Many biologists interpret "species" as the fundamental unit into which populations of organisms can be classified. However, what is considered to constitute a species varies by taxonomic group as well as the purpose for which this classification is being used. The biological species concept, which defines species as interbreeding populations that are reproductively isolated from other populations, is a useful definition, particularly for thinking about how many species of sexually reproducing animals and plants arise.

There are four geographic modes of speciation that are based on the extent to which the incipient species (populations that are in the process of forming distinct species) are geographically isolated from one another. Allopatric speciation occurs in populations that became separated by a geographic barrier. Peripatric speciation, also known as founder effect speciation, is a special type of allopatric speciation. It occurs when a small population becomes isolated from its parent species. Parapatric speciation arises between neighboring populations that share small zones of contact and exhibit modest gene exchange. Sympatric speciation occurs within a single, freely interbreeding population, and is believed to occur only rarely. These modes were first described for animals and also are useful for distinguishing patterns of speciation in plants.

Allopatric speciation is the evolution of reproductive isolation in populations that are separated by geographic barriers. What constitutes a geographic barrier is not strictly defined, rather, it can be understood as any environmental factor that prevents or dramatically reduces gene flow between two populations. Thus, while geographic barriers most commonly result from large-scale climatic and geological events (mountain formation, glaciation, continental drift), they can also result from strict habitat preferences that "microgeographically" isolate populations.

Geographic isolation prevents gene flow among previously interbreeding populations and allows them to evolve independently. This almost inevitably leads to divergence between the two populations over time as distinct evolutionary changes accumulate: different mutations arise in the different populations, genetic drift fixes different genes in the populations, and the populations undergo different adaptive changes in response to natural selection. Over time, the two populations may become reproductively incompatible or isolated, essentially as a by-product of the genetic divergence of other traits. Eventually, the two (initially identical) species will no longer interbreed, even if they are brought back into contact with one another under natural conditions. Allopatric speciation is considered to be the most common of the known modes of speciation.

Peripatric speciation is a type of allopatric speciation. In both of these geographic modes of speciation, a single population becomes divided into two independent populations that can no longer interbreed because they are separated by some physical barrier. Because of the separation, the two populations evolve independently and eventually become reproductively incompatible. The distinction between allopatric and peripatric speciation is the relative sizes of the populations involved. In allopatric speciation, a population is separated into two relatively large independent populations. In contrast, in peripatric speciation, only a small fraction of the original population becomes geographically isolated. Peripatric speciation originally was known as founder effect speciation because it can occur when a few individuals (the founders) colonize a new habitat, such as an island, thereby establishing a new population away from the parent population.

The same genetic forces drive the evolution of reproductive isolation in both allopatric and peripatric speciation: mutation, natural selection, and genetic drift. However, in peripatric speciation, evolution may occur on a faster time scale because small populations are more susceptible to the random effects of genetic drift. In addition, it is likely that there will be a period of rapid selection and adaptation if the colonists' new habitat is substantially different from their original environment. For example, the founder effect has been used to explain the rapid speciation of Hawaiian fruit flies (Drosophila). Approximately 500 species of Drosophila currently inhabit the Hawaiian archipelago, and all are believed to have descended from a common ancestor that reached the island of Kauai (the oldest of the volcanic islands) over five million years ago. Some believe that as new Hawaiian islands formed as a result of volcanic activity, they were colonized by small groups of Drosophila from the older islands. Because these founders represented only a fraction of the genetic variability present in the parent species, it is likely that genetic drift played a large role in the evolution of genetic distinctiveness between species of Hawaiian Drosophila. In addition, the founders evolved through the process of natural selection to adapt to aspects of the new environment, such as the endemic plant hosts.

The founder effect has been invoked in the speciation events of the Hawaiian Drosophila because so many species were formed in such a relatively short time; the standard allopatric model does not predict that several hundred speciation events should occur in only a few million years. However, the importance of the founder-induced speciation is debated. Some have suggested that it rarely occurs, especially compared to the more standard allopatric model of speciation.

Both allopatric and peripatric speciation occur when populations are physically separated and therefore do not exchange genes. In contrast, parapatric speciation involves the evolution of reproductive isolation within a population where gene exchange is possible because there is no physical barrier separating individuals. However, although the population is continuous, it does not interbreed randomly and the degree of gene exchange is modest. For example, if the population of a single species expands its range, some individuals may grow in new areas with distinct environmental conditions. Over time, the "subpopulation" that inhabits the new area, or a fringe region adjacent to a new area, has potential to become genetically distinct from the rest of the population as it adapts to the new environmental conditions. As genetic differences accumulate, gene flow between the incipient species may slow. Eventually, if selection pressures are strong enough, reproductive isolation will evolve and the subpopulation will become a new species.

One of the best documented examples of parapatric speciation involves the evolution of tolerance to heavy metals in the subpopulation of grass Anthoxanthum odoratum. Populations of A. odorantum growing in close proximity to abandoned mines were observed to have diverged from neighboring populations as a result of selection pressure for heavy metal tolerance. In addition to evolving tolerance to heavy metals, the new populations self-pollinate and flower at different times. These characteristics reproductively isolate the heavy-metal tolerant populations.

In sympatric speciation, reproductive isolation is said to arise within a single, freely, and randomly interbreeding population in the absence of any spatial segregation. Thus, gene flow is initially restricted by biological features of organisms rather than by geography or distance. Because even low levels of gene exchange can swamp out the build up of genetic differentiation that is required for speciation, the occurrence of sympatric speciation is highly debated and controversial. Models of sympatric speciation propose various evolutionary forces and processes as the driving force behind the genetic divergence required for reproductive isolation in sympatry, including diversifying selection (a form of natural selection) and polyploidy (when multiple, duplicate copies of the genome are present within individuals). 

When populations inhabit environments with multiple resources and microhabitats, some individuals may possess traits or characteristics that allow them to use one of the resources and/or microhabitats more efficiently. Over time, diversifying selection can cause the population to split into genetically distinct groups that are adapted to discreet niches or the use of different resources within the environment. If selection pressures are strong enough to overcome gene exchange in the population, speciation can occur in sympatry.

An example of sympatric speciation resulting from diversifying selection may be found in flies of the genus Rhagoletis. These flies exhibit strong fidelity to the host plants in which they mate and leave their offspring to develop. Until the mid-nineteenth century, Rhagoletis in the northeastern United States used hawthorns exclusively as their host plant. However, when apples were introduced in some areas approximately 150 years ago, a new "race" of Rhagoletis appeared that inhabits apples rather than hawthorns. Because hawthorns and apples are often found in the same geographic area, the hawthorn and apple-maggot flies can exist in trees that are only yards apart. Many consider that the hawthorn flies are the parent species of the apple flies and that the speciation event was initiated by genetic variations that caused some members of the original population to be attracted to new hosts. This argues for sympatric speciation in Rhagoletis. However, this claim has come under debate. For example, some argue that the hawthorn and apple-maggot flies descended from distinct, independent lineages, through allopatric speciation.

While many models of sympatric speciation remain somewhat controversial among evolutionary biologists, most (if not all) agree that sympatric speciation can occur through polyploidy, the inheritance of more than two basic genome copies as a result of errors during cell division. Polyploids (organisms with more than two duplicate sets of chromosomes) are named according to the number of chromosome sets they have within their nuclei: a triploid has three sets of chromosomes (3n), a tetraploid has four sets (4n), etc.

Polyploid organisms are immediately reproductively isolated from their diploid parent species. For example, a failure during meiosis can cause diploid (2n) parent species to produce tetraploid (4n) offspring. However, crosses between a diploid and a tetraploid will result in inviable or sterile offspring due to abnormal chromosomal pairings during mitosis or meiosis. In fact, for the tetraploid organism to successfully reproduce, it must fertilize itself or mate with another tetraploid. Thus, polyploidy can result in instantaneous speciation in a single genetic event. Polyploidy also provides an immediate way for hybrids of otherwise incompatible parent genomes to produce fertile offspring.

Polyploidy is very common in plant species. It is estimated that 35% of flowering plant species are polyploid. While relatively rare, polyploidy is also found in animal species, such as the frog Hyla versicolor, a tetraploid derived from the diploid Hyla chrysoscelis.