Non-random neutral evolution.

Title: Non-random neutral evolution.
Authors: Singer, Gregory A. C.
Date: 2002
Abstract: In this study, we investigate the causes and consequences of directional neutral evolution. We believe this is an evolutionary force that has not received the attention its importance to DNA and protein evolution warrants. Traditional sequence analyses rely upon models that assume homogeneity of nucleotide and amino acid compositions across different lineages, but our examinations of modern sequences show that this assumption is often violated. Our findings imply that periods of directional changes to the nucleotide or amino acid compositions of biological sequences have occurred in the past. Moreover, we demonstrate that these directional changes are very common and can be quite extreme. We show that modifications to the genetic code---a phenomenon that is common among mitochondrial genomes---can cause directional changes to the amino acid composition of proteins. Codon reassignments shift the relative number of codons assigned to each amino acid, and when coupled with neutral evolution over a period of time these changes will lead to a corresponding shift in the relative amino acid usages within the protein. More common causes of directional changes to the amino acid composition of proteins are mutation biases in the DNA. In particular, we show that biases to the relative proportions of A+T and G+C are capable of bringing about amino acid composition changes to the proteins the DNA encodes, with AT-rich DNA favouring the encoding of the FYMINK amino acids, and GC-rich DNA favouring the encoding of GARP amino acids. We show that this effect is both pervasive across all kingdoms of life, and that it also affects every protein within the genome---whether highly or loosely conserved. Finally, we show that directional neutral evolution in the DNA can operate in the presence of purifying selection in transmembrane domains. Since selection does not preclude neutral evolution if there are multiple favourable mutations possible, DNA mutation bias is able to influence the direction of evolution of the transmembrane domains without interfering with their fitness. We extend this same notion to include the possibility of mutation biases biasing the outcome of positive selection, as well.
CollectionTh├Ęses, 1910 - 2010 // Theses, 1910 - 2010
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