Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within lineages. Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book The Origin of Species. He also identified sexual selection as a likely mechanism, but found it problematic.
There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments. Whether genetic drift is a minor or major contributor to speciation is the subject matter of much ongoing discussion.
Rapid sympatric speciation can take place through polyploidy, such as by doubling of chromosome number; the result is progeny which are immediately reproductively isolated from the parent population. New species can also be created through hybridisation followed, if the hybrid is favoured by natural selection, by reproductive isolation.
In addressing the question of the origin of species, there are two key issues: (1) what are the evolutionary mechanisms of speciation, and (2) what accounts for the separateness and individuality of species in the biota? Since Charles Darwin's time, efforts to understand the nature of species have primarily focused on the first aspect, and it is now widely agreed that the critical factor behind the origin of new species is reproductive isolation. Next we focus on the second aspect of the origin of species.
In On the Origin of Species (1859), Darwin interpreted biological evolution in terms of natural selection, but was perplexed by the clustering of organisms into species. Chapter 6 of Darwin's book is entitled "Difficulties of the Theory." In discussing these "difficulties" he noted "Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?" This dilemma can be referred to as the absence or rarity of transitional varieties in habitat space.
Another dilemma, related to the first one, is the absence or rarity of transitional varieties in time. Darwin pointed out that by the theory of natural selection "innumerable transitional forms must have existed," and wondered "why do we not find them embedded in countless numbers in the crust of the earth." That clearly defined species actually do exist in nature in both space and time implies that some fundamental feature of natural selection operates to generate and maintain species.
It has been argued that the resolution of Darwin's first dilemma lies in the fact that out-crossing sexual reproduction has an intrinsic cost of rarity. The cost of rarity arises as follows. If, on a resource gradient, a large number of separate species evolve, each exquisitely adapted to a very narrow band on that gradient, each species will, of necessity, consist of very few members. Finding a mate under these circumstances may present difficulties when many of the individuals in the neighborhood belong to other species. Under these circumstances, if any species’ population size happens, by chance, to increase (at the expense of one or other of its neighboring species, if the environment is saturated), this will immediately make it easier for its members to find sexual partners. The members of the neighboring species, whose population sizes have decreased, experience greater difficulty in finding mates, and therefore form pairs less frequently than the larger species. This has a snowball effect, with large species growing at the expense of the smaller, rarer species, eventually driving them to extinction. Eventually, only a few species remain, each distinctly different from the other. The cost of rarity not only involves the costs of failure to find a mate, but also indirect costs such as the cost of communication in seeking out a partner at low population densities.
Rarity brings with it other costs. Rare and unusual features are very seldom advantageous. In most instances, they indicate a (non-silent) mutation, which is almost certain to be deleterious. It therefore behooves sexual creatures to avoid mates sporting rare or unusual features (koinophilia). Sexual populations therefore rapidly shed rare or peripheral phenotypic features, thus canalizing the entire external appearance, as illustrated in the accompanying illustration of the African pygmy kingfisher, Ispidina picta. This uniformity of all the adult members of a sexual species has stimulated the proliferation of field guides on birds, mammals, reptiles, insects, and many other taxa, in which a species can be described with a single illustration (or two, in the case of sexual dimorphism). Once a population has become as homogeneous in appearance as is typical of most species (and is illustrated in the photograph of the African pygmy kingfisher), its members will avoid mating with members of other populations that look different from themselves. Thus, the avoidance of mates displaying rare and unusual phenotypic features inevitably leads to reproductive isolation, one of the hallmarks of speciation.
In the contrasting case of organisms that reproduce asexually, there is no cost of rarity; consequently, there are only benefits to fine-scale adaptation. Thus, asexual organisms very frequently show the continuous variation in form (often in many different directions) that Darwin expected evolution to produce, making their classification into "species" (more correctly, morphospecies) very difficult.
One example of natural speciation is the diversity of the three-spined stickleback, a marine fish that, after the last glacial period, has undergone speciation into new freshwater colonies in isolated lakes and streams. Over an estimated 10,000 generations, the sticklebacks show structural differences that are greater than those seen between different genera of fish including variations in fins, changes in the number or size of their bony plates, variable jaw structure, and color differences.
During allopatric (from the ancient Greek allos, "other" + patrā, "fatherland") speciation, a population splits into two geographically isolated populations (for example, by habitat fragmentation due to geographical change such as mountain formation). The isolated populations then undergo genotypic or phenotypic divergence as: (a) they become subjected to dissimilar selective pressures; (b) they independently undergo genetic drift; (c) different mutations arise in the two populations. When the populations come back into contact, they have evolved such that they are reproductively isolated and are no longer capable of exchanging genes. Island genetics is the term associated with the tendency of small, isolated genetic pools to produce unusual traits. Examples include insular dwarfism and the radical changes among certain famous island chains, for example on Komodo. The Galápagos Islands are particularly famous for their influence on Charles Darwin. During his five weeks there he heard that Galápagos tortoises could be identified by island, and noticed that finches differed from one island to another, but it was only nine months later that he reflected that such facts could show that species were changeable. When he returned to England, his speculation on evolution deepened after experts informed him that these were separate species, not just varieties, and famously that other differing Galápagos birds were all species of finches. Though the finches were less important for Darwin, more recent research has shown the birds now known as Darwin's finches to be a classic case of adaptive evolutionary radiation.
In peripatric speciation, a subform of allopatric speciation, new species are formed in isolated, smaller peripheral populations that are prevented from exchanging genes with the main population. It is related to the concept of a founder effect, since small populations often undergo bottlenecks. Genetic drift is often proposed to play a significant role in peripatric speciation.
In parapatric speciation, there is only partial separation of the zones of two diverging populations afforded by geography; individuals of each species may come in contact or cross habitats from time to time, but reduced fitness of the heterozygote leads to selection for behaviours or mechanisms that prevent their interbreeding. Parapatric speciation is modelled on continuous variation within a "single," connected habitat acting as a source of natural selection rather than the effects of isolation of habitats produced in peripatric and allopatric speciation.
Parapatric speciation may be associated with differential landscape-dependent selection. Even if there is a gene flow between two populations, strong differential selection may impede assimilation and different species may eventually develop. Habitat differences may be more important in the development of reproductive isolation than the isolation time. Caucasian rock lizards Darevskia rudis, D. valentini and D. portschinskii all hybridize with each other in their hybrid zone; however, hybridization is stronger between D. portschinskii and D. rudis, which separated earlier but live in similar habitats than between D. valentini and two other species, which separated later but live in climatically different habitats.
Ecologists refer to parapatric and peripatric speciation in terms of ecological niches. A niche must be available in order for a new species to be successful. Ring species such as Larus gulls have been claimed to illustrate speciation in progress, though the situation may be more complex. The grass Anthoxanthum odoratum may be starting parapatric speciation in areas of mine contamination.
Sympatric speciation is the formation of two or more descendant species from a single ancestral species all occupying the same geographic location.
The best known example of sympatric speciation is that of the cichlids of East Africa inhabiting the Rift Valley lakes, particularly Lake Victoria, Lake Malawi and Lake Tanganyika. There are over 800 described species, and according to estimates, there could be well over 1,600 species in the region. Their evolution is cited as an example of both natural and sexual selection. A 2008 study suggests that sympatric speciation has occurred in Tennessee cave salamanders. Sympatric speciation driven by ecological factors may also account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake Baikal.
Budding speciation has been proposed as a particular form of sympatric speciation, whereby small groups of individuals become progressively more isolated from the ancestral stock by breeding preferentially with one another. This type of speciation would be driven by the conjunction of various advantages of inbreeding such as the expression of advantageous recessive phenotypes, reducing the recombination load, and reducing the cost of sex 
The hawthorn fly (Rhagoletis pomonella), also known as the apple maggot fly, appears to be undergoing sympatric speciation. Different populations of hawthorn fly feed on different fruits. A distinct population emerged in North America in the 19th century some time after apples, a non-native species, were introduced. This apple-feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. The current hawthorn feeding population does not normally feed on apples. Some evidence, such as that six out of thirteen allozyme loci are different, that hawthorn flies mature later in the season and take longer to mature than apple flies; and that there is little evidence of interbreeding (researchers have documented a 4-6% hybridization rate) suggests that sympatric speciation is occurring.
Reinforcement, sometimes referred to as the Wallace effect, is the process by which natural selection increases reproductive isolation. It may occur after two populations of the same species are separated and then come back into contact. If their reproductive isolation was complete, then they will have already developed into two separate incompatible species. If their reproductive isolation is incomplete, then further mating between the populations will produce hybrids, which may or may not be fertile. If the hybrids are infertile, or fertile but less fit than their ancestors, then there will be further reproductive isolation and speciation has essentially occurred (e.g., as in horses and donkeys).
The reasoning behind this is that if the parents of the hybrid offspring each have naturally selected traits for their own certain environments, the hybrid offspring will bear traits from both, therefore would not fit either ecological niche as well as either parent. The low fitness of the hybrids would cause selection to favor assortative mating, which would control hybridization. This is sometimes called the Wallace effect after the evolutionary biologist Alfred Russel Wallace who suggested in the late 19th century that it might be an important factor in speciation.
Conversely, if the hybrid offspring are more fit than their ancestors, then the populations will merge back into the same species within the area they are in contact.
Reinforcement favoring reproductive isolation is required for both parapatric and sympatric speciation. Without reinforcement, the geographic area of contact between different forms of the same species, called their "hybrid zone," will not develop into a boundary between the different species. Hybrid zones are regions where diverged populations meet and interbreed. Hybrid offspring are very common in these regions, which are usually created by diverged species coming into secondary contact. Without reinforcement, the two species would have uncontrollable inbreeding. Reinforcement may be induced in artificial selection experiments as described below.
Ecological selection is "the interaction of individuals with their environment during resource acquisition". Natural selection is inherently involved in the process of speciation, whereby, "under ecological speciation, populations in different environments, or populations exploiting different resources, experience contrasting natural selection pressures on the traits that directly or indirectly bring about the evolution of reproductive isolation". Evidence for the role ecology plays in the process of speciation exists. Studies of stickleback populations support ecologically-linked speciation arising as a by-product, alongside numerous studies of parallel speciation, where isolation evolves between independent populations of species adapting to contrasting environments than between independent populations adapting to similar environments. Ecological speciation occurs with much of the evidence, "...accumulated from top-down studies of adaptation and reproductive isolation".
It is widely appreciated that sexual selection could drive speciation in many clades, independently of natural selection. However the term “speciation”, in this context, tends to be used in two different, but not mutually exclusive senses. The first and most commonly used sense refers to the “birth” of new species. That is, the splitting of an existing species into two separate species, or the budding off of a new species from a parent species, both driven by a biological "fashion fad" (a preference for a feature, or features, in one or both sexes, that do not necessarily have any adaptive qualities). In the second sense, "speciation" refers to the wide-spread tendency of sexual creatures to be grouped into clearly defined species, rather than forming a continuum of phenotypes both in time and space - which would be the more obvious or logical consequence of natural selection. This was indeed recognized by Darwin as problematic, and included in his On the Origin of Species (1859), under the heading "Difficulties with the Theory". There are several suggestions as to how mate choice might play a significant role in resolving Darwin’s dilemma.
New species have been created by animal husbandry, but the dates and methods of the initiation of such species are not clear. Often, the domestic counterpart of the wild ancestor can still interbreed and produce fertile offspring as in the case of domestic cattle, that can be considered the same species as several varieties of wild ox, gaur, yak, etc., or domestic sheep that can interbreed with the mouflon.
The best-documented creations of new species in the laboratory were performed in the late 1980s. William R. Rice and George W. Salt bred Drosophila melanogaster fruit flies using a maze with three different choices of habitat such as light/dark and wet/dry. Each generation was placed into the maze, and the groups of flies that came out of two of the eight exits were set apart to breed with each other in their respective groups. After thirty-five generations, the two groups and their offspring were isolated reproductively because of their strong habitat preferences: they mated only within the areas they preferred, and so did not mate with flies that preferred the other areas. The history of such attempts is described by Rice and Elen E. Hostert (1993). Diane Dodd used a laboratory experiment to show how reproductive isolation can evolve in Drosophila pseudoobscura fruit flies after several generations by placing them in different media, starch- and maltose-based media.
Dodd's experiment has been easy for many others to replicate, including with other kinds of fruit flies and foods. Research in 2005 has shown that this rapid evolution of reproductive isolation may in fact be a relic of infection by Wolbachia bacteria.
Alternatively, these observations are consistent with the notion that sexual creatures are inherently reluctant to mate with individuals whose appearance or behavior is different from the norm. The risk that such deviations are due to heritable maladaptations is very high. Thus, if a sexual creature, unable to predict natural selection's future direction, is conditioned to produce the fittest offspring possible, it will avoid mates with unusual habits or features. Sexual creatures will then inevitably tend to group themselves into reproductively isolated species.
Few speciation genes have been found. They usually involve the reinforcement process of late stages of speciation. In 2008, a speciation gene causing reproductive isolation was reported. It causes hybrid sterility between related subspecies. The order of speciation of three groups from a common ancestor may be unclear or unknown; a collection of three such species is referred to as a "trichotomy."
Polyploidy is a mechanism that has caused many rapid speciation events in sympatry because offspring of, for example, tetraploid x diploid matings often result in triploid sterile progeny. However, not all polyploids are reproductively isolated from their parental plants, and gene flow may still occur for example through triploid hybrid x diploid matings that produce tetraploids, or matings between meiotically unreduced gametes from diploids and gametes from tetraploids (see also hybrid speciation).
It has been suggested that many of the existing plant and most animal species have undergone an event of polyploidization in their evolutionary history. Reproduction of successful polyploid species is sometimes asexual, by parthenogenesis or apomixis, as for unknown reasons many asexual organisms are polyploid. Rare instances of polyploid mammals are known, but most often result in prenatal death.
Hybridization between two different species sometimes leads to a distinct phenotype. This phenotype can also be fitter than the parental lineage and as such natural selection may then favor these individuals. Eventually, if reproductive isolation is achieved, it may lead to a separate species. However, reproductive isolation between hybrids and their parents is particularly difficult to achieve and thus hybrid speciation is considered an extremely rare event. The Mariana mallard is thought to have arisen from hybrid speciation.
Hybridization is an important means of speciation in plants, since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals. Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis. Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations.
Hybridization without change in chromosome number is called homoploid hybrid speciation. It is considered very rare but has been shown in Heliconius butterflies  and sunflowers. Polyploid speciation, which involves changes in chromosome number, is a more common phenomenon, especially in plant species.
Theodosius Dobzhansky, who studied fruit flies in the early days of genetic research in 1930s, speculated that parts of chromosomes that switch from one location to another might cause a species to split into two different species. He mapped out how it might be possible for sections of chromosomes to relocate themselves in a genome. Those mobile sections can cause sterility in inter-species hybrids, which can act as a speciation pressure. In theory, his idea was sound, but scientists long debated whether it actually happened in nature. Eventually a competing theory involving the gradual accumulation of mutations was shown to occur in nature so often that geneticists largely dismissed the moving gene hypothesis. However, 2006 research shows that jumping of a gene from one chromosome to another can contribute to the birth of new species. This validates the reproductive isolation mechanism, a key component of speciation.
There is debate as to the rate at which speciation events occur over geologic time. While some evolutionary biologists claim that speciation events have remained relatively constant and gradual over time (known as "Phyletic gradualism" - see diagram), some palaeontologists such as Niles Eldredge and Stephen Jay Gould have argued that species usually remain unchanged over long stretches of time, and that speciation occurs only over relatively brief intervals, a view known as punctuated equilibrium. (See diagram, and Darwin's dilemma.)
Evolution can be extremely rapid, as shown in the creation of domesticated animals and plants in a very short geological space of time, spanning only a few tens of thousands of years. Maize (Zea mays), for instance, was created in Mexico in only a few thousand years, starting about 7,000 to 12,000 years ago. This raises the question of why the long term rate of evolution is far slower than is theoretically possible.
Evolution is imposed on species or groups. It is not planned or striven for in some Lamarckist way. The mutations on which the process depends are random events, and, except for the "silent mutations" which do not affect the functionality or appearance of the carrier, are thus usually disadvantageous, and their chance of proving to be useful in the future is vanishingly small. Therefore, while a species or group might benefit from being able to adapt to a new environment by accumulating a wide range of genetic variation, this is to the detriment of the individuals who have to carry these mutations until a small, unpredictable minority of them ultimately contributes to such an adaptation. Thus, the capability to evolve would require group selection, a concept discredited by (for example) George C. Williams, John Maynard Smith and Richard Dawkins as selectively disadvantageous to the individual.
The resolution to Darwin's second dilemma might thus come about as follows:
If sexual individuals are disadvantaged by passing mutations on to their offspring, they will avoid mutant mates with strange or unusual characteristics. Mutations that affect the external appearance of their carriers will then rarely be passed on to the next and subsequent generations. They would therefore seldom be tested by natural selection. Evolution is, therefore, effectively halted or slowed down considerably. The only mutations that can accumulate in a population, on this punctuated equilibrium view, are ones that have no noticeable effect on the outward appearance and functionality of their bearers (i.e., they are "silent" or "neutral mutations," which can be, and are, used to trace the relatedness and age of populations and species.) This argument implies that evolution can only occur if mutant mates cannot be avoided, as a result of a severe scarcity of potential mates. This is most likely to occur in small, isolated communities. These occur most commonly on small islands, in remote valleys, lakes, river systems, or caves, or during the aftermath of a mass extinction. Under these circumstances, not only is the choice of mates severely restricted but population bottlenecks, founder effects, genetic drift and inbreeding cause rapid, random changes in the isolated population's genetic composition. Furthermore, hybridization with a related species trapped in the same isolate might introduce additional genetic changes. If an isolated population such as this survives its genetic upheavals, and subsequently expands into an unoccupied niche, or into a niche in which it has an advantage over its competitors, a new species, or subspecies, will have come in being. In geological terms this will be an abrupt event. A resumption of avoiding mutant mates will thereafter result, once again, in evolutionary stagnation.
In apparent confirmation of this punctuated equilibrium view of evolution, the fossil record of an evolutionary progression typically consists of species that suddenly appear, and ultimately disappear, hundreds of thousands or millions of years later, without any change in external appearance. Graphically, these fossil species are represented by lines parallel with the time axis, whose lengths depict how long each of them existed. The fact that the lines remain parallel with the time axis illustrates the unchanging appearance of each of the fossil species depicted on the graph. During each species' existence new species appear at random intervals, each also lasting many hundreds of thousands of years before disappearing without a change in appearance. The exact relatedness of these concurrent species is generally impossible to determine. This is illustrated in the diagram depicting the distribution of hominin species through time since the hominins separated from the line that led to the evolution of our closest living primate relatives, the chimpanzees.
One of his greatest anxieties was that the "incompleteness" of the fossil record would be used to criticize his thory: that the apparent "gaps" in fossil succession could be cited as negative evidence, at the very least, for his proposal that all organisms have descended by minute and gradual modifications from a common ancestor.
The near-simultaneous appearance of most modern animal body plans in the Cambrian explosion suggests a brief interval of rapid phenotypic and genetic evolution, which Darwin believed were too fast to be explained by natural selection.
The Phenotypic Differences between Carrion and Hooded Crows across the Hybridization Zone in Europe are Unlikely to be due to Assortative Mating.— Commentary by Mazhuvancherry K. Unnikrishnan and H. S. Akhila
In evolutionary biology, adaptive radiation is a process in which organisms diversify rapidly from an ancestral species into a multitude of new forms, particularly when a change in the environment makes new resources available, creates new challenges, or opens new environmental niches. Starting with a recent single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits. The prototypical example of adaptive radiation is finch speciation on the Galapagos ("Darwin's finches"), but examples are known from around the world.Allopatric speciation
Allopatric speciation (from Ancient Greek ἄλλος, allos, meaning "other", and πατρίς, patris, "fatherland"), also referred to as geographic speciation, vicariant speciation, or its earlier name, the dumbbell model, is a mode of speciation that occurs when biological populations of the same species become isolated from each other to an extent that prevents or interferes with gene flow.
Various geographic changes can arise such as the movement of continents, and the formation of mountains, islands, bodies of water, or glaciers. Human activity such as agriculture or developments can also change the distribution of species populations. These factors can substantially alter a region's geography, resulting in the separation of a species population into isolated subpopulations. The vicariant populations then undergo genetic changes as they become subjected to different selective pressures, experience genetic drift, and accumulate different mutations in the separated populations gene pools. The barriers prevent the exchange of genetic information between the two populations leading to reproductive isolation. If the two populations come into contact they will be unable to reproduce—effectively speciating. Other isolating factors such as population dispersal leading to emigration can cause speciation (for instance, the dispersal and isolation of a species on an oceanic island) and is considered a special case of allopatric speciation called peripatric speciation.
Allopatric speciation is typically subdivided into two major models: vicariance and peripatric. Both models differ from one another by virtue of their population sizes and geographic isolating mechanisms. The terms allopatry and vicariance are often used in biogeography to describe the relationship between organisms whose ranges do not significantly overlap but are immediately adjacent to each other—they do not occur together or only occur within in a narrow zone of contact. Historically, the language used to refer to modes of speciation directly reflected biogeographical distributions. As such, allopatry is a geographical distribution opposed to sympatry (speciation within the same area). Furthermore, the terms allopatric, vicariant, and geographical speciation are often used interchangeably in the scientific literature. This article will follow a similar theme, with the exception of special cases such as peripatric, centrifugal, among others.
Observation of nature creates difficulties in witnessing allopatric speciation from "start-to-finish" as it operates as a dynamic process. From this arises a host of various issues in defining species, defining isolating barriers, measuring reproductive isolation, among others. Nevertheless, verbal and mathematical models, laboratory experiments, and empirical evidence overwhelmingly supports the occurrence of allopatric speciation in nature. Mathematical modeling of the genetic basis of reproductive isolation supports the plausibility of allopatric speciation; whereas laboratory experiments of Drosophila and other animal and plant species have confirmed that reproductive isolation evolves as a byproduct of natural selection.Cospeciation
Cospeciation is a form of coevolution in which the speciation of one species dictates speciation of another species and is most commonly studied in host-parasite relationships. In the case of a host-parasite relationship, if two hosts of the same species get within close proximity of each other, parasites of the same species from each host are able to move between individuals and mate with the parasites on the other host. However, if a speciation event occurs in the host species, the parasites will no longer be able to "cross over" because the two new host species no longer mate and, if the speciation event is due to a geographic separation, it is very unlikely the two hosts will interact at all with each other. The lack of proximity between the hosts ultimately prevents the populations of parasites from interacting and mating. This can ultimately lead to speciation within the parasite.According to Fahrenholz's rule, first proposed by Heinrich Fahrenholz in 1913, when host-parasite cospeciation has occurred, the phylogenies of the host and parasite come to mirror each other. In host-parasite phylogenies, and all species phylogenies for that matter, perfect mirroring is rare. Host-parasite phylogenies can be altered by host switching, extinction, independent speciation, and other ecological events, making cospeciation harder to detect. However, cospeciation is not limited to parasitism, but has been documented in symbiotic relationships like those of gut microbes in primates.Divergent evolution
Divergent evolution or divergent selection is the accumulation of differences between closely related species populations, leading to speciation. Divergent evolution is typically exhibited when two populations become separated by a geographic barrier (such as in allopatric or peripatric speciation) and experience different selective pressures that drive adaptions to their new environment. After many generations and continual evolution, the populations become unable to interbreed with one another. The American naturalist J. T. Gulick (1832-1923) was the first to use the term "divergent evolution", with its use becoming widespread in modern evolutionary literature. Classic examples of divergence in nature are the adaptive radiation of the finches of the Galapagos or the coloration differences in populations of a species that live in different habitats such as with pocket mice and fence lizards.The term can also be applied in molecular evolution, such as to proteins that derive from homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication) can illustrate divergent evolution. Through gene duplication, it is possible for divergent evolution to occur between two genes within a species. Similarities between species that have diverged are due to their common origin, so such similarities are homologies. In contrast, convergent evolution arises when an adaptation has arisen independently, creating analogous structures such as the wings of birds and of insects.Ecological speciation
Ecological speciation is the process by which ecologically based divergent selection between different environments leads to the creation of reproductive barriers between populations. This is often the result of selection over traits which are genetically correlated to reproductive isolation, thus speciation occurs as a by-product of adaptive divergence.Ecological selection is "the interaction of individuals with their environment during resource acquisition". Natural selection is inherently involved in the process of speciation, whereby, "under ecological speciation, populations in different environments, or populations exploiting different resources, experience contrasting natural selection pressures on the traits that directly or indirectly bring about the evolution of reproductive isolation". Evidence for the role ecology plays in the process of speciation exists. Studies of stickleback populations support ecologically-linked speciation arising as a by-product, alongside numerous studies of parallel speciation—of which, substantiates speciation's occurrence in nature.
The key difference between ecological speciation and other kinds of speciation, is that it is triggered by divergent natural selection among different habitats; as opposed to other kinds of speciation processes, like random genetic drift, the fixation of incompatible mutations in populations experiencing similar selective pressures, or various forms of sexual selection not involving selection on ecologically relevant traits. Ecological speciation can occur either in allopatry, sympatry, or parapatry. The only requirement being that speciation occurs as a result of adaptation to different ecological or micro-ecological conditions.Some debate exists over the framework concerning the delineation of whether a speciation event is ecological or nonecological. "The pervasive effect of selection suggests that adaptive evolution and speciation are inseparable, casting doubt on whether speciation is ever nonecological".Gene flow
In population genetics, gene flow (also known as gene migration or allele flow) is the transfer of genetic variation from one population to another. If the rate of gene flow is high enough, then two populations are considered to have equivalent genetic diversity and therefore effectively be a single population. It has been shown that it takes only "One migrant per generation" to prevent populations from diverging due to drift. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity within the populations, by modifying the allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to full speciation. In some cases migration may also result in the addition of novel genetic variants to the gene pool of a species or population.
There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there is long distances between populations, and when there are small population sizes. Mobility plays an important role in the migration rate, as highly mobile individuals tend to have greater migratory prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.History of speciation
The scientific study of speciation — how species evolve to become new species — began around the time of Charles Darwin in the middle of the 19th century. Many naturalists at the time recognized the relationship between biogeography (the way species are distributed) and the evolution of species. The 20th century saw the growth of the field of speciation, with major contributors such as Ernst Mayr researching and documenting species' geographic patterns and relationships. The field grew in prominence with the modern evolutionary synthesis in the early part of that century. Since then, research on speciation has expanded immensely.
The language of speciation has grown more complex. Debate over classification schemes on the mechanisms of speciation and reproductive isolation continue. The 21st century has seen a resurgence in the study of speciation, with new techniques such as molecular phylogenetics and systematics. Speciation has largely been divided into discrete modes that correspond to rates of gene flow between two incipient populations. Today however, research has driven the development of alternative schemes and the discovery of new processes of speciation.Hominini
The Hominini, or hominins, form a taxonomic tribe of the subfamily Homininae ("hominines"). Hominini includes genus Homo (humans), but excludes genus Gorilla (gorillas). As of 2019, there is no consensus on whether it should include genus Pan (the chimpanzees), the question being closely tied to the complex speciation process connecting humans and chimpanzees and the development of bipedalism in proto-humans.
The tribe was originally introduced by John Edward Gray (1824), long before any details on the speciation of Pan and Homo were known. Gray's tribe Hominini by definition includes both Pan and Homo. This definition is still adhered to in the proposal by Mann and Weiss (1996), which divides Hominini into three subtribes, Panina (containing Pan), Hominina ("homininans", containing Homo "humans"), and Australopithecina (containing several extinct "australopithecine" genera).Alternatively, Hominini is taken to exclude Pan. In this case, Panini ("panins", Delson 1977) may be used to refer to the tribe containing Pan as its only genus.Minority dissenting nomenclatures include Gorilla in Hominini and Pan in Homo (Goodman et al. 1998), or both Pan and Gorilla in Homo (Watson et al. 2001).Hybrid speciation
Hybrid speciation is a form of speciation where hybridization between two different species leads to a new species, reproductively isolated from the parent species. From the 1940s, reproductive isolation between hybrids and their parents was thought to be particularly difficult to achieve and thus hybrid species were thought to be extremely rare. With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a fairly common phenomenon, particularly in plants. In botanical nomenclature, a hybrid species is also called a nothospecies. Hybrid species are by their nature polyphyletic.Monotypic taxon
In biology, a monotypic taxon is a taxonomic group (taxon) that contains only one immediately subordinate taxon.A monotypic species is one that does not include subspecies or smaller, infraspecific taxa. In the case of genera, the term "unispecific" or "monospecific" is sometimes preferred.
In botanical nomenclature, a monotypic genus is a genus in the special case where a genus and a single species are simultaneously described.In contrast an oligotypic taxon contains more than one but only a very few subordinate taxa.Parapatric speciation
In parapatric speciation, two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes. This mode of speciation has three distinguishing characteristics: 1) mating occurs non-randomly, 2) gene flow occurs unequally, and 3) populations exist in either continuous or discontinuous geographic ranges. This distribution pattern may be the result of unequal dispersal, incomplete geographical barriers, or divergent expressions of behavior, among other things. Parapatric speciation predicts that hybrid zones will often exist at the junction between the two populations.
In biogeography, the terms parapatric and parapatry are often used to describe the relationship between organisms whose ranges do not significantly overlap but are immediately adjacent to each other; they do not occur together except in a narrow contact zone. Parapatry is a geographical distribution opposed to sympatry (same area) and allopatry or peripatry (two similar cases of distinct areas).
Various "forms" of parapatry have been proposed and are discussed below. Coyne and Orr in Speciation categorise these forms into three groups: clinal (environmental gradients), "stepping-stone" (discrete populations), and stasipatric speciation in concordance with most of the parapatric speciation literature. Henceforth, the models are subdivided following a similar format.
Charles Darwin was the first to propose this mode of speciation. It was not until 1930 when Ronald Fisher published The Genetical Theory of Natural Selection where he outlined a verbal theoretical model of clinal speciation. In 1981, Joseph Felsenstein proposed an alternative, "discrete population" model (the "stepping-stone model). Since Darwin, a great deal of research has been conducted on parapatric speciation—concluding that its mechanisms are theoretically plausible, "and has most certainly occurred in nature".Peripatric speciation
Peripatric speciation is a mode of speciation in which a new species is formed from an isolated peripheral population. Since peripatric speciation resembles allopatric speciation, in that populations are isolated and prevented from exchanging genes, it can often be difficult to distinguish between them. Nevertheless, the primary characteristic of peripatric speciation proposes that one of the populations is much smaller than the other. The terms peripatric and peripatry are often used in biogeography, referring to organisms whose ranges are closely adjacent but do not overlap, being separated where these organisms do not occur—for example on an oceanic island compared to the mainland. Such organisms are usually closely related (e.g. sister species); their distribution being the result of peripatric speciation.
The concept of peripatric speciation was first outlined by the evolutionary biologist Ernst Mayr in 1954. Since then, other alternative models have been developed such as centrifugal speciation, that posits that a species' population experiences periods of geographic range expansion followed by shrinking periods, leaving behind small isolated populations on the periphery of the main population. Other models have involved the effects of sexual selection on limited population sizes. Other related models of peripherally isolated populations based on chromosomal rearrangements have been developed such as budding speciation and quantum speciation.
The existence of peripatric speciation is supported by observational evidence and laboratory experiments. Scientists observing the patterns of a species biogeographic distribution and its phylogenetic relationships are able to reconstruct the historical process by which they diverged. Further, oceanic islands are often the subject of peripatric speciation research due to their isolated habitats—with the Hawaiian Islands widely represented in much of the scientific literature.Punctuated equilibrium
Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that once species appear in the fossil record the population will become stable, showing little evolutionary change for most of its geological history. This state of little or no morphological change is called stasis. When significant evolutionary change occurs, the theory proposes that it is generally restricted to rare and geologically rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which a species splits into two distinct species, rather than one species gradually transforming into another.Punctuated equilibrium is commonly contrasted against phyletic gradualism, the idea that evolution generally occurs uniformly and by the steady and gradual transformation of whole lineages (called anagenesis). In this view, evolution is seen as generally smooth and continuous.In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing their theory and called it punctuated equilibria. Their paper built upon Ernst Mayr's model of geographic speciation, I. Michael Lerner's theories of developmental and genetic homeostasis, and their own empirical research. Eldredge and Gould proposed that the degree of gradualism commonly attributed to Charles Darwin is virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species.Reinforcement (speciation)
Reinforcement is a process of speciation where natural selection increases the reproductive isolation between two populations of species. This occurs as a result of selection acting against the production of hybrid individuals of low fitness. The idea was originally developed by Alfred Russel Wallace and is sometimes referred to as the Wallace effect. The modern concept of reinforcement originates from Theodosius Dobzhansky. He envisioned a species separated allopatrically, where secondary contact of the two populations mate, producing hybrids with lower fitness. Natural selection results from the hybrid's inability to produce viable offspring; thus members of one species who do not mate with members of the other have greater reproductive success. This favors the evolution of greater prezygotic isolation (differences in behavior or biology that inhibit formation of hybrid zygotes). Reinforcement is one of the few cases in which selection can favor an increase in prezygotic isolation, influencing the process of speciation directly. This aspect has been particularly appealing among evolutionary biologists.The support for reinforcement has fluctuated since its inception, and terminological confusion and differences in usage over history have led to multiple meanings and complications. Various objections have been raised by evolutionary biologists as to the plausibility of its occurrence. Since the 1990s, data from theory, experiments, and nature have overcome many of the past objections, rendering reinforcement widely accepted, though its prevalence in nature remains unknown.Numerous models have been developed to understand its operation in nature, most relying on several facets: genetics, population structures, influences of selection, and mating behaviors. Empirical support for reinforcement exists, both in the laboratory and in nature. Documented examples are found in a wide range of organisms: both vertebrates and invertebrates, fungi, and plants. The secondary contact of originally separated incipient species (the initial stage of speciation) is increasing due to human activities such as the introduction of invasive species or the modification of natural habitats. This has implications for measures of biodiversity and may become more relevant in the future.Sequence homology
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs).Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous.Species
In biology, a species (ˌ/ˈspiːʃiːz/, (listen) is the basic unit of classification and a taxonomic rank, as well as a unit of biodiversity, but it has proven difficult to find a satisfactory definition. Scientists and conservationists need a species definition which allows them to work, regardless of the theoretical difficulties. If as Carl Linnaeus thought, species were fixed and clearly distinct from one another, there would be no problem, but evolutionary processes cause species to change continually, and to grade into one another. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, when looked at more closely it is problematic. For example, with hybridisation, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies. Problems also arise when dealing with fossils, since reproduction cannot be examined; the concept of the chronospecies is therefore used in palaeontology. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche.
All species are given a two-part name, a "binomial". The first part of a binomial is the genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes in zoological nomenclature). For example, Boa constrictor is one of four species of the genus Boa.
Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time. Charles Darwin's 1859 book The Origin of Species explained how species could arise by natural selection. That understanding was greatly extended in the 20th century through genetics and population ecology. Genetic variability arises from mutations and recombination, while organisms themselves are mobile, leading to geographical isolation and genetic drift with varying selection pressures. Genes can sometimes be exchanged between species by horizontal gene transfer; new species can arise rapidly through hybridisation and polyploidy; and species may become extinct for a variety of reasons. Viruses are a special case, driven by a balance of mutation and selection, and can be treated as quasispecies.
As a practical matter, species concepts may be used to define species that are then used to measure biodiversity, though whether this is a good measure is disputed, as other measures are possible.Species complex
In biology, a species complex is a group of closely related species that are very similar in appearance to the point that the boundaries between them are often unclear. Terms sometimes used synonymously but with more precise meanings are: cryptic species for two or more species hidden under one species name, sibling species for two cryptic species that are each other's closest relative, and species flock for a group of closely related species living in the same habitat. As informal taxonomic ranks, species group, species aggregate, and superspecies are also in use.
Two or more taxa once considered conspecific (of the same species) may later be subdivided into infraspecific taxa (taxa within a species, such as bacterial strains or plant varieties), but this is not a species complex.
A species complex is in most cases a monophyletic group with a common ancestor, although there are exceptions. It may represent an early stage after speciation, but may also have been separated for a long time period without evolving morphological differences. Hybrid speciation can be a component in the evolution of a species complex.
Species complexes exist in all groups of organisms. They are identified by the rigorous study of differences between individual species, making use of minute morphological details, tests of reproductive isolation, or DNA-based methods such as molecular phylogenetics or DNA barcoding. The existence of extremely similar species may cause local and global species diversity to be underestimated. Recognizing similar but distinct species is important for disease and pest control, and in conservation biology, although drawing dividing lines between species can be inherently difficult.Sympatric speciation
Sympatric speciation is the evolution of a new species from a surviving ancestral species while both continue to inhabit the same geographic region. In evolutionary biology and biogeography, sympatric and sympatry are terms referring to organisms whose ranges overlap so that they occur together at least in some places. If these organisms are closely related (e.g. sister species), such a distribution may be the result of sympatric speciation. Etymologically, sympatry is derived from the Greek roots συν ("together") and πατρίς ("homeland"). The term was invented by Edward Bagnall Poulton in 1904, who explains the derivation.Sympatric speciation is one of three traditional geographic modes of speciation. Allopatric speciation is the evolution of species caused by the geographic isolation of two or more populations of a species. In this case, divergence is facilitated by the absence of gene flow. Parapatric speciation is the evolution of geographically adjacent populations into distinct species. In this case, divergence occurs despite limited interbreeding where the two diverging groups come into contact. In sympatric speciation, there is no geographic constraint to interbreeding. These categories are special cases of a continuum from zero (sympatric) to complete (allopatric) spatial segregation of diverging groups.In multicellular eukaryotic organisms, sympatric speciation is a plausible process that is known to occur, but the frequency with which it occurs is not known.
In bacteria, however, the analogous process (defined as "the origin of new bacterial species that occupy definable ecological niches") might be more common because bacteria are less constrained by the homogenizing effects of sexual reproduction and are prone to comparatively dramatic and rapid genetic change through horizontal gene transfer.Sympatry
In biology, two related species or populations are considered sympatric when they exist in the same geographic area and thus frequently encounter one another. An initially interbreeding population that splits into two or more distinct species sharing a common range exemplifies sympatric speciation. Such speciation may be a product of reproductive isolation – which prevents hybrid offspring from being viable or able to reproduce, thereby reducing gene flow – that results in genetic divergence. Sympatric speciation does not imply secondary contact, which is speciation or divergence in allopatry followed by range expansions leading to an area of sympatry. Sympatric species or taxa in secondary contact may or may not interbreed.