Species

Classical forms

In his biology, Aristotle used the term γένος (génos) to mean a kind, such as a bird or fish, and εἶδος (eidos) to mean a specific form within a kind, such as (within the birds) the crane, eagle, crow, or sparrow. These terms were translated into Latin as "genus" and "species", though they do not correspond to the Linnean terms thus named; today the birds are a class, the cranes are a family, and the crows a genus. A kind was distinguished by its attributes; for instance, a bird has feathers, a beak, wings, a hard-shelled egg, and warm blood. A form was distinguished by being shared by all its members, the young inheriting any variations they might have from their parents. Aristotle believed all kinds and forms to be distinct and unchanging. His approach remained influential until the Renaissance.

Fixed species

When observers in the Early Modern period began to develop systems of organization for living things, they placed each kind of animal or plant into a context. Many of these early delineation schemes would now be considered whimsical: schemes included consanguinity based on colour (all plants with yellow flowers) or behaviour (snakes, scorpions and certain biting ants). John Ray (1686), an English naturalist, was the first to give a biological definition of the term "species", as follows:

No surer criterion for determining species has occurred to me than the distinguishing features that perpetuate themselves in propagation from seed. Thus, no matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as to distinguish a species... Animals likewise that differ specifically preserve their distinct species permanently; one species never springs from the seed of another nor vice versa.

In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics, and not simply based upon differences. He established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was still widely believed that there was no organic connection between species, no matter how similar they appeared. This view was influenced by European scholarly and religious education, which held that the categories of life are dictated by God, forming an Aristotelian hierarchy, the scala naturae or great chain of being. However, whether or not it was supposed to be fixed, the scala (a ladder) inherently implied the possibility of climbing.

Species that could change

By the 19th century, 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, described the transmutation of species, proposing that a species could change over time, in a radical departure from Aristotelian thinking.

In 1859, Charles Darwin and Alfred Russel Wallace provided a compelling account of evolution and the formation of new species. Darwin argued that it was populations that evolved, not individuals, by natural selection from naturally occurring variation among individuals. This required a new definition of species. Darwin concluded that species are what they appear to be: ideas, provisionally useful for naming groups of interacting individuals. "I look at the term species", he wrote, "as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other ... It does not essentially differ from the word variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for convenience sake."

Common and scientific names

The commonly used names for kinds of organisms are often ambiguous: "cat" could mean the domestic cat, Felis catus, or the cat family, Felidae. Another problem with common names is that they often vary from place to place, so that puma, cougar, catamount, panther, painter and mountain lion all mean Puma concolor in various parts of America, while "panther" may also mean the jaguar (Panthera onca) of Latin America or the leopard (Panthera pardus) of Africa and Asia. In contrast, the scientific names of species are chosen to be unique and universal; they are in two parts used together: the genus as in Puma, and the specific epithet as in concolor.

Species description

A species is given a name when a type specimen is described formally by a scientist, in a paper that assigns it a scientific name. The name becomes a validly published name (in botany) or an available name (in zoology) when the paper is accepted for publication. The type material is provided for other scientists to examine, often in the research collection of a major museum. Scientists are asked to choose names that, in the words of the International Code of Zoological Nomenclature, are "appropriate, compact, euphonious, memorable, and do not cause offence."

Abbreviations

Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." (standing for species pluralis, the Latin for multiple species) in the plural in place of the specific name or epithet (e.g. Canis sp.) This commonly occurs when authors are confident that some individuals belong to a particular genus but are not sure to which exact species they belong, as is common in paleontology. Authors may also use "spp." as a short way of saying that something applies to many species within a genus, but not to all. If scientists mean that something applies to all species within a genus, they use the genus name without the specific name or epithet. The names of genera and species are usually printed in italics. Abbreviations such as "sp." should not be italicized.

Identification codes

Various codes have been devised to provide identifiers for species, including:

Lumping and splitting

The naming of a particular species, including which genus (and higher taxa) it is placed in, is a hypothesis about the evolutionary relationships and distinguishability of that group of organisms. As further information comes to hand, the hypothesis may be confirmed or refuted. Sometimes, especially in the past when communication was more difficult, taxonomists working in isolation have given two distinct names to individual organisms later identified as the same species. When two named species are discovered to be of the same species, the older species name is usually retained, and the newer species name dropped, a process called synonymization, or colloquially, as lumping. Dividing a taxon into multiple, often new, taxa is called splitting. Taxonomists are often referred to as "lumpers" or "splitters" by their colleagues, depending on their personal approach to recognizing differences or commonalities between organisms.

Mayr's biological species concept

Most modern textbooks use Ernst Mayr's definition, known as the Biological Species Concept. It is also called a reproductive or isolation concept. This defines a species as

groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups".

It can be argued that this definition is a natural consequence of the effect of sexual reproduction on the dynamics of natural selection. Mayr's definition excludes unusual or artificial matings that result from deliberate human action, or occur only in captivity, or that involve animals capable of mating but that do not normally do so in the wild.

The species problem

It is difficult to define a species in a way that applies to all organisms. The debate about how to define a species is called the Species Problem. The problem was already current in 1859, when Darwin wrote in On the Origin of Species:

No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.

When Mayr's concept breaks down

A simple textbook definition, following Mayr's concept, works well for most multi-celled organisms, but breaks down in several situations:

Species identification is made difficult by discordance between molecular and morphological investigations; these can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). In addition, horizontal gene transfer (HGT) makes it difficult to define a species. All species definitions assume that an organism acquires its genes from one or two parents very like the "daughter" organism, but that is not what happens in HGT. There is strong evidence of HGT between very dissimilar groups of prokaryotes, and at least occasionally between dissimilar groups of eukaryotes, including some crustaceans and echinoderms.

The evolutionary biologist James Mallet concludes that

there is no easy way to tell whether related geographic or temporal forms belong to the same or different species. Species gaps can be verified only locally and at a point of time. One is forced to admit that Darwin's insight is correct: any local reality or integrity of species is greatly reduced over large geographic ranges and time periods.

Aggregates of microspecies

The species concept is further weakened by the existence of microspecies, groups of organisms, including many plants, with very little genetic variability, usually forming species aggregates. For example, the dandelion Taraxacum officinale and the blackberry Rubus fruticosus are aggregates with many microspecies—perhaps 400 in the case of the blackberry and over 200 in the dandelion, complicated by hybridization, apomixis, and polyploidy, making gene flow between populations difficult to determine, and their taxonomy debatable.

Species complexes occur in insects such as Heliconius butterflies, vertebrates such as Hypsiboas treefrogs, and fungi such as the fly agaric.

Hybridisation

Natural hybridisation presents a challenge to the concept of a reproductively isolated species, as fertile hybrids permit gene flow between two populations. For example, the carrion crow Corvus corone and the hooded crow Corvus cornix appear and are classified as separate species, yet they hybridise freely where their geographical ranges overlap.

Ring species

A ring species is a connected series of neighbouring populations, each of which can sexually interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" population. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing the ring. Ring species thus present a difficulty for any species concept that relies on reproductive isolation. However, ring species are at best rare. Proposed examples include the herring gull-lesser black-backed gull complex around the North pole, the Ensatina eschscholtzii group of 19 populations of salamanders in America, and the greenish warbler in Asia, but there is evidence that none form genuine rings.

Attempts at definition

Biologists and taxonomists have made many attempts to define species, beginning from morphology and moving towards genetics. Early taxonomists such as Linnaeus had no option but to describe what they saw: this was later formalised as the typological or morphological species concept. Mayr emphasised reproductive isolation, but this, like other species concepts, is hard or even impossible to test. Later biologists have tried to refine Mayr's definition with the recognition and cohesion concepts, among others. Many of the concepts are quite similar or overlap, so they are not easy to count: the biologist R. L. Mayden recorded about 24 concepts, and the philosopher of science John Wilkins counted 26.

Typological or morphological species

A typological species is a group of organisms in which individuals conform to certain fixed properties (a type), so that even pre-literate people often recognize the same taxon as do modern taxonomists. The clusters of variations or phenotypes within specimens (i.e. longer or 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, different phenotypes are not necessarily different species (e.g. a four-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies.

Recognition and cohesion species

A mate-recognition species is a group of sexually reproducing organisms that recognize one another as potential mates. Expanding on this to allow for post-mating isolation, a cohesion species is the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion 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.

Vavilovian species

Nikolai Vavilov developed ways to define and conceive of Linnaean species. He saw species as systems, each an integral entity consisting of closely interlinked components. He emphasized the variability within species, relativity of taxonomic criteria and the accumulation of genetic variation within a species. From the evolutionary point of view he compared species to knots in evolutionary chains. Building on V.L. Komarov's aphorism: "a species is a morphological system plus geographic distinctness", in 1930, Vavilov defined a "Linnaean species" as "an isolated complex dynamic morph-physiological system bound in its origin to a certain environment and area".

Genetic similarity

In microbiology, genes can move freely even between distantly related bacteria, possibly extending to the whole bacterial domain. As a rule of thumb, microbiologists have assumed that kinds of Bacteria or Archaea with 16S ribosomal RNA gene sequences more similar than 97% to each other need to be checked by DNA-DNA Hybridization to decide if they belong to the same species or not. This concept was narrowed in 2006 to a similarity of 98.7%.

DNA-DNA hybridization results have however sometimes led to misleading conclusions about species, as with the pomarine skua – great skua.

Evolutionary species

A single evolutionary lineage of organisms within which genes can be shared, and that maintains its integrity with respect to other lineages through both time and space. At some point in the evolution of such a group, some members may diverge from the main population and evolve into a subspecies, a process that may eventually lead to the formation of a new species if isolation (geographical or ecological) is maintained. New species evolve from previous species via a speciation process. A species that gives rise to another species is a paraphyletic species, or paraspecies. The single lineage of ancestor-descendant population which has its own evolutionary tendencies and historical fates and is distinct from other lineages.

Phylogenetic or cladistic species

A phylogenetic or cladistic species is an evolutionarily divergent lineage, one that has maintained its hereditary integrity through time and space. A cladistic species is the smallest group of populations that can be distinguished by a unique set of morphological or genetic traits. Molecular markers may be used to determine genetic similarities in the nuclear or mitochondrial DNA of various species. For example, in a study done on fungi, studying the nucleotide characters using cladistic species produced the most accurate results in recognizing the numerous fungi species of all the concepts studied.

Unlike the Biological Species Concept, a cladistic species does not rely on reproductive isolation, so it is independent of processes that are integral in other concepts. It works for asexual lineages, and can detect recent divergences, which the Morphological Species Concept cannot. However, it does not work in every situation, and may require more than one polymorphic locus to give an accurate result. The concept may lead to splitting of existing species, for example of Bovidae, into many new ones.

Ecological species

An ecological species is 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

A genetic species as defined by Robert Baker and Robert Bradley is a set of genetically isolated interbreeding populations. This is similar to Mayr's Biological Species Concept, but stresses genetic rather than reproductive isolation.

Evolutionarily significant unit

An evolutionarily significant unit (ESU) or "wildlife species" is a population of organisms considered distinct for purposes of conservation.

Phenetic species

A phenetic species is a set of organisms which have a similar phenotype to each other, but a different phenotype from other sets of organisms.

Change

Species are subject to change, whether by evolving into new species, exchanging genes with other species, or by becoming extinct.

Speciation

The evolutionary process by which biological populations evolve to become distinct species is called speciation. Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book The Origin of Species. Speciation depends on a measure of reproductive isolation, a reduced gene flow. This occurs most easily in allopatric speciation, where populations are separated geographically and can diverge gradually as mutations accumulate. Reproductive isolation is threatened by hybridisation, but this can be selected against once a pair of populations have incompatible alleles of the same gene, as described in the Bateson–Dobzhansky–Muller model.

Exchange of genes between species

Horizontal gene transfer between organisms in different species, either through hybridization, antigenic shift, or reassortment, is sometimes an important source of genetic variation. Viruses can transfer genes between species. Bacteria can exchange plasmids with bacteria of other species, including some apparently distantly related ones in different phylogenetic domains, making analysis of their relationships difficult.

Extinction

A species is extinct when the last individual of that species dies, but it may be functionally extinct well before that moment. It is estimated that over 99 percent of all species that ever lived on Earth, some five billion species, are now extinct. Some of these were in mass extinctions such as those at the ends of the Permian, Triassic and Cretaceous periods. Mass extinctions had a variety of causes including volcanic activity, climate change, and changes in oceanic and atmospheric chemistry, and they in turn had major effects on Earth's ecology, atmosphere, land surface, and waters.