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• W2915072818 endingPage "264" @default.
• W2915072818 startingPage "253" @default.
• W2915072818 abstract "Single-nucleotide variants or mutations (e.g., point mutations) are less common than other variations and mutations, and cannot generate observed genomic diversity. Genomic elements such as short tandem repeats, ribosomal RNA gene arrays, or transposable elements have extremely high mutation rates that likely contribute most mutations in eukaryotic genomes. These high-rate elements are very diverse and their importance depends on their biological context. For example, in prokaryotes the more important such elements are plasmids and integrative and conjugative elements. Functional elements with very high mutation rates behave very differently than functional elements with low mutation rates in evolution. Specifically, the same mutation can occur multiple times in different lineages, and evolution is no longer mutation-limited. Extant genomes are largely shaped by global transposition, copy-number fluctuation, and rearrangement of DNA sequences rather than by substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution and undermine common models of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short sequences. The scale and extent of this ‘non-substitution’ variation has recently come into focus through the advent of new genomic technologies; however, it is still not widely considered in genotype–phenotype association studies. In this review we identify common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns. Extant genomes are largely shaped by global transposition, copy-number fluctuation, and rearrangement of DNA sequences rather than by substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution and undermine common models of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short sequences. The scale and extent of this ‘non-substitution’ variation has recently come into focus through the advent of new genomic technologies; however, it is still not widely considered in genotype–phenotype association studies. In this review we identify common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns. when favorable mutations occur in populations, they tend to increase in frequency over time until they dominate the population as a result of positive selection. In hard sweeps, positive selection is very strong and the mutation goes to fixation very quickly. In soft sweeps, selection is weaker and multiple mutations are simultaneously under positive selection, leading to complex population dynamics which are more difficult to detect and interpret. a model of molecular evolution under which it is assumed that all mutations take place at different sites. Under this assumption, parallel (or recurrent) mutation does not occur. This condition is satisfied by simply assuming that the number of sites in the genome is infinite, while keeping the mutation rate constant, such that the probability of mutation at any specific site becomes infinitesimally small. a mutation that occurs at the same locus as another previous mutation, but independently from the same starting allele, usually in different genetic lineages. Mutations at the same locus in the same lineage are called ‘stepwise’ mutations. the total number of mutations arising across the entire population of an organism. Either a larger population or a higher rate of per-locus mutation can increase this measure. Sometimes written as θ. regions of genomes consisting of many copies of ribosomal RNA genes, which vary dramatically in copy number across species and individuals while remaining conserved in the sequence of each gene. regions of DNA consisting of tandemly repeated DNA sequences at high copy number. This copy number mutates rapidly. Genomic regions such as telomeres and centromeres tend to consist of satellite DNA. Short tandem repeats (STRs), also called microsatellites, consist of very short repeat units (<10 nt). a mutation that replaces a nucleotide at a single position (A, C, G, T) with one of the other three nucleotides. DNA elements that reproduce themselves in genomes via ‘cut-and-paste’ or ‘copy-and-paste’ mechanisms, leading to large insertions and deletions of DNA. Sometimes called ‘selfish DNA’ or ‘jumping genes’." @default.
• W2915072818 created "2019-03-02" @default.
• W2915072818 creator A5049813467 @default.
• W2915072818 creator A5050779824 @default.
• W2915072818 creator A5084831697 @default.
• W2915072818 creator A5091676211 @default.
• W2915072818 date "2019-04-01" @default.
• W2915072818 modified "2023-10-12" @default.
• W2915072818 title "Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates" @default.
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