Biomedical subjects

B A Salisbury

Publications and source records attributed to B A Salisbury.

3 recordsLinked to original sources

PubMed2001

A tree obscured by vines: horizontal gene transfer and the median tree method of estimating species phylogeny.

A phylogeny is a tree graph representation of genealogical relationships between biological objects. It is of general interest to estimate the phylogeny of whole organisms (species trees) using bio-molecular sequences. When multiple sequences are available for each organism such as with whole genome data, individual phylogenies estimated by each molecule (gene trees) may not be concordant. The lack of concordance may be due to actual biological mechanisms such as horizontal transfer of the molecules. Here, we present a new phylogeny estimation method designed to estimate the species tree despite such horizontal transfer. It uses the idea that horizontal transfer distorts distance relationships between pairs of species but a median estimate of the distances is robust to such distortions. We demonstrate the utility of our method using a simulation study.

Algorithms↗

PubMed2001

Ancestral state estimation and taxon sampling density.

A set of experiments based on simulation and analysis found that using the parsimony algorithm for ancestral state estimation can benefit from increased sampling of terminal taxa. Estimation at the base of small clades showed strong sensitivity to tree topology and number of descendent tips. These effects were largely driven by the creation and negation of ambiguity across a topology. Root state and internal state estimation showed similar behavior. We conclude that increased taxon sampling density is generally advisable, and attention to topological effects may be advisable in evaluating the confidence placed in state estimation. We also explore the factors affecting ancestral state estimation and conjecture that as taxa are added to a tree, the total amount of information for root state estimation depends on the tree topology and distance to root state of added taxa. For a pure-birth model tree, we conjecture that the addition of N taxa increases root state information in proportion to log(N).

Algorithms↗

PubMed1999

Misinformative characters and phylogeny shape.

The discrepancy between theoretical and observed distributions of tree shapes in recent surveys of phylogeny estimates has lead to investigations of possible biological and methodological causes. I investigated whether the phylogenetic quality of characters is related to the tree shape on which they evolve. Simulated evolution revealed shape-related tendencies for characters to indicate correct cladistic relationships; these differences were measured by examining the characters directly, without deriving any phylogeny estimates. Tree stemminess indices correlated strongly with character quality when characters evolved either speciationally or phyletically. Tree balance was a significant correlate of character quality under speciational evolution but not under phyletic evolution. These results help explain the findings of other simulation studies. With additional study of the behavior of evolving characters and their interaction with phylogenetic methods, we might be able to increase the accuracy of tree estimation and compensate for potential biases related to shape. These results give further reason for caution in trusting phylogeny estimates.

Biological Evolution↗