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PubMed2000

Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides.

The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the Southern Hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as several relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, we examine several hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias. Although most workers consider Lepidogalaxias to be an unusual scaled member of the Southern Hemisphere galaxioids, it has also been suggested that this species is related to the Northern Hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid, and the alternative hypothesized esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae, and the loss of this migratory phase may be a major cause of speciation.

Animals↗

PubMed2001

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

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

History, 20th Century↗

PubMedDate not supplied

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known.

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.

Biometry↗

PubMedDate not supplied

Character analysis in morphological phylogenetics: problems and solutions.

Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (definition, delimitation, and ordering of character states) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modification of Thiele's approach) is proposed that allows quantitative traits to be analyzed as continuous variables. The problem of scaling or weighting quantitative characters relative to qualitative characters (and to each other) is reviewed, and three possible solutions are described. The new coding method is applied to data from hoplocercid lizards, and the results show the sensitivity of phylogenetic conclusions to different scaling methods. Although some authors reject the use of continuous, overlapping, quantitative characters in phylogenetic analysis, quantitative data from hoplocercid lizards that are coded using the new approach contain significant phylogenetic structure and exhibit levels of homoplasy similar to those seen in data that are coded qualitatively.

Animals↗

PubMed2002

Phylogenetic balance and ecological evenness.

The frequency distribution of numbers of species in taxonomic groups, where many species belong to a few very diverse higher taxa, is mirrored by that of species in most communities, where many individuals belong to a few very abundant species. Various hypotheses mechanistically link a species' community abundance with the diversity of the higher level taxon (genus, family, order) to which it belongs, but empirical data are equivocal about general trends in the relation between rank-taxon diversity and mean abundance. One reason for this inconclusive result may be the effect of the semisubjective nature of rank-based classification. We assessed the relationship between clade diversity and mean species abundance for two diverse tropical tree communities, using both traditional rank-based analysis and two new phylogenetic analyses (based on the ratio of individuals to taxa at each node in the phylogeny). Both rank-based and phylogenetic analyses using taxonomic ranks above the species level as terminal taxa detected a trend associating common species with species-rich families. In contrast, phylogenetic analyses using species as terminal taxa could not distinguish the observed distribution of species abundances from a random distribution with respect to clade diversity. The difference between these results might be due to (1) the absence of a real phylogeny-wide relationship between clade abundance and diversity, (2) the influence of poor phylogenetic resolution within families in our phylogenies, or (3) insufficient sensitivity of our metrics to subtle tree-wide effects. Further development and application of phylogeny-based methods for testing abundance-diversity relationships is needed.

Ecology↗

PubMed2003

When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders.

Convergence, i.e., similarity between organisms that is not the direct result of shared phylogenetic history (and that may instead result from independent adaptations to similar environments), is a fundamental issue that lies at the interface of systematics and evolutionary biology. Although convergence is often cited as an important problem in morphological phylogenetics, there have been few well-documented examples of strongly supported and misleading phylogenetic estimates that result from adaptive convergence in morphology. In this article, we propose criteria that can be used to infer whether or not a phylogenetic analysis has been misled by convergence. We then apply these criteria in a study of central Texas cave salamanders (genus Eurycea). Morphological characters (apparently related to cave-dwelling habitat use) support a clade uniting the species E. rathbuni and E. tridentifera, whereas mitochondrial DNA sequences and allozyme data show that these two species are not closely related. We suggest that a likely explanation for the paucity of examples of strongly misleading morphological convergence is that the conditions under which adaptive convergence is most likely to produce strongly misleading results are limited. Specifically, convergence is most likely to be problematic in groups (such as the central Texas Eurycea) in which most species are morphologically very similar and some of the species have invaded and adapted to a novel selective environment.

Adaptation, Biological↗

PubMed2003

Missing data, incomplete taxa, and phylogenetic accuracy.

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.

Computer Simulation↗

PubMed2003

Canonical phylogenetic ordination.

A phylogenetic comparative method is proposed for estimating historical effects on comparative data using the partitions that compose a cladogram, i.e., its monophyletic groups. Two basic matrices, Y and X, are defined in the context of an ordinary linear model. Y contains the comparative data measured over t taxa. X consists of an initial tree matrix that contains all the xj monophyletic groups (each coded separately as a binary indicator variable) of the phylogenetic tree available for those taxa. The method seeks to define the subset of groups, i.e., a reduced tree matrix, that best explains the patterns in Y. This definition is accomplished via regression or canonical ordination (depending on the dimensionality of Y) coupled with Monte Carlo permutations. It is argued here that unrestricted permutations (i.e., under an equiprobable model) are valid for testing this specific kind of groupwise hypothesis. Phylogeny is either partialled out or, more properly, incorporated into the analysis in the form of component variation. Direct extensions allow for testing ecomorphological data controlled by phylogeny in a variation partitioning approach. Currently available statistical techniques make this method applicable under most univariate/multivariate models and metrics; two-way phylogenetic effects can be estimated as well. The simplest case (univariate Y), tested with simulations, yielded acceptable type I error rates. Applications presented include examples from evolutionary ethology, ecology, and ecomorphology. Results showed that the new technique detected previously overlooked variation clearly associated with phylogeny and that many phylogenetic effects on comparative data may occur at particular groups rather than across the entire tree.

Animals↗

PubMed2004

Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae).

The internal transcribed spacer (ITS) of nuclear ribosomal DNA has been widely used by systematists for reconstructing phylogenies of closely related taxa. Although the occurrence of ITS putative pseudogenes is well documented for many groups of animals and plants, the potential utility of these pseudogenes in phylogenetic analyses has often been underestimated or even ignored in part because of deletions that make unambiguous alignment difficult. In addition, long branches often can lead to spurious relationships, particularly in parsimony analyses. We have discovered unusually high levels of ITS polymorphism (up to 30%, 40%, and 14%, respectively) in three tropical tree species of the coffee family (Rubiaceae), Adinauclea fagifolia, Haldina cordifolia, and Mitragyna rubrostipulata. Both secondary structure stability and patterns of nucleotide substitutions in a highly conserved region (5.8S gene) were used for distinguishing presumed functional sequences from putative pseudogenes. The combination of both criteria was the most powerful approach. The sequences from A. fagifolia appear to be a mix of functional genes and highly distinct putative pseudogenes, whereas those from H. cordifolia and M. rubrostipulata were identified as putative pseudogenes. We explored the potential utility of the identified putative pseudogenes in the phylogenetic analyses of Naucleeae sensu lato. Both Bayesian and parsimony trees identified the same monophyletic groups and indicated that the polymorphisms do not transcend species boundaries, implying that they do not predate the divergence of these three species. The resulting trees are similar to those produced by previous analyses of chloroplast genes. In contrast to results of previous studies therefore, divergent putative pseudogenes can be useful for phylogenetic analyses, especially when no sequences of their functional counterparts are available. Our studies clearly show that ITS polymorphism may not necessarily mislead phylogenetic inference. Despite using many different PCR conditions (different primers, higher denaturing temperatures, and absence or presence of DMSO and BSA-TMACl), we recovered only a few functional ITS copies from A. fagifolia and none from H. cordifolia and M. rubrostipulata, which suggests that PCR selection is occurring and/or the presumed functional alleles are located at minor loci (with few ribosomal DNA copies).

Base Composition↗

PubMed2006

Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.

Reversible-jump Markov chain Monte Carlo (RJ-MCMC) is a technique for simultaneously evaluating multiple related (but not necessarily nested) statistical models that has recently been applied to the problem of phylogenetic model selection. Here we use a simulation approach to assess the performance of this method and compare it to Akaike weights, a measure of model uncertainty that is based on the Akaike information criterion. Under conditions where the assumptions of the candidate models matched the generating conditions, both Bayesian and AIC-based methods perform well. The 95% credible interval contained the generating model close to 95% of the time. However, the size of the credible interval differed with the Bayesian credible set containing approximately 25% to 50% fewer models than an AIC-based credible interval. The posterior probability was a better indicator of the correct model than the Akaike weight when all assumptions were met but both measures performed similarly when some model assumptions were violated. Models in the Bayesian posterior distribution were also more similar to the generating model in their number of parameters and were less biased in their complexity. In contrast, Akaike-weighted models were more distant from the generating model and biased towards slightly greater complexity. The AIC-based credible interval appeared to be more robust to the violation of the rate homogeneity assumption. Both AIC and Bayesian approaches suggest that substantial uncertainty can accompany the choice of model for phylogenetic analyses, suggesting that alternative candidate models should be examined in analysis of phylogenetic data. [AIC; Akaike weights; Bayesian phylogenetics; model averaging; model selection; model uncertainty; posterior probability; reversible jump.].

Bayes Theorem↗

PubMed2006

Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models.

A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide strong support at key nodes that were equivocal based on other molecular markers. Combining LSU sequences with those of the small subunit of the nuclear ribosome (SSU or 18S), we present a detailed working hypothesis of medusozoan relationships and discuss character evolution within this diverse clade. Stauromedusae, comprising the benthic, so-called stalked jellyfish, appears to be the sister group of all other medusozoans, implying that the free-swimming medusa stage, the motor nerve net, and statocysts of ecto-endodermal origin are features derived within Medusozoa. Cubozoans, which have had uncertain phylogenetic affinities since the elucidation of their life cycles, form a clade-named Acraspeda-with the scyphozoan groups Coronatae, Rhizostomeae, and Semaeostomeae. The polyps of both cubozoans and hydrozoans appear to be secondarily simplified. Hydrozoa is comprised by two well-supported clades, Trachylina and Hydroidolina. The position of Limnomedusae within Trachylina indicates that the ancestral hydrozoan had a biphasic life cycle and that the medusa was formed via an entocodon. Recently hypothesized homologies between the entocodon and bilaterian mesoderm are therefore suspect. Laingiomedusae, which has often been viewed as a close ally of the trachyline group Narcomedusae, is instead shown to be unambiguously a member of Hydroidolina. The important model organisms of the Hydra species complex are part of a clade, Aplanulata, with other hydrozoans possessing direct development not involving a ciliated planula stage. Finally, applying phylogenetic mixture models to our data proved to be of little additional value over a more traditional phylogenetic approach involving explicit hypothesis testing and bootstrap analyses under multiple optimality criteria. [18S; 28S; Cubozoa; Hydrozoa; medusa; molecular systematics; polyp; Scyphozoa; Staurozoa.].

Animals↗

PubMed2006

Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis.

The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.

Animals↗

PubMed2005

Mitochondrial phylogenetics and evolution of mysticete whales.

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.

Animals↗

PubMed2005

Phylogenetic diversity and the greedy algorithm.

Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the "phylogenetic diversity" of any subset of the species is the sum of the edge weights of the minimal subtree connecting the species. This measure is relevant in biodiversity conservation where one may wish to compare different subsets of species according to how much evolutionary variation they encompass. In this note we show that phylogenetic diversity has an attractive mathematical property that ensures that we can solve the following problem easily by the greedy algorithm: find a subset of the species of any given size k of maximal phylogenetic diversity. We also describe an extension of this result that also allows weights to be assigned to species.

Algorithms↗

PubMed2005

Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences.

Mitochondrial DNA (mtDNA) sequences are comonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect assymetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa (34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand assymetry, where one strand is biased in favor of A and C, whereas the other strand has reverse bias, i.e. in favor of T and G. the origin of this strand bias can be related to assymetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigrioupus (Maxillopoda), Branchiostoma (Cephalochordata) Florometra (Echinodermata), and Katharina (Mollusca). It is proposed that assymetric mutational constraints have been independantly reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of assymetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda, This new approach provides a better congruence with nuclear analyses based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.

Animals↗

PubMed2005

Phylogenetic relationships, divergence time estimation, and global biogeographic patterns of calopterygoid damselflies (odonata, zygoptera) inferred from ribosomal DNA sequences.

The calopterygoid superfamily (Calopterygidae + Hetaerinidae) is composed of more than twenty genera in two families: the Calopterygidae (at least 17) and the Hetaerinidae (at least 4). Here, 62 calopterygoid (ingroup) taxa representing 18 genera and 15 outgroup taxa are subjected to phylogenetic analysis using the ribosomal 18S and 5.8S genes and internal transcribed spacers (ITS1, ITS2). The five other families of calopterid affinity (Polythoridae, Dicteriadidae, Amphipterygidae, Euphaeidae, and Chlorocyphidae) are included in the outgroup. For phylogenetic inference, we applied maximum parsimony, maximum likelihood, and the Bayesian inference methods. A molecular phylogeny combined with a geographic analysis produced a well-supported phylogenetic hypothesis that partly confirms the traditional taxonomy and describes distributional patterns. A monophyletic origin of the calopterygoids emerges, revealing the Hetaerinid clade as sister group to the Calopterygidae sensu strictu. Within Calopterygidae, seven clades of subfamily rank are recognized. Phylogenetic dating was performed with semiparametric rate smoothing by penalized likelihood, using seven reference fossils for calibration. Divergence time based on the ribosomal genes and spacers and fossil constraints indicate that Calopteryginae (10 genera, approximately 50% of all Calopterygid taxa studied here), Vestalinae (1 genus), and Hetaerinidae (1 genus out of 4 studied here) started radiating around 65 Mya (K/T boundary). The South American Iridictyon (without distinctive morphology except for wing venation) and Southeast Asian Noguchiphaea (with distinctive morphology) are older (about 86 My) and may be survivors of old clades with a Gondwanian range that went extinct at the K/T boundary. The same reasoning (and an even older age, ca. 150 My) applies to the amphipterygids Rimanella and Pentaphlebia (South America-Africa). The extant Calopterygidae show particular species and genus richness between west China and Japan, with genera originating between the early Oligocene and Pleistocene. Much of that richness probably extended much wider in preglacial times. The Holarctic Calopteryx, of Miocene age, was deeply affected by the climatic cooling of the Pliocene and by the Pleistocene glaciations. Its North American and Japanese representatives are of Miocene and Pliocene age, respectively, but its impoverished Euro-Siberian taxa are late Pliocene-Pleistocene, showing reinvasion, speciation, and introgression events. The five other calopterid families combine with the Calopterygidae and Hetaerinidae to form the monophyletic cohort Caloptera, with Polythoridae, Dicteriadidae, and Amphipterygidae sister group to Calopterygoidea. The crown node age of the latter three families has an age of about 157 My, but the Dicteriadidae and Polythoridae themselves are of Eocene age, and the same is true for the Euphaeidae and Chlorocyphidae. The cohort Caloptera itself, with about 197 My of age, goes back to the early Jurassic.

Animals↗

PubMed2006

Phylogenetic diversity within seconds.

We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branch-lengths of the minimal subtree connecting the taxa in the subset. We introduce two time-efficient algorithms (greedy and pruning) to compute a subset of size k with maximal phylogenetic diversity in O(n log k) and O[n + (n-k) log (n-k)] time, respectively. The greedy algorithm is an efficient implementation of the so-called greedy strategy (Steel, 2005; Pardi and Goldman, 2005), whereas the pruning algorithm provides an alternative description of the same problem. Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more.

Algorithms↗

PubMed1998

Is it better to add taxa or characters to a difficult phylogenetic problem?

The effects on phylogenetic accuracy of adding characters and/or taxa were explored using data generated by computer simulation. The conditions of this study were constrained but allowed for systematic investigation of certain parameters. The starting point for the study was a four-taxon tree in the "Felsenstein zone," representing a difficult phylogenetic problem with an extreme situation of long branch attraction. Taxa were added sequentially to this tree in a manner specifically designed to break up the long branches, and for each tree data matrices of different sizes were simulated. Phylogenetic trees were reconstructed from these data using the criteria of parsimony and maximum likelihood. Phylogenetic accuracy was measured in three ways: (1) proportion of trees that are completely correct, (2) proportion of correctly reconstructed branches in all trees, and (3) proportion of trees in which the original four-taxon statement is correctly reconstructed. Accuracy improved dramatically with the addition of taxa and much more slowly with the addition of characters. If taxa can be added to break up long branches, it is much more preferable to add taxa than characters.

Classification↗