The commonly used names for plant and animal taxa sometimes correspond to species: for example, "lion," "walrus," and "Camphor tree" – each refers to a species. In other cases common names do not: for example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Elk (Wapiti). The last two species were once considered a single species, illustrating how species boundaries may change with increased scientific knowledge.
Each species is placed within a single genus. This is a hypothesis that the species is more closely related to other species within its genus than to species of other genera. All species are given a binomial name consisting of the generic name and specific name (or specific epithet). For example, Pinus palustris (commonly known as the Longleaf Pine). The taxonomic ranks are life, domain, kingdom, phylum, class, order, family, genus, and species.
A usable definition of the word "species" and reliable methods of identifying particular species are essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple examples of a proposed species must be studied for unifying characters before it can be regarded as a species. Extinct species known only from fossils are generally difficult to give precise taxonomic rankings to.
Because of the difficulties with both defining and tallying the total numbers of different species in the world, it is estimated that there are anywhere between 2 and 100 million different species.
In scientific classification, a species is assigned a two-part name, treated as Latin, although roots from any language can be used as well as names of locales or individuals. The genus is listed first (with its leading letter capitalized), followed by a second term: for example, gray wolves belong to the species Canis lupus, coyotes to Canis latrans, golden jackals to Canis aureus, etc., and all of those belong to the genus Canis (which also contains many other species). The name of the species is the whole binomial, not just the second term (which may be called specific name for animals).
The binomial naming convention that is used, later formalized in the biological codes of nomenclature, was first used by Leonhart Fuchs and introduced as the standard by Carolus Linnaeus in his 1758 classical work Systema Naturae 10th edition. As a result, it is sometimes called the "binomial nomenclature." At that time, the chief biological theory was that species represented independent acts of creation by God and were therefore considered objectively real and immutable.
In books and articles that use the genus and species names are usually printed in italics. If using "sp." and "spp.," these should not be italicized.
It is surprisingly difficult to define the word "species" in a way that applies to all naturally occurring organisms, and the debate among biologists about how to define "species" and how to identify actual species is called the species problem.
Most textbooks follow Ernst Mayr's definition of a species as all the individual organisms of a natural population that generally interbreed at maturity in the wild and whose interbreeding produces fertile offspring.
Various parts of this definition are there to exclude some unusual or artificial matings:
The typical textbook definition above works well for most multi-celled organisms, but there are several types of situations in which it breaks down:
Horizontal gene transfer makes it even more difficult to define the word "species". There is strong evidence of horizontal gene transfer between very dissimilar groups of procaryotes, and possibly between dissimilar groups of single-celled eucaryotes; and Williamson argues that there is evidence for it in some crustaceans and echinoderms. All definitions of the word "species" assume that an organism gets all its genes from one or two parents which are very like that organism, but horizontal gene transfer makes that assumption false.
Practically, biologists define species as populations of organisms that have a high level of genetic similarity. This may reflect an adaptation to the same niche, and the transfer of genetic material from one individual to others, through a variety of possible means. The exact level of similarity used in such a definition is arbitrary, but this is the most common definition used for organisms that reproduce asexually, such as some plants and microorganisms.
This lack of any clear species concept in microbiology has led to some authors arguing that the term "species" is not useful when studying bacterial evolution. Instead they see genes as moving freely between even distantly-related bacteria, with the entire bacterial domain being a single gene pool.
In the study of sexually reproducing organisms, where genetic material is shared through the process of reproduction, the ability of two organisms to interbreed and produce fertile offspring is generally accepted as a simple indicator that the organisms chare enough genes to be considered members of the same species. Thus a "species" is a group of interbreeding organisms.
This definition can be extended to say that a species is a group of organisms that could potentially interbreed - fish could still be classed as the same species even if they live in different lakes, as long as they could still interbreed were they ever to come into contact with each other. On the other hand, there are many examples of series of three or more distinct populations, where individuals of the population in the middle can interbreed with the populations to either side, but individuals of the populations on either side cannot interbreed. Thus, one could argue that these populations constitute a single species, or two distinct species. This is not a paradox; it is evidence that species are defined by gene frequencies, and thus have fuzzy boundaries.
Consequently, any single, universal definition of "species" is necessarily arbitrary. Instead, biologists have proposed a range of definitions; which definition a biologists uses is a pragmatic choice, depending on the particularities of that biologist's research. Typological species : A group of organisms in which individuals are members of the species if they sufficiently conform to certain fixed properties. The clusters of variations or phenotypes within specimens (i.e. longer and shorter tails) would differentiate the species. This method was used as a "classical" method of determining species, such as with Linnaeus early in evolutionary theory. However, we now know that different phenotypes do not always constitute different species (e.g.: a 4-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies. Morphological species : A population or group of populations that differs morphologically from other populations. For example, we can distinguish between a chicken and a duck because they have different shaped bills and the duck has webbed feet. Species have been defined in this way since well before the beginning of recorded history. This species concept is much criticised because more recent genetic data reveal that genetically distinct populations may look very similar and, contrarily, large morphological differences sometimes exist between very closely-related populations. Nonetheless, most species known have been described solely from morphology. Biological / Isolation species : A set of actually or potentially interbreeding populations. This is generally a useful formulation for scientists working with living examples of the higher taxa like mammals, fish, and birds, but meaningless for organisms that do not reproduce sexually. It does not distinguish between the theoretical possibility of interbreeding and the actual likelihood of gene flow between populations and is thus impractical in instances of allopatric (geographically isolated) populations. The results of breeding experiments done in artificial conditions may or may not reflect what would happen if the same organisms encountered each other in the wild, making it difficult to gauge whether or not the results of such experiments are meaningful in reference to natural populations. Biological / reproductive species : Two organisms that are able to reproduce naturally to produce fertile offspring. Organisms that can reproduce but almost always make infertile hybrids, such as a mule or hinny, are not considered to be the same species. Mate-recognition species : A group of organisms that are known to recognize one another as potential mates. Like the isolation species concept above, it applies only to organisms that reproduce sexually. Unlike the isolation species concept, it focuses specifically on pre-mating reproductive isolation. Phylogenetic (Cladistic)/ Evolutionary / Darwinian species : A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. At some point in the progress of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. Subspecies as such are not recognized under this approach; either a population is a phylogenetic species or it is not taxonomically distinguishable. Ecological species: A set of organisms adapted to a particular set of resources, called a niche, in the environment. According to this concept, populations form the discrete phenetic clusters that we recognize as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters Genetic species : based on similarity of DNA of individuals or populations. Techniques to compare similarity of DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding). Phenetic species: based on phenotypes Recognition species: based on shared reproductive systems, including mating behavior Microspecies : Species that reproduce without meiosis or fertilization so that each generation is genetically identical to the previous generation. See also apomixis. Cohesion species : Most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. This is an expansion of the mate-recognition species concept to allow for post-mating isolation mechanisms; no matter whether populations can hybridize successfully, they are still distinct cohesion species if the amount of hybridization is insufficient to completely mix their respective gene pools. Evolutionarily Significant Unit (ESU) : An evolutionarily significant unit is a population of organisms that is considered distinct for purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several possible definitions, which coincide with definitions of species.
In practice, these definitions often coincide, and the differences between them are more a matter of emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective, or can be applied in all cases without resorting to judgment. Given the complexity of life, some have argued that such an objective definition is in all likelihood impossible, and biologists should settle for the most practical definition. For most vertebrates, this is the biological species concept (BSC), and to a lesser extent (or for different purposes) the phylogenetic species concept (PSC). Many BSC subspecies are considered species under the PSC; the difference between the BSC and the PSC can be summed up insofar as that the BSC defines a species as a consequence of manifest evolutionary history, while the PSC defines a species as a consequence of manifest evolutionary potential. Thus, a PSC species is "made" as soon as an evolutionary lineage has started to separate, while a BSC species starts to exist only when the lineage separation is complete. Accordingly, there can be considerable conflict between alternative classifications based upon the PSC versus BSC, as they differ completely in their treatment of taxa that would be considered subspecies under the latter model (e.g., the numerous subspecies of honey bees).
After thousands of years of use, the concept remains central to biology and a host of related fields, and yet also remains at times ill-defined.
Traditionally, researchers relied on observations of anatomical differences, and on observations of whether different populations were able to interbreed successfully, to distinguish species; both anatomy and breeding behavior are still important to assigning species status. As a result of the revolutionary (and still ongoing) advance in microbiological research techniques, including DNA analysis, in the last few decades, a great deal of additional knowledge about the differences and similarities between species has become available. Many populations which were formerly regarded as separate species are now considered to be a single taxon, and many formerly grouped populations have been split. Any taxonomic level (species, genus, family, etc.) can be synonymized or split, and at higher taxonomic levels, these revisions have been still more profound.
From a taxonomical point of view, groups within a species can be defined as being of a taxon hierarchically lower than a species. In zoology only the subspecies is used, while in botany the variety, subvariety, and form are used as well. In conservation biology, the concept of evolutionary significant units (ESU) is used, which may be define either species or smaller distinct population segments.
In general, for large, complex, organisms that reproduce sexually (such as mammals and birds), one of several variations on the isolation or biological species concept is employed. Often, the distinction between different species, even quite closely related ones, is simple. Horses (Equus caballus) and donkeys (Equus asinus) are easily told apart even without study or training, and yet are so closely related that they can interbreed after a fashion. Because the result, a mule or hinny, is not fertile, they are clearly separate species.
But many cases are more difficult to decide. This is where the isolation species concept diverges from the evolutionary species concept. Both agree that a species is a lineage that maintains its integrity over time, that is diagnosably different from other lineages (else we could not recognise it), is reproductively isolated (else the lineage would merge into others, given the chance to do so), and has a working intra-species recognition system (without which it could not continue). In practice, both also agree that a species must have its own independent evolutionary history—otherwise the characteristics just mentioned would not apply. The species concepts differ in that the evolutionary species concept does not make predictions about the future of the population: it simply records that which is already known. In contrast, the isolation species concept refuses to assign the rank of species to populations that, in the best judgement of the researcher, would recombine with other populations if given the chance to do so.
In theory, it would be possible to recognise even the tiniest of differences as sufficient to delineate a separate species, provided only that the difference is clear and consistent (and that other criteria are met). There is no universal rule to state the smallest allowable difference between two species, but in general, very trivial differences are ignored on the twin grounds of simple practicality, and genetic similarity: if two population groups are so close that the distinction between them rests on an obscure and microscopic difference in morphology, or a single base substitution in a DNA sequence, then a demonstration of restricted gene flow between the populations will probably be difficult in any case.
More typically, one or other of the following requirements must be met:
Sometimes it is not possible to isolate a single difference between species, and several factors must be taken in combination. This is often the case with plants in particular. In eucalypts, for example, Corymbia ficifolia cannot be reliably distinguished from its close relative Corymbia calophylla by any single measure (and sometimes individual trees cannot be definitely assigned to either species), but populations of Corymbia can be clearly told apart by comparing the colour of flowers, bark, and buds, number of flowers for a given size of tree, and the shape of the leaves and fruit.
When using a combination of characteristics to distinguish between populations, it is necessary to use a reasonably small number of factors (if more than a handful are needed, the genetic difference between the populations is likely to be insignificant and is unlikely to endure into the future), and to choose factors that are functionally independent (height and weight, for example, should usually be considered as one factor, not two).
In the earliest works of science, a species was simply an individual organism that represented a group of similar or nearly identical organisms. No other relationships beyond that group were implied. Aristotle used the words genus and species to mean generic and specific categories. Aristotle and other pre-Darwinian scientists took the species to be distinct and unchanging, with an "essence", like the chemical elements. When early observers began to develop systems of organization for living things, they began to place formerly isolated species into a context. Many of these early delineation schemes would now be considered whimsical and these included consanguinity based on color (all plants with yellow flowers) or behavior (snakes, scorpions and certain biting ants).
In the 18th century Carolus Linnaeus classified organisms according to differences in the form of reproductive apparatus. Although his system of classification sorts organisms according to degrees of similarity, it made no claims about the relationship between similar species. At that time, it was still widely believed that there was no organic connection between species, no matter how similar they appeared. This approach also suggested a type of idealism: the notion that each species existed as an "ideal form". Although there are always differences (although sometimes minute) between individual organisms, Linnaeus considered such variation problematic. He strove to identify individual organisms that were exemplary of the species, and considered other non-exemplary organisms to be deviant and imperfect.
By the 19th century most naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, offered one of the first logical arguments against creationism. The new emphasis was on determining how a species could change over time. Lamarck suggested that an organism could pass on an acquired trait to its offspring, i.e., the giraffe's long neck was attributed to generations of giraffes stretching to reach the leaves of higher treetops (this well-known and simplistic example, however, does not do justice to the breadth and subtlety of Lamarck's ideas). With the acceptance of the natural selection idea of Charles Darwin in the 1860s, however, Lamarck's view of goal-oriented evolution, also known as a teleological process, was eclipsed. Recent interest in inheritance of acquired characteristics centers around epigenetic processes, e.g. methylation, that do not affect DNA sequences, but instead alter expression in an inheritable manner. Thus, neo-lamarckism, as it is sometimes termed, is not a challenge to the theory of evolution by natural selection.
Charles Darwin and Alfred Wallace provided what scientists now consider as the most powerful and compelling theory of evolution. Darwin argued that it was populations that evolved, not individuals. His argument relied on a radical shift in perspective from that of Linnaeus: rather than defining species in ideal terms (and searching for an ideal representative and rejecting deviations), Darwin considered variation among individuals to be natural. He further argued that variation, far from being problematic, actually provides the explanation for the existence of distinct species.
Darwin's work drew on Thomas Malthus' insight that the rate of growth of a biological population will always outpace the rate of growth of the resources in the environment, such as the food supply. As a result, Darwin argued, not all the members of a population will be able to survive and reproduce. Those that did will, on average, be the ones possessing variations—however slight—that make them slightly better adapted to the environment. If these variable traits are heritable, then the offspring of the survivors will also possess them. Thus, over many generations, adaptive variations will accumulate in the population, while counter-adaptive will be eliminated.
It should be emphasized that whether a variation is adaptive or non-adaptive depends on the environment: different environments favor different traits. Since the environment effectively selects which organisms live to reproduce, it is the environment (the "fight for existence") that selects the traits to be passed on. This is the theory of evolution by natural selection. In this model, the length of a giraffe's neck would be explained by positing that proto-giraffes with longer necks would have had a significant reproductive advantage to those with shorter necks. Over many generations, the entire population would be a species of long-necked animals.
In 1859, when Darwin published his theory of natural selection, the mechanism behind the inheritance of individual traits was unknown. Although Darwin made some speculations on how traits are inherited (pangenesis), his theory relies only on the fact that inheritable traits exist, and are variable (which makes his accomplishment even more remarkable.) Although Gregor Mendel's paper on genetics was published in 1866, its significance was not recognized. It was not until 1900 that his work was rediscovered by Hugo de Vries, Carl Correns and Erich von Tschermak, who realised that the "inheritable traits" in Darwin's theory are genes.
The theory of the evolution of species through natural selection has two important implications for discussions of species -- consequences that fundamentally challenge the assumptions behind Linnaeus' taxonomy. First, it suggests that species are not just similar, they may actually be related. Some students of Darwin argue that all species are descended from a common ancestor. Second, it supposes that "species" are not homogeneous, fixed, permanent things; members of a species are all different, and over time species change. This suggests that species do not have any clear boundaries but are rather momentary statistical effects of constantly changing gene-frequencies. One may still use Linnaeus' taxonomy to identify individual plants and animals, but one can no longer think of species as independent and immutable.
The rise of a new species from a parental line is called speciation. There is no clear line demarcating the ancestral species from the descendant species.
Although the current scientific understanding of species suggests that there is no rigorous and comprehensive way to distinguish between different species in all cases, biologists continue to seek concrete ways to operationalize the idea. One of the most popular biological definitions of species is in terms of reproductive isolation; if two creatures cannot reproduce to produce fertile offspring, then they are in different species. This definition captures a number of intuitive species boundaries, but it remains imperfect. It has nothing to say about species that reproduce asexually, for example, and it is very difficult to apply to extinct species. Moreover, boundaries between species are often fuzzy: there are examples where members of one population can produce fertile offspring with a second population, and members of the second population can produce fertile offspring with members of a third population, but members of the first and third population cannot produces fertile offspring. Consequently, some people reject this definition of a species.
Richard Dawkins defines two organisms as conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides (The Blind Watchmaker, p. 118). However, most if not all taxonomists would strongly disagree. For example, in many amphibians, most notably in New Zealand's Leiopelma frogs, the genome consists of "core" chromosomes which are mostly invariable and accessory chromosomes, of which exist a number of possible combinations. Even though the chromosome numbers are highly variable between populations, these can interbreed successfully and form a single evolutionary unit. In plants, polyploidy is extremely commonplace with few restrictions on interbreeding; as individuals with an odd number of chromosome sets are usually sterile, depending on the actual number of chromosome sets present, this results in the odd situation where some individuals of the same evolutionary unit can interbreed with certain others and some cannot, with all populations being eventually linked as to form a common gene pool.
The classification of species has been profoundly affected by technological advances that have allowed researchers to determine relatedness based on molecular markers, starting with the comparatively crude blood plasma precipitation assays in the mid-20th century to Charles Sibley's ground-breaking DNA-DNA hybridisation studies in the 1970s leading to DNA sequencing techniques. The results of these techniques caused revolutionary changes in the higher taxonomic categories (such as phyla and classes), resulting in the reordering of many branches of the phylogenetic tree (see also: molecular phylogeny). For taxonomic categories below genera, the results have been mixed so far; the pace of evolutionary change on the molecular level is rather slow, yielding clear differences only after considerable periods of reproductive separation. DNA-DNA hybridization results have led to misleading conclusions, the Pomarine Skua - Great Skua phenomenon being a famous example. Turtles have been determined to evolve with just one-eighth of the speed of other reptiles on the molecular level, and the rate of molecular evolution in albatrosses is half of what is found in the rather closely related storm-petrels. The hybridization technique is now obsolete and is replaced by more reliable computational approaches for sequence comparison. Molecular taxonomy is not directly based on the evolutionary processes, but rather on the overall change brought upon by these processes. The processes that lead to the generation and maintenance of variation such as mutation, crossover and selection are not uniform (see also molecular clock). DNA is only extremely rarely a direct target of natural selection rather than changes in the DNA sequence enduring over generations being a result of the latter; for example, silent transition-transversion combinations would alter the melting point of the DNA sequence, but not the sequence of the encoded proteins and thus are a possible example where, for example in microorganisms, a mutation confers a change in fitness all by itself.