Plant Molecular Evolution

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Title: Plant Molecular Evolution
Author: Strain, Errol Alan
Advisors: Jeff Thorne, Committee Member
Michael Purugganan, Committee Member
William Atchley, Committee Member
Spencer Muse, Committee Chair
Abstract: The current dissertation looks at the molecular evolution of protein-coding genes in the flowering plant Arabidopsis thaliana and within two RNA viruses, humanimmunodeficiency virus (HIV) and Astroviridae. We analyzed members of the receptor-like kinase (RLK) gene family in Arabidopsis thaliana for positive selection. Likelihood analysis found evidence for positive selection in 12 of the 52 RLK family sequences groups. These 12 groups represent 97 of the 403 sequences analyzed. The majority of genes in groups subject to positive selection have not been functionally characterized, but sites under selection are predominantly located in the extracellular region. In HIV we use Akaike Information Criteria (AIC) based model averaging for models of nucleotide evolution to examine estimates of genetic distance and the ratio of transition⁄transversion (ts⁄tv). AIC weighted estimates of distance and ts/tv were shown to be robust relative to model assumptions. AIC weighted estimates of the ts⁄tv ratio in simulated HIV sequences generally had less variance than similar estimates made by selecting the single best scoring AIC model. Astroviruses are a leading cause of viral gastroenteritis in infants worldwide and little is known about the mechanisms of astrovirus-induced diarrhea or the virally encoded components responsible for disease. We report the genomic sequence of nine novel TAstV-2 isolates. Nucleotide and amino acid identities for the isolates were generally > 90% conserved. Phylogenies constructed using genomic RNA and the individual open reading frames (ORF) provide evidence for recombination and indicate differences in substitution rates between non-structural and structural genes. Analysis of the viral capsid genes using codon models of evolution indicate site-specific positive selection in both turkey and human astroviruses.
Date: 2006-08-07
Degree: PhD
Discipline: Bioinformatics

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