How much genetic variation exists in natural populations? Before easy access to DNA sequences themselves, genotypic variants or polymorphisms were examined at the level of chromosome banding, particularly in the salivary glands of Drosophila, and through genetically based variation in enzymes as revealed through allozyme electrophoresis. Studies of enzyme variation in the mid-1960s by Lewontin and Hubby working with Drosophila pseudoobscura showed that an unexpectedly high number of loci were polymorphic (two or more alleles were found in 30% of all loci examined) and that over all loci nearly every individual was genetically unique. This work prompted the question of what was responsible for all this genetic variation, and in particular, did natural selection maintain this polymorphism or was the variation selectively neutral, being influenced only by processes of random genetic drift? That many loci are in fact polymorphic has been confirmed more recently with information directly from DNA sequences of both protein-coding and noncoding regions of DNA.
How is this variation then expressed in the observable phenotype? The link between the genotype and the phenotype is often relatively straightforward. Many phenotypic traits are determined by only one or a few genetic loci. However, other traits are influenced not by one or two loci, but by many loci, each with a relatively small effect; here, the link between genotype and phenotype is described by quantitative genetics. Usually such traits have measurable genetic and environmental components and frequently an interaction between the two. For such traits, the amount of variation that is "genetic" is described as the heritability, usually denoted h2, which can be estimated through breeding studies or by examining relatives of known genetic relatedness. Crosses of inbred lines that differ in traits of interest can be used to determine the inheritance, approximate number, and relative importance of loci responsible for variation in those traits. In such analyses, loci responsible for variation in quantitative traits are termed quantitative trait loci.
The origins of genetic variability rest in the processes of mutation, which are typically classified by the type of change caused by the mutational event. Mutations can arise through substitution (one nucleotide is replaced by another), recombination (crossing over and gene conversion), deletion (one or more nucleotides are removed), insertion (one or more nucleotides are added), or inversion (180° rotation of a double-stranded DNA segment). In protein-coding regions, some nucleotide substitutions do not change the amino acid for which they code and such substitutions are termed synonymous or silent. Substitutions that change the amino acid are termed nonsynonymous. Rates of mutation vary widely and can be influenced by the internal genetic environment as well as by the external environment. Aspects of the genetic environment that have been shown to affect rates of mutation include the functional role of the region (whether coding or not) and, for a given base, its position within a gene (e.g., stems or loops of ribosomal DNA) or within a codon (e.g., third positions change much more frequently than first or second positions due to redundancy in the genetic code). Rates of mutation are also affected by genome size and type, i.e., whether organellar or nuclear. For example, in insects, rates of mutation for protein-coding regions are typically higher for haploid mitochondrial DNA than for diploid nuclear DNA, a fact usually attributed to a lack of an efficient mechanism for DNA repair in insect mitochondrial DNA. Recent findings have shown that parts of the genomes of organisms may originate from other sources. For example, recent research on Orthoptera and Diptera has revealed nuclear DNA inserts of what were previously mitochondrial genes, and transposable elements, highly mobile pieces of DNA, are likely widespread in insect nuclear genomes. Of course, rates of mutation are also affected by external environmental variables, such as temperature and radiation.
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