Efficacy or convenience? Model‐based approaches to phylogeny estimation using morphological data

Model‐based approaches (e.g. maximum likelihood, Bayesian inference) are widely used with molecular data, where they might be more appropriate than maximum parsimony for estimating phylogenies under various models of molecular evolution. Recently, there has been an increase in the application of model‐based approaches with morphological (mainly fossil) data; however, there is some doubt as to the effectiveness of the model of morphological evolution. The input parameters (prior probabilities) for the model are unclear, particularly when concerned with unobserved character states. Despite this, some systematists are suggesting superiority of these model‐based methods over maximum parsimony based on, for example, increased resolution or, in the current study, the preferred phylogenetic placement of an iconic taxon. Here, we revisit a recently published analysis implying such superiority and document the discrepancies between parsimony‐based and model‐based approaches to phylogeny estimation. We find that although some taxa are shifted back to their “traditional” phylogenetic placement, other clades are disturbed. The model‐based phylogenies are better resolved; however, due to the lack of an appropriate model of morphological evolution, the increase in resolving power is probably not meaningful. Similarly, some of the preferred phylogenetic positions of taxa, particularly of labile taxa such as Archaeopteryx, are based solely on analyses employing maximum parsimony as the optimality criterion. Poor resolution and labile taxa indicate a need for further examination of the morphology and not a change in method.     

Homology assessment in parsimony and model‐based analyses: two sides of the same coin

The present paper is mainly concerned with homology assessment through phylogenetic analyses. It raises a fundamental question: What are the epistemological differences between modern parsimony and model‐based analyses in relation to homology assessment and phylogenetic inference? Although these methods usually achieve concordant topological results, they may generate discordant inferences of character evolution from the same datasets. This indicates that method selection has serious implications for evolutionary scenarios and classificatory arrangements. Notwithstanding that parsimony and model‐based approaches use the Hennigian concepts of monophyly and synapomorphy, they employ different epistemological ways of dealing with the monophyly/synapomorphy relationship. Independently of their differences, these analyses should take into account all relevant evidence in support of the phylogenetic inferences. A focus on morphological homologues means that they must be included in data matrices, evaluated as part of the phylogenetic analysis, and cannot be ignored in calculation of the tree(s) length (parsimony), maximum‐likelihood (maximum‐likelihood), and posterior probabilities (Bayes).     

The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters

We tested whether it is beneficial for the accuracy of phylogenetic inference to sample characters that are evolving under different sets of parameters, using both Bayesian MCMC (Markov chain Monte Carlo) and parsimony approaches. We examined differential rates of evolution among characters, differential character-state frequencies and character-state space, and differential relative branch lengths among characters. We also compared the relative performance of parsimony and Bayesian analyses by progressively incorporating more of these heterogeneous parameters and progressively increasing the severity of this heterogeneity. Bayesian analyses performed better than parsimony when heterogeneous simulation parameters were incorporated into the substitution model. However, parsimony outperformed Bayesian MCMC when heterogeneous simulation parameters were not incorporated into the Bayesian substitution model. The higher the rate of evolution simulated, the better parsimony performed relative to Bayesian analyses. Bayesian and parsimony analyses converged in their performance as the number of simulated heterogeneous model parameters increased. Up to a point, rate heterogeneity among sites was generally advantageous for phylogenetic inference using both approaches. In contrast, branch-length heterogeneity was generally disadvantageous for phylogenetic inference using both parsimony and Bayesian approaches. Parsimony was found to be more conservative than Bayesian analyses, in that it resolved fewer incorrect clades.
© The Willi Hennig Society 2006.     

Do model‐based phylogenetic analyses perform better than parsimony? A test with empirical data

The use of model‐based methods to infer a phylogenetic tree from a given data set is frequently motivated by the truism that under certain circumstances the parsimony approach (MP) may produce incorrect topologies, while explicit model‐based approaches are believed to avoid this problem. In the realm of empirical data from actual taxa, it is not known (or knowable) how commonly MP, maximum‐likelihood or Bayesian inference are inaccurate. To test the perceived need for “sophisticated” model‐based approaches, we assessed the degree of congruence between empirical phylogenetic hypotheses generated by alternative methods applied to DNA sequence data in a sample of 1000 recently published articles. Of 504 articles that employed multiple methods, only two exhibited strongly supported incongruence among alternative methods. This result suggests that the MP approach does not produce deviant hypotheses of relationship due to convergent evolution in long branches. Our finding therefore indicates that the use of multiple analytical methods is largely superfluous. We encourage the use of analytical approaches unencumbered by ad hoc assumptions that sap the explanatory power of the evidence. © The Willi Hennig Society 2010.     

Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.     

Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach

Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has been the only feasible combined approach but is highly sensitive to long-branch attraction. Recent development of stochastic models for discrete morphological characters and computationally efficient methods for Bayesian inference has enabled combined molecular and morphological data analysis with rigorous statistical approaches less prone to such inconsistencies. We present the first statistically founded analysis of a metazoan data set based on a combination of morphological and molecular data and compare the results with a traditional parsimony analysis. Interestingly, the Bayesian analyses demonstrate a high degree of congruence between morphological and molecular data, and both data sets contribute to the result of the combined analysis. Additionally, they resolve several irregularities obtained in previous studies and show high credibility values for controversial groups such as the ecdysozoans and lophotrochozoans. Parsimony, on the contrary, shows conflicting results, with morphology being congruent to the Bayesian results and the molecular data set producing peculiarities that are largely reflected in the combined analysis.     

Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts

The field of phylogenetic tree estimation has been dominated by three broad classes of methods: distance-based approaches, parsimony and likelihood-based methods (including maximum likelihood (ML) and Bayesian approaches). Here we introduce two new approaches to tree inference: pairwise likelihood estimation and a distance-based method that estimates the number of substitutions along the paths through the tree. Our results include the derivation of the formulae for the probability that two leaves will be identical at a site given a number of substitutions along the path connecting them. We also derive the posterior probability of the number of substitutions along a path between two sequences. The calculations for the posterior probabilities are exact for group-based, symmetric models of character evolution, but are only approximate for more general models.     

Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a single body of data; however, both classes of methods can be used to perform severe tests. The assumption of descent with modification is insufficient background knowledge to justify cladistic parsimony as a method for assessing degree of corroboration. Invoking equivalency between parsimony methods and likelihood models that assume no common mechanism emphasizes the necessity of additional assumptions, at least some of which are probabilistic in nature. Incongruent characters do not qualify as falsifiers of phylogenetic hypotheses except under extremely unrealistic evolutionary models; therefore, justifications of parsimony methods as falsificationist based on the idea that they minimize the ad hoc dismissal of falsifiers are questionable. Probabilistic concepts such as degree of corroboration and likelihood provide a more appropriate framework for understanding how phylogenetics conforms with Popper's philosophy of science. Likelihood ratio tests do not assume what is at issue but instead are methods for testing hypotheses according to an accepted standard of statistical significance and for incorporating considerations about test severity. These tests are fundamentally similar to Popper's degree of corroboration in being based on the relationship between the probability of the evidence e in the presence versus absence of the hypothesis h, i.e., between p(e|hb) and p(e|b), where b is the background knowledge. Both parsimony and likelihood methods are inductive in that their inferences (particular trees) contain more information than (and therefore do not follow necessarily from) the observations upon which they are based; however, both are deductive in that their conclusions (tree lengths and likelihoods) follow necessarily from their premises (particular trees, observed character state distributions, and evolutionary models). For these and other reasons, phylogenetic likelihood methods are highly compatible with Karl Popper's philosophy of science and offer several advantages over parsimony methods in this context.     

Estimating trees from filtered data: Identifiability of models for morphological phylogenetics

As an alternative to parsimony analyses, stochastic models have been proposed ( [Lewis, 2001] and [Nylander et al., 2004]) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A key feature of these models is that they account for ascertainment bias, in that only varying, or parsimony-informative characters are observed. However, statistical consistency of such model-based inference requires that the model parameters be identifiable from the joint distribution they entail, and this issue has not been addressed.Here we prove that parameters for several such models, with finite state spaces of arbitrary size, are identifiable, provided the tree has at least eight leaves. If the tree topology is already known, then seven leaves suffice for identifiability of the numerical parameters. The method of proof involves first inferring a full distribution of both parsimony-informative and non-informative pattern joint probabilities from the parsimony-informative ones, using phylogenetic invariants. The failure of identifiability of the tree parameter for four-taxon trees is also investigated.     

A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters

The root lesion nematodes of the genus Pratylenchus Filipjev, 1936 are migratory endoparasites of plant roots, considered among the most widespread and important nematode parasites in a variety of crops. We obtained gene sequences from the D2 and D3 expansion segments of 28S rRNA partial and 18S rRNA from 31 populations belonging to 11 valid and two unidentified species of root lesion nematodes and five outgroup taxa. These datasets were analyzed using maximum parsimony and Bayesian inference. The alignments were generated using the secondary structure models for these molecules and analyzed with Bayesian inference under the standard models and the complex model, considering helices under the doublet model and loops and bulges under the general time reversible model. The phylogenetic informativeness of morphological characters is tested by reconstruction of their histories on rRNA based trees using parallel parsimony and Bayesian approaches. Phylogenetic and sequence analyses of the 28S D2–D3 dataset with 145 accessions for 28 species and 18S dataset with 68 accessions for 15 species confirmed among large numbers of geographical diverse isolates that most classical morphospecies are monophyletic. Phylogenetic analyses revealed at least six distinct major clades of examined Pratylenchus species and these clades are generally congruent with those defined by characters derived from lip patterns, numbers of lip annules, and spermatheca shape. Morphological results suggest the need for sophisticated character discovery and analysis for morphology based phylogenetics in nematodes.     

Exploring myrmecophily based on the phylogenetic interrelationships of Falagonia Sharp, 1883 (Coleoptera: Staphylinidae: Aleocharinae) and allied genera

The taxonomy of Lomechusini Fleming has a complex history. Recent studies have shown that this group is polyphyletic; however, little is known about the evolutionary interrelationships among its constituent genera. The goals of the present study are to infer the phylogenetic relationships of Falagonia Sharp and closely related genera; to define the boundaries of those genera based on synapomorphic characters; and to explore the evolution of myrmecophily within the lineage. The phylogenetic analyses are based exclusively on morphological characters of adults. A total of 36 operational taxonomic units were used for the analysis. The best trees were selected based on maximum parsimony and Bayesian inference. During the parsimony reconstruction, different weighting strategies were used to recover the most robust phylogenetic hypothesis. Although minor differences were observed in the results of the different analyses, the topologies were consistent throughout. Several groups of genera proposed by Seevers (1965), such as the ‘Tetradonia’ and ‘Ecitopora’ groups, were not recovered. Thus, these may represent nonmonophyletic groups that were based on nonsynapomorphic diagnostic characters. Our analyses consistently recovered the genera Asheidium Santiago‐Jiménez, Delgadoidium Santiago‐Jiménez, Falagonia, Newtonidium Santiago‐Jiménez, Pseudofalagonia Santiago‐Jiménez, Sharpidium Santiago‐Jiménez, Tetradonia Wasmann and Thayeridium Santiago‐Jiménez, forming a monophyletic group that we have called the ‘Asheidium complex’. Falagonia mexicana Sharp shows seven autapomorphies, none of which were used to establish the genus. Based on the phylogenetic results, myrmecophily has evolved independently at least three times within the lineage. This study, based on morphological characters, is one of the first approaches towards gaining an understanding of the phylogenetic relationships within the polyphyletic tribe Lomechusini.     

Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes

Background  

The use of molecular genetic data in phylogenetic systematics has revolutionized this field of research in that several taxonomic groupings defined by traditional taxonomic approaches have been rejected by molecular data. The taxonomic classification of the oribatid mite group Circumdehiscentiae ("Higher Oribatida") is largely based on morphological characters and several different classification schemes, all based upon the validity of diagnostic morphological characters, have been proposed by various authors. The aims of this study were to test the appropriateness of the current taxonomic classification schemes for the Circumdehiscentiae and to trace the evolution of the main diagnostic traits (the four nymphal traits scalps, centrodorsal setae, sclerits and wrinkled cuticle plus octotaxic system and pteromorphs both in adults) on the basis of a molecular phylogenetic hypothesis by means of parsimony, likelihood and Bayesian approaches.     

Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference--with their explicit probabilistic basis--are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Journeys through discrete‐character morphospace: synthesizing phylogeny,tempo, and disparity

Palaeontologists have long employed discrete categorical data to capture morphological variation in fossil species, using the resulting character–taxon matrices to measure evolutionary tempo, infer phylogenies and capture morphological disparity. However, to date these have been seen as separate approaches despite a common goal of understanding morphological evolution over deep time. Here I argue that there are clear advantages to considering these three lines of enquiry in a single space: the phylomorphospace. Conceptually these high‐dimensional spaces capture how a phylogenetic tree explores morphospace and allow us to consider important process questions around evolutionary rates, constraints, convergence and directional trends. Currently the literature contains fundamentally different approaches used to generate such spaces, with no direct comparison between them, despite the differing evolutionary histories they imply. Here I directly compare five different phylomorphospace approaches, three with direct literature equivalents and two that are novel. I use a single empirical case study of coelurosaurian theropod dinosaurs (152 taxa, 853 characters) to show that under many analyses the literature‐derived approaches tend to reflect introduced phylogenetic (rather than the intended morphological) signal. The two novel approaches, which produce limited ancestral state estimates prior to ordination, are able to minimize this phylogenetic signal and thus exhibit more realistic amounts of phylogenetic signal, rate heterogeneity, and convergent evolution.     

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference

AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters.     

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。     

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.     

Parsimony, likelihood, and simplicity

The latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own (instead of the homogeneous branch lengths assumed in current likelihood models), the results for likelihood and parsimony are identical. Parsimony, however, can also be derived from simpler models, involving fewer parameters. Therefore, parsimony provides (as many authors had argued before) the simplest explanation of the data, or the most realistic, depending on one's views. If (as argued by likelihoodists) phylogenetic inference is to use the simplest model that provides sufficient explanation of the data, the starting point of phylogenetic analyses should be parsimony, not maximum likelihood. If the addition of new parameters (which increase the likelihood) to a parsimony estimation is seen as desirable, this may lead to a preference for results based on current likelihood models. If the addition of parameters is continued, however, the results will eventually come back to the same place where they had started, since allowing each character a branch length of its own also produces parsimony. Parsimony can be justified by very different types of models—either very complex or very simple. This suggests that parsimony does have a unique place among methods of phylogenetic estimation.