusions
We benchmark several known metrics to measure 2D-distances in a matrix of homologies and we compare PhylDiag to i-ADHoRe 3.0 on real and simulated data. We show that PhylDiag correctly identifies small synteny blocks even with insertions, deletions, incorrect annotations or micro-inversions. Finally, PhylDiag allowed us to identify the most relevant distance metric for 2D-distance calculation between homologies.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-268) contains supplementary material, which is available to authorized users. 相似文献10.
Interior-branch and bootstrap tests of phylogenetic trees 总被引:19,自引:3,他引:16
We have compared statistical properties of the interior-branch and
bootstrap tests of phylogenetic trees when the neighbor-joining tree-
building method is used. For each interior branch of a predetermined
topology, the interior-branch and bootstrap tests provide the confidence
values, PC and PB, respectively, that indicate the extent of statistical
support of the sequence cluster generated by the branch. In phylogenetic
analysis these two values are often interpreted in the same way, and if PC
and PB are high (say, > or = 0.95), the sequence cluster is regarded as
reliable. We have shown that PC is in fact the complement of the P-value
used in the standard statistical test, but PB is not. Actually, the
bootstrap test usually underestimates the extent of statistical support of
species clusters. The relationship between the confidence values obtained
by the two tests varies with both the topology and expected branch lengths
of the true (model) tree. The most conspicuous difference between PC and PB
is observed when the true tree is starlike, and there is a tendency for the
difference to increase as the number of sequences in the tree increases.
The reason for this is that the bootstrap test tends to become
progressively more conservative as the number of sequences in the tree
increases. Unlike the bootstrap, the interior-branch test has the same
statistical properties irrespective of the number of sequences used when a
predetermined tree is considered. Therefore, the interior-branch test
appears to be preferable to the bootstrap test as long as unbiased
estimators of evolutionary distances are used. However, when the
interior-branch is applied to a tree estimated from a given data set, PC
may give an overestimate of statistical confidence. For this case, we
developed a method for computing a modified version (P'C) of the PC value
and showed that this P'C tends to give a conservative estimate of
statistical confidence, though it is not as conservative as PB. In this
paper we have introduced a model in which evolutionary distances between
sequences follow a multivariate normal distribution. This model allowed us
to study the relationships between the two tests analytically.
相似文献
11.
Mossel E 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2007,4(1):108-116
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree T on n leaves with a path metric d, consider the pairwise distances {d(u,v)} between leaves. It is well known that these determine the tree and the d length of all edges. Here, we consider distortions d of d such that, for all leaves u and v, it holds that |d(u,v)-dmacr(u,v)|1.....T0 such that the true tree T may be obtained from that forest by adding alpha-1 edges and alpha-1les2-Omega(M/g)n. Our distorted metric result implies a reconstruction algorithm of phylogenetic forests with a small number of trees from sequences of length logarithmic in the number of species. The reconstruction algorithm is applicable for the general Markov model. Both the distorted metric result and its applications to phylogeny are almost tight 相似文献
12.
Richard Holmquist 《Journal of molecular evolution》1978,12(1):17-24
Summary The augmentation procedure of G.W. Moore leads to correct estimates of the total number of nucleotide substitutions separating two genes descendent from a common ancestor provided the data base is sufficiently dense. These estimates are in agreement with the true distance values from simulations of known evolutionary pathways. The estimates, on the average, are unbiased: they neither overaugment nor underaugment seriously. The variance of the population of augmented distance values reflects accurately the variance of the population of true distance values and is thus not abnormally large due to procedural defects in the algorithm.The augmented distances are in agreement with stochastic models tested on real data when the latter take proper account of the restricted mutability of codons resulting from natural selection.When the experimental data base is not dense, the augmented distance values and population variance may underestimate both the true distance values and their variance. This has a logical consequence that there exist significant and numerous errors in the ancestral sequences reconstructed by the parsimony principle from such data bases.The restrictions, resulting from natural selection, on the mutability of different nucleotide sites is shown to bear critically on the accuracy of estimates of the total number of nucleotide replacements made by stochastic models. 相似文献
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Evolutionary branching, which is a coevolutionary phenomenon of the development of two or more distinctive traits from a single trait in a population, is the issue of recent studies on adaptive dynamics. In previous studies, it was revealed that trait variance is a minimum requirement for evolutionary branching, and that it does not play an important role in the formation of an evolutionary pattern of branching. Here we demonstrate that the trait evolution exhibits various evolutionary branching paths starting from an identical initial trait to different evolutional terminus traits as determined by only changing the assumption of trait variance. The key feature of this phenomenon is the topological configuration of equilibria and the initial point in the manifold of dimorphism from which dimorphic branches develop. This suggests that the existing monomorphic or polymorphic set in a population is not an unique inevitable consequence of an identical initial phenotype. 相似文献
16.
We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade that is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P values from these individual tests. By controlling the familywise error rate or the false discovery rate (FDR), 4 different tree test methods are evaluated through simulation methods. It shows that the combination of the approximately unbiased (AU) test and the FDR-controlling procedure provides strong power along with reasonable type I error rate and less heavy computation. 相似文献
17.
Gabriel Cardona Mercè Llabrés Francesc Rosselló Gabriel Valiente 《Journal of mathematical biology》2010,61(2):253-276
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths
between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic
trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are
metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable
way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This
allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics
in spaces
Mn(\mathbb R){\mathcal{M}_n(\mathbb {R})} of real-valued n × n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined
in this way using L
p
metrics on
Mn(\mathbb R){\mathcal{M}_n(\mathbb {R})}, with ${p \in \mathbb {R}_{ >0 }}${p \in \mathbb {R}_{ >0 }}. 相似文献
18.
Liang Liu Lili Yu LauraKubatko Dennis K. Pearl Scott V. Edwards 《Molecular phylogenetics and evolution》2009,53(1):320-328
We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces. 相似文献
19.
Castresana J 《Genome biology》2007,8(6):216
A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies. 相似文献
20.
Joel D. Velasco 《Biology & philosophy》2008,23(4):455-473
Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology
remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most
often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that
a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance
and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be
derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by
the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications
may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying
Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and
about macroevolutionary processes more generally. 相似文献