Syst. Biol. 50(5) 2001

Housworth and Martins

Abstract. 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., with polytomies) are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., 4 taxa belong together in a sub-clade). It can be used to conduct comparative analyses when the phylogeny is only partially resolved or used in other randomization tests in which large numbers of possible phylogenies are needed. [Keywords: phylogeny, phylogenetic analysis, comparative method, branching process, combinatorics]


Abstract. Ontogenetic trajectories are commonly quantified by characterizing changes in the sizes and shapes of organisms over the course of development. This formulation of ontogenetic transformations can be misleading in that it ignores critical aspects of the biological processes responsible for constructing morphology. Hypothetical examples are used to illustrate some of the shortcomings of methods that rely exclusively on size and shape data for ontogenetic analyses. By characterizing growth as a vector field, and representing growth vectors as complex numbers, it is possible to simultaneously analyze size, shape, and growth processes. The utility of such an approach is demonstrated in a study of shape and growth process variation in turtle shells. [Growth; morphometrics; ontogeny; size; shape; Testudines]

Medina et al.

Abstract.— Sea hares within the genus Aplysia are important neurobiological model organisms, and as studies based on different Aplysia species appear in the literature, a phylogenetic framework has become essential. We present a phylogenetic hypothesis for this genus, based on portions of two mitochondrial genes (12S and 16S). In addition, we reconstruct the evolution of several behavioral characters of interest to neurobiologists in order to illustrate the potential benefits of a phylogeny for the genus Aplysia. These benefits include the determination of ancestral traits, the direction and timing of evolution of characters, prediction of the distribution of traits, and identification of cases of independent acquisition of traits within lineages. This last benefit may prove especially useful in understanding the linkage between behaviors and their underlying neurological basis. [Opisthobranchia, Anaspidea, Aplysia phylogeny, Sea Hare, neurobiology of inking, neurobiology of swimming]

O'Keefe and Wagner

Abstract. The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complimentary change in another . Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny, and therefore assume that non-phylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis prior to phylogeny reconstruction, or may be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of non-phylogenetic correlation in character suites can be attributed to chance alone. We apply these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers, and identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix. [correlated character evolution, character independence, compatibility, similarity coefficient, character weighting]

Renner and Hon

Abstract.— Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yielded almost identical topologies that were used to trace the evolution of the two sexual systems. The African species, which is dioecious, was sister to all neotropical species, and the monoecious species formed a grade basal to a large dioecious Andean clade. Dioecy evolved a second time within the monoecious grade. Geographical mapping of 6496 herbarium collections from all species sorted by sexual system showed that monoecy is confined to low-lying areas (<700 m) in the Amazon basin and southern Central America. The only morphological trait with a strong phylogenetic signal is leaf margin shape (entire or toothed) even though this character also correlates with altitude, probably reflecting selection on leaf shapes by temperature and rainfall regimes. The data do not reject the molecular clock, and branch lengths suggest that the shift to dioecy in the lowlands occurred many million years after the shift to dioecy in the ancestor of the Andean clade. [Dioecy, altitudinal distribution of sexual systems, sexual system evolution, molecular clock, monoecy]


Abstract. Maximum likelihood estimation of phylogenetic trees from nucleotide sequences is completely consistent when nucleotide substitution is governed by the general time reversible (GTR) model with rates that vary over sites according to the invariable sites plus gamma (I+G) distribution. [Maximum likelihood; phylogeny estimation; consistency; general time reversible model; rate heterogeneity]


Abstract. 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 it is coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (character state definition, delimitation, and ordering) 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 do contain significant phylogenetic structure, and exhibit levels of homoplasy that are similar to those seen in data that are coded qualitatively. [Character coding; morphology, phylogenetics; quantitative characters; weighting]