Biomedical subjects

W P Maddison

Publications and source records attributed to W P Maddison.

9 recordsLinked to original sources

PubMed2001

A combined molecular approach to phylogeny of the jumping spider subfamily dendryphantinae (araneae: salticidae).

Four gene regions were sequenced for 30 species of jumping spiders, most from the subfamily Dendryphantinae, to investigate their molecular phylogeny and evolution. These are three regions from the mitochondria (ca. 560 bp of 16S plus adjacent tRNA, 1047 bp of cytochrome oxidase 1 (CO1), and 414 bp of NADH1 (ND1) and one region from the nuclear genome (ca. 750 bp of 28S). Parsimony and likelihood analyses of these gene regions separately and together support the monophyly of the dendryphantines as delimited previously by morphological characters. A group of elongate-bodied genera are placed as basal among the dendryphantines, and previously proposed relationships of Poultonella, Paraphidippus, and Sassacus vitis are confirmed. Comparison of overall rates of molecular evolution indicates striking differences across the gene regions, with highest divergence in ND1, CO1, 16S, and 28S in decreasing order. All four regions are characterized by both within- and among-site rate variation. Phylogenetic results from CO1 conflict conspicuously with phylogenetic results from the other genes and morphological data. Attempts to account for potential sources of this conflict (e.g., accommodating biased base composition, high homoplasy, within- and among-site rate variation, etc.) are largely unsuccessful.

Animals↗

PubMed2001

Phylogenetic utility and evidence for multiple copies of elongation factor-1alpha in the spider genus Habronattus (Araneae: Salticidae).

In the continuing quest for informative genes for use in molecular systematics, the protein-coding gene Elongation factor-1alpha (EF-1alpha) has rapidly become one of the most prevalent "single-copy" nuclear genes utilized, particularly in arthropods. This paper explores the molecular evolutionary dynamics and phylogenetic utility of EF-1alpha in the salticid spider genus Habronattus. As has been reported for other arthropod lineages, our studies indicate that multiple (two) copies of EF-1alpha exist in Habronattus. These copies differ in intron structure and thus in size, making it possible to easily separate PCR amplification products. We present data for an intronless EF-1alpha copy for three Habronattus species. The presence of nonsense mutations and generally elevated rates of amino acid change suggest that this copy is evolving under relaxed functional constraints in Habronattus. A larger taxon sample (50 species plus outgroups) is presented for an EF-1alpha copy that includes both intron and exon regions. Characteristics of both regions suggest that this is a functional, orthologous copy in the species sampled. Maximum-likelihood relative-rate comparisons show that exon third codon sites are evolving more than 100 times as fast as second codon sites in these sequences and that intron sites are evolving about twice as fast as exon third sites. In combination, the EF-1alpha data provide robust, species-level phylogenetic signal that is largely congruent with morphologically well supported areas of Habronattus phylogeny. The recovery of some novel clades, and the unexpected fragmentation of others, suggests areas requiring further phylogenetic attention.

Amino Acid Sequence↗

PubMed2000

Testing character correlation using pairwise comparisons on a phylogeny.

In comparative biology, pairwise comparisons of species or genes (terminal taxa) are used to detect character associations. For instance, if pairs of species contrasting in the state of a particular character are examined, the member of a pair with a particular state might be more likely than the other member to show a particular state in a second character. Pairs are chosen so as to be phylogenetically separate, that is, the path between members of a pair, along the branches of the tree, does not touch the path of any other pair. On a given phylogenetic tree, pairs must be chosen carefully to achieve the maximum possible number of pairs while maintaining phylogenetic separation. Many alternative sets of pairs may have this maximum number. Algorithms are developed that find all taxon pairings that maximize the number of pairs without constraint, or with the constraint that members of each pair have contrasting states in a binary character, or that they have contrasting states in two binary characters. The comparisons chosen by these algorithms, although phylogenetically separate on the tree, are not necessarily statistically independent.

Anatomy, Comparative↗

PubMed1997

NEXUS: an extensible file format for systematic information.

NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.

Animals↗

PubMed1994

Phylogenetic analysis supports horizontal transfer of P transposable elements.

Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from a number of different analyses are highly consistent and reveal a P-element phylogeny that contradicts the phylogeny of the species. At least three instances of horizontal transfer are necessary to explain this incongruence, but other explanations cannot be ruled out at this time.

Animals↗

PubMed1992

Estimation of levels of gene flow from DNA sequence data.

We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).

Computer Simulation↗

PubMed1990

Detecting isolation by distance using phylogenies of genes.

We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.

Computer Simulation↗

PubMed1989

A cladistic measure of gene flow inferred from the phylogenies of alleles.

A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.

Alleles↗

PubMed1989

Interactive analysis of phylogeny and character evolution using the computer program MacClade.

Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.

Animals↗