The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
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paper_title: Molecular Evolution: A phylogenetic approach

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The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of Molecular Phylogenetics
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paper_title: Parsimony in Systematics: Philosophical Issues

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Systematists observe patterns of sameness and difference in the characteristics of taxa. On this basis, they attempt to reach conclusions about phylogenetic relationships. Parsimony and other principles of inference have been proposed to bridge the gap. Methods have proliferated, as have justifications and criticisms of them; the question of which method is most reasonable has become increasingly controversial. Methods differ in their specifications of what information must be available if phylogenetic inference is to be undertaken and in their view of the kind of hypothesis that can be constructed using phylogenetic inference. Parsimony stipulates that the investigator must be able to distinguish between the ancestral (plesiomorphic) and the derived (apomorphic) form of every characteristic used. t Given this information, the preferred geneological hypothesis is the one that requires the fewest homoplasies. A homoplasy occurs when two taxa independently evolve the same state of some character; the concept subsumes both parallelism and convergence. Parsimony may also be described as holding that synapomorphies--matches with respect to derived characteristics---count as evidence of a phylogenetic relationship, but that simplesiomorphies~matches with respect to ancestral characteristics---do not. Synapomorphy and simplesiomorphy do not imply homology; matchings may be due to inheritance from a common ancestor or to independent evolution.
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paper_title: The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [ =neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Far-r-is’s method, Sattath and Tversky’s method, Li’s method, and Tateno et al.‘s modified Fan-is method. The new, neighbor-joining method and Sattath and Tversky’s method are shown to be generally better than the other methods.
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paper_title: Phylogenomics and the reconstruction of the tree of life

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As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
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paper_title: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

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Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the “discrete gamma model,” uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called “fixed-rates model,” classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368–376) model, which assumes a single rate for all the sites.
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paper_title: Taxon Sampling and the Accuracy of Large Phylogenies

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Department of Ecology and Evolution, State University of New York, Stony Brook, NY 11794-5245 , USA; E-mail: rannala@life.bio.sunysb.edu Department of Biology, University of Rochester, Rochester, NY 14627-0211 , USA Department of Biology, Galton Laboratory, University College London, 4 Stephenson Way, London NW1 2HE, England Department of Integrative Biology, University of California, Berkeley, California 94720-3140 , USA
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paper_title: Accuracy of Phylogenetic Analysis Including and Excluding Polymorphic Characters

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Intraspecific variation is ubiquitous in systematic characters, yet systematists often do not deal with polymorphism explicity. For example, morphological systematists typically exclude characters in which any or "too much" polymorphism is observed, and molecular systematists often avoid intraspecific variation by sampling a single individual per species. Recent empirical studies have suggested that polymorphic characters contain significant phylogenetic information but are more homoplastic than fixed characters. Given these two observations, should including polymorphic characters increase or decrease accuracy? We addressed this question using simu- lated data sets that also show a strong relationship between homoplasy and intraspecific vari- ability. Data sets were generated with eight species, two alleles per locus, and a variety of branch lengths, number of loci, and sample sizes (individuals sampled per species). The data sets were analyzed using eight parsimony coding methods (with and without a priori and successive weighting) and different variability thresholds for excluding polymorphic characters. Excluding polymorphic characters decreased accuracy under almost all conditions examined, even when only the more variable characters were excluded. Sampling a single individual per species also consistently decreased accuracy. Thus, two common approaches for dealing with intraspecific variation in morphological and molecular systematics can give relatively poor estimates of phy- logeny. In contrast, the unweighted frequency method, including polymorphic characters and sampling a reasonable number of individuals per species (n a 5), can give accurate results under a variety of conditions. (Accuracy; coding methods; computer simulations; parsimony; polymor- phic characters; sample size; weighting.)
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paper_title: The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.

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The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of the methods were violated to varying degrees on three model four-taxon trees. The performance of the methods was evaluated with respect to ability to correctly estimate the unrooted four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of the 36 cases in which the assumptions of both methods were satisfied. In 133 of 180 of the simulations in which the assumptions of the maximum-likelihood and neighbor-joining methods were violated, maximum likelihood outperformed neighbor joining. These results are consistent with a general superiority of maximum likelihood over neighbor joining under comparable conditions. They extend and clarify an earlier study that found an advantage for neighbor joining over maximum likelihood for gamma-distributed mutation rates.
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paper_title: General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa

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Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least with respect to the maximum parsimony method, has been given the catch phrase "long branches attract." It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclu- sions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by com- parison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. (Maximum parsimony; inconsistency; large phylogenies; long branches.)
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paper_title: Gene tree discordance , phylogenetic inference and the multispecies coalescent

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The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.
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paper_title: Rapid neighbourjoining

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The neighbour-joining method reconstructs phylogenies by iteratively joining pairs of nodes until a single node remains. The criterion for which pair of nodes to merge is based on both the distance between the pair and the average distance to the rest of the nodes. In this paper, we present a new search strategy for the optimisation criteria used for selecting the next pair to merge and we show empirically that the new search strategy is superior to other state-of-the-art neighbour-joining implementations.
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paper_title: Branch Support and Tree Stability

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—Branch support is quantified as the extra length needed to lose a branch in the consensus of near-most-parsimonious trees. This approach is based solely on the original data, as opposed to the data perturbation used in the bootstrap procedure. If trees have been generated by Farris's successive approximations approach to character weighting, branch support should be examined in terms of weighted extra length needed to lose a branch. The sum of all branch support values over the tree divided by the length of the most parsimonious tree[s] provides a new index, the total support index. This index is a measure of tree stability in terms of supported resolutions, which is of prime importance in cladistic analysis.
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paper_title: A review of long-branch attraction

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The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall wasps are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic ‘‘the guinea-pig is not a rodent’’ hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + G + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup. � The Willi Hennig Society 2005.
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paper_title: Evolutionary trees from DNA sequences: A maximum likelihood approach

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The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
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paper_title: Phylogenies from Molecular Sequences: Inference and Reliability

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Article de synthese sur les methodes d'obtention de phylogenese a partir de sequences moleculaires, tests statistiques des phylogeneses et simulations sur ordinateur
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paper_title: Approaches for Assessing Phylogenetic Accuracy

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?Accuracy of phylogenetic methods may be assessed in terms of consistency, efficiency, and robustness. Four principal methods have been used for assessing phylogenetic accuracy: simulation, known phylogenies, statistical analyses, and congruence studies. Simulation studies are useful for studying accuracy of methods under idealized conditions and can be used to make general predic? tions about the behavior of methods if the limitations of the models are taken into account. Studies of known phylogenies can be used to test predictions from simulation studies, thus providing a check on the robustness of the models (and possibly suggesting refinements for future simulations). Statistical analyses allow general predictions to be applied to specific results, facilitate assessments as to whether or not sufficient data have been collected to formulate a robust conclusion, and indicate whether a given data set is any more structured than random noise. Finally, congruence studies of multiple data sets can be used to assess the degree to which independent results agree and thus the minimum proportion of the findings that can be attributed to an underlying phylogeny. These differ? ent methods of assessing phylogenetic accuracy are largely complementary, and the results are consis? tent in identifying a large class of problems that are amenable to phylogenetic reconstruction. [Phy? logeny; accuracy; simulations; experimental evolution; statistics; congruence; consistency; efficiency; robustness.] Phylogenetic analyses have become com? monplace throughout the biological disci? plines during the past few decades. This in? creased emphasis on evolutionary history is a direct result of the realization of the im? portance of understanding phylogenetic background as a prerequisite to interpreting virtually any biological system in a compar? ative context. However, the increased uti? lization of phylogenetic approaches has been driven at least as much by technologi? cal and methodological advances as by con? ceptual advances. In particular, advances in algorithm development, computer technol? ogy, and molecular biology have made phy? logenetic analyses feasible for almost any problem involving biological lineages, from viral epidemics in extant human popula? tions (e.g., Ou et al., 1992) to the origins of the earliest lineages of life (e.g., Olsen, 1987). Phylogenetic applications depend on accurate reconstructions of phylogenetic trees; therefore, it is natural that systematists should wonder about the accuracy of their reconstructed trees. This issue of Sys? tematic Biology contains reviews of the four approaches that systematists have explored to examine phylogenetic accuracy and as1 E-mail: hillis@bull.zo.utexas.edu. sess confidence in their results: evolution? ary simulations (Huelsenbeck, 1995), explo? ration of known (observed) phylogenies (briefly reviewed here), statistical evalua? tions (Li and Zharkikh, 1995), and congru? ence studies (Miyamoto and Fitch, 1995). I evaluating phylogenetic accuracy, there are two common goals: one may ask about general properties of phylogenetic methods or about a specific phylogenetic es? timate. A systematist may address how well a given method works under different cir? cumstances (e.g., different evolutionary conditions, different amounts of informa? tion, different types of trees, etc.). Such studies may ask about phylogenetic perfor? mance of a single method or may compare several methods. This approach primarily involves numerical simulations and investi? gation of known phylogenies. On the other hand, statistical and congruence studies tend to address specific questions of phylo? genetic accuracy, i.e., how much confidence can be placed in a specific phylogenetic re? sult? Of course, the distinction is not always clear because simulations can be used to ad? dress confidence in a particular empirical result (e.g., Hillis et al., 1994a) and general conclusions about the relative accuracy of phylogenetic methods can come from statis? tical or congruence studies (e.g., Penny et
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paper_title: The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction

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We analyze the performance of the popular class of neighbor-joining methods of phylogeny reconstruction. In particular, we find conditions under which these methods will determine the correct tree topology and show that these perform as well as possible in a certain sense. We also give indications of the performance of these methods when the conditions necessary to show that they determine the entire tree topology correctly, do not hold. We use these results to demonstrate an upper bound on the amount of data necessary to reconstruct the topology with high confidence.
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paper_title: Evaluation of the Strategy of Long-Branch Subdivision to Improve the Accuracy of Phylogenetic Methods

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Methods for reconstructing evolutionary history are sensitive to the number and position of taxa included in the analysis (e.g., Gauthier et al., 1988; Hendy and Penny, 1989; Lecointre et al., 1993; Poe, 1998). Figure 1 illustrates this phenomenon using parsimony analyses of a sample of four Anolis lizard species from a large matrix of morphological and molecular data (Poe, 2001). Any of the three possible relationships for these species can be obtained by including appropriate additional species in the same analysis. In addition to demonstrating the instability of results relative to taxon sampling, this example shows conclusively that addition of taxa may be beneficial to the accuracy of a phylogenetic analysis but also may be detrimental to accuracy. This conclusion holds because it is possible to change any of the topological results either by adding or by subtracting taxa, and even though we do not know which of these three trees is the true tree, we can assume that one of them is correct and two of them are wrong. One might think that the sensitivity to taxon sampling shown in Figure 1 is restricted to certain methods or to poorly supported trees. Unfortunately this is not the case, as shown in the example in Figure 2. These trees were reconstructed using the mitochondrial DNA sequence data of Jackman et al. (1999) for Anolis lizards. Tree a in Figure 2 is obtained when these taxa are analyzed alone using maximum likelihood and minimum evolution under complex models (HKY + G; Hasegawa et al., 1985; Yang, 1994; parameter values estimated from data) and using parsimony with equal weights for all character changes. Tree b is obtained using these same methods but running the analyses including three other lizard species. This comparison shows that sensitivity to taxon sampling may occur even with strongly supported trees and diverse methods of estimation (and shows that high bootstrap values and strongly supported congruence between methods are not necessarily predictors of accuracy). The above examples show the potentially extreme sensitivity of phylogenetic methods to taxon sampling, but they are of little help in devising a taxon sampling strategy for maximizing the accuracy of a phylogenetic analysis. When a researcher is interested in the relationships of a set of clades from which exemplar taxa are chosen, is it better or worse to include additional taxa in the analysis? Clearly, simply including more taxa without additional character information can be detrimental to accuracy, because more characters are needed to resolve a greater number of nodes. However, addition of more taxa adds information about evolutionary history (e.g., Gauthier et al., 1988), which seems likely to have a positive effect on accuracy. Given these potentially opposing effects, what is the best taxon-sampling strategy for maximizing the accuracy of phylogenetic analyses? Phylogenies that include lineages that have undergone extensive evolution are difficult to reconstruct because of the phenomenon of long branch attraction (Felsenstein, 1978; Huelsenbeck and Hillis, 1993). Thus, a beneficial sampling strategy might involve shortening long branches by including additional taxa, assuming that such taxa exist (Hendy and Penny, 1989). This strategy has been evaluated for the parsimony method by Graybeal (1998) and by Poe and Swofford (1999). Graybeal fulfilled Hendy and Penny’s (1989) prediction that long-branch subdivision can have a strong beneficial effect on the accuracy of estimation of four-taxon trees in the Felsenstein zone of two long opposing branches and a short internal branch. Poe and Swofford (1999) examined a wider range of model trees and discovered several conditions of the kind discussed by Zharkikh and Li (1993) under which long-branch subdivision was detrimental to accuracy. The taxon sampling strategy of long-branch subdivision (LBS) has not been examined for methods other than parsimony. Poe and Swofford (1999) suggested that phylogenetic methods that take branch lengths into account are less likely to be affected by the problems of LBS that afflicted their application of the parsimony method. Pollock and Bruno (2000:1858) concluded that “the notion that added taxa can decrease accuracy . . . should be abandoned as an artifact of parsimony.” Although it seems likely that LBS will be beneficial when the model
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paper_title: Phylogeny estimation: traditional and Bayesian approaches

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The construction of evolutionary trees is now a standard part of exploratory sequence analysis. Bayesian methods for estimating trees have recently been proposed as a faster method of incorporating the power of complex statistical models into the process. Researchers who rely on comparative analyses need to understand the theoretical and practical motivations that underlie these new techniques, and how they differ from previous methods. The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.
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paper_title: Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo.

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We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump (RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.
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paper_title: When phylogenetic assumptions are violated: base compositional heterogeneity and among‐site rate variation in beetle mitochondrial phylogenomics

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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.
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paper_title: Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle

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The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary least-squares (OLS) fitting of a metric to a tree structure. The traditional approach to using ME has been to start with the Neighbor Joining (NJ) topology for a given matrix and then do a topological search from that starting point. The first stage requires O(n(3)) time, where n is the number of taxa, while the current implementations of the second are in O(p n(3)) or more, where p is the number of swaps performed by the program. In this paper, we examine a greedy approach to minimum evolution which produces a starting topology in O(n(2)) time. Moreover, we provide an algorithm that searches for the best topology using nearest neighbor interchanges (NNIs), where the cost of doing p NNIs is O(n(2) + p n), i.e., O(n(2)) in practice because p is always much smaller than n. The Greedy Minimum Evolution (GME) algorithm, when used in combination with NNIs, produces trees which are fairly close to NJ trees in terms of topological accuracy. We also examine ME under a balanced weighting scheme, where sibling subtrees have equal weight, as opposed to the standard "unweighted" OLS, where all taxa have the same weight so that the weight of a subtree is equal to the number of its taxa. The balanced minimum evolution scheme (BME) runs slower than the OLS version, requiring O(n(2) x diam(T)) operations to build the starting tree and O(p n x diam(T)) to perform the NNIs, where diam(T) is the topological diameter of the output tree. In the usual Yule-Harding distribution on phylogenetic trees, the diameter expectation is in log(n), so our algorithms are in practice faster that NJ. Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy.
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paper_title: The Logical Basis of Phylogenetic Taxonomy

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Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The following points are made: (1) cladograms, rather than trees or hybrid cladogram-trees, provide the framework for the simplest graphical depiction of phylogenetic definitions; (2) a complete notational scheme for phylogenetic definitions is presented that distinguishes symbolic notation from shorthand and longhand versions; (3) phylogenetic definitions are composed of three components (paradigm, specifier, qualifier) arranged in two fundamental patterns-node and stem; (4) apomorphies do not constitute a fundamental definitional pattern but rather serve to qualify a stem-based definition (as do time and geographic range); (5) formulation of phylogenetic definitions involves three heuristic criteria (stability, simplicity, prior use); (6) reasoned definitional revision is encouraged and better defined (textual substitution, first-and second-order revision); and (7) a database, TaxonSearch, allows rapid recall of taxonomic and definitional information.
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paper_title: CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

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The recently-developed statistical method known as the bootstrap can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, asmore » envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters. 8 references, 2 figures, 1 table.« less
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paper_title: Taxon sampling, bioinformatics, and phylogenomics.

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Taxon sampling is often thought to be of extreme importance for phylogenetic inference, and increased sampling of taxa is commonly advocated as a solution to resolving problematic phylogenies. Another solution is to increase the number of sites (by sequencing additional genes) sampled for each taxon. In an ideal world, one would like to increase samples of both taxa and genes, but taxon sampling has not kept up with the pace of gene sampling increase because of the increasing ease and emphasis on genome sequencing. ::: ::: The question of taxon sampling is necessarily driven by resource limitation. The precise scope of “sufficient” taxon sampling is always dependent on questions being addressed. If we need to know the complete phylogeny of a genus, we must sample the genus exhaustively. In experimental design, partial sampling is an issue only when certain taxa can stand as proxies for the clades to which they belong (clade-based or stratified sampling; see Hillis, 1998). In bioinformatics studies, taxon sampling is restricted by the data availability in genetic databases (database-restricted sampling). Clearly, the nature of the problem in these two research programs is different. In stratified sampling, we are interested in knowing whether to sequence more genes per species or fewer genes for a large number of species per clade. In contrast, in database-restricted sampling it is important to know whether the overall accuracy of inferred phylogenetic trees for small taxa sets is similar to that of trees inferred from larger taxa sets. We recently addressed the issue of the database-restricted sampling (Rosenberg and Kumar, 2001) and concluded that although there was a consistent decrease in error when using more taxa, the decrease was generally minor relative to the number of taxa added to the data set. ::: ::: Pollock et al. (2002) challenged this conclusion by modifying our measure of the phylogenetic error. This measure, ΔE, differs from ours in that we used the difference in error between the subsampled tree [ES] and full sampled tree [EP], whereas Pollock et al. (2002) divided this difference by ES to measure the relative reduction in error. ΔE plotted against the number of additional taxa in the full sampled tree (=66 minus the number of taxa in the subsample tree) shows a clear positive effect (Pollock et al., 2002: Figs. 4, 5). Unfortunately, this impressive result brings little biological benefit, as clearly shown by a scatterplot of the average number of additional branches inferred correctly in each case (Fig. 1). In no instance are there more than 1.5 additional branches reconstructed correctly, even though the number of taxa has often increased many fold. For instance, more than doubling the number of taxa only led to an average increase of 0.7 additional correct branches (points in the middle of the x-axis in Fig. 1). This fact was clearly noted in our original article: “Note that even though ES is greater than EG and EP for very small subsamples (<10 taxa), the difference in phylogenetic error is usually much smaller than one branch per tree” (Rosenberg and Kumar, 2001: 10754). Therefore, although an increase in the number of taxa sampled will lead to improvement in accuracy, the improvement is minimal, particularly when we consider the amount of data (in terms of the number of total nucleotides) being added. We do not advocate using fewer taxa when more are available, as is clear from the results presented by Rosenberg and Kumar (2001:10754). ::: ::: ::: ::: Figure 1 ::: ::: Number of branches reconstructed correctly with increased taxon sampling. (a) All simulated genes. (b) Genes with rates >0.7 and >500 sites (after Pollock et al., 2002). ::: ::: ::: ::: ::: ::: Figure 4 ::: ::: Plot of the percentage of times interordinal branches were reconstructed correctly when the total number of bases was held constant. In each comparison, the data set with fewer taxa (and more sites per taxon) is always plotted on the x-axis. The dotted ... ::: ::: ::: ::: Zwickl and Hillis (2002) also challenged conclusions reached by Rosenberg and Kumar (2001) by using the concept of tree diameter (the maximum distance between all pairs of taxa) to partition genes with different subsampled sets of taxa for analysis. They showed that four-taxon subsamples with a smaller tree diameter generate more accurate results than those subsamples with larger tree diameters. This result is expected because, with sequence divergence and length kept constant, the larger diameter four-taxon trees will encompass higher average divergence and would thus involve larger estimation errors. Furthermore, for the simulations involving the model tree in Figure 2a, four-taxon data sets containing sequences with larger diameters would include interordinal relationships (with many small interior branches) more frequently than would small diameter samples (see also Zwickl and Hillis, 2002: Fig. 3a). Therefore, Zwickl and Hillis’s study is an examination of the phylogenetic error at different evolutionary divergence cross sections of the phylogenetic tree specifically simulated. This and the complete absence of resource limitation (a must for any sampling study) clearly establish that Zwickl and Hillis have not evaluated either stratified or database-restricted taxon-sampling problems. Therefore, Zwickl and Hillis were not correct in stating that their results are in contradiction with our previous results (Rosenberg and Kumar, 2001). In fact, Zwickl and Hillis’s results represent another facet of statistical analysis of the same data. Also, Zwickl and Hillis took issue with our choice of a fast heuristic search used in computer simulations (Rosenberg and Kumar, 2001). We chose this strategy based on results of multiple previous studies, which showed that the most optimal tree is often more optimal than the true tree and that the fast and more exhaustive searches produce trees with comparable phylogenetic errors (Kumar, 1996; Nei et al., 1998; Takahashi and Nei, 2000). Zwickl and Hillis found that with the maximum parsimony (MP) method for the given data set, the TBR searches produced topologies that had less error than those from NNI. This result (based on a single simulation data set) seems to be in conflict with previous studies. We plan to evaluate this result more thoroughly analytically and by computer simulation in the future. ::: ::: ::: ::: Figure 2 ::: ::: Model tree for the simulations based on the Eutherian mammal tree from Murphy et al. (2001) and Eizrik et al. (2001). (a) Full 66-taxon tree; interordinal relationships are represented by thick branches designated with letters. (b) Phylogenetic relationships ... ::: ::: ::: ::: ::: ::: Figure 3 ::: ::: Plot of the percentage of times the interordinal branches were reconstructed correctly in 66-taxon trees versus n-taxon trees, where n = 15, 30, and 45. These values are for all genes and all replicates. The dotted lines indicate a 1:1 relationship. Analyses ... ::: ::: ::: ::: However, we extrapolated our database-restricted sampling and random sampling results to conclude that the phylogenetic trees with fewer taxa but large numbers of genes per taxon may be more accurate than those with many taxa but fewer genes (Rosenberg and Kumar, 2001). Neither Pollock et al. (2002) nor Zwickl and Hillis (2002) addressed that issue, which lies at the heart of the experimental design. Here, we tackle this issue along with biological relevance of many other assumptions made and conclusions reached by Rosenberg and Kumar (2001) that Zwickl and Hillis (2002) objected to. We show that the conclusions reached by Rosenberg and Kumar (2001) are applicable for both phyloinformatic and phylogenomic studies.
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paper_title: Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference.

paper_content:

Because a constant rate of DNA sequence evolution cannot be assumed to be ubiquitous, relaxed molecular clock inference models have proven useful when estimating rates and divergence dates. Furthermore, it has been recently suggested that using relaxed molecular clocks may provide superior accuracy and precision in phylogenetic inference compared with traditional time-free methods that do not incorporate a molecular clock. We perform a simulation study to determine if assuming a relaxed molecular clock does indeed improve the quality of phylogenetic inference. We analyze sequence data simulated under various rate distributions using relaxed-clocks, strict-clocks, and time-free Bayesian phylogenetic inference models. Our results indicate that no difference exists in the quality of phylogenetic inference between assuming a relaxed molecular clock and making no assumption about the clock-likeness of sequence evolution. This pattern is likely due to the bias-variance trade-off inherent in this type of phylogenetic inference. We also compared the quality of inference between Bayesian and maximum likelihood time-free inference models and found them to be qualitatively similar.
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paper_title: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

paper_content:

Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.
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paper_title: Phylogenomics: the beginning of incongruence

paper_content:

Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence.
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paper_title: Evidence for a clade of nematodes, arthropods and other moulting animals

paper_content:

The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear1. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting2,3. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel1,4, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses4,5. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres6. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinor-hynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other.
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paper_title: The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets

paper_content:

Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by ribosomal DNA (rDNA) data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria. Here, we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa. In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the data sets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear rDNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria. By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone be explained by long-branch attraction. After trimming a published phylogenomic data set, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian. In further explorations of these data sets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the Whelan and Goldman amino acid substitution model changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria. Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered. Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic data set. These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration when investigating the phylogenetic placement of highly divergent taxa.
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paper_title: Evolutionary relationships of eukaryotic kingdoms

paper_content:

The evolutionary relationships of four eukaryotic kingdoms—Animalia, Plantae, Fungi, and Protista—remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants is lacking, and a preferred branching order of these and other eukaryotic lineages is still controversial even though molecular sequences from diverse eukaryotic taxa have been analyzed. We report a statistical analysis of 214 sequences of nuclear small-subunit ribosomal RNA (srRNA) gene undertaken to clarify these evolutionary relationships. We have considered the variability of substitution rates and the nonindependence of nucleotide substitution across sites in the srRNA gene in testing alternative hypotheses regarding the branching patterns of eukaryote phylogeny. We find that the rates of evolution among sites in the srRNA sequences vary substantially and are approximately gamma distributed with size and shape parameter equal to 0.76. Our results suggest that (1) the animals and true fungi are indeed closer to each other than to any other “crown” group in the eukaryote tree, (2) red algae are the closest relatives of animals, true fungi, and green plants, and (3) the heterokonts and alveolates probably evolved prior to the divergence of red algae and animal-fungus-green-plant lineages. Furthermore, our analyses indicate that the branching order of the eukaryotic lineages that diverged prior to the evolution of alveolates may be generally difficult to resolve with the srRNA sequence data.
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paper_title: Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.

paper_content:

Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). However, it received little additional support. In fact, several multigene analyses strongly argued against this new phylogeny. These latter studies were based on a large amount of sequence data and therefore showed an apparently strong statistical support. Yet, they covered only a few taxa (those for which complete genomes were available), making systematic artifacts of tree reconstruction more probable. Here we expand this sparse taxonomic sampling and analyze a large data set (146 genes, 35,371 positions) from a diverse sample of animals (35 species). Our study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies. A refined analysis of our data set excluding the most biased genes provides strong support in favor of the new animal phylogeny and in addition suggests that urochordates are more closely related to vertebrates than are cephalochordates. These findings have important implications for the interpretation of morphological and genomic data.
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paper_title: A general comparison of relaxed molecular clock models.

paper_content:

Several models have been proposed to relax the molecular clock in order to estimate divergence times. However, it is unclear which model has the best fit to real data and should therefore be used to perform molecular dating. In particular, we do not know whether rate autocorrelation should be considered or which prior on divergence times should be used. In this work, we propose a general bench mark of alternative relaxed clock models. We have reimplemented most of the already existing models, including the popular lognormal model, as well as various prior choices for divergence times (birth-death, Dirichlet, uniform), in a common Bayesian statistical framework. We also propose a new autocorrelated model, called the "CIR" process, with well-defined stationary properties. We assess the relative fitness of these models and priors, when applied to 3 different protein data sets from eukaryotes, vertebrates, and mammals, by computing Bayes factors using a numerical method called thermodynamic integration. We find that the 2 autocorrelated models, CIR and lognormal, have a similar fit and clearly outperform uncorrelated models on all 3 data sets. In contrast, the optimal choice for the divergence time prior is more dependent on the data investigated. Altogether, our results provide useful guidelines for model choice in the field of molecular dating while opening the way to more extensive model comparisons.
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paper_title: Base-Compositional Heterogeneity in the RAG1 Locus among Didelphid Marsupials: Implications for Phylogenetic Inference and the Evolution of GC Content

paper_content:

Although theoretical studies have suggested that base-compositional heterogeneity can adversely affect phylo- genetic reconstruction, only a few empirical examples of this phenomenon, mostly among ancient lineages (with divergence dates >100 Mya), have been reported. In the course of our phylogenetic research on the New World marsupial family Didelphidae, we sequenced 2790 bp of the RAGl exon from exemplar species of most extant genera. Phylogenetic analysis of these sequences recovered an anomalous node consisting of two clades previously shown to be distantly related based on analyses of other molecular data. These two clades show significantly increased GC content at RAGl third codon positions, and the resulting convergence in base composition is strong enough to overwhelm phylogenetic signal from other genes (and morphology) in most analyses of concatenated datasets. This base-compositional convergence occurred relatively re- cently (over tens rather than hundreds of millions of years), and the affected gene region is still in a state of evolutionary disequilibrium. Both mutation rate and substitution rate are higher in GC-rich didelphid taxa, observations consistent with RAGl sequences having experienced a higher rate of recombination in the convergent lineages. (Biased gene conversion; Didelphidae; nucleotide composition; phytogeny; RAGl; recombination.)
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paper_title: Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling

paper_content:

The debate about whether phylogenetic accuracy is most efficiently increased by sampling more charac ters or more taxa is certainly not new (e.g., Kim, 1996; Graybeal, 1998; Poe, 1998a,b; Rannala et al., 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rosenburg and Kumar, 2001; Pollock et al., 2002; Zwickl and Hillis, 2002; Rosenberg and Kumar, 2003; Hillis et al., 2003). However, the recent increase of whole genomic sequences available from an assortment of distantly related taxa makes this debate highly relevant to researchers across fields of bi ology. Recently, Rokas et al. (2003) argued that the true species tree can be recovered despite conflicting phylo genetic signal between genes if enough genes are used in the analysis. Using the bootstrap proportion (BP) as a measure of phylogenetic accuracy, they concluded that approximately 20 genes are needed to ensure a robustly supported tree (>95% BP) for their study group of eight yeast taxa. From these empirical results, they generalized that most molecular phylogenetic studies have probably included insufficient numbers of genes to confidently re solve relationships within their respective focal groups. This approach to measuring accuracy can be sensitive to method inconsistency, or the failure to converge on the correct tree as the data set becomes infinitely large. When a method is inconsistent, measures of support such as nonparametric bootstrapping can increase as more se quence data are added?but in support of the wrong phy logeny (Phillips et al., 2004; Collins et al., 2005; Delsuc et al., 2005). Although most methods perform well over most of tree space (Huelsenbeck, 1995; Poe, 2003), regions of inconsistency have been identified in the literature for all of the most commonly used phylogenetic meth ods. For example, compositional bias can affect the accu racy of minimum evolution (Phillips et al., 2004), model misspecification may affect parametric methods such as maximum likelihood (ML) (Poe, 2003; Philippe et al, 2005; Collins et al., 2005), and branch-length asymme try can lead to inconsistency in maximum parsimony (Felsenstein, 1978; Hendy and Penny, 1989). Parsimony is particularly prone to long-branch attraction (LBA), an analytical artifact in which two taxa on long branches are incorrectly placed as sister taxa (Felsenstein, 1978; Hendy and Penny, 1989; Huelsenbeck and Hillis, 1993). Although there are many reasons for conflicting phylo genetic signal between genes, one relevant reason could be related to method inconsistency: differing rates of evo lution between genes could cause a particular method to be inconsistent for some genes and not for others. We argue that by addressing this source of conflict between genes, fewer genes may be needed to return an accu rate phylogeny. One source of conflict in the Rokas et al. (2003) data set may be nonstationarity: taxa that differ from the others in their base compositional bias may be erroneously drawn together as sister taxa (Collins et al., 2005). Here, we show that an additional source of conflict between the 106 genes in the Rokas et al. data set may be branch-length asymmetry. Using simulations of 106 genes from the Rokas et al. data set on a 79-taxon yeast phylogeny, we additionally show that when genes are added to a data set, support for the wrong reconstruc tion can increase when there is LBA. However, when taxa are added to the analysis, support for the correct reconstruction increases, and fewer genes are needed to achieve accuracy.
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paper_title: Evolutionary trees from DNA sequences: A maximum likelihood approach

paper_content:

The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
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paper_title: Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference.

paper_content:

Convergence in nucleotide composition (CNC) in unrelated lineages is a factor potentially affecting the performance of most phylogeny reconstruction methods. Such convergence has deleterious effects because unrelated lineages show similarities due to similar nucleotide compositions and not shared histories. While some methods (such as the LogDet/paralinear distance measure) avoid this pitfall, the amount of convergence in nucleotide composition necessary to deceive other phylogenetic methods has never been quantified. We examined analytically the relationship between convergence in nucleotide composition and the consistency of parsimony as a phylogenetic estimator for four taxa. Our results show that rather extreme amounts of convergence are necessary before parsimony begins to prefer the incorrect tree. Ancillary observations are that (for unweighted Fitch parsimony) transition/transversion bias contributes to the impact of CNC and, for a given amount of CNC and fixed branch lengths, data sets exhibiting substantial site-to-site rate heterogeneity present fewer difficulties than data sets in which rates are homogeneous. We conclude by reexamining a data set originally used to illustrate the problems caused by CNC. Using simulations, we show that in this case the convergence in nucleotide composition alone is insufficient to cause any commonly used methods to fail, and accounting for other evolutionary factors (such as site-to-site rate heterogeneity) can give a correct inference without accounting for CNC.
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paper_title: The evolutionary position of nematodes

paper_content:

BackgroundThe complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes.ResultsWe tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.ConclusionWe conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.
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paper_title: The phylogenetic potential of entire 26S rDNA sequences in plants.

paper_content:

18S ribosomal RNA genes are the most widely used nuclear sequences for phylogeny reconstruction at higher taxonomic levels in plants. However, due to a conservative rate of evolution, 18S rDNA alone sometimes provides too few phylogenetically informative characters to resolve relationships adequately. Previous studies using partial sequences have suggested the potential of 26S or large-subunit (LSU) rDNA for phylogeny retrieval at taxonomic levels comparable to those investigated with 18S rDNA. Here we explore the patterns of molecular evolution of entire 26S rDNA sequences and their impact on phylogeny retrieval. We present a protocol for PCR amplification and sequencing of entire (approximately 3.4 kb) 26S rDNA sequences as single amplicons, as well as primers that can be used for amplification and sequencing. These primers proved useful in angiosperms and Gnetales and likely have broader applicability. With these protocols and primers, entire 26S rDNA sequences were generated for a diverse array of 15 seed plants, including basal eudicots, monocots, and higher eudicots, plus two representatives of Gnetales. Comparisons of sequence dissimilarity indicate that expansion segments (or divergence domains) evolve 6.4 to 10.2 times as fast as conserved core regions of 26S rDNA sequences in plants. Additional comparisons indicate that 26S rDNA evolves 1.6 to 2.2 times as fast as and provides 3.3 times as many phylogenetically informative characters as 18S rDNA; compared to the chloroplast gene rbcL, 26S rDNA evolves at 0.44 to 1.0 times its rate and provides 2.0 times as many phylogenetically informative characters. Expansion segment sequences analyzed here evolve 1.2 to 3.0 times faster than rbcL, providing 1.5 times the number of informative characters. Plant expansion segments have a pattern of evolution distinct from that found in animals, exhibiting less cryptic sequence simplicity, a lower frequency of insertion and deletion, and greater phylogenetic potential.
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paper_title: BEAST: Bayesian evolutionary analysis by sampling trees

paper_content:

The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
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paper_title: More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

paper_content:

The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.
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paper_title: Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin.

paper_content:

Relationships among the ecdysozoans, or molting animals, have been difficult to resolve. Here, we use nearly complete 28S+18S ribosomal RNA gene sequences to estimate the relations of 35 ecdysozoan taxa, including newly obtained 28S sequences from 25 of these. The tree-building algorithms were likelihood-based Bayesian inference and minimum-evolution analysis of LogDet-transformed distances, and hypotheses were tested wth parametric bootstrapping. Better taxonomic resolution and recovery of established taxa were obtained here, especially with Bayesian inference, than in previous parsimony-based studies that used 18S rRNA sequences (or 18S plus small parts of 28S). In our gene trees, priapulan worms represent the basal ecdysozoans, followed by nematomorphs, or nematomorphs plus nematodes, followed by Panarthropoda. Panarthropoda was monophyletic with high support, although the relationships among its three phyla (arthropods, onychophorans, tardigrades) remain uncertain. The four groups of arthropods-hexapods (insects and related forms), crustaceans, chelicerates (spiders, scorpions, horseshoe crabs), and myriapods (centipedes, millipedes, and relatives)-formed two well-supported clades: Hexapoda in a paraphyletic crustacea (Pancrustacea), and 'Chelicerata+Myriapoda' (a clade that we name 'Paradoxopoda'). Pycnogonids (sea spiders) were either chelicerates or part of the 'chelicerate+myriapod' clade, but not basal arthropods. Certain clades derived from morphological taxonomy, such as Mandibulata, Atelocerata, Schizoramia, Maxillopoda and Cycloneuralia, are inconsistent with these rRNA data. The 28S gene contained more signal than the 18S gene, and contributed to the improved phylogenetic resolution. Our findings are similar to those obtained from mitochondrial and nuclear (e.g., elongation factor, RNA polymerase, Hox) protein-encoding genes, and should revive interest in using rRNA genes to study arthropod and ecdysozoan relationships.
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paper_title: Taxon sampling revisited

paper_content:

Phylogenies that include long, unbranched lineages can be difficult to reconstruct. This is because long-branch taxa (such as rapidly evolving species) may share character states by chance more often than more closely related taxa share derived character states through common ancestry1. Despite Kim's warning that added taxa can decrease accuracy2, some authors have argued that the negative impact of this error, called ‘long-branch attraction’, is minimized when slowly evolving lineages are included to subdivide long branches3,4,5. From this they have concluded that increasing the number of species sampled per lineage results in better accuracy than increasing the number of characters per species6. We find, using computer simulations, that adding characters can be the more favourable strategy, even for long-branched trees, and that adding slowly evolving taxa to subdivide long branches can reduce accuracy.
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paper_title: Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?

paper_content:

The study of metazoan evolution has fascinated biologists for centuries, and it will certainly keep doing so. Recent interest on the origin of metazoan body plans, early metazoan evolution, genetic mechanisms generating disparity and diversity, molecular clock information, paleontology, and biogeochemistry is contributing to a better understanding of the current phyletic diversity. Unfortunately, the pattern of the metazoan tree of life still shows some important gaps in knowledge. It is the aim of this article to review some of the most important issues related to the inference of the metazoan tree, and point towards possible ways of solving certain obscure aspects in the history of animal evolution. A new hypothesis of the metazoan diversification during the Cambrian explosion is proposed by synthesizing ideas from phylogenetics, molecular evolution, paleontology, and developmental biology.
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paper_title: Models of amino acid substitution and applications to mitochondrial protein evolution

paper_content:

Models of amino acid substitution were developed and compared using maximum likelihood. Two kinds of models are considered. "Empirical" models do not explicitly consider factors that shape protein evolution, but attempt to summarize the substitution pattern from large quantities of real data. "Mechanistic" models are formulated at the codon level and separate mutational biases at the nucleotide level from selective constraints at the amino acid level. They account for features of sequence evolution, such as transition-transversion bias and base or codon frequency biases, and make use of physicochemical distances between amino acids to specify nonsynonymous substitution rates. A general approach is presented that transforms a Markov model of codon substitution into a model of amino acid replacement. Protein sequences from the entire mitochondrial genomes of 20 mammalian species were analyzed using different models. The mechanistic models were found to fit the data better than empirical models derived from large databases. Both the mutational distance between amino acids (determined by the genetic code and mutational biases such as the transition-transversion bias) and the physicochemical distance are found to have strong effects on amino acid substitution rates. A significant proportion of amino acid substitutions appeared to have involved more than one codon position, indicating that nucleotide substitutions at neighboring sites may be correlated. Rates of amino acid substitution were found to be highly variable among sites.
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paper_title: Genome-scale approaches to resolving incongruence in molecular phylogenies

paper_content:

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.
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paper_title: Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

paper_content:

Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with chordates in a coelomate clade, whereas nematodes, which lack a coelome, occupy a basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA and several proteins, joins nematodes with arthropods in a clade of molting animals, Ecdysozoa. We performed a phylogenetic analysis of over 500 sets of orthologous proteins, which are represented in plants, animals, and fungi, using maximum likelihood, maximum parsimony, and distance methods. Additionally, to increase the statistical power of topology tests, the same methods were applied to concatenated alignments of subunits of eight conserved macromolecular complexes. The majority of the methods, when applied to most of the orthologous clusters, both concatenated and individual, grouped the fly with humans to the exclusion of the nematode, in support of the coelomate phylogeny. Trees were also constructed using information on insertions and deletions in orthologous proteins, combinations of domains in multidomain proteins, and presence-absence of species in clusters of orthologs. All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss.
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paper_title: Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?

paper_content:

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.
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paper_title: Molecular Evolution: A phylogenetic approach

paper_content:

The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of Molecular Phylogenetics
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paper_title: Broad phylogenomic sampling improves resolution of the animal tree of life

paper_content:

This paper describes and discusses almost 40 megabases of expressed sequence tags (EST) clones from the DNA of animals from 21 phyla, including 11 animals for which genomic or EST data were previously lacking. The conclusions confirm ideas long established by anatomy, but raise new and interesting evolutionary relationships.
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paper_title: Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?

paper_content:

Rosenberg and Kumar (2001) addressed the importance of taxon sampling in phylogenetic analysis and concluded that phylogenetic error is “largely independent of taxon sample size” (2001:10756) and that their “results do not provide evidence in favor of adding taxa to problematic phylogenies” (2001:10756). In response to these conclusions, Zwickl and Hillis (2002) and Pollock et al. (2002) conducted additional simulations and reanalyzed the data presented by Rosenberg and Kumar (2001). Zwickl and Hillis and Pollock et al. showed that these conclusions of Rosenberg and Kumar could not be supported either by analyses of their original data or by new simulations that corrected a number of deficiencies in Rosenberg and Kumar’s original experimental design. Both Zwickl and Hillis and Pollock et al. found that increased taxon sampling resulted in greatly reduced phylogenetic estimation error, and Pollock et al. showed that the benefits of increased taxon sampling were similar to adding an equivalent amount of sequence length for the same taxa (in the ranges simulated by Rosenberg and Kumar). ::: ::: In their response, Rosenberg and Kumar (2002) focused on a slightly different conclusion from that in their original paper, which was that “longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference” (2001:10751). In 2001, Rosenberg and Kumar argued that the beneficial effect of increasing taxa was 10-fold lower than the beneficial effect of increasing sequence length and that the effects of increased taxon sampling for the same genes were negligible (“largely independently” of phylogenetic error). Rosenberg and Kumar (2002) have now concluded that the beneficial effect of increasing taxon sample size is not small, but they suggested that the benefit comes simply from the overall increase in size of the data matrix (the total number of characters × taxa). Furthermore, they maintained that there is a greater benefit to increasing the total sequence length for few taxa than can be obtained by increasing taxon sampling for the same genes. Here, we discuss the two sets of conclusions reached by Rosenberg and Kumar (2001, 2002).
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paper_title: Increased taxon sampling is advantageous for phylogenetic inference.

paper_content:

Until recently, it was believed that complex phylogenies might be extremely difficult to reconstruct due to the phenomenal rate of increase in the number of possible phylogenies as the number of taxa increases. However, Hillis (1996) showed through simulation that, for at least one complex phylogeny of angiosperms with 228 taxa, reconstruction was far more accurate than expected, even with relatively modest amounts of DNA sequence data. This led to a flurry of papers on the subject of taxon sampling and phylogenetic reconstruction, with focus quickly shifting from the question of whether complex phylogenies can be reconstructed to whether and how much an existing phylogeny can be improved through increased taxon sampling (Hillis, 1998; Kim, 1998; Poe, 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rannala et al., 1998; Yang, 1998). Although a statistician might intuitively believe that it is generally better (or at least no worse) to increase the amount of data to resolve a question in statistical inference, the benefits of taxon addition for phylogenetic inference remain controversial. Some researchers have argued that taxon addition can decrease accuracy (Kim, 1996,1998), while others believe that increased sampling improves accuracy (Graybeal, 1998; Hillis, 1996, 1998; Murphy et al., 2001; Poe, 1998; Pollock and Bruno, 2000; Pollock et al., 2000; Soltis et al., 1999). The reasons that different papers come to apparently contradictory conclusions deserve careful consideration. ::: ::: An often cited factor affecting the benefits of taxon addition is the phenomenon of long-branch attraction (LBA). Some phylogenetic methods have a bias toward preferential clustering of long branches, leading to erroneous results when those long branches do not actually represent a monophyletic assemblage (Felsenstein, 1978; Hendy and Penny, 1989). This phenomenon has been cited in favor of increased taxon sampling, since sampling can be designed to break up long branches (Hillis, 1998). However, increased sampling has also been implicated as a potential cause of LBA because addition of a new long branch may wrongly attract a pre-existing long branch that had previously been inferred correctly (Poe and Swofford, 1999; Rannala et al., 1998). LBA may also explain some simulations that have found problems in phylogeny estimation when sampling outside the taxonomic group of interest (but see Pollock and Bruno [2000] for an alternative explanation). Outside sampling in these simulations tended to add long branches, which tended to attract the longest unbroken branch in the group of interest (Hillis, 1998; Rannala et al., 1998). The degree to which LBA is a problem depends greatly on the method of analysis, and LBA is much less of a problem for maximum likelihood (ML) than for parsimony or distance methods (Bruno and Halpern, 1999). ::: ::: A recent paper on the subject of taxon addition (Rosenberg and Kumar, 2001) concludes that increased taxon sampling is of little benefit to phylogenetic inference when compared to increasing sequence length. We disagree with their interpretation and believe that their data support the importance of increased taxon sampling. In addition, some of their data were simulated under extreme conditions (i.e., substitution rates that were very high or low, or sequences that were unreasonably short). Large error values and nonlinear relationships at these extremes make it difficult to interpret effects for the majority of the range, and averaging across the entire range is inappropriate. Moreover, we do not believe that Rosenberg and Kumar (2001) used the most appropriate metric to measure the relative effect of taxon addition. Our reanalysis of their simulated data indicates that increased taxon sampling is highly beneficial for phylogenetic inference.
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paper_title: Phylogenomics and the reconstruction of the tree of life

paper_content:

As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
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paper_title: Homoplasy Increases Phylogenetic Structure

paper_content:

According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants—shows the opposite: although rapidly evolving and highly homoplastic, third positions contain most of the phylogenetic structure in the data. Frequency of change should thus be used with caution as a criterion for weighting or selecting characters.
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paper_title: Experimental Design Criteria in Phylogenetics: Where to Add Taxa

paper_content:

Accurate phylogenetic inference is a topic of intensive research and debate and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model, and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early 20th century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998. Proc. R. Soc. Lond. B. 265: 1779-1786) thus allows investigation of "where to add taxa" in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behavior of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants. (A-optimality; D-optimality; E-optimality; experimental design; Fisher information; phylogenetics; taxon sampling.) Nylander (2001) formulates the problem of taxon sampling as: "Given a sample of taxa and a method of analysis, certain properties of the data could render the reconstruction of the true tree difficult or even impossi ble. Furthermore, a different sample of taxa could have facilitated the reconstruction, or conversely, even made it more difficult." Examples from the literature illustrate that the addition or deletion of even a single taxon can change the inferred phylogenetic relationships and there is a general consensus on the importance of, and sensitiv ity to, taxon sampling (e.g., Poe, 2003; Soltis et al., 2004; Martin et al., 2005).
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paper_title: Phylogenetic information and experimental design in molecular systematics

paper_content:

Despite the widespread perception that evolutionary inference from molecular sequences is a statistical problem, there has been very little attention paid to questions of experimental design. Previous consideration of this topic has led to little more than an empirical folklore regarding the choice of suitable genes for analysis, and to dispute over the best choice of taxa for inclusion in data sets. I introduce what I believe are new methods that permit the quantification of phylogenetic information in a sequence alignment. The methods use likelihood calculations based on Markov-process models of nucleotide substitution allied with phylogenetic trees, and allow a general approach to optimal experimental design. Two examples are given, illustrating realistic problems in experimental design in molecular phylogenetics and suggesting more general conclusions about the choice of genomic regions, sequence lengths and taxa for evolutionary studies.
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paper_title: How Many Genes Should a Systematist Sample ? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence

paper_content:

How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix
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paper_title: Missing data, incomplete taxa, and phylogenetic accuracy.

paper_content:

The problem of missing data is often considered to be the most important obstacle in reconstructing the phylogeny of fossil taxa and in combining data from diverse characters and taxa for phylogenetic analysis. Empirical and theoretical studies show that including highly incomplete taxa can lead to multiple equally parsimonious trees, poorly resolved consensus trees, and decreased phylogenetic accuracy. However, the mechanisms that cause incomplete taxa to be problematic have remained unclear. It has been widely assumed that incomplete taxa are problematic because of the proportion or amount of missing data that they bear. In this study, I use simulations to show that the reduced accuracy associated with including incomplete taxa is caused by these taxa bearing too few complete characters rather than too many missing data cells. This seemingly subtle distinction has a number of important implications. First, the so-called missing data problem for incomplete taxa is, paradoxically, not directly related to their amount or proportion of missing data. Thus, the level of completeness alone should not guide the exclusion of taxa (contrary to common practice), and these results may explain why empirical studies have sometimes found little relationship between the completeness of a taxon and its impact on an analysis. These results also (1) suggest a more effective strategy for dealing with incomplete taxa, (2) call into question a justification of the controversial phylogenetic supertree approach, and (3) show the potential for the accurate phylogenetic placement of highly incomplete taxa, both when combining diverse data sets and when analyzing relationships of fossil taxa.
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paper_title: General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa

paper_content:

Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least with respect to the maximum parsimony method, has been given the catch phrase "long branches attract." It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclu- sions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by com- parison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. (Maximum parsimony; inconsistency; large phylogenies; long branches.)
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paper_title: Information Theory and an Extension of the Maximum Likelihood Principle

paper_content:

In this paper it is shown that the classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion. This observation shows an extension of the principle to provide answers to many practical problems of statistical model fitting.
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paper_title: Fisher information and stochastic complexity

paper_content:

By taking into account the Fisher information and removing an inherent redundancy in earlier two-part codes, a sharper code length as the stochastic complexity and the associated universal process are derived for a class of parametric processes. The main condition required is that the maximum-likelihood estimates satisfy the central limit theorem. The same code length is also obtained from the so-called maximum-likelihood code.
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paper_title: More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

paper_content:

The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.
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paper_title: Genome-scale approaches to resolving incongruence in molecular phylogenies

paper_content:

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.
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paper_title: Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

paper_content:

A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolution of the characters added for resolution of the phylogeny in question. Clearly, the addition of characters evolving at optimal rates will have much greater impact upon accurate phylogenetic analysis than will the addition of characters with an inappropriate rate of evolution. Development of practical analytical predictions of the asymptotic impact of adding additional taxa would complement computational investigations of the relative utility of these two methods of expanding acquired data. Accordingly, we here formulate a measure of the phylogenetic informativeness of the additional sampling of character states from a new taxon added to the canonical phylogenetic quartet. We derive the optimal rate of evolution for characters assessed in taxa to be sampled and a metric of informativeness based on the rate of evolution of the characters assessed in the new taxon and the distance of the new taxon from the internode of interest. Calculation of the informativeness per base pair of additional character sampling for included taxa versus additional character sampling for novel taxa can be used to estimate cost-effectiveness and optimal efficiency of phylogenetic experimental design. The approach requires estimation of rates of evolution of individual sites based on an alignment of genes orthologous to those to be sequenced, which may be identified in a well-established clade of sister taxa or of related taxa diverging at a deeper phylogenetic scale. Some approximate idea of the potential phylogenetic relationships of taxa to be sequenced is also desirable, such as may be obtained from ribosomal RNA sequence alone. Application to the solution of recalcitrant unresolved nodes in an otherwise well-known phylogeny is the most obvious application. We validate the theory by analysis of its predictions regarding the phylogenetic informativeness for taxon addition of 46 amino acid alignments of 21 fungal taxa. Gene and taxon sampling according to the theory herein and following a "deepest ingroup" heuristic are shown to provide significantly improved resolution of specified deep internodes.
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paper_title: Profiling Phylogenetic Informativeness

paper_content:

The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.
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paper_title: Incomplete taxon sampling is not a problem for phylogenetic inference

paper_content:

A major issue in all data collection for molecular phylogenetics is taxon sampling, which refers to the use of data from only a small representative set of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated. To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters--rates of evolution, species sampling, and gene lengths--determined from data available in genomic databases. A comparison of the true tree with trees constructed by using taxa subsamples and trees constructed by using all taxa shows that the amount of phylogenetic error per internal branch is similar; a result that holds true for the neighbor-joining, minimum evolution, maximum parsimony, and maximum likelihood methods. Furthermore, our results show that even though trees inferred by using progressively larger taxa subsamples of a real data set become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogenetic error per internal branch. Our results suggest that longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference.
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paper_title: Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias

paper_content:

These recommendations, taken at face val? ue, appear to be in direct conflict with re? gard to advice on taxon sampling. The pa? pers in this issue extend these studies and modify these recommendations on the ba? sis of analyses of real data sets (Soltis et al., 1998; Poe, 1998), simulations (Graybeal, 1998), and theoretical considerations (Kim, 1998). One conclusion from reading these papers is that whether increased taxonom? ic sampling helps or hinders the process of accurate phylogenetic estimation depends to a great extent on how accuracy is eval? uated and what is meant by "taxonomic sampling."
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paper_title: Sensitivity of Phylogeny Estimation to Taxonomic Sampling

paper_content:

Recent studies have shown that addition or deletion of taxa from a data matrix can change the estimate of phylogeny. I used 29 data sets from the literature to examine the effect of taxon sampling on phylogeny estimation within data sets. I then used multiple regression to assess the effect of number of taxa, number of characters, homoplasy, strength of support, and tree symmetry on the sensitivity of data sets to taxonomic sampling. Sensitivity to sampling was measured by mapping characters from a matrix of culled taxa onto optimal trees for that reduced matrix and onto the pruned optimal tree for the entire matrix, then comparing the length of the reduced tree to the length of the pruned complete tree. Within-data-set patterns can be described by a second-order equation relating fraction of taxa sampled to sensitivity to sampling. Multiple regression analyses found number of taxa to be a signi® cant predictor of sensitivity to sampling; retention index, number of informative characters, total support index, and tree symmetry were nonsigni® cant predictors. I derived a predictive regression equation relating fraction of taxa sam- pled and number of taxa potentially sampled to sensitivity to taxonomic sampling and calculated values for this equation within the bounds of the variables examined. The length difference be- tween the complete tree and a subsampled tree was generally small (average difference of 0± 2.9 steps), indicating that subsampling taxa is probably not an important problem for most phylo- genetic analyses using up to 20 taxa. (Multiple regression; modeling; phylogeny estimation; tax- onomic sampling.)
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paper_title: General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa

paper_content:

Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least with respect to the maximum parsimony method, has been given the catch phrase "long branches attract." It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclu- sions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by com- parison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. (Maximum parsimony; inconsistency; large phylogenies; long branches.)
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paper_title: Inferring Complex Phylogenies Using Parsimony: An Empirical Approach Using Three Large DNA Data Sets for Angiosperms

paper_content:

To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbcL (1,428 bp), and atpB (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA 1 rbcL 1 atpB data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given suf® cient signal. In this case, and probably most others, suf® cient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of $ 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa. (Large data sets, parsimony, phylogeny.)
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paper_title: Taxon sampling revisited

paper_content:

Phylogenies that include long, unbranched lineages can be difficult to reconstruct. This is because long-branch taxa (such as rapidly evolving species) may share character states by chance more often than more closely related taxa share derived character states through common ancestry1. Despite Kim's warning that added taxa can decrease accuracy2, some authors have argued that the negative impact of this error, called ‘long-branch attraction’, is minimized when slowly evolving lineages are included to subdivide long branches3,4,5. From this they have concluded that increasing the number of species sampled per lineage results in better accuracy than increasing the number of characters per species6. We find, using computer simulations, that adding characters can be the more favourable strategy, even for long-branched trees, and that adding slowly evolving taxa to subdivide long branches can reduce accuracy.
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paper_title: Large-scale phylogenies and measuring the performance of phylogenetic estimators.

paper_content:

Performance measures of phylogenetic estimation methods such as accuracy, consistency, and power are an attempt at summarizing an ensemble of a given estimator's behavior. These summaries characterize an ensemble behavior with a single number, leading to a variety of definitions. In particular, the relationships between different performance measures such as accuracy and consistency or accuracy and error depend on the exact definition of these measures. In addition, it is relatively common to use large-sample behavior to infer similar behavior for small samples. In fact, large-sample results such as the claimed asymptotic efficiency of the maximum-likelihood estimator are often uninformative for small samples. Conversely, small-sample behavior using simulations is sometimes used to imply large-sample behavior such as consistency. However, such extrapolation is often difficult. How the performance of a phylogenetic estimator scales with the addition of taxa must be qualified with respect to whether the whole tree is being estimated or a fixed subset of taxa is being estimated. It must also be qualified with respect to how tree models are sampled. Over the ensemble of all possible trees of a given size, the performance of the estimators for the whole tree estimate suffers when the tree size becomes larger. However, under certain models of cladogenesis, the estimate can improve with the addition of taxa. In fact, at all numbers of taxa there are subsets of tree models that are easier to estimate than others. This suggests that with judicious addition or subtraction of taxa we can move from tree models that are more difficult to estimate at one number of taxa to those that are easier to estimate at another number of taxa.
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paper_title: Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?

paper_content:

Rosenberg and Kumar (2001) addressed the importance of taxon sampling in phylogenetic analysis and concluded that phylogenetic error is “largely independent of taxon sample size” (2001:10756) and that their “results do not provide evidence in favor of adding taxa to problematic phylogenies” (2001:10756). In response to these conclusions, Zwickl and Hillis (2002) and Pollock et al. (2002) conducted additional simulations and reanalyzed the data presented by Rosenberg and Kumar (2001). Zwickl and Hillis and Pollock et al. showed that these conclusions of Rosenberg and Kumar could not be supported either by analyses of their original data or by new simulations that corrected a number of deficiencies in Rosenberg and Kumar’s original experimental design. Both Zwickl and Hillis and Pollock et al. found that increased taxon sampling resulted in greatly reduced phylogenetic estimation error, and Pollock et al. showed that the benefits of increased taxon sampling were similar to adding an equivalent amount of sequence length for the same taxa (in the ranges simulated by Rosenberg and Kumar). ::: ::: In their response, Rosenberg and Kumar (2002) focused on a slightly different conclusion from that in their original paper, which was that “longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference” (2001:10751). In 2001, Rosenberg and Kumar argued that the beneficial effect of increasing taxa was 10-fold lower than the beneficial effect of increasing sequence length and that the effects of increased taxon sampling for the same genes were negligible (“largely independently” of phylogenetic error). Rosenberg and Kumar (2002) have now concluded that the beneficial effect of increasing taxon sample size is not small, but they suggested that the benefit comes simply from the overall increase in size of the data matrix (the total number of characters × taxa). Furthermore, they maintained that there is a greater benefit to increasing the total sequence length for few taxa than can be obtained by increasing taxon sampling for the same genes. Here, we discuss the two sets of conclusions reached by Rosenberg and Kumar (2001, 2002).
---
paper_title: Increased taxon sampling is advantageous for phylogenetic inference.

paper_content:

Until recently, it was believed that complex phylogenies might be extremely difficult to reconstruct due to the phenomenal rate of increase in the number of possible phylogenies as the number of taxa increases. However, Hillis (1996) showed through simulation that, for at least one complex phylogeny of angiosperms with 228 taxa, reconstruction was far more accurate than expected, even with relatively modest amounts of DNA sequence data. This led to a flurry of papers on the subject of taxon sampling and phylogenetic reconstruction, with focus quickly shifting from the question of whether complex phylogenies can be reconstructed to whether and how much an existing phylogeny can be improved through increased taxon sampling (Hillis, 1998; Kim, 1998; Poe, 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rannala et al., 1998; Yang, 1998). Although a statistician might intuitively believe that it is generally better (or at least no worse) to increase the amount of data to resolve a question in statistical inference, the benefits of taxon addition for phylogenetic inference remain controversial. Some researchers have argued that taxon addition can decrease accuracy (Kim, 1996,1998), while others believe that increased sampling improves accuracy (Graybeal, 1998; Hillis, 1996, 1998; Murphy et al., 2001; Poe, 1998; Pollock and Bruno, 2000; Pollock et al., 2000; Soltis et al., 1999). The reasons that different papers come to apparently contradictory conclusions deserve careful consideration. ::: ::: An often cited factor affecting the benefits of taxon addition is the phenomenon of long-branch attraction (LBA). Some phylogenetic methods have a bias toward preferential clustering of long branches, leading to erroneous results when those long branches do not actually represent a monophyletic assemblage (Felsenstein, 1978; Hendy and Penny, 1989). This phenomenon has been cited in favor of increased taxon sampling, since sampling can be designed to break up long branches (Hillis, 1998). However, increased sampling has also been implicated as a potential cause of LBA because addition of a new long branch may wrongly attract a pre-existing long branch that had previously been inferred correctly (Poe and Swofford, 1999; Rannala et al., 1998). LBA may also explain some simulations that have found problems in phylogeny estimation when sampling outside the taxonomic group of interest (but see Pollock and Bruno [2000] for an alternative explanation). Outside sampling in these simulations tended to add long branches, which tended to attract the longest unbroken branch in the group of interest (Hillis, 1998; Rannala et al., 1998). The degree to which LBA is a problem depends greatly on the method of analysis, and LBA is much less of a problem for maximum likelihood (ML) than for parsimony or distance methods (Bruno and Halpern, 1999). ::: ::: A recent paper on the subject of taxon addition (Rosenberg and Kumar, 2001) concludes that increased taxon sampling is of little benefit to phylogenetic inference when compared to increasing sequence length. We disagree with their interpretation and believe that their data support the importance of increased taxon sampling. In addition, some of their data were simulated under extreme conditions (i.e., substitution rates that were very high or low, or sequences that were unreasonably short). Large error values and nonlinear relationships at these extremes make it difficult to interpret effects for the majority of the range, and averaging across the entire range is inappropriate. Moreover, we do not believe that Rosenberg and Kumar (2001) used the most appropriate metric to measure the relative effect of taxon addition. Our reanalysis of their simulated data indicates that increased taxon sampling is highly beneficial for phylogenetic inference.
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paper_title: Missing data, incomplete taxa, and phylogenetic accuracy.

paper_content:

The problem of missing data is often considered to be the most important obstacle in reconstructing the phylogeny of fossil taxa and in combining data from diverse characters and taxa for phylogenetic analysis. Empirical and theoretical studies show that including highly incomplete taxa can lead to multiple equally parsimonious trees, poorly resolved consensus trees, and decreased phylogenetic accuracy. However, the mechanisms that cause incomplete taxa to be problematic have remained unclear. It has been widely assumed that incomplete taxa are problematic because of the proportion or amount of missing data that they bear. In this study, I use simulations to show that the reduced accuracy associated with including incomplete taxa is caused by these taxa bearing too few complete characters rather than too many missing data cells. This seemingly subtle distinction has a number of important implications. First, the so-called missing data problem for incomplete taxa is, paradoxically, not directly related to their amount or proportion of missing data. Thus, the level of completeness alone should not guide the exclusion of taxa (contrary to common practice), and these results may explain why empirical studies have sometimes found little relationship between the completeness of a taxon and its impact on an analysis. These results also (1) suggest a more effective strategy for dealing with incomplete taxa, (2) call into question a justification of the controversial phylogenetic supertree approach, and (3) show the potential for the accurate phylogenetic placement of highly incomplete taxa, both when combining diverse data sets and when analyzing relationships of fossil taxa.
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paper_title: Sensitivity of Phylogeny Estimation to Taxonomic Sampling

paper_content:

Recent studies have shown that addition or deletion of taxa from a data matrix can change the estimate of phylogeny. I used 29 data sets from the literature to examine the effect of taxon sampling on phylogeny estimation within data sets. I then used multiple regression to assess the effect of number of taxa, number of characters, homoplasy, strength of support, and tree symmetry on the sensitivity of data sets to taxonomic sampling. Sensitivity to sampling was measured by mapping characters from a matrix of culled taxa onto optimal trees for that reduced matrix and onto the pruned optimal tree for the entire matrix, then comparing the length of the reduced tree to the length of the pruned complete tree. Within-data-set patterns can be described by a second-order equation relating fraction of taxa sampled to sensitivity to sampling. Multiple regression analyses found number of taxa to be a signi® cant predictor of sensitivity to sampling; retention index, number of informative characters, total support index, and tree symmetry were nonsigni® cant predictors. I derived a predictive regression equation relating fraction of taxa sam- pled and number of taxa potentially sampled to sensitivity to taxonomic sampling and calculated values for this equation within the bounds of the variables examined. The length difference be- tween the complete tree and a subsampled tree was generally small (average difference of 0± 2.9 steps), indicating that subsampling taxa is probably not an important problem for most phylo- genetic analyses using up to 20 taxa. (Multiple regression; modeling; phylogeny estimation; tax- onomic sampling.)
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paper_title: Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling

paper_content:

The debate about whether phylogenetic accuracy is most efficiently increased by sampling more charac ters or more taxa is certainly not new (e.g., Kim, 1996; Graybeal, 1998; Poe, 1998a,b; Rannala et al., 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rosenburg and Kumar, 2001; Pollock et al., 2002; Zwickl and Hillis, 2002; Rosenberg and Kumar, 2003; Hillis et al., 2003). However, the recent increase of whole genomic sequences available from an assortment of distantly related taxa makes this debate highly relevant to researchers across fields of bi ology. Recently, Rokas et al. (2003) argued that the true species tree can be recovered despite conflicting phylo genetic signal between genes if enough genes are used in the analysis. Using the bootstrap proportion (BP) as a measure of phylogenetic accuracy, they concluded that approximately 20 genes are needed to ensure a robustly supported tree (>95% BP) for their study group of eight yeast taxa. From these empirical results, they generalized that most molecular phylogenetic studies have probably included insufficient numbers of genes to confidently re solve relationships within their respective focal groups. This approach to measuring accuracy can be sensitive to method inconsistency, or the failure to converge on the correct tree as the data set becomes infinitely large. When a method is inconsistent, measures of support such as nonparametric bootstrapping can increase as more se quence data are added?but in support of the wrong phy logeny (Phillips et al., 2004; Collins et al., 2005; Delsuc et al., 2005). Although most methods perform well over most of tree space (Huelsenbeck, 1995; Poe, 2003), regions of inconsistency have been identified in the literature for all of the most commonly used phylogenetic meth ods. For example, compositional bias can affect the accu racy of minimum evolution (Phillips et al., 2004), model misspecification may affect parametric methods such as maximum likelihood (ML) (Poe, 2003; Philippe et al, 2005; Collins et al., 2005), and branch-length asymme try can lead to inconsistency in maximum parsimony (Felsenstein, 1978; Hendy and Penny, 1989). Parsimony is particularly prone to long-branch attraction (LBA), an analytical artifact in which two taxa on long branches are incorrectly placed as sister taxa (Felsenstein, 1978; Hendy and Penny, 1989; Huelsenbeck and Hillis, 1993). Although there are many reasons for conflicting phylo genetic signal between genes, one relevant reason could be related to method inconsistency: differing rates of evo lution between genes could cause a particular method to be inconsistent for some genes and not for others. We argue that by addressing this source of conflict between genes, fewer genes may be needed to return an accu rate phylogeny. One source of conflict in the Rokas et al. (2003) data set may be nonstationarity: taxa that differ from the others in their base compositional bias may be erroneously drawn together as sister taxa (Collins et al., 2005). Here, we show that an additional source of conflict between the 106 genes in the Rokas et al. data set may be branch-length asymmetry. Using simulations of 106 genes from the Rokas et al. data set on a 79-taxon yeast phylogeny, we additionally show that when genes are added to a data set, support for the wrong reconstruc tion can increase when there is LBA. However, when taxa are added to the analysis, support for the correct reconstruction increases, and fewer genes are needed to achieve accuracy.
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paper_title: More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

paper_content:

The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.
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paper_title: Incomplete taxon sampling is not a problem for phylogenetic inference

paper_content:

A major issue in all data collection for molecular phylogenetics is taxon sampling, which refers to the use of data from only a small representative set of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated. To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters--rates of evolution, species sampling, and gene lengths--determined from data available in genomic databases. A comparison of the true tree with trees constructed by using taxa subsamples and trees constructed by using all taxa shows that the amount of phylogenetic error per internal branch is similar; a result that holds true for the neighbor-joining, minimum evolution, maximum parsimony, and maximum likelihood methods. Furthermore, our results show that even though trees inferred by using progressively larger taxa subsamples of a real data set become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogenetic error per internal branch. Our results suggest that longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference.
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paper_title: Large-scale phylogenies and measuring the performance of phylogenetic estimators.

paper_content:

Performance measures of phylogenetic estimation methods such as accuracy, consistency, and power are an attempt at summarizing an ensemble of a given estimator's behavior. These summaries characterize an ensemble behavior with a single number, leading to a variety of definitions. In particular, the relationships between different performance measures such as accuracy and consistency or accuracy and error depend on the exact definition of these measures. In addition, it is relatively common to use large-sample behavior to infer similar behavior for small samples. In fact, large-sample results such as the claimed asymptotic efficiency of the maximum-likelihood estimator are often uninformative for small samples. Conversely, small-sample behavior using simulations is sometimes used to imply large-sample behavior such as consistency. However, such extrapolation is often difficult. How the performance of a phylogenetic estimator scales with the addition of taxa must be qualified with respect to whether the whole tree is being estimated or a fixed subset of taxa is being estimated. It must also be qualified with respect to how tree models are sampled. Over the ensemble of all possible trees of a given size, the performance of the estimators for the whole tree estimate suffers when the tree size becomes larger. However, under certain models of cladogenesis, the estimate can improve with the addition of taxa. In fact, at all numbers of taxa there are subsets of tree models that are easier to estimate than others. This suggests that with judicious addition or subtraction of taxa we can move from tree models that are more difficult to estimate at one number of taxa to those that are easier to estimate at another number of taxa.
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paper_title: Taxon sampling, bioinformatics, and phylogenomics.

paper_content:

Taxon sampling is often thought to be of extreme importance for phylogenetic inference, and increased sampling of taxa is commonly advocated as a solution to resolving problematic phylogenies. Another solution is to increase the number of sites (by sequencing additional genes) sampled for each taxon. In an ideal world, one would like to increase samples of both taxa and genes, but taxon sampling has not kept up with the pace of gene sampling increase because of the increasing ease and emphasis on genome sequencing. ::: ::: The question of taxon sampling is necessarily driven by resource limitation. The precise scope of “sufficient” taxon sampling is always dependent on questions being addressed. If we need to know the complete phylogeny of a genus, we must sample the genus exhaustively. In experimental design, partial sampling is an issue only when certain taxa can stand as proxies for the clades to which they belong (clade-based or stratified sampling; see Hillis, 1998). In bioinformatics studies, taxon sampling is restricted by the data availability in genetic databases (database-restricted sampling). Clearly, the nature of the problem in these two research programs is different. In stratified sampling, we are interested in knowing whether to sequence more genes per species or fewer genes for a large number of species per clade. In contrast, in database-restricted sampling it is important to know whether the overall accuracy of inferred phylogenetic trees for small taxa sets is similar to that of trees inferred from larger taxa sets. We recently addressed the issue of the database-restricted sampling (Rosenberg and Kumar, 2001) and concluded that although there was a consistent decrease in error when using more taxa, the decrease was generally minor relative to the number of taxa added to the data set. ::: ::: Pollock et al. (2002) challenged this conclusion by modifying our measure of the phylogenetic error. This measure, ΔE, differs from ours in that we used the difference in error between the subsampled tree [ES] and full sampled tree [EP], whereas Pollock et al. (2002) divided this difference by ES to measure the relative reduction in error. ΔE plotted against the number of additional taxa in the full sampled tree (=66 minus the number of taxa in the subsample tree) shows a clear positive effect (Pollock et al., 2002: Figs. 4, 5). Unfortunately, this impressive result brings little biological benefit, as clearly shown by a scatterplot of the average number of additional branches inferred correctly in each case (Fig. 1). In no instance are there more than 1.5 additional branches reconstructed correctly, even though the number of taxa has often increased many fold. For instance, more than doubling the number of taxa only led to an average increase of 0.7 additional correct branches (points in the middle of the x-axis in Fig. 1). This fact was clearly noted in our original article: “Note that even though ES is greater than EG and EP for very small subsamples (<10 taxa), the difference in phylogenetic error is usually much smaller than one branch per tree” (Rosenberg and Kumar, 2001: 10754). Therefore, although an increase in the number of taxa sampled will lead to improvement in accuracy, the improvement is minimal, particularly when we consider the amount of data (in terms of the number of total nucleotides) being added. We do not advocate using fewer taxa when more are available, as is clear from the results presented by Rosenberg and Kumar (2001:10754). ::: ::: ::: ::: Figure 1 ::: ::: Number of branches reconstructed correctly with increased taxon sampling. (a) All simulated genes. (b) Genes with rates >0.7 and >500 sites (after Pollock et al., 2002). ::: ::: ::: ::: ::: ::: Figure 4 ::: ::: Plot of the percentage of times interordinal branches were reconstructed correctly when the total number of bases was held constant. In each comparison, the data set with fewer taxa (and more sites per taxon) is always plotted on the x-axis. The dotted ... ::: ::: ::: ::: Zwickl and Hillis (2002) also challenged conclusions reached by Rosenberg and Kumar (2001) by using the concept of tree diameter (the maximum distance between all pairs of taxa) to partition genes with different subsampled sets of taxa for analysis. They showed that four-taxon subsamples with a smaller tree diameter generate more accurate results than those subsamples with larger tree diameters. This result is expected because, with sequence divergence and length kept constant, the larger diameter four-taxon trees will encompass higher average divergence and would thus involve larger estimation errors. Furthermore, for the simulations involving the model tree in Figure 2a, four-taxon data sets containing sequences with larger diameters would include interordinal relationships (with many small interior branches) more frequently than would small diameter samples (see also Zwickl and Hillis, 2002: Fig. 3a). Therefore, Zwickl and Hillis’s study is an examination of the phylogenetic error at different evolutionary divergence cross sections of the phylogenetic tree specifically simulated. This and the complete absence of resource limitation (a must for any sampling study) clearly establish that Zwickl and Hillis have not evaluated either stratified or database-restricted taxon-sampling problems. Therefore, Zwickl and Hillis were not correct in stating that their results are in contradiction with our previous results (Rosenberg and Kumar, 2001). In fact, Zwickl and Hillis’s results represent another facet of statistical analysis of the same data. Also, Zwickl and Hillis took issue with our choice of a fast heuristic search used in computer simulations (Rosenberg and Kumar, 2001). We chose this strategy based on results of multiple previous studies, which showed that the most optimal tree is often more optimal than the true tree and that the fast and more exhaustive searches produce trees with comparable phylogenetic errors (Kumar, 1996; Nei et al., 1998; Takahashi and Nei, 2000). Zwickl and Hillis found that with the maximum parsimony (MP) method for the given data set, the TBR searches produced topologies that had less error than those from NNI. This result (based on a single simulation data set) seems to be in conflict with previous studies. We plan to evaluate this result more thoroughly analytically and by computer simulation in the future. ::: ::: ::: ::: Figure 2 ::: ::: Model tree for the simulations based on the Eutherian mammal tree from Murphy et al. (2001) and Eizrik et al. (2001). (a) Full 66-taxon tree; interordinal relationships are represented by thick branches designated with letters. (b) Phylogenetic relationships ... ::: ::: ::: ::: ::: ::: Figure 3 ::: ::: Plot of the percentage of times the interordinal branches were reconstructed correctly in 66-taxon trees versus n-taxon trees, where n = 15, 30, and 45. These values are for all genes and all replicates. The dotted lines indicate a 1:1 relationship. Analyses ... ::: ::: ::: ::: However, we extrapolated our database-restricted sampling and random sampling results to conclude that the phylogenetic trees with fewer taxa but large numbers of genes per taxon may be more accurate than those with many taxa but fewer genes (Rosenberg and Kumar, 2001). Neither Pollock et al. (2002) nor Zwickl and Hillis (2002) addressed that issue, which lies at the heart of the experimental design. Here, we tackle this issue along with biological relevance of many other assumptions made and conclusions reached by Rosenberg and Kumar (2001) that Zwickl and Hillis (2002) objected to. We show that the conclusions reached by Rosenberg and Kumar (2001) are applicable for both phyloinformatic and phylogenomic studies.
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paper_title: Taxon sampling and the accuracy of phylogenetic analyses

paper_content:

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge- netic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incor- rect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applica- tions of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computa- tional power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.
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paper_title: Molecular Evolution: A phylogenetic approach

paper_content:

The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of Molecular Phylogenetics
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paper_title: Broad phylogenomic sampling improves resolution of the animal tree of life

paper_content:

This paper describes and discusses almost 40 megabases of expressed sequence tags (EST) clones from the DNA of animals from 21 phyla, including 11 animals for which genomic or EST data were previously lacking. The conclusions confirm ideas long established by anatomy, but raise new and interesting evolutionary relationships.
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paper_title: Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics

paper_content:

Background ::: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices.
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paper_title: Genome trees and the tree of life

paper_content:

Abstract Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a ‘Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal ‘species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.
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paper_title: Phylogenomics and the reconstruction of the tree of life

paper_content:

As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
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paper_title: How Many Genes Should a Systematist Sample ? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence

paper_content:

How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix
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paper_title: General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa

paper_content:

Inconsistency of phylogenetic estimations refers to the property of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This property, at least with respect to the maximum parsimony method, has been given the catch phrase "long branches attract." It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclu- sions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by com- parison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. (Maximum parsimony; inconsistency; large phylogenies; long branches.)
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paper_title: The tree of eukaryotes

paper_content:

Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical ‘supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.
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paper_title: Large-scale sequencing and the new animal phylogeny

paper_content:

Although comparisons of gene sequences have revolutionised our understanding of the animal phylogenetic tree, it has become clear that, to avoid errors in tree reconstruction, a large number of genes from many species must be considered: too few genes and stochastic errors predominate, too few taxa and systematic errors appear. We argue here that, to gather many sequences from many taxa, the best use of resources is to sequence a small number of expressed sequence tags (1000–5000 per species) from as many taxa as possible. This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme.
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paper_title: Gene Trees in Species Trees

paper_content:

Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and ex- tinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relation- ships. Each of the processes of discord could yield a different parsimony criterion for reconstruct- ing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the prob- ability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of inter- breeding. (Biogeography; coalescence; coevolution; evolution; gene duplication; gene genealogy; gene trees; horizontal transfer; hybridization; lineage sorting; parsimony; phylogeny; species con- cepts; species trees; tree reconciliation.)
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paper_title: Genome-scale approaches to resolving incongruence in molecular phylogenies

paper_content:

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.
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paper_title: Incomplete taxon sampling is not a problem for phylogenetic inference

paper_content:

A major issue in all data collection for molecular phylogenetics is taxon sampling, which refers to the use of data from only a small representative set of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated. To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters--rates of evolution, species sampling, and gene lengths--determined from data available in genomic databases. A comparison of the true tree with trees constructed by using taxa subsamples and trees constructed by using all taxa shows that the amount of phylogenetic error per internal branch is similar; a result that holds true for the neighbor-joining, minimum evolution, maximum parsimony, and maximum likelihood methods. Furthermore, our results show that even though trees inferred by using progressively larger taxa subsamples of a real data set become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogenetic error per internal branch. Our results suggest that longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference.
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paper_title: Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?

paper_content:

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.
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paper_title: The importance of taxon sampling in genomic studies: an example from the cyclooxygenases of teleost fishes.

paper_content:

Comparative genomic studies must often rely on single model species and exemplars to represent the genetic variation both within and among different major groups, because of technological, financial, and time constraints. This study of the cyclooxygenases from teleost fishes serves as a reminder that caution is required in these cases, since such incomplete taxon sampling can lead to errors in the interpretation and prediction of genome evolution, function, and structure.
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paper_title: The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies.

paper_content:

We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the 'Mouse Goat' and the 'Irish Elk'. Previous primary analyses have included only a small portion of the species diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid phylogenetic estimates for a large number of species. However, single-gene phylogenies often differ dramatically from studies involving multiple datasets suggesting that they often are unreliable. However, based on recovery of benchmark clades-clades supported in prior studies based on multiple independent datasets-and recovery of undisputed traditional taxonomic groups, Cytb performs extraordinarily well in resolving cetartiodactyl phylogeny when taxon sampling is dense. Missing data, however, (taxa with partial sequences) can compromise phylogenetic accuracy, suggesting a tradeoff between the benefits of adding taxa and introducing question marks. In the full data, a few species with a short sequences appear misplaced, however, sequence length alone seems a poor predictor of this phenomenon as other taxa with equally short sequences were not conspicuously misplaced. Although we recommend awaiting a better supported phylogeny based on more character data to reconsider classification and taxonomy within Cetartiodactyla, the new phylogenetic hypotheses provided here represent the currently best available tool for comparative species-level studies within this group. Cytb has been sequenced for a large percentage of mammals and appears to be a reliable phylogenetic marker as long as taxon sampling is dense. Therefore, an opportunity exists now to reconstruct detailed phylogenies of most of the major mammalian clades to rapidly provide much needed tools for species-level comparative studies.
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paper_title: Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?

paper_content:

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.
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Title: The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

Section 1: INTRODUCTION
Description 1: Write about the background of phylogenetic inference, the importance of taxon sampling, and the purpose of the review.

Section 2: THE NATURE OF MOLECULAR SEQUENCE-BASED TAXA
Description 2: Discuss issues related to taxon sampling of molecular sequence data, including conflicting signals, inadequate rates of sequence evolution, and violation of method assumptions.

Section 3: QUANTIFYING TAXON INFORMATIVENESS
Description 3: Address the problem of finding criteria to select the most informative set of taxa for phylogenetic inference and explore the measures to quantify informativeness.

Section 4: THE 1990S: A DECADE OF DEBATE
Description 4: Review the studies and debates from the 1990s on the impact of taxon sampling on phylogenetic inference accuracy and the challenges encountered.

Section 5: THE 2000s: YET ANOTHER DECADE OF CONTROVERSY
Description 5: Summarize the ongoing debates and findings in the 2000s regarding the influence of taxon sampling on phylogenetic inference, highlighting significant studies and their conclusions.

Section 6: GENOME-SCALE APPROACHES
Description 6: Discuss the impact of genome-scale data on phylogenetic inference and the implications of using large amounts of data from multiple loci for taxon sampling.

Section 7: ARRIVING AT A CONSENSUS AFTER TWO DECADES OF CONTROVERSY?
Description 7: Present the emerging consensus on the importance of taxon sampling for producing accurate phylogenies and the persisting debates regarding the best practices.

Section 8: CONCLUSION
Description 8: Summarize the key points discussed in the review about taxon sampling issues and their impact on phylogenetic inference, and suggest directions for future research.