New genes are an important source of evolutionary novelty and adaptation. The most common origin of new genes in eukaryotes is by gene duplication that happens when there is an error in DNA replication.
Whole genome duplication is much rarer but has been a key event in the evolution of the genome in many groups of organisms, especially plants.
New genes can be acquired from unrelated species by horizontal gene transfer. HGT is particularly common in prokaryotes, in which it has enabled the rapid evolution of traits, including antibiotic resistance.
Most gene duplicates degenerate into nonfunctional pseudogenes. Some duplicates survive, however, and evolve to specialize in one of the functions of the original gene, or to take on a new function. The result is a gene family: a set of loci that originated by gene duplication and that typically have related biochemical roles.
Chromosomal deletions can eliminate functioning genes. Natural selection can cause a deletion to increase in frequency, for example when the deleted gene codes for a protein that increases the risk of infection.
Most mutations that change the amino acid of a protein (nonsynonymous mutations) are deleterious and are removed from the population by purifying selection. Mutations in coding sequences that do not change the protein’s amino acid sequence (synonymous mutations) have only very weak effects on fitness and evolve largely by random drift. Nonsynonymous mutations that are beneficial are the rarest of all, but their fixation by positive selection is the basis of much adaptive evolution.
The dN/dS ratio provides a rough measure of the relative contributions of drift and selection to the evolution of a gene. The ratio is given by the frequency of differences in the DNA sequence for the gene in two species that are nonsynonymous divided by the frequency of differences that are synonymous. Typically this ratio is less than 1, which is expected when most nonsynonymous changes are eliminated by purifying selection but some synonymous changes have become fixed by drift. Occasionally genes have a dN/dS ratio greater than 1, which strongly suggests that nonsynonymous changes have become fixed by positive selection.
The fraction of protein differences among species caused by adaptive evolution versus genetic drift varies greatly among groups of organisms. About half the differences are adaptive in species with very large population sizes (e.g., Drosophila and free-living bacteria). In species with a small effective population size, including humans, drift is much stronger and so the fraction of adaptive differences is much smaller.
Another important route to adaptation comes from changes in how genes are expressed. Recent research shows that changes in gene expression have been key to adaptation to new environments in many species, including humans.
In eukaryotes, almost all genes have introns. These allow the mRNA to be spliced in different ways to make a variety of proteins. Chromosome mutations that bring together exons from different genes have yielded new genes with novel functions.
Chromosome numbers change by fusion and fission. In some cases, fissions and fusions have become fixed not because they increase fitness but because they benefit from meiotic drive.
Chromosome inversions can spread by several mechanisms. One is when they bind together beneficial combinations of alleles at two or more loci.
Genome size varies dramatically among species. In viruses and prokaryotes, almost all of the genome is coding sequence. In animals and plants, most of the genome is noncoding, and the quantity of noncoding DNA differs greatly among species.
Transposable elements, which are genetic parasites, are a major component of the noncoding DNA and account for much of the variation in genome size among species of eukaryotes.
Whole genome duplication, which is particularly common in plants, is responsible for the large differences in gene number seen among some closely related groups of organisms.