Plant Molecular Evolution

Astrovirus;Model Averaging;Arabidopsis;Molecular Evolution;AIC;Receptor Like Kinases

Strain, Errol Alan ; Jeff Thorne, Committee Member,Michael Purugganan, Committee Member,William Atchley, Committee Member,Spencer Muse, Committee Chair,Strain, Errol Alan ; Jeff Thorne ; Committee Member ; Michael Purugganan ; Committee Member ; William Atchley ; Committee Member ; Spencer Muse ; Committee Chair

University:North Carolina State University

关键词: Astrovirus;    Model Averaging;    Arabidopsis;    Molecular Evolution;    AIC;    Receptor Like Kinases;   

Others  :  https://repository.lib.ncsu.edu/bitstream/handle/1840.16/5360/etd.pdf?sequence=1&isAllowed=y

美国|英语

来源: null

【 摘 要 】

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 inArabidopsis thaliana for positive selection.Likelihood analysis found evidence for positive selection in 12 of the 52 RLK family sequences groups.These 12 groupsrepresent 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 arepredominantly located in the extracellular region. In HIV we use Akaike Information Criteria (AIC) based model averaging formodels 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 shownto 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 byselecting the single best scoring AIC model. Astroviruses are a leading cause of viral gastroenteritis in infants worldwide andlittle is known about the mechanisms of astrovirus-induced diarrhea or the virally encoded components responsible for disease. We report the genomic sequence of ninenovel TAstV-2 isolates.Nucleotide and amino acid identities for the isolates were generally > 90% conserved.Phylogenies constructed using genomic RNA and theindividual open reading frames (ORF) provide evidence for recombination and indicate differences in substitution rates between non-structural and structural genes.Analysis ofthe viral capsid genes using codon models of evolution indicate site-specific positive selection in both turkey and human astroviruses.