Bayesian model adequacy and choice in phylogenetics

Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.     

The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The phylogenetic placement of the monotypic crab plover Dromasardeola (Aves, Charadriiformes) remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix). Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers), in agreement with previously published DNA-DNA hybridization studies.     

An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds

Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (, and ) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods ( and ) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment.     

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

Fossil taxa are critical to inferences of historical diversity and the origins of modern biodiversity, but realizing their evolutionary significance is contingent on restoring fossil species to their correct position within the tree of life. For most fossil species, morphology is the only source of data for phylogenetic inference; this has traditionally been analysed using parsimony, the predominance of which is currently challenged by the development of probabilistic models that achieve greater phylogenetic accuracy. Here, based on simulated and empirical datasets, we explore the relative efficacy of competing phylogenetic methods in terms of clade support. We characterize clade support using bootstrapping for parsimony and Maximum Likelihood, and intrinsic Bayesian posterior probabilities, collapsing branches that exhibit less than 50% support. Ignoring node support, Bayesian inference is the most accurate method in estimating the tree used to simulate the data. After assessing clade support, Bayesian and Maximum Likelihood exhibit comparable levels of accuracy, and parsimony remains the least accurate method. However, Maximum Likelihood is less precise than Bayesian phylogeny estimation, and Bayesian inference recaptures more correct nodes with higher support compared to all other methods, including Maximum Likelihood. We assess the effects of these findings on empirical phylogenies. Our results indicate probabilistic methods should be favoured over parsimony.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

Molecular phylogeny of Stentor (Ciliophora: Heterotrichea) based on small subunit ribosomal RNA sequences

To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally.     

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford–Olsen–Waddell–Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.     

Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data

Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches are temporally very long relative to internal branches. We present new mitochondrial DNA sequences, approximately 2,100 base pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families, to examine these relationships. Parsimony analysis of these mtDNA sequences supports monophyly of all families except Proteidae, but yields a tree largely unresolved with respect to interfamilial relationships and the phylogenetic positions of the proteid genera Necturus and Proteus. In contrast, Bayesian and maximum-likelihood analyses of the mtDNA data produce a topology concordant with phylogenetic results from nuclear-encoded rRNA sequences, and they statistically reject monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Phylogenetic simulations based on our mitochondrial DNA sequences reveal that Bayesian analyses outperform parsimony in reconstructing short branches located deep in the phylogenetic history of a taxon. However, phylogenetic conflicts between our results and a recent analysis of nuclear RAG-1 gene sequences suggest that statistical rejection of a monophyletic Salamandroidea by Bayesian analyses of our mitochondrial genomic data is probably erroneous. Bayesian and likelihood-based analyses may overestimate phylogenetic precision when estimating short branches located deep in a phylogeny from data showing substitutional saturation; an analysis of nucleotide substitutions indicates that these methods may be overly sensitive to a relatively small number of sites that show substitutions judged uncommon by the favored evolutionary model.     

Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1

The most plausible origin of HIV-1 group M is an SIV lineage currently represented by SIVcpz isolated from the chimpanzee subspecies Pan troglodytes troglodytes. The origin of HIV-1 group O is less clear. Putative recombination between any of the HIV-1 and SIVcpz sequences was tested using bootscanning and Bayesian-scanning plots, as well as a new method using a Bayesian multiple change-point (BMCP) model to infer parental sequences and crossing-over points. We found that in the case of highly divergent sequences, such as HIV-1/SIVcpz, Bayesian scanning and BMCP methods are more appropriate than bootscanning analysis to investigate spatial phylogenetic variation, including estimating the boundaries of the regions with discordant evolutionary relationships and the levels of support of the phylogenetic clusters under study. According to the Bayesian scanning plots and BMCP method, there was strong evidence for discordant phylogenetic clustering throughout the genome: (1) HIV-1 group O clustered with SIVcpzANT/TAN in middle pol, and partial vif/env; (2) SIVcpzGab1 clustered with SIVcpzANT/TAN in 3'pol/vif, and middle env; (3) HIV-1 group O grouped with SIVcpzCamUS and SIVcpzGab1 in p17/p24; (4) HIV-1 group M was more closely related to SIVcpzCamUS in 3'gag/pol and in middle pol, whereas in partial gp120 group M clustered with group O. Conditionally independent phylogenetic analysis inferred by maximum likelihood (ML) and Bayesian methods further confirmed these findings. The discordant phylogenetic relationships between the HIV-1/SIVcpz sequences may have been caused by ancient recombination events, but they are also due, at least in part, to altered rates of evolution between parental SIVcpz lineages.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Dissolving the star-tree paradox

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy prior as a solution (or rather dissolution) of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet.     

When phylogenetic assumptions are violated: base compositional heterogeneity and among‐site rate variation in beetle mitochondrial phylogenomics

The ability to generate large molecular datasets for phylogenetic studies benefits biologists, but such data expansion introduces numerous analytical problems. A typical molecular phylogenetic study implicitly assumes that sequences evolve under stationary, reversible and homogeneous conditions, but this assumption is often violated in real datasets. When an analysis of large molecular datasets results in unexpected relationships, it often reflects violation of phylogenetic assumptions, rather than a correct phylogeny. Molecular evolutionary phenomena such as base compositional heterogeneity and among‐site rate variation are known to affect phylogenetic inference, resulting in incorrect phylogenetic relationships. The ability of methods to overcome such bias has not been measured on real and complex datasets. We investigated how base compositional heterogeneity and among‐site rate variation affect phylogenetic inference in the context of a mitochondrial genome phylogeny of the insect order Coleoptera. We show statistically that our dataset is affected by base compositional heterogeneity regardless of how the data are partitioned or recoded. Among‐site rate variation is shown by comparing topologies generated using models of evolution with and without a rate variation parameter in a Bayesian framework. When compared for their effectiveness in dealing with systematic bias, standard phylogenetic methods tend to perform poorly, and parsimony without any data transformation performs worst. Two methods designed specifically to overcome systematic bias, LogDet and a Bayesian method implementing variable composition vectors, can overcome some level of base compositional heterogeneity, but are still affected by among‐site rate variation. A large degree of variation in both noise and phylogenetic signal among all three codon positions is observed. We caution and argue that more data exploration is imperative, especially when many genes are included in an analysis.     

利用DNA序列构建系统树的方法介绍

利用DNA序列进行系统发生分析是分子进化研究的必要手段。构建系统树的方法有距离法、简约法、最大似然法以及贝叶斯推断法等。要解决特定的系统发生问题,首先要挑选合理的分类群及序列,尽量减少数据的偏倚,然后选择构树方法,最后还要对结果进行评价并给出进化学上的解释。本文讨论了挑选数据的原则及存在的问题,介绍了几种构树方法的基本原理及步骤,并列举了它们的优缺点。Abstract: Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.     

Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

Background  

Explicit evolutionary models are required in maximum-likelihood and Bayesian inference, the two methods that are overwhelmingly used in phylogenetic studies of DNA sequence data. Appropriate selection of nucleotide substitution models is important because the use of incorrect models can mislead phylogenetic inference. To better understand the performance of different model-selection criteria, we used 33,600 simulated data sets to analyse the accuracy, precision, dissimilarity, and biases of the hierarchical likelihood-ratio test, Akaike information criterion, Bayesian information criterion, and decision theory.     

Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony,likelihood, and Bayesian approaches

The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis.     

Constraining prior probabilities of phylogenetic trees

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form.     

Molecular phylogenetics: principles and practice

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.     

The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species

The 16,678 bp mitochondrial genome of the Chrysolophus pictus has been sequenced in this paper. To determine the phylogentic position of C. pictus with related species within Phasianidae, the phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 12 heavy-strand-encoded protein genes. The phylogenetic analysis was carried out using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed similar topology and consistently suggested that C. pictus shared a close relationship with Phasianus versicolor. The results also showed that the Meleagris gallopavo possessed a basal phylogenetic position within Phasianidae, which may imply that it should be classified into the Phasianidae.     

Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.     

以雾灵山夜蛾科为材料评估进化模型对DNA条码分类的影响

为了探究进化模型对DNA条形码分类的影响, 本研究以雾灵山夜蛾科44个种的标本为材料, 获得COI基因序列。使用邻接法（neighbor-joining）、 最大简约法（maximum parsimony）、 最大似然法（maximum likelihood）以及贝叶斯法（Bayesian inference）构建系统发育树, 并且对邻接法的12种模型、 最大似然法的7种模型、 贝叶斯法的2种模型进行模型成功率的评估。结果表明, 邻接法的12种模型成功率相差不大, 较稳定; 最大似然法及贝叶斯法的不同模型成功率存在明显差异, 不稳定; 最大简约法不基于模型, 成功率比较稳定。邻接法及最大似然法共有6种相同的模型, 这6种模型在不同的方法中成功率存在差异。此外, 分子数据中存在单个物种仅有一条序列的情况, 显著降低了模型成功率, 表明在DNA条形码研究中, 每个物种需要有多个样本。