Biomedical subjects

Colleen T Webb

Publications and source records attributed to Colleen T Webb.

5 recordsLinked to original sources

PubMed2006

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference.

AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters.

Computer Simulation↗

PubMed2006

Classic flea-borne transmission does not drive plague epizootics in prairie dogs.

We lack a clear understanding of the enzootic maintenance of the bacterium (Yersinia pestis) that causes plague and the sporadic epizootics that occur in its natural rodent hosts. A key to elucidating these epidemiological dynamics is determining the dominant transmission routes of plague. Plague can be acquired from the bites of infectious fleas (which is generally considered to occur via a blocked flea vector), inhalation of infectious respiratory droplets, or contact with a short-term infectious reservoir. We present results from a plague modeling approach that includes transmission from all three sources of infection simultaneously and uses sensitivity analysis to determine their relative importance. Our model is completely parameterized by using data from the literature and our own field studies of plague in the black-tailed prairie dog (Cynomys ludovicianus). Results of the model are qualitatively and quantitatively consistent with independent data from our field sites. Although infectious fleas might be an important source of infection and transmission via blocked fleas is a dominant paradigm in the literature, our model clearly predicts that this form of transmission cannot drive epizootics in prairie dogs. Rather, a short-term reservoir is required for epizootic dynamics. Several short-term reservoirs have the potential to affect the prairie dog system. Our model predictions of the residence time of the short-term reservoir suggest that other small mammals, infectious prairie dog carcasses, fleas that transmit plague without blockage of the digestive tract, or some combination of these three are the most likely of the candidate infectious reservoirs.

Animals↗

PubMed2006

How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants.

Greater phylogenetic signal is often found in parsimony-based analyses of third codon positions of protein-coding genes relative to their corresponding first and second codon positions, even for early-derived ("basal") clades. We used the Soltis et al. (2000; Bot. J. Linn. Soc. 133:381-461) data matrix of atpB and rbcL from 567 seed plants to quantify how each of six factors (observed character-state space, frequencies of observed character states, substitution probabilities among nucleotides, rate heterogeneity among sites, overall rate of evolution, and number of parsimony-informative characters) contributed to this phenomenon. Each of these six factors was estimated from the original data matrix for parsimony-informative third codon positions considered separately from first and second codon positions combined. One of the most parsimonious trees found was used as the constraint topology; branch lengths were estimated using likelihood-based distances, and characters were simulated on this tree. Differential frequencies of observed character states were found to be the most limiting of the factors simulated for all three codon positions. Differential frequencies of observed character states and differential substitution probabilities among states were relatively advantageous for first and second codon positions. In contrast, differential numbers of observed character states, differential rate heterogeneity among sites, the greater number of parsimony-informative characters, and the higher overall rate of evolution were relatively advantageous for third codon positions. The amount of possible synapomorphy was predictive of the overall success of resolution.

Base Sequence↗

PubMed2005

Pair statistics clarify percolation properties of spatially explicit simulations.

Dispersal is a fundamental control on the spatial structure of a population. We investigate the precise mechanism by which a mixed strategy of short- and long-distance dispersal affects spatial patterning. Using techniques from pair approximation and percolation theory, we demonstrate that dispersal controls the extent to which a population is completely connected by modulating the proportion of neighboring sites which are simultaneously occupied. We show that near the percolation threshold this pair statistic, rather than other metrics proposed earlier, best explains clustering, and we suggest more general circumstances under which this may hold.

Cluster Analysis↗

PubMed2002

Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae.

Patterns of similarity between genomes of related species reflect the distribution of selective constraint within DNA. We analyzed alignments of 142 orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae and found a mosaic pattern with regions of high similarity (phylogenetic footprints) interspersed with non-alignable sequences. Footprints cover approximately 20% of intergenic regions, often occur in clumps and are rare within 5' UTRs but common within 3' UTRs. The footprints have a higher ratio of transitions to transversions than expected at random and a higher GC content than the rest of the intergenic region. The number of footprints and the GC content of footprints within an intergenic region are higher when genes are oriented so that their 5' ends form the boundaries of the intergenic region. Overall, the patterns and characteristics identified here, along with other comparative and experimental studies, suggest that many footprints have a regulatory function, although other types of function are also possible. These conclusions may be quite general across eukaryotes, and the characteristics of conserved regulatory elements determined from genomic comparisons can be useful in prediction of regulation sites within individual DNA sequences.

Animals↗