Broughton et al.
Abstract. Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. These results suggest that down-weighting transitions may be unwarranted in many cases. This conclusion was supported by the fact that a range of transition: transversion weighting schemes applied to various mitochondrial genes and genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective. [homoplasy, consistency, weighted parsimony, character evolution, transitions, transversions]
Brown et al.
Abstract. Community ecologists are increasingly aware that the regional history of taxon diversification can have an important influence on community structure. Likewise, systematists recognize that ecological context can have an important influence on the processes of speciation and extinction that create patterns of descent. We present a phylogenetic analysis of 33 species of a North American radiation of damselflies (Zygoptera: Coenagrionidae: Enallagma Selys), which have been well-studied ecologically, in order to elucidate the evolutionary mechanisms that have contributed to differences in diversity between larval habitats (lakes with and without fish predators). Analysis of molecular variation in 842 bp of the mitochondrial cytochrome oxidase I and II subunit and the intervening Leu-tRNA and 37 morphological characters resulted in three well-defined clades that are only partially congruent with previous phylogenetic hypotheses. Molecular and morphological data partitions were significantly incongruent. Lack of haplotype monophyly within species and small levels of sequence divergence (<1%) between related species in 3 of the 4 clades suggests that recent, and parallel, speciation has been an important source of community diversity. Reconstruction of habitat preference over the phylogeny suggests that the greater species diversity in fish-lake habitats is due to the recency of shifts into the fishless-lake habit, although a difference in speciation or extinction rates between the two habitats is difficult to exclude as an additional mechanism. [Coenagrionidae, habitat shifts, mitochondrial DNA, molecular systematics, Odonata, species diversity].
Flores et al.
Abstract. Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isozymes, and morphological characters, were used to propose a new phylogeny and to test previously published hypotheses about the phylogenetic positions of basal clades of the lizard genus Sceloporus and the relationship of Sceloporus to the former genus "Sator". In accord with earlier studies, our results grouped "Sator" internal to Sceloporus, and both support a hypothesis of transgulfian vicariance for the origin of the former genus "Sator" on islands in the Sea of Cortez. Robustness of support for internal nodes in our best tree was established though widely used indices (bootstrap proportions, decay values) but also through congruence among independent data partitions. Several deep nodes in the tree recovered by a number of methods, including equally weighted and differentially weighted parsimony, and maximum likelihood models, are only weakly supported by the traditional indices, and this methodological concordance is taken as evidence for insensitivity of the deep structure of the topology to alternate assumptions. [Character congruence; parsimony; weighted parsimony; maximum likelihood; phylogeny; biogeography; Sceloporus.]
Abstract. Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino-Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino-Hasegawa test place important restrictions on its applicability. In particular, it is only valid when the topologies being compared are specified a priori. Unfortunately, this means that the Kishino-Hasegawa may be severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies has been selected for testing because it is the maximum likelihood topology for the data set at hand. We review the theory of the Kishino-Hasegawa test, and contend that for the majority of popular applications the Kishino-Hasegawa test should not be used. Previously published results from invalid applications of the Kishino-Hasegawa test should be treated extremely cautiously. All future applications should employ appropriate alternative tests instead. Such alternative tests, both non-parametric and parametric, are also reviewed. We give two examples which illustrate the importance of our contentions. [Kishino-Hasegawa test; maximum likelihood; phylogeny; Shimodaira-Hasegawa test; statistical tests; tree topology]
Lutzoni et al.
Abstract. Phylogenetic analyses of non-protein coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers (ITS) and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions no matter which optimization criteria are used. This problem is particularly acute in large scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. This three-step procedure consists first of delimiting homologous regions of the alignment containing ambiguously aligned sequences. Second, each ambiguously aligned region is unequivocally coded as a new character that replaces its respective ambiguous region. Third, each of these coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the highest similarity and the lowest number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony. [Character coding; character-state weighting; crocodile 12S mtrDNA; indel-rich region; insect 16S mtrDNA; intron; large scale phylogenies; molecular phylogenies; multiple sequence alignment; non-protein coding DNA sequences; ribosomal RNA genes.]
Rohlf and Corti
Abstract. The relatively new two-block partial least-squares method for analyzing the covariance between two sets of variables is described and contrasted with the well-known method of canonical correlation analysis. Their statistical properties, types of answers, and visualization techniques are discussed. Examples are given to show its usefulness in comparing two sets of variablesespecially when one or both of the sets of variables are shape variables from a geometric morphometric study. [Partial least squares, morphometrics, canonical correlation, covariance, visualization, Plethodon, Mus musculus domesticus.]
Abstract. Phylogenetic analyses of large data sets pose special challenges. Among these is an apparent tendency for bootstrap support for a clade to decline with increased taxon sampling of that clade. We document this decline in data sets of increasing numbers of taxa in Astragalus, the most species-rich angiosperm genus. Support for one sub-clade, Neo-Astragalus, declined monotonically with increased sampling of taxa inside Neo-Astragalus, irrespective of whether parsimony or neighbor-joining methods were employed, or of which particular heuristic search algorithm was used (more stringent algorithms did tend to yield higher support, however). Three possible explanations for this decline were examined, including (1) mistaken assignment of the most recent common ancestor of the taxon sample (and its bootstrap support) with the most recent common ancestor of the clade it is sampled from; (2) computational limitations of heuristic search strategies; (3) statistical bias in bootstrap proportions; especially owing to random homoplasy distributed among taxa. The best explanation appears to be (3), although computational shortcomings (2) may explain some of the problem. The bootstrap proportion, as currently employed in phylogenetic analysis, does not accurately capture the classical notion of confidence assessments on the null hypothesis of non-monophyly, especially in large data sets. More accurate assessments of confidence as type I error levels (relying on iterated bootstrap methods) remove most of the monotonic decline in confidence with increasing numbers of taxa. [bootstrap, phylogeny reconstruction, taxon sampling, species richness]
Abstract. Landmark-based morphometric methods must estimate translation, rotation, and scaling (or, nuisance) parameters in order to remove non-shape variation from a set of digitized figures. The error in the estimation of these nuisance parameters will be reflected in the covariance structure of the coordinates, such as the residuals from a superimposition, or any linear combination of the coordinates, such as the partial warp and standard uniform scores. A simulation experiment was used to compare the ability of the generalized resistant fit (GRF) and a relative warp analysis (RWA) to estimate known covariance matrices with various levels of correlation and variance structure. Random covariance matrices were perturbed in order to vary (1) the magnitude of the average correlation among coordinates, (2) the number of landmarks with excessive variance, and (3) the magnitude of the excessive variance. The covariance structure was applied to random figures with between 6 and 20 landmarks. The results show the expected performance of GRF and RWA across a broad spectrum of conditions. The performance of both GRF and RWA depended most strongly on the number of landmarks. RWA performance decreased slightly when there was one or a few landmarks with excessive variance. GRF performance peaked when about 25% of the landmarks had excessive variance. In general, both RWA and GRF performed better at estimating the direction of the first principal axis of the covariance matrix than the structure of the entire covariance matrix. RWA tended to outperform GRF when more than about 75% of the coordinates had excessive variance. When fewer than 75% of the coordinates had excessive variance, the relative performance of RWA and GRF depended on the magnitude of the excessive variance; when the landmarks with excessive variance had standard deviations of greater than or equal to four times that of the minimum standard deviation, GRF regularly outperformed RWA. [Simulation; superimposition; partial warps; relative warps analysis; covariance structure; principal components analysis; shape; resistant fit]
Waters et al.
Abstract. 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 a number of relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, a number of hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias are examined. While 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; the alternative hypothesised 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. [mtDNA, phylogeny, Gondwana, biogeography, diadromy, evolution, molecular clock, secondary structure]
Wilkinson et al.
Abstract. In decay analyses the support for a particular split in most-parsimonious trees is its decay index, i.e., the extra steps required of the shortest trees that do not include the split. By focusing solely upon the support for splits, traditional decay analysis may provide an incomplete and potentially misleading summary of the support for phylogenetic relationships common to the most-parsimonious tree(s). Here, we introduce double decay analysis, a new approach to assessing support for phylogenetic relationships. Double decay analysis is the determination of the decay indices of all n-taxon statements/partitions common to the most-parsimonious tree(s). The results of double decay analyses are presented in a partition table, but various approaches to graphical representation of the results, including the use of reduced consensus support trees, are also discussed. Double decay analysis provides a more comprehensive summary and facilitates a better understanding of the strengths and weaknesses of complex phylogenetic hypotheses than does traditional decay analysis. The limitations of traditional decay analyses and the utility of double decay analyses are illustrated with both contrived data and real data for sauropod dinosaurs. [Parsimony; support; decay analysis; consensus; phylogeny; Sauropoda.]