Vision has profound effects on the evolution of organisms by affecting survivorship through such basic behaviors as mating preference, foraging strategies and prey preference. Its importance is strongly indicated by the presence of visual pigments in a whole array of organisms ranging from bacteria to human. Using both blind cave fish and eyed river fish of the characid, Astyanax fasciatus, we propose to investigate the patterns of nucleotide and amino acid obtained will contribute in understanding functional adaptation and possible degeneration of vision. By constructing genomic DNA libraries, cloning and nucleotide sequencing and using the polymerase chain reaction (PCR) and direct sequencing, we plan to characterize all visual pigment genes from both blind cave fish and eyed river fish. In addition, we will determine which visual pigment genes are expressed in the eyes of the river fish and the pineal organs of the two types of fish. This will be achieved using PCR amplification of cDNA made from RNA of these organs followed by direct sequencing. The DNA sequences obtained will be used to evaluate the biological implications of the mutation accumulations by considering statistics such as (1) rates of transitional and transversional changes, (2) rates of nucleotide substitution, (3) rates of synonymous and nonsynonymous changes, and (4) codon usage. These quantities will be evaluated by considering different functional domains of the visual pigments, i.e., intracellular, extracellular, and seven transmembrane segments and will be used to construct phylogenetic trees and to estimate the lengths of the different branches. Origin, direction, and speed of nucleotide and amino acid substitutions will also be evaluated. Furthermore, these and other sequences of guanine nucleotide binding protein coupled receptor genes will be used to make inference on the neutral as well as adaptive evolutions.
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