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D L Swofford

Publications and source records attributed to D L Swofford.

9 recordsLinked to original sources
PubMed1999

Multiple local maxima for likelihoods of phylogenetic trees: a simulation study.

Steel demonstrated that the maximum-likelihood function for a phylogenetic tree may have multiple local maxima. If this phenomenon were general, it would compromise the applicability of maximum likelihood as an optimality criterion for phylogenetic trees. In several simulation studies reported on in this paper, the true tree, and other trees of very high likelihood, rarely had multiple maxima. Our results thus provide reassurance that the value of maximum likelihood as a tree selection criterion is not compromised by the presence of multiple local maxima--the best estimates of the true tree are not likely to have them. This result holds true even when an incorrect nucleotide substitution model is used for tree selection.

Base Sequence↗
PubMed1998

A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences.

We have developed a rapid parsimony method for reconstructing ancestral nucleotide states that allows calculation of initial branch lengths that are good approximations to optimal maximum-likelihood estimates under several commonly used substitution models. Use of these approximate branch lengths (rather than fixed arbitrary values) as starting points significantly reduces the time required for iteration to a solution that maximizes the likelihood of a tree. These branch lengths are close enough to the optimal values that they can be used without further iteration to calculate approximate maximum-likelihood scores that are very close to the "exact" scores found by iteration. Several strategies are described for using these approximate scores to substantially reduce times needed for maximum-likelihood tree searches.

Animals↗
PubMed1997

Evolution of the mitochondrial cytochrome oxidase II gene in collembola.

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.

Amino Acid Sequence↗
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↗