The theory of evolution was developed to explain how the diversity of life on Earth arose. The theory hypothesizes that organisms have evolved from earlier forms through a series of mutations. Most mutations are either benign or harmful, but the beneficial ones allow an organism to leave more offspring. These beneficial mutations are then handed down to future generations. Eventually, enough mutations accumulate that an entirely new species emerges.
Beneficial mutations can take several forms. Chief among them are mutations that allow a species to adapt to a new ecological niche (e.g., the ability to obtain food from a new source); adaptations that allow them to compete better for resources in an established hierarchy (e.g., an increase in size as protection against predators); and changes that make one gender of a species more appealing to the opposite sex (e.g., the fabulous plumage of some birds).
The original motivation for the theory of evolution was the fact that species of animals were extremely diverse, and yet clearly related to each other. Among the most famous (although perhaps not the best) examples are the birds that inhabit the Galapagos Islands. The finches are clearly related, but each has different features that are matched to its diet (e.g., insects or seeds) and habitat (e.g., the ground or trees). Charles Darwin's explanation was that all of the species of finch descended from a common ancestor, and that the species diverged as mutations allowed them to fill new roles in the ecosystem.
Darwin, and the scientists that have followed in his wake, extended this idea to explain the genera, phyla, kingdoms, etc. of biological taxonomy. That all life shares a common ancestor is suggested by the similarities of bone structure in species as diverse as whales and dogs; by the similarities in the embryonic development of frogs, fishes, and humans; by organs that appear to have little use in humans, but that do have uses for related species, such as the appendix; and by the fossil record that was known even in Darwin's time.
The theory of evolution is supported by continuing discoveries in the fossil record, by the emergence of our modern understanding of genetics and its relation to DNA, by the underlying similarities between the genetic codes of all life, and even by laboratory experiments on rapidly-reproducing bacteria.
Darwin and his contemporaries were aware that the fossil record contained species that are now extinct. Modern tools have now revealed many more similarities between modern and ancient species. Many more fossils have emerged of species that appear to represent ancestors of modern ones, including dinosaurs that have bird-like features (the most famous is Archaeopteryx) There are also numerous species that appear to be dead-ends, such as the mysterious small humanoid, Homo floresienses. If evolution were not a good description of how species emerged, there would be no reason for such fossils to exist.
The discovery of chromosomes as carriers of genetic information is also viewed as a validation of evolutionary theory. When Darwin first proposed his theory of evolution, it was evident that there was a large piece missing from this theory: he hadn't proposed a mechanism that would work to pass mutations from a single parent to its progeny. For a mutation from one parent to be passed down to its offspring, it must not be diluted by the contribution from the other parent. Something had to allow mutations from one parent to be passed down whole. Darwin apparently was not aware of Gregory Mendel's contemporary work on gene theory. Mendel hypothesized that offspring receive one set of genes from each parent, and that traits are expressed based on the combination of pairs of genes. We now know Mendel was basically correct, and that genes allow mutations to be passed to offspring. Moreover, we know that much of that genetic information is encoded in the DNA within our chromosomes.
Once DNA was discovered, it became possible to examine the relationship between species on a molecular level. It is a remarkable verification of evolutionary theory that the molecular code underlying similar species is very similar. Humans and chimpanzees, for instance, share 98% of their DNA and nearly all of their identified genes, including many errors in the genes. This strongly suggests that they have evolved from common ancestors.
Finally, evolution appears to have been observed in the laboratory. An evolutionary biologist, Richard Lenski, has been allowing strains of E. coli bacteria to breed for twenty years. Suddenly, about 31,500 generations into the process, a strain of the bacteria suddenly became able to metabolize the chemical citrate. It is not yet clear what genetic changes were needed for the bacteria to use this new chemical as food. Nonetheless, this may well be the first case in which scientists have seen evolution occur under controlled conditions.
Although it is widely appreciated that gene theory has a multitude of practical uses in biology, it may be a bit harder to think of applications that specifically evolve evolutionary theory. One such application are the flu vaccines that are produced each year, which are developed based on an expectation of how the influenza virus will evolve.
Experiments are also underway to coax bacteria to evolve to metabolize new chemicals, in the hopes that this could make it easier to synthesize biofuels.
Evolutionary theory has also influenced a class of computer algorithms (genetic algorithms) that are used for solving complex optimization problems.
Evolution is now connected intimately with genetic theory. Genetic theory provides a mechanism by which random mutations can occur and be passed on to progeny, and because the genetic code of various species can be used to trace their evolutionary relationships. Evolutionary theory helps researchers to understand how and why the genetic codes of species change with time.
Evolution is also a key part of our understanding of the natural history of the Earth. It was not until 1905, over 20 years after the death of Darwin, that radiometric dating of rocks established that the Earth is billions of years old. That vast time span is probably required for evolution to occur. Indeed, multi-celled life emerged only 600 million years ago (the Precambrian era), over 4 billion years after the formation of the Earth.
Many details about how evolution has operated remain to be understood. Looking at the fossil record, it is uncertain what caused the Cambrian Explosion 545 million years ago, when the number and complexity of multi-celled organisms increased dramatically over the span of perhaps 10 million years.
There is still debate over how species are related, such as dinosaurs and birds, and what the geographical origin is of important species, such as Homo erectus.
There is also debate over the relative importance of random genetic drift compared to natural selection. The latter is often cited as the main driver of evolution, but not every difference between species appears related to a clear competitive advantage.