Species
A species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. It can be 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. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour, or ecological niche. In addition, palaeontologists use the concept of the chronospecies since fossil reproduction cannot be examined. The most recent rigorous estimate for the total number of species of eukaryotes is between 8 and 8.7 million. About 14% of these had been described by 2011. All species are given a two-part name, a "binomen". The first part of a binomen is the name of a genus to which the species belongs. The second part is called the specific name or the specific epithet. For example, Boa constrictor is one of the species of the genus Boa, with constrictor being the specific name.
While the definitions given above may seem adequate at first glance, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clonal lineage is potentially a microspecies. Although none of these are entirely satisfactory definitions, and while the concept of species may not be a perfect model of life, it is still a useful tool to scientists and conservationists for studying life on Earth, regardless of the theoretical difficulties. If species were fixed and distinct from one another, there would be no problem, but evolutionary processes cause species to change. This obliges taxonomists to decide, for example, when enough change has occurred to declare that a fossil lineage should be divided into multiple chronospecies, or when populations have diverged to have enough distinct character states to be described as cladistic species.
Species and higher taxa were seen from Aristotle until the 18th century as categories 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 On 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 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.
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. Ernst Mayr emphasised reproductive isolation, but this, like other species concepts, can be hard or even impossible to test for groups of organisms separated in space or time. 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. Wilkins further grouped the species concepts into seven basic kinds of concepts: agamospecies for asexual organisms biospecies for reproductively isolated sexual organisms ecospecies based on ecological niches evolutionary species based on lineage genetic species based on gene pool morphospecies based on form or phenotype and taxonomic species, a species as determined by a taxonomist.Typological or morphological species
A typological species is a group of organisms in which individuals conform to certain fixed properties, so that even pre-literate people often recognise the same taxon as do modern taxonomists. Modern-day field guides and identification websites such as iNaturalist use this concept. The clusters of variations or phenotypes within specimens 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. Species named in this manner are called morphospecies.In the 1970s, Robert R. Sokal, Theodore J. Crovello and Peter Sneath proposed a variation on the morphological species concept, a phenetic species, defined as a set of organisms with a similar phenotype to each other, but a different phenotype from other sets of organisms. It differs from the morphological species concept in including a numerical measure of distance or similarity to cluster entities based on multivariate comparisons of a reasonably large number of phenotypic traits.
Recognition and cohesion species
A mate-recognition species is a group of sexually reproducing organisms that recognise 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 hybridise successfully, they are still distinct cohesion species if the amount of hybridisation is insufficient to completely mix their respective gene pools. A further development of the recognition concept is provided by the biosemiotic concept of species.Genetic similarity and barcode species
Single locus (barcoding)
In microbiology, genes can move freely even between distantly related bacteria, possibly extending to the whole bacterial domain. As a rule of thumb, microbiologists had assumed that members of Bacteria or Archaea with 16S ribosomal RNA gene sequences more similar than 97% to each other need to be checked by DNA–DNA hybridisation to decide if they belong to the same species. This concept was narrowed in 2006 to a similarity of 98.7%.The 16S sequence is an example of a single locus which is simple enough for non-specialists to apply and, in most cases, sufficient to distinguish species. Using a single easy-to-use locus to distinguish taxa is called DNA barcoding. One of the barcodes for eukaryotes is a region of mitochondrial DNA within the gene for cytochrome c oxidase. A database, Barcode of Life Data System, contains DNA barcode sequences from over 190,000 species. However, scientists such as Rob DeSalle have expressed concern that classical taxonomy and DNA barcoding, which they consider a misnomer, need to be reconciled, as they delimit species differently. Genetic introgression mediated by endosymbionts and other vectors can further make barcodes ineffective in the identification of species.
A singular locus can be a good proxy of time of divergence assuming the chosen locus evolved like most of the rest of the genome. This assumption can be broken by horizontal gene transfer affecting the locus itself. Rapid modes of evolution separating biological species over a short timespan would also decouple the species concept from time itself. Among bacteria, there are several cases where very different genomes share 99.9% 16S identity.
Multilocus comparison
Using multiple loci for comparison provides more phylogenetic signal compared to comparing versions of the same loci as more mutations can be captured. As a result, it provides improved taxonomic resolution compared to single-locus comparison, giving results more similar to the expensive "gold standard" of whole genome comparison at a small increase in cost.Even when whole genomes are available, there are good reasons to only compare select genes: many genes are not universally found in all genomes, so they provide limited taxonomic signal while still adding to the computational cost of comparison. In situations like this, tens to hundreds of loci may be extracted from each genome and used together. As with comparisons with fewer loci, marker genes used for this purpose should be genes with low rates of horizontal transfer and gene duplication, few known instances of horizontal transfer, and high occurrence in the sampled genomes. With prokaryotes, marker genes can be used to delimit taxa down to the genus level, with whole-genome comparison reserved to separate species from each other.
Whole genome comparison
The surefire way to capture all gene flow among populations is to compare their entire genomes. The average nucleotide identity method quantifies genetic distance between entire genomes, using regions of about 10,000 base pairs. With enough data from genomes of one genus, algorithms can be used to categorize species, as for Pseudomonas avellanae in 2013, and for all sequenced bacteria and archaea since 2020. Observed ANI values among prokaryotic sequences appear to have an "ANI gap" at 85–95%, suggesting that a genetic boundary suitable for defining a species concept is present.Phylogenetic or cladistic species
A phylogenetic or cladistic species is "the smallest aggregation of populations or lineages diagnosable by a unique combination of character states in comparable individuals ". The empirical basis – observed character states – provides the evidence to support hypotheses about evolutionarily divergent lineages that have maintained their hereditary integrity through time and space. Molecular markers may be used to determine diagnostic genetic differences 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 recognising the numerous fungi species of all the concepts studied. Versions of the phylogenetic species concept that emphasise monophyly or diagnosability may lead to splitting of existing species, for example in Bovidae, by recognising old subspecies as species, despite the fact that there are no reproductive barriers, and populations may intergrade morphologically. Others have called this approach taxonomic inflation, diluting the species concept and making taxonomy unstable. Yet others defend this approach, considering "taxonomic inflation" pejorative and labelling the opposing view as "taxonomic conservatism"; claiming it is politically expedient to split species and recognise smaller populations at the species level, because this means they can more easily be included as endangered in the IUCN red list and can attract conservation legislation and funding.Unlike the biological species concept, a cladistic species does not rely on reproductive isolation – its criteria are independent of processes that are integral in other concepts. Therefore, it applies to asexual lineages. However, it does not always provide clear cut and intuitively satisfying boundaries between taxa, and may require multiple sources of evidence, such as more than one polymorphic locus, to give plausible results.