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Please use this identifier to cite or link to this item: http://hdl.handle.net/1807/24561

Title: Investigating Molecular Evolution of Rhodopsin Using Likelihood/Bayesian Phylogenetic Methods
Authors: Du, Jingjing
Advisor: Chang, Belinda
Department: Ecology and Evolutionary Biology
Keywords: Molecular Evolution
Likelihood and Bayesian methods
Phylogenetics
Rhodopsin
Natural Selection
Codon Usage Bias
Nocturnality
Early mammals
Visual Pigment
Adaptive Evolution
Vision
GPCR
Issue Date: 22-Jul-2010
Abstract: Rhodopsin, a visual pigment protein found in retinal photoreceptors, mediates vision at low-light levels. Recent studies focusing primarily in human and mouse have challenged the assumption of neutral evolution of synonymous substitutions in mammals. Using recently developed likelihood-based codon models accounting for mutational bias and selection, we find significant evidence for selective constraint on synonymous substitutions in mammalian rhodopsins, and a preference for cytosine at 3rd codon positions. A second project investigated adaptive evolution in rhodopsin, in view of theories of nocturnality in early mammals. We detected a significant acceleration of non-synonymous substitution rates at the origins of therian mammals, and a tendency of synonymous substitutions towards C-ending codons prior to that. These findings suggest an evolutionary scenario in which synonymous substitutions that increase mRNA stability and/or translation efficiency may have preceded adaptive non-synonymous evolution in early mammalian rhodopsins. These findings have important implications for theories of early mammalian nocturnality.
URI: http://hdl.handle.net/1807/24561
Appears in Collections:Master
Department of Ecology & Evolutionary Biology - Master theses

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