species

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, is hard or even impossible to test.{{cite journal |last1=Mallet |first1=James |title=A species definition for the modern synthesis |journal=Trends in Ecology & Evolution |date=1995 |volume=10 |issue=7 |pages=294–299 |doi=10.1016/0169-5347(95)90031-4 |pmid=21237047 |bibcode=1995TEcoE..10..294M }} Later biologists have tried to refine Mayr's definition with the recognition and cohesion concepts, among others.{{cite journal |last1=Masters |first1=J. C. |last2=Spencer |first2=H. G. |title=Why We Need a New Genetic Species Concept |journal=Systematic Zoology |date=1989 |volume=38 |issue=3 |pages=270–279 |doi=10.2307/2992287 |jstor=2992287}} 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,{{cite book |last1=Mayden |first1=R. L. |editor1-last=Claridge |editor1-first=M. F. |editor2-first=H. A. |editor2-last=Dawah |editor3-first=M. R. |editor3-last=Wilson |chapter=A hierarchy of species concepts: the denouement of the species problem |title=The Units of Biodiversity – Species in Practice Special Volume 54 |date=1997 |publisher=Systematics Association}} and the philosopher of science John Wilkins counted 26.{{cite web |title=Species Concepts |url=https://blogs.scientificamerican.com/evo-eco-lab/species-concepts/ |publisher=Scientific American |access-date=14 March 2017 |date=20 April 2012 |url-status=live |archive-url=https://web.archive.org/web/20170314154734/https://blogs.scientificamerican.com/evo-eco-lab/species-concepts/ |archive-date=14 March 2017 |df=dmy-all }} Wilkins further grouped the species concepts into seven basic kinds of concepts: (1) agamospecies for asexual organisms (2) biospecies for reproductively isolated sexual organisms (3) ecospecies based on ecological niches (4) evolutionary species based on lineage (5) genetic species based on gene pool (6) morphospecies based on form or phenotype and (7) taxonomic species, a species as determined by a taxonomist.{{sfn|Zachos|2016|p=79}}

{{anchor|Typological species}}

File:Eurasian_blue_tit_Lancashire.jpgs share the same coloration, unmistakably identifying the morphospecies.{{cite book |last1=Gooders |first1=John |title= Kingfisher Field Guide to the Birds of Britain and Ireland|page=246 |publisher=Kingfisher Books |date=1986 |isbn=978-0-86272-139-8}}]]

A typological species is a group of organisms in which individuals conform to certain fixed properties (a type, which may be defined by a chosen 'nominal species'), so that even pre-literate people often recognise the same taxon as do modern taxonomists.{{cite book |last1=Gould |first1=Stephen Jay |author-link=Stephen Jay Gould |chapter=A Quahog is a Quahog |title=In: The Panda's Thumb: More Reflections in Natural History |location=New York |publisher=W.W. Norton & Company |date=1980 |pages=[https://archive.org/details/pandasthumb000step/page/204 204–213] |isbn=978-0-393-30023-9 |chapter-url=https://archive.org/details/pandasthumb000step/page/204 }}{{cite book |last=Maynard Smith |first=John |author-link=John Maynard Smith |title=Evolutionary Genetics |publisher=Oxford University Press |date=1989 |pages=273–274 |isbn=978-0-19-854215-5}} The clusters of variations or phenotypes within specimens (such as 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 two-winged mother is not a different species). Species named in this manner are called morphospecies.{{cite journal |last=Ruse |first=Michael |author-link=Michael Ruse |title=Definitions of Species in Biology |journal=The British Journal for the Philosophy of Science |volume=20 |issue=2 |pages=97–119 |year=1969 |jstor=686173 |doi=10.1093/bjps/20.2.97|s2cid=121580839 }}{{cite journal |last=Lewin |first=Ralph A. |author-link=Ralph A. Lewin |title=Three Species Concepts |journal=Taxon |year=1981 |volume=30|issue=3 |pages=609–613 |doi=10.2307/1219942|jstor=1219942 |bibcode=1981Taxon..30..609L }}

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.{{harvnb|Claridge|Dawah|Wilson|1997|p=404}} 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.{{cite journal |last=Ghiselin |first=Michael T. |author-link=Michael Ghiselin |title=A Radical Solution to the Species Problem |journal=Systematic Biology |volume=23 |issue=4 |pages=536–544 |year=1974 |doi=10.1093/sysbio/23.4.536|url=https://philpapers.org/rec/GHIARS }}

{{anchor|Recognition species|Cohesion species}}

A mate-recognition species is a group of sexually reproducing organisms that recognise one another as potential mates.Claridge et al.:408–409.{{cite book |last=Paterson |first=H. E. H. |date=1985 |title=Monograph No. 4: The recognition concept of species |chapter=Species and Speciation |editor1-last=Vrba |editor1-first=E. S. |publisher=Transvaal Museum |location=Pretoria}} 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.{{cite encyclopedia |last=Mallet |first=James |author-link=James Mallet |title=Species, Concepts of |url=http://www.ucl.ac.uk/taxome/jim/Sp/species.pdf |publisher=Blackwell |editor1-last=Calow |editor1-first=P. |encyclopedia=Encyclopaedia of Ecology and Environmental Management |pages=709–711 |isbn=978-0-632-05546-3 |url-status=live |archive-url=https://web.archive.org/web/20161019152621/http://www.ucl.ac.uk/taxome/jim/Sp/species.pdf |archive-date=19 October 2016 |df=dmy-all |date=28 September 1999 }} A further development of the recognition concept is provided by the biosemiotic concept of species.{{cite journal |last=Kull |first=Kalevi |author-link=Kalevi Kull |date=2016 |title=The biosemiotic concept of the species |journal=Biosemiotics |volume=9 |pages=61–71 |url=https://www.academia.edu/23574109 |doi=10.1007/s12304-016-9259-2 |s2cid=18470078 |url-status=live |archive-url=https://web.archive.org/web/20180207144820/http://www.academia.edu/23574109/The_Biosemiotic_Concept_of_the_Species |archive-date=7 February 2018 |df=dmy-all }}

{{anchor|Genetic similarity|Barcode species}}

{{See also |Bacterial taxonomy#Species concept}}

File:Cytochrome C Oxidase 1OCC in Membrane 2.png for the cytochrome c oxidase enzyme is used to distinguish species in the Barcode of Life Data Systems database.]]

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 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.{{cite journal |last1=Stackebrandt |first1=E. |last2=Goebel |first2=B. M. |title=Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology |journal=International Journal of Systematic Bacteriology |year=1994 |volume=44 |issue=4 |pages=846–849 |doi=10.1099/00207713-44-4-846 |doi-access=free }} This concept was narrowed in 2006 to a similarity of 98.7%.{{cite journal |last1=Stackebrandt |first1=E. |last2=Ebers |first2=J. |title=Taxonomic parameters revisited: tarnished gold standards |journal=Microbiology Today |year=2006 |volume=33 |issue=4 |pages=152–155 |url=https://microbiologysociety.org/uploads/assets/uploaded/a8800d1f-de21-432d-a5399c13c9ad1643.pdf |url-status=live |archive-url=https://web.archive.org/web/20180325022016/https://microbiologysociety.org/uploads/assets/uploaded/a8800d1f-de21-432d-a5399c13c9ad1643.pdf |archive-date=25 March 2018 |df=dmy-all}}

The average nucleotide identity (ANI) 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,{{cite journal |doi=10.1007/s10142-015-0433-4 |pmid=25722247 |title=Insights from 20 years of bacterial genome sequencing |journal=Functional & Integrative Genomics |volume=15 |issue=2 |pages=141–161 |year=2015 |last1=Land |first1=Miriam |last2=Hauser |first2=Loren |last3=Jun |first3=Se-Ran |last4=Nookaew |first4=Intawat |last5=Leuze |first5=Michael R. |last6=Ahn |first6=Tae-Hyuk |last7=Karpinets |first7=Tatiana |last8=Lund |first8=Ole |last9=Kora |first9=Guruprased |last10=Wassenaar |first10=Trudy |last11=Poudel |first11=Suresh |last12=Ussery |first12=David W. |pmc=4361730}} 50px This article contains quotations from this source, which is available under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International (CC BY 4.0)] {{Webarchive|url=https://web.archive.org/web/20171016050101/https://creativecommons.org/licenses/by/4.0/ |date=16 October 2017 }} license. and for all sequenced bacteria and archaea since 2020.{{cite journal |last1=Parks |first1=D. H. |last2=Chuvochina |first2=M. |last3=Chaumeil |first3=P. A. |last4=Rinke |first4=C. |last5=Mussig |first5=A. J. |last6=Hugenholtz |first6=P. |title=A complete domain-to-species taxonomy for Bacteria and Archaea |journal=Nature Biotechnology |date=September 2020 |volume=38 |issue=9 |pages=1079–1086 |doi=10.1038/s41587-020-0501-8 |pmid=32341564 |url=https://www.researchgate.net/publication/340954053 |biorxiv=10.1101/771964 |s2cid=216560589 }} Observed ANI values among sequences appear to have an "ANI gap" at 85–95%, suggesting that a genetic boundary suitable for defining a species concept is present.{{cite journal |last1=Rodriguez-R |first1=Luis M. |last2=Jain |first2=Chirag |last3=Conrad |first3=Roth E. |last4=Aluru |first4=Srinivas |last5=Konstantinidis |first5=Konstantinos T. |title=Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species" |journal=Nature Communications |date=7 July 2021 |volume=12 |issue=1 |page=4060 |doi=10.1038/s41467-021-24129-1 |doi-access=free|pmid=34234115 |pmc=8263725 |bibcode=2021NatCo..12.4060R }}

DNA barcoding has been proposed as a way to distinguish species suitable even for non-specialists to use.{{cite web |title=What Is DNA Barcoding? |url=http://www.barcodeoflife.org/content/about/what-dna-barcoding |publisher=Barcode of Life |access-date=11 October 2017 |url-status=live |archive-url=https://web.archive.org/web/20170701081215/http://www.barcodeoflife.org/content/about/what-dna-barcoding |archive-date=1 July 2017 |df=dmy-all }} One of the barcodes 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.{{cite journal |last1=Ratnasingham |first1=Sujeevan |last2=Hebert |first2=Paul D. N. |title=BOLD: The Barcode of Life Data System |journal=Molecular Ecology Notes |year=2007 |volume=7 |issue=3 |pages=355–364 |doi=10.1111/j.1471-8286.2007.01678.x |pmid=18784790 |pmc=1890991}}{{cite journal |last=Stoeckle |first=Mark |title=DNA Barcoding Ready for Breakout |journal=GeneWatch |date=November–December 2013 |volume=26 |issue=5 |url=http://www.councilforresponsiblegenetics.org/genewatch/GeneWatchPage.aspx?pageId=510 |access-date=25 March 2018 |archive-date=3 April 2014 |archive-url=https://web.archive.org/web/20140403101448/http://www.councilforresponsiblegenetics.org/genewatch/genewatchpage.aspx?pageid=510 }} 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.{{cite journal |last1=DeSalle |first1=R. |last2=Egan |first2=M. G. |last3=Siddall |first3=M. |title=The unholy trinity: taxonomy, species delimitation and DNA barcoding |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=360 |issue=1462 |year=2005 |pages=1905–1916 |doi=10.1098/rstb.2005.1722 |pmid=16214748 |pmc=1609226}} Genetic introgression mediated by endosymbionts and other vectors can further make barcodes ineffective in the identification of species.{{cite journal |last1=Whitworth |first1=T. L. |last2=Dawson |first2=R. D. |last3=Magalon |first3=H. |last4=Baudry |first4=E. |doi=10.1098/rspb.2007.0062 |pmid=17472911 |pmc=2493573 |title=DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae) |journal=Proceedings of the Royal Society B: Biological Sciences |volume=274 |issue=1619 |pages=1731–1739 |year=2007 }}

{{anchor |Phylogenetic species |Cladistic species |Phylogenetic species concept}}

{{anchor |Phylogenetic, cladistic, or evolutionary species}}

File:Cladistic species.svg

A phylogenetic or cladistic species is "the smallest aggregation of populations (sexual) or lineages (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts)".{{cite journal |last1=Nixon |first1=K. C. |last2=Wheeler |first2=Q. D. |year=1990 |title=An amplification of the phylogenetic species concept |journal=Cladistics |volume=6 |issue=3 |pages=211–223 |doi=10.1111/j.1096-0031.1990.tb00541.x |s2cid=84095773 |doi-access=free }} 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.Wheeler, Quentin D.; Platnick, Norman I. 2000. The phylogenetic species concept (sensu Wheeler & Platnick). In: {{harvnb|Wheeler|Meier2000|pp=55–69}}{{cite journal |last1=Giraud |first1=T. |author2=Refrégier, G. |author3=Le Gac, M. |author4=de Vienne, D. M. |author5=Hood, M. E. |year=2008 |title=Speciation in Fungi |journal=Fungal Genetics and Biology |volume=45 |issue=6 |pages=791–802 |doi=10.1016/j.fgb.2008.02.001|pmid=18346919 }}{{cite book |last=Bernardo |first=J. |year=2011 |chapter=A critical appraisal of the meaning and diagnosability of cryptic evolutionary diversity, and its implications for conservation in the face of climate change |pages=380–438 |title=Climate Change, Ecology and Systematics. Systematics Association Special Series |editor1-first=T. |editor1-last=Hodkinson |editor2-first=M. |editor2-last=Jones |editor3-first=S. |editor3-last=Waldren |editor4-first=J. |editor4-last=Parnell |publisher=Cambridge University Press |isbn=978-0-521-76609-8}}.Brower, Andrew V. Z. and Randall T. Schuh. (2021). Biological Systematics: Principles and Applications. Cornell University Press, Ithaca, NY. Molecular markers may be used to determine diagnostic genetic differences in the nuclear or mitochondrial DNA of various species.{{cite journal |author1=Giraud, T. |author2=Refrégier, G. |author3=Le Gac, M. |author4=de Vienne, D. M. |author5=Hood, M. E. |year=2008 |title=Speciation in Fungi |journal=Fungal Genetics and Biology |volume=45 |issue=6 |pages=791–802 |doi=10.1016/j.fgb.2008.02.001|pmid=18346919 }}{{cite journal |author1=Taylor, J. W. |author2=Jacobson, D. J. |author3=Kroken, S. |author4=Kasuga, T. |author5=Geiser, D. M. |author6=Hibbett, D. S. |author7=Fisher, M. C. |year=2000 |title=Phylogenetic species recognition and species concepts in fungi |journal=Fungal Genetics and Biology |volume=31 |issue=1 | pages=21–32 |doi=10.1006/fgbi.2000.1228 |pmid=11118132|s2cid=2551424 }} 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.{{cite journal|last1=Taylor |first1=J. W. |last2=Turner |first2=E. |last3=Townsend |first3=J. P. |last4=Dettman |first4=J. R. |last5=Jacobson |first5=D. |title=Eukaryotic microbes, species recognition and the geographic limits of species: Examples from the kingdom Fungi |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |volume=361 |issue=1475 |pages=1947–1963 |year=2006 |pmc=1764934 |doi=10.1098/rstb.2006.1923 |pmid=17062413}} Versions of the phylogenetic species concept that emphasise monophyly or diagnosability{{sfn|Zachos|2016|pp=91–92}} 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.Groves, C.; Grubb, P. 2011. Ungulate taxonomy. Baltimore, MD: The Johns Hopkins University Press. Others have called this approach taxonomic inflation, diluting the species concept and making taxonomy unstable.{{cite journal |last1=Heller |first1=R. |author2=Frandsen, P. |author3=Lorenzen, E. D. |author4=Siegismund, H. R. |year=2013 |title=Are there really twice as many bovid species as we thought? |journal=Systematic Biology |volume=62 |issue=3 |pages=490–493 |doi=10.1093/sysbio/syt004 |pmid=23362112 |doi-access=free|hdl=10400.7/566 |hdl-access=free }} 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.{{cite journal |last1=Cotterill |first1=F. |author2=Taylor, P. |author3=Gippoliti, S. |year=2014 |title=Why one century of phenetics is enough: Response to 'are there really twice as many bovid species as we thought?' |journal=Systematic Biology |volume=63 |issue=5|pages=819–832 |doi=10.1093/sysbio/syu003|display-authors=etal |pmid=24415680 |doi-access=free }}

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.

An evolutionary species, suggested by George Gaylord Simpson in 1951, is "an entity composed of organisms which maintains its identity from other such entities through time and over space, and which has its own independent evolutionary fate and historical tendencies".{{cite journal |last1=Laporte |first1=L. O. F. |title=Simpson on species |doi=10.1007/BF01058629 |journal=Journal of the History of Biology |volume=27 |issue=1 |pages=141–159 |year=1994 |pmid=11639257|s2cid=34975382 }} This differs from the biological species concept in embodying persistence over time. Wiley and Mayden stated that they see the evolutionary species concept as "identical" to Willi Hennig's species-as-lineages concept, and asserted that the biological species concept, "the several versions" of the phylogenetic species concept, and the idea that species are of the same kind as higher taxa are not suitable for biodiversity studies (with the intention of estimating the number of species accurately). They further suggested that the concept works for both asexual and sexually-reproducing species.{{harvnb|Wheeler|Meier|2000|pp=70–92, 146–160, 198–208}} A version of the concept is Kevin de Queiroz's "General Lineage Concept of Species".{{cite book |last=de Queiroz |first=Kevin |year=1998 |chapter=The general lineage concept of species, species criteria, and the process of speciation |pages=57–75 |editor1=D. J. Howard |editor2=S. H. Berlocher |title=Endless forms: species and speciation |publisher=Oxford University Press }}

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 recognise as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters.{{cite book |last=Ridley |first=Mark |author-link=Mark Ridley (zoologist) |title=Evolution |publisher=Blackwell Science |chapter=The Idea of Species |edition=2nd |page=719 |isbn=978-0-86542-495-1}}

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.{{cite journal |last1=Baker |first1=Robert J. |last2=Bradley |first2=Robert D. |title=Speciation in Mammals and the Genetic Species Concept |journal=Journal of Mammalogy |date=2006 |volume=87 |issue=4 |pages=643–662 |doi=10.1644/06-MAMM-F-038R2.1 |pmid=19890476 |pmc=2771874}} In the 21st century, a genetic species could be established by comparing DNA sequences. Earlier, other methods were available, such as comparing karyotypes (sets of chromosomes) and allozymes (enzyme variants).{{cite journal |last1=Baker |first1=Robert J. |last2=Bradley |first2=Robert D. |title=Speciation in Mammals and the Genetic Species Concept |journal=Journal of Mammalogy |volume=87 |issue=4 |year=2006 |pages=643–662 |doi=10.1644/06-MAMM-F-038R2.1|pmid=19890476 |pmc=2771874 }}

An evolutionarily significant unit (ESU) or "wildlife species"{{cite web |author=Government of Canada. Committee on the Status of Endangered Wildlife in Canada |url=http://www.cosepac.gc.ca/eng/sct0/assessment_process_e.cfm |title=COSEWIC's Assessment Process and Criteria |publisher=Cosepac.gc.ca |access-date=7 April 2015 |archive-url=https://web.archive.org/web/20150412232417/http://www.cosepac.gc.ca/eng/sct0/assessment_process_e.cfm |archive-date=12 April 2015 |df=dmy-all }} is a population of organisms considered distinct for purposes of conservation.{{cite web |last1=DeWeerdt |first1=Sarah |title=What Really is an Evolutionarily Significant Unit? |url=http://conservationmagazine.org/2002/07/what-really-is-an-evolutionarily-significant-unit/ |publisher=University of Washington |access-date=1 December 2016 |date=29 July 2002 |url-status=live |archive-url=https://web.archive.org/web/20170205155325/http://www.conservationmagazine.org/2002/07/what-really-is-an-evolutionarily-significant-unit/ |archive-date=5 February 2017 |df=dmy-all}}

File:Chronospecies.svg is defined in a single lineage (solid line) whose morphology changes with time. At some point, palaeontologists judge that enough change has occurred that two species (A and B), separated in time and anatomy, once existed.]]

{{main|Chronospecies}}

In palaeontology, with only comparative anatomy (morphology) and histology{{cite book |last1=de Buffrénil |first1=Vivian |last2=de Ricqlès |first2=Armand J |last3=Zylberberg |first3=Louise |last4=Padian |first4=Kevin |last5=Laurin |first5=Michel |last6=Quilhac |first6=Alexandra |title=Vertebrate skeletal histology and paleohistology |date=2021 |publisher=CRC Press |location=Boca Raton, FL |isbn=978-1-351-18957-6 |pages=xii + 825|url=https://books.google.com/books?id=tJcwEAAAQBAJ&dq=Vertebrate+Skeletal+Histology+and+Paleohistology&pg=PT8}} from fossils as evidence, the concept of a chronospecies can be applied. During anagenesis (evolution, not necessarily involving branching), some palaeontologists seek to identify a sequence of species, each one derived from the phyletically extinct one before through continuous, slow and more or less uniform change. In such a time sequence, some palaeontologists assess how much change is required for a morphologically distinct form to be considered a different species from its ancestors.{{cite web |title=Chronospecies |url=http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095611471 |publisher=Oxford Reference |access-date=12 January 2018 |url-status=live |archive-url=https://web.archive.org/web/20141001151656/http://www.oxfordreference.com/view/10.1093/oi/authority.20110803095611471 |archive-date=1 October 2014 |df=dmy-all}}{{cite web |last1=Carr |first1=Steven M. |title=Evolutionary species and chronospecies |url=https://www.mun.ca/biology/scarr/Evolutionary_vs_Chronospecies.html |publisher=Memorial University Newfoundland and Labrador |access-date=12 January 2018 |date=2005 |url-status=live |archive-url=https://web.archive.org/web/20160310075417/http://www.mun.ca/biology/scarr/Evolutionary_vs_Chronospecies.html |archive-date=10 March 2016 |df=dmy-all}}{{cite journal |last=Dzik |first=J. |year=1985 |title=Typologic versus population concepts of chronospecies: implications for ammonite biostratigraphy |journal=Acta Palaeontologica Polonica |volume=30 |issue=1–2 |pages=71–92 |url=https://www.app.pan.pl/archive/published/app30/app30-071.pdf |url-status=live |archive-url=https://web.archive.org/web/20170313080626/http://www.app.pan.pl/archive/published/app30/app30-071.pdf |archive-date=13 March 2017 |df=dmy-all}}{{cite book |last1=O'Brien |first1=Michael J. |last2=Lyman|first2=R. Lee |title=Applying Evolutionary Archaeology: A Systematic Approach |url=https://books.google.com/books?id=IkAOBwAAQBAJ&pg=PA146 |year=2007|publisher=Springer |isbn=978-0-306-47468-2|pages=146–149|url-status=live|archive-url=https://web.archive.org/web/20180207144819/https://books.google.com/books?id=IkAOBwAAQBAJ&pg=PA146|archive-date=7 February 2018|df=dmy-all}}

{{main|Viral quasispecies}}

Viruses have enormous populations, are doubtfully living since they consist of little more than a string of DNA or RNA in a protein coat, and mutate rapidly. All of these factors make conventional species concepts largely inapplicable.{{cite journal |last=Van Regenmortel |first=Marc H. V. |title=Logical puzzles and scientific controversies: The nature of species, viruses and living organisms |journal=Systematic and Applied Microbiology |volume=33 |issue=1 |pages=1–6|year=2010 |doi=10.1016/j.syapm.2009.11.001 |pmid=20005655 |bibcode=2010SyApM..33....1V }} A viral quasispecies is a group of genotypes related by similar mutations, competing within a highly mutagenic environment, and hence governed by a mutation–selection balance. It is predicted that a viral quasispecies at a low but evolutionarily neutral and highly connected (that is, flat) region in the fitness landscape will outcompete a quasispecies located at a higher but narrower fitness peak in which the surrounding mutants are unfit, "the quasispecies effect" or the "survival of the flattest". There is no suggestion that a viral quasispecies resembles a traditional biological species.{{cite journal |last1=van Nimwegen |first1=Erik |last2=Crutchfield |first2=James P. |last3=Huynen |first3=Martijn |title=Neutral evolution of mutational robustness |date=August 1999 |journal=PNAS |volume=96 |issue=17 |pages=9716–9720 |doi=10.1073/pnas.96.17.9716 |pmid=10449760 |pmc=22276 |bibcode=1999PNAS...96.9716V |arxiv=adap-org/9903006 |doi-access=free }}{{cite journal |last1=Wilke |first1=Claus O. |last2=Wang |first2=Jia Lan |last3=Ofria |first3=Charles |last4=Lenski |first4=Richard E. |last5=Adami |first5=Christoph |title=Evolution of digital organisms at high mutation rates leads to survival of the flattest |journal=Nature |volume=412 |issue=6844 |year=2001 |pages=331–333 |doi=10.1038/35085569|pmid=11460163 |url=https://authors.library.caltech.edu/56230/2/412331a0_S1.pdf |bibcode=2001Natur.412..331W |s2cid=1482925 }}{{cite journal |last1=Elena |first1=S. F. |last2=Agudelo-Romero |first2=P. |last3=Carrasco |first3=P. |last4=Codoñer |first4=F. M. |last5=Martín |first5=S. |last6=Torres-Barceló |first6=C. |last7=Sanjuán |first7=R. |display-authors=3 |title=Experimental evolution of plant RNA viruses |journal=Heredity |volume=100 |issue=5 |year=2008 |pages=478–483 |doi=10.1038/sj.hdy.6801088 |pmid=18253158 |pmc=7094686 |doi-access=free |bibcode=2008Hered.100..478E }} The International Committee on Taxonomy of Viruses has since 1962 developed a universal taxonomic scheme for viruses; this has stabilised viral taxonomy.{{Cite book |title=Virus Taxonomy Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses |last1=King |first1=Andrew M.Q. |last2=Lefkowitz |first2=E. |last3=Adams |first3=M. J. |last4=Carstens |first4=E. B. |publisher=Elsevier |year=2012 |isbn=978-0-12-384684-6 |url=http://www.sciencedirect.com/science/book/9780123846846#ancp4 |access-date=13 April 2017 |archive-url=https://web.archive.org/web/20171210163802/http://www.sciencedirect.com/science/book/9780123846846#ancp4 |archive-date=10 December 2017 |url-status=live }}{{cite journal |last1=Fauquet |first1=C. M. |last2=Fargette |first2=D. |title=International Committee on Taxonomy of Viruses and the 3,142 unassigned species |journal=Virology Journal |volume=2 |page=64 |year=2005 |pmid=16105179 |pmc=1208960 |doi=10.1186/1743-422X-2-64 |doi-access=free }}{{cite journal |last=Gibbs |first=A. J. |title= Viral taxonomy needs a spring clean; its exploration era is over |journal=Virology Journal |volume=10 |page=254 |year=2013 |pmid= 23938184 |pmc=3751428 |doi=10.1186/1743-422X-10-254 |doi-access=free }}

File:Ernst Mayr PLoS.jpg proposed the widely used Biological Species Concept of reproductive isolation in 1942.]]

Most modern textbooks make use of Ernst Mayr's 1942 definition,{{cite book |last=Mayr |first=Ernst |author-link=Ernst Mayr |year=1942 |title=Systematics and the Origin of Species |url=https://archive.org/details/systematicsorigi0000mayr_p8z7 |url-access=registration |publisher=Columbia University Press |place=New York}}Wheeler, pp. 17–29 known as the biological species concept, as a basis for further discussion on the definition of species. It is also called a reproductive or isolation concept. This defines a species as{{cite journal |last=de Queiroz |first=K. |title=Ernst Mayr and the modern concept of species |journal=PNAS |volume=102 |issue=Supplement 1 |pages=6600–6607 |year=2005 |pmid=15851674 |pmc=1131873 |doi=10.1073/pnas.0502030102|doi-access=free|bibcode=2005PNAS..102.6600D }}

{{blockquote|groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups.}}

It has been argued that this definition is a natural consequence of the effect of sexual reproduction on the dynamics of natural selection.{{cite journal |last1=Hopf |first1=F. A. |last2=Hopf |first2=F. W. |date=1985 |title=The role of the Allee effect on species packing |journal=Theoretical Population Biology |volume=27 |issue=1 |pages=27–50 |doi=10.1016/0040-5809(85)90014-0|bibcode=1985TPBio..27...27H }}{{cite journal |last1=Bernstein |first1=H. |last2=Byerly |first2=H. C. |last3=Hopf |first3=F. A. |last4=Michod |first4=R.E. |title=Sex and the emergence of species |journal=Journal of Theoretical Biology |volume=117 |issue=4 |pages=665–690 |date=1985 |pmid=4094459 |doi=10.1016/S0022-5193(85)80246-0|bibcode=1985JThBi.117..665B }}{{cite book |last1=Bernstein |first1=Carol |last2=Bernstein |first2=Harris |title=Aging, sex, and DNA repair |publisher=Academic Press |location=Boston |year=1991 |isbn=978-0-12-092860-6}}{{cite book |last=Michod |first=Richard E. |title=Eros and Evolution: A Natural Philosophy of Sex |url=https://archive.org/details/erosevolutionnat0000mich |url-access=registration |publisher=Addison-Wesley |year=1995 |isbn=978-0-201-44232-8 }} Mayr's use of the adjective "potentially" has been a point of debate; some interpretations exclude unusual or artificial matings that occur only in captivity, or that involve animals capable of mating but that do not normally do so in the wild.

It is difficult to define a species in a way that applies to all organisms.{{Citation|title=Fuzzy species revisited |last=Hanage |first=William P. |journal=BMC Biology |year=2013 |volume=11 |issue=41 |page=41 |doi=10.1186/1741-7007-11-41 |pmid=23587266 |pmc=3626887 |doi-access=free }} The debate about species concepts is called the species problem.{{cite journal |last=Koch |first=H. |year=2010 |title=Combining morphology and DNA barcoding resolves the taxonomy of Western Malagasy Liotrigona Moure, 1961 |journal=African Invertebrates |volume=51 |issue=2 |pages=413–421 |doi=10.5733/afin.051.0210 |doi-access=free |url=https://www.uthfa.com/wp-content/uploads/2016/08/Koch_AFRICAN_INVERTEBRATES_2010_51_413-421.pdf |url-status=live |archive-url=https://web.archive.org/web/20161201213741/https://www.uthfa.com/wp-content/uploads/2016/08/Koch_AFRICAN_INVERTEBRATES_2010_51_413-421.pdf |archive-date=1 December 2016 |df=dmy-all}}{{cite journal |last=De Queiroz |first=K. |title=Species concepts and species delimitation |journal=Systematic Biology |volume=56 |issue=6 |pages=879–886 |year=2007 |pmid=18027281 |doi=10.1080/10635150701701083|doi-access=free }}{{cite journal |author1=Fraser, C. |author2=Alm, E. J. |author3=Polz, M. F. |author4=Spratt, B. G. |author5=Hanage, W. P. |title=The bacterial species challenge: making sense of genetic and ecological diversity |journal=Science |volume=323 |issue=5915 |pages=741–746 |date=2009 |pmid=19197054 |doi=10.1126/science.1159388 |bibcode=2009Sci...323..741F |s2cid=15763831 }}{{Closed access}} The problem was recognised even in 1859, when Darwin wrote in On the Origin of Species:

{{blockquote|I was much struck how entirely vague and arbitrary is the distinction between species and varieties.{{cite wikisource|chapter=Chapter II|wslink=On the Origin of Species (1859)|plaintitle=On the Origin of Species (1859)|last=|first=|year=|publisher=|page=|wspage=|scan=}}}}

He went on to write:

{{blockquote|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.{{cite web |url=http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F373&pageseq=59 |title=Darwin 1859 Chapter II, p. 59 |publisher=Darwin-online.org.uk |access-date=25 November 2012 |url-status=live |archive-url=https://web.archive.org/web/20121021034500/http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F373&pageseq=59 |archive-date=21 October 2012 |df=dmy-all }}}}

File:Inoceramus cripsii Creta sup Bergamo.JPGs are limited to morphological evidence when deciding whether fossil life-forms like these Inoceramus bivalves formed a separate species.]]

Many authors have argued that a simple textbook definition, following Mayr's concept, works well for most multi-celled organisms, but breaks down in several situations:

• When organisms reproduce asexually, as in single-celled organisms such as bacteria and other prokaryotes,{{cite journal |doi=10.1038/nrmicro1236 |pmid=16138101 |title=Opinion: Re-evaluating prokaryotic species |journal=Nature Reviews Microbiology |volume=3 |issue=9 |pages=733–9 |year=2005 |last1=Gevers |first1=Dirk |last2=Cohan |first2=Frederick M. |last3=Lawrence |first3=Jeffrey G. |last4=Spratt |first4=Brian G. |last5=Coenye |first5=Tom |last6=Feil |first6=Edward J. |last7=Stackebrandt |first7=Erko|last8=De Peer |first8=Yves Van |last9=Vandamme |first9=Peter |last10=Thompson |first10=Fabiano L. |last11=Swings |first11=Jean|s2cid=41706247 |url=https://biblio.ugent.be/publication/329526/file/3072252 }} and parthenogenetic or apomictic multi-celled organisms. DNA barcoding and phylogenetics are commonly used in these cases.{{cite book |last=Templeton |first=A. R. |year=1989 |title=Speciation and its Consequences |chapter=The meaning of species and speciation: A genetic perspective |publisher=Sinauer Associates |editor1-first=D. |editor1-last=Otte |editor2-first=J. A. |editor2-last=Endler |pages=3–27}}{{cite book |author1=Edward G. Reekie |author2=Fakhri A. Bazzaz |title=Reproductive allocation in plants |url=https://books.google.com/books?id=_KJdaiLKAogC&pg=PA99 |year=2005 |publisher=Academic Press |isbn=978-0-12-088386-8 |page=99 |url-status=live |archive-url=https://web.archive.org/web/20130617224832/http://books.google.com/books?id=_KJdaiLKAogC&pg=PA99 |archive-date=17 June 2013 |df=dmy-all }}{{Cite journal |last1=Rosselló-Mora |first1=Ramon |last2=Amann |first2=Rudolf |date=January 2001 |title=The species concept for prokaryotes |journal=FEMS Microbiology Reviews |volume=25 |issue=1 |pages=39–67 |doi=10.1111/j.1574-6976.2001.tb00571.x |pmid=11152940 |df=dmy-all |doi-access=free }} The term quasispecies is sometimes used for rapidly mutating entities like viruses.{{Cite journal |last1=Andino |first1=Raul |last2=Domingo |first2=Esteban |title=Viral quasispecies |journal=Virology |volume=479–480 |pages=46–51 |doi=10.1016/j.virol.2015.03.022 |pmid=25824477 |df=dmy-all |pmc=4826558 |year=2015 }}{{Cite book |last1=Biebricher |first1=C. K. |last2=Eigen |first2=M. |chapter=What is a Quasispecies? |title=Quasispecies: Concept and Implications for Virology |volume=299 |year=2006 |publisher=Springer |isbn=978-3-540-26397-5 |series=Current Topics in Microbiology and Immunology |pages=1–31 |doi=10.1007/3-540-26397-7_1|pmid=16568894 }}
• When scientists do not know whether two morphologically similar groups of organisms are capable of interbreeding; this is the case with all extinct life-forms in palaeontology, as breeding experiments are not possible.{{cite journal |last=Teueman |first=A. E. |title=The Species-Concept in Palaeontology |journal=Geological Magazine |date=2009 |volume=61 |issue=8 |pages=355–360 |doi=10.1017/S001675680008660X |url=https://www.cambridge.org/core/journals/geological-magazine/article/div-classtitlethe-species-concept-in-palaeontologydiv/A203CDD72F8979A98B134274082C1A1D# |url-status=live |archive-url=https://web.archive.org/web/20170314155325/https://www.cambridge.org/core/journals/geological-magazine/article/div-classtitlethe-species-concept-in-palaeontologydiv/A203CDD72F8979A98B134274082C1A1D |archive-date=14 March 2017 |df=dmy-all |bibcode=1924GeoM...61..355T |s2cid=84339122 }}
• When hybridisation permits substantial gene flow between species.{{sfn|Zachos|2016|p=101}}
• In ring species, when members of adjacent populations in a widely continuous distribution range interbreed successfully but members of more distant populations do not.{{sfn|Zachos|2016|pp=156–157}}

{{multiple image

|align=right

|width = 150

|image1 = Willow Warbler Phylloscopus trochilus.jpg

|alt1 = Willow warbler

|image2 = Common Chiff-Chaff - Italy S4E1681 (19081363189) (cropped).jpg

|alt2 = Chiffchaff

|footer = The willow warbler and chiffchaff are almost identical in appearance but do not interbreed.

}}

Species identification is made difficult by discordance between molecular and morphological investigations; these can be categorised 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).{{cite journal |year=2014 |title=How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth |journal=BioEssays |volume=36 |issue=10 |pages=950–959 |doi=10.1002/bies.201400056 |last1=Lahr |first1=D. J. |last2=Laughinghouse |first2=H. D. |author3=Oliverio, A. M. |author4=Gao, F. |author5=Katz, L. A. |pmid=25156897 |pmc=4288574}} 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.{{cite journal |last=Bapteste |first=E. |date=May 2005 |title=Do orthologous gene phylogenies really support tree-thinking? |journal=BMC Evolutionary Biology |volume=5 |issue=33 |page=33 |doi=10.1186/1471-2148-5-33 |display-authors=etal |pmid=15913459 |pmc=1156881 |doi-access=free |bibcode=2005BMCEE...5...33B }} There is strong evidence of HGT between very dissimilar groups of prokaryotes, and at least occasionally between dissimilar groups of eukaryotes,{{cite web |url=http://bioinfosu.okstate.edu/MG/MGW3/MG334.html |last=Melcher |first=Ulrich |date=2001 |title=Molecular genetics: Horizontal gene transfer |publisher=Oklahoma State University |archive-url=https://web.archive.org/web/20160304071146/http://bioinfosu.okstate.edu/MG/MGW3/MG334.html |archive-date=4 March 2016 |df=dmy-all }} including some crustaceans and echinoderms.{{cite book |last=Williamson |first=David I. |title=The Origins of Larvae |publisher=Kluwer |year=2003 |isbn=978-1-4020-1514-4}}

The evolutionary biologist James Mallet concludes that

{{blockquote|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.}}

The botanist Brent Mishler{{cite book |last=Mishler |first=Brent D. |title=Species problems and beyond: contemporary issues in philosophy and practice |date=2022 |publisher=CRC Press, Taylor & Francis Group |isbn=978-0-367-85560-4 |editor1=Wilkins, John S. |publication-place=Boca Raton |chapter=Ecology, evolution, and systematics in a post-species world |oclc=1273727987 |author-link=Brent Mishler |editor2=Zachos, Frank E. |editor3=Pavlinov, Igor}} argued that the species concept is not valid, notably because gene flux decreases gradually rather than in discrete steps, which hampers objective delimitation of species.{{cite book |last=Mishler |first=Brent D. |editor1-last=Wilson |editor1-first=R. |chapter=Getting Rid of Species? |title=Species: New Interdisciplinary Essays |date=1999 |publisher=MIT Press |pages=307–315 |url=https://pdfs.semanticscholar.org/672e/7dbe0b756ec853fdb0a3580aca4dffb6f64b.pdf |isbn=978-0-262-73123-2 |url-status=live |archive-url=https://web.archive.org/web/20180110174246/https://pdfs.semanticscholar.org/672e/7dbe0b756ec853fdb0a3580aca4dffb6f64b.pdf |archive-date=10 January 2018 |df=dmy-all }} Indeed, complex and unstable patterns of gene flux have been observed in cichlid teleosts of the East African Great Lakes.{{cite journal |last1=Salzburger |first1=Walter |title=Understanding explosive diversification through cichlid fish genomics |journal=Nature Reviews Genetics |date=November 2018 |volume=19 |issue=11 |pages=705–717 |doi=10.1038/s41576-018-0043-9 |pmid=30111830 |s2cid=52008986 |language=en |issn=1471-0064}} Wilkins argued that "if we were being true to evolution and the consequent phylogenetic approach to taxa, we should replace it with a 'smallest clade' idea" (a phylogenetic species concept).{{cite book |last=Wilkins |first=John S. |title=Species problems and beyond: contemporary issues in philosophy and practice |date=2022 |publisher=CRC Press, Taylor & Francis Group |isbn=978-0-367-85560-4 |editor1=Wilkins, John S. |publication-place=Boca Raton |chapter=The Good Species |oclc=1273727987 |editor2=Zachos, Frank E. |editor3=Pavlinov, Igor}} Mishler and Wilkins{{cite journal |last1=Mishler |first1=Brent D. |author1-link=Brent Mishler |last2=Wilkins |first2=John S. |title=The Hunting of the SNaRC: A Snarky Solution to the Species Problem |journal=Philosophy, Theory, and Practice in Biology |publisher=University of Michigan Library |volume=10 |issue=20220112 |year=2018 |doi=10.3998/ptpbio.16039257.0010.001 |doi-access=free |hdl=2027/spo.16039257.0010.001 |hdl-access=free }} and others{{cite book |last1=Laurin |first1=Michel |title=The Advent of PhyloCode: The Continuing Evolution of Biological Nomenclature |date=3 August 2023 |publisher=CRC Press |isbn=978-1-003-09282-7 |page=xv + 209 |doi=10.1201/9781003092827 |url=https://www.taylorfrancis.com/books/mono/10.1201/9781003092827/advent-phylocode-michel-laurin}} concur with this approach, even though this would raise difficulties in biological nomenclature. Wilkins cited the ichthyologist Charles Tate Regan's early 20th century remark that "a species is whatever a suitably qualified biologist chooses to call a species". Wilkins noted that the philosopher Philip Kitcher called this the "cynical species concept",{{cite journal |last=Kitcher |first=Philip |author-link=Philip Kitcher |date=June 1984 |title=Species |journal=Philosophy of Science |volume=51 |issue=2 |pages=308–333 |doi=10.1086/289182 |s2cid=224836299 |quote=I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists.}} and arguing that far from being cynical, it usefully leads to an empirical taxonomy for any given group, based on taxonomists' experience. Other biologists have gone further and argued that we should abandon species entirely, and refer to the "Least Inclusive Taxonomic Units" (LITUs),{{cite journal |last1=Pleijel |first1=F. |last2=Rouse |first2=G. W. |title=Least-inclusive taxonomic unit: a new taxonomic concept for biology |journal=Proceedings of the Royal Society of London. Series B: Biological Sciences |date=22 March 2000 |volume=267 |issue=1443 |pages=627–630 |doi=10.1098/rspb.2000.1048 |pmid=10787169 |pmc=1690571 |language=en |issn=0962-8452}} a view that would be coherent with current evolutionary theory.

{{main|Species complex}}

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.{{cite book |last=Heywood |first=V. H. |year=1962 |title=Symposium on Biosystematics, Montreal, October 1962 |chapter=The 'species aggregate' in theory and practice |editor1-last=Heywood |editor1-first=V. H. |editor2-last=Löve |editor2-first=Á. |pages=26–36}} 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,{{cite book |last=Pimentel |first=David |title=Biological Invasions: Economic and Environmental Costs of Alien Plant, Animal, and Microbe Species |url=https://books.google.com/books?id=90jRBQAAQBAJ&pg=PA92 |year=2014 |publisher=CRC Press |isbn=978-1-4200-4166-8 |page=92 |url-status=live |archive-url=https://web.archive.org/web/20180207144819/https://books.google.com/books?id=90jRBQAAQBAJ&pg=PA92 |archive-date=7 February 2018 |df=dmy-all }} complicated by hybridisation, apomixis and polyploidy, making gene flow between populations difficult to determine, and their taxonomy debatable.{{cite journal |last=Jarvis |first=C. E. |year=1992 |title=Seventy-Two Proposals for the Conservation of Types of Selected Linnaean Generic Names, the Report of Subcommittee 3C on the Lectotypification of Linnaean Generic Names |journal=Taxon |volume=41 |issue=3 |pages=552–583 |jstor=1222833 |doi=10.2307/1222833|bibcode=1992Taxon..41..552J }}{{cite journal |last=Wittzell |first=Hakan |year=1999 |title=Chloroplast DNA variation and reticulate evolution in sexual and apomictic sections of dandelions |journal=Molecular Ecology |volume=8 |pages=2023–2035 |doi=10.1046/j.1365-294x.1999.00807.x |pmid=10632854 |issue=12 |bibcode=1999MolEc...8.2023W |s2cid=25180463 }}{{cite journal |last=Dijk |first=Peter J. van |year=2003 |title=Ecological and evolutionary opportunities of apomixis: insights from Taraxacum and Chondrilla |journal=Philosophical Transactions of the Royal Society B |volume=358 |pages=1113–1121 |doi=10.1098/rstb.2003.1302 |pmid=12831477 |issue=1434 |pmc=1693208}} Species complexes occur in insects such as Heliconius butterflies,{{cite journal |last1=Mallet |first1=James |author1-link=James Mallet |last2=Beltrán |first2=M. |last3=Neukirchen |first3=W. |last4=Linares |first4=M. |title=Natural hybridization in heliconiine butterflies: the species boundary as a continuum |year=2007 |journal=BMC Evolutionary Biology |volume=7 |issue=1 |page=28 |doi=10.1186/1471-2148-7-28 |doi-access=free |pmid=17319954 |pmc=1821009|bibcode=2007BMCEE...7...28M }} vertebrates such as Hypsiboas treefrogs,{{cite journal |last1=Ron |first1=Santiago |last2=Caminer |first2=Marcel |title=Systematics of treefrogs of the Hypsiboas calcaratus and Hypsiboas fasciatus species complex (Anura, Hylidae) with the description of four new species |journal=ZooKeys |issue=370 |year=2014 |pages=1–68 |doi=10.3897/zookeys.370.6291 |pmid=24478591 |pmc=3904076|bibcode=2014ZooK..370....1C |doi-access=free }} and fungi such as the fly agaric.{{cite journal |last1=Geml |first1=J. |last2=Tulloss |first2=R. E. |last3=Laursen |first3=G. A. |last4=Sasanova |first4=N. A. |last5=Taylor |first5=D. L. |year=2008 |title=Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete |journal=Molecular Phylogenetics and Evolution |volume=48 |issue=2 |pages=694–701 |doi=10.1016/j.ympev.2008.04.029 |pmid=18547823|bibcode=2008MolPE..48..694G |s2cid=619242 }}

File:Ripe, ripening, and green blackberries.jpg|Blackberries belong to any of hundreds of microspecies of the Rubus fruticosus species aggregate.

File:Heliconius mimicry.png|The butterfly genus Heliconius contains many similar species.

File:Systematics-of-treefrogs-of-the-Hypsiboas-calcaratus-and-Hypsiboas-fasciatus-species-complex-(Anura-ZooKeys-370-001-g009.jpg|The Hypsiboas calcaratus–fasciatus species complex contains at least six species of treefrog.

{{main|Hybrid (biology)}}

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 can hybridise where their geographical ranges overlap.{{cite web |title=Defining a species |url=http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_41 |publisher=University of California Berkeley |access-date=12 March 2017 |url-status=live |archive-url=https://web.archive.org/web/20170313042614/http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_41 |archive-date=13 March 2017 |df=dmy-all }}

File:Krähe_65(loz) (cropped).JPG|Carrion crow

File:Corvus cornix (Scops).jpg|Hybrid with dark belly

File:Wrona_Siwa.jpg|Hooded crow

{{main|Ring species}}

A ring species is a connected series of neighbouring populations, each of which can sexually interbreed with adjacent 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.{{sfn|Zachos|2016|p=188}} 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.{{cite book |last=Stamos |first=David N. |title=The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology |url=https://books.google.com/books?id=KT02AAAAQBAJ&pg=PA330 |date=2003 |publisher=Lexington Books |isbn=978-0-7391-6118-0 |page=330 |url-status=live |archive-url=https://web.archive.org/web/20170312134720/https://books.google.com/books?id=KT02AAAAQBAJ&pg=PA330 |archive-date=12 March 2017 |df=dmy-all }} 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,{{cite journal |doi=10.1093/sysbio/41.3.273 |title=Evolutionary Relationships Within the Ensatina eschscholtzii Complex Confirm the Ring Species Interpretation |journal=Systematic Biology |volume=41 |issue=3 |pages=273–291 |year=1992 |last1=Moritz |first1=C. |last2=Schneider |first2=C. J. |last3=Wake |first3=D. B. |url=http://theantlife.com/wp-content/uploads/2014/03/Mortiz-etal-1992_Ring-species-interpretation-confirmed-in-salamanders.pdf |url-status=live |archive-url=https://web.archive.org/web/20180112160100/http://theantlife.com/wp-content/uploads/2014/03/Mortiz-etal-1992_Ring-species-interpretation-confirmed-in-salamanders.pdf|archive-date=12 January 2018|df=dmy-all}} and the greenish warbler in Asia,{{cite journal|doi=10.1126/science.1105201 |pmid=15662011 |title=Speciation by Distance in a Ring Species |journal=Science |volume=307 |issue=5708 |pages=414–6 |year=2005 |last1=Irwin |first1=D. E. |last2=Bensch |first2=Staffan |last3=Irwin |first3=Jessica H. |last4=Price |first4=Trevor D. |bibcode=2005Sci...307..414I |s2cid=18347146 }} but many so-called ring species have turned out to be the result of misclassification leading to questions on whether there really are any ring species.{{cite journal |doi=10.1016/j.jcz.2007.07.004 |title=Ring species – Do they exist in birds? |journal=Zoologischer Anzeiger|volume=246 |issue=4 |pages=315–324 |year=2007 |last1=Martens |first1=Jochen |last2=Päckert |first2=Martin|bibcode=2007ZooAn.246..315M }}{{cite journal |author1=Alcaide, M. |author2=Scordato, E. S. C. |author3=Price, T. D. |author4=Irwin, D. E. |date=2014 |title=Genomic divergence in a ring species complex |journal=Nature |volume=511 |issue=7507|pages=83–85 |doi=10.1038/nature13285 |pmid=24870239|bibcode=2014Natur.511...83A|hdl=10261/101651 |s2cid=4458956 |hdl-access=free }}{{cite journal |last1=Liebers |first1=Dorit |last2=Knijff |first2=Peter de |last3=Helbig |first3=Andreas J. |title=The herring gull complex is not a ring species |journal= Proceedings of the Royal Society of London. Series B: Biological Sciences|date=2004 |volume=271 |issue=1542 |pages=893–901 |doi=10.1098/rspb.2004.2679 |pmc=1691675 |pmid=15255043}}{{cite journal |last=Highton |first=R. |date=1998 |title=Is Ensatina eschscholtzii a ring species? |journal=Herpetologica |volume=54 |issue=2 |pages=254–278 |jstor=3893431 }}

File:Ring species seagull.svg|Seven "species" of Larus gulls interbreed in a ring around the Arctic.

File:PT05 ubt.jpeg|Opposite ends of the ring: a herring gull (Larus argentatus) (front) and a lesser black-backed gull (Larus fuscus) in Norway

File:Greenish Warbler Sikkim India 11.05.2014.jpg|A greenish warbler, Phylloscopus trochiloides

File:Greenish warbler ring.svg|Presumed evolution of five "species" of greenish warblers around the Himalayas

File:Mountain-lion-01623.jpg.]]

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 (except for some inter-code homonyms); they are in two parts used together: the genus as in Puma, and the specific epithet as in concolor.{{cite web |title=A Word About Species Names ... |url=http://www.sms.si.edu/irlspec/NamSpecies.htm |publisher=Smithsonian Marine Station at Fort Pierce |access-date=11 March 2017 |url-status=live |archive-url=https://web.archive.org/web/20170324161039/http://www.sms.si.edu/IRLSpec/NamSpecies.htm |archive-date=24 March 2017 |df=dmy-all }}{{cite news |last1=Hone |first1=Dave |title=What's in a name? Why scientific names are important |url=https://www.theguardian.com/science/lost-worlds/2013/jun/19/dinosaurs-fossils |access-date=11 March 2017 |work=The Guardian |date=19 June 2013 |url-status=live |archive-url=https://web.archive.org/web/20170215220511/https://www.theguardian.com/science/lost-worlds/2013/jun/19/dinosaurs-fossils |archive-date=15 February 2017 |df=dmy-all }}

File:Lacerta plica holotype - ZooKeys-355-049-g005.jpg (holotype) of Lacerta plica, described by Linnaeus in 1758]]

{{main|Species description}}

A species is given a taxonomic name when a type specimen is described formally, in a publication that assigns it a unique scientific name. The description typically provides means for identifying the new species, which may not be based solely on morphology{{Cite journal |last1=Lawley |first1=Jonathan W. |last2=Gamero-Mora |first2=Edgar |last3=Maronna |first3=Maximiliano M. |last4=Chiaverano |first4=Luciano M. |last5=Stampar |first5=Sérgio N. |last6=Hopcroft |first6=Russell R. |last7=Collins |first7=Allen G. |last8=Morandini |first8=André C. |date=2022-09-29 |title=Morphology is not always useful for diagnosis, and that's ok: Species hypotheses should not be bound to a class of data. Reply to Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590) |url=https://sajs.co.za/article/view/14495 |journal=South African Journal of Science |volume=118 |issue=9/10 |doi=10.17159/sajs.2022/14495 |s2cid=252562185 |doi-access=free }} (see cryptic species), differentiating it from other previously described and related or confusable species and provides a validly published name (in botany) or an available name (in zoology) when the paper is accepted for publication. The type material is usually held in a permanent repository, often the research collection of a major museum or university, that allows independent verification and the means to compare specimens.One example of an abstract of an article naming a new species can be found at {{cite journal |title=Methylobacterium cerastii sp. nov., a novel species isolated from the leaf surface of Cerastium holosteoides |first1=S. |last1=Wellner |first2=N. |last2=Lodders |first3=P. |last3=Kämpfer |year=2012 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=62 |issue=Pt 4 |pages=917–924 |doi=10.1099/ijs.0.030767-0 |pmid=21669927 |doi-access=free }}{{citation |last=Hitchcock |first=A. S. |year=1921 |title=The Type Concept in Systematic Botany |journal=American Journal of Botany |volume=8 |issue=5 |pages=251–255 |jstor=2434993 |doi=10.2307/2434993|url=https://www.biodiversitylibrary.org/part/314424 }}{{cite web |last1=Nicholson |first1=Dan H. |title=Botanical nomenclature, types, & standard reference works |url=http://botany.si.edu/references/botlinks/dhntyp.htm |publisher=Smithsonian National Museum of Natural History, Department of Botany |access-date=17 November 2015 |url-status=live |archive-url=https://web.archive.org/web/20150916184608/http://botany.si.edu/references/botlinks/dhntyp.htm |archive-date=16 September 2015 |df=dmy-all }} Describers of new species 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".{{cite web|access-date=18 June 2011|url=http://www.nhm.ac.uk/hosted-sites/iczn/code/|title=International Code of Zoological Nomenclature, Recommendation 25C|url-status=live|archive-url=https://web.archive.org/web/20110608184753/http://www.nhm.ac.uk/hosted-sites/iczn/code/|archive-date=8 June 2011|df=dmy-all}}

{{main|Open nomenclature}}

Books and articles sometimes intentionally do not identify species fully, using the abbreviation "sp." in the singular or "spp." (standing for species pluralis, 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. However, abbreviations such as "sp." should not be italicised.

When a species' identity is not clear, a specialist may use "cf." before the epithet to indicate that confirmation is required. The abbreviations "nr." (near) or "aff." (affine) may be used when the identity is unclear but when the species appears to be similar to the species mentioned after.{{cite book |last=Winston |first=Judith E. |title=Describing species. Practical taxonomic procedure for biologists |publisher=Columbia University Press |place=New York|year=1999 |pages=141–144}}

With the rise of online databases, codes have been devised to provide identifiers for species that are already defined, including:

• National Center for Biotechnology Information (NCBI) employs a numeric 'taxid' or Taxonomy identifier, a "stable unique identifier", e.g., the taxid of Homo sapiens is 9606.{{cite web |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Home – Taxonomy – NCBI |publisher=Ncbi.nlm.nih.gov |date=19 October 2012 |access-date=25 November 2012 |url-status=live |archive-url=https://web.archive.org/web/20180207144820/https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock |archive-date=7 February 2018 |df=dmy-all }}
• Kyoto Encyclopedia of Genes and Genomes (KEGG) employs a three- or four-letter code for a limited number of organisms; in this code, for example, H. sapiens is simply hsa.{{cite web |url=http://www.genome.jp/kegg/catalog/org_list.html |title=KEGG Organisms: Complete Genomes |publisher=Genome.jp |access-date=25 November 2012 |url-status=live |archive-url=https://web.archive.org/web/20121014160440/http://www.genome.jp/kegg/catalog/org_list.html |archive-date=14 October 2012 |df=dmy-all }}
• UniProt employs an "organism mnemonic" of not more than five alphanumeric characters, e.g., HUMAN for H. sapiens.{{cite web |url=https://www.uniprot.org/help/taxonomy |title=Taxonomy |website=Uniprot.org |access-date=25 November 2012 |url-status=live |archive-url=https://web.archive.org/web/20121127091404/http://www.uniprot.org/help/taxonomy |archive-date=27 November 2012 |df=dmy-all }}
• Integrated Taxonomic Information System (ITIS) provides a unique number for each species. The LSID for Homo sapiens is urn:lsid:catalogueoflife.org:taxon:4da6736d-d35f-11e6-9d3f-bc764e092680:col20170225.{{cite web |title=ITIS: Homo sapiens |url=http://www.catalogueoflife.org/col/details/species/id/e3b90576561f93a8ac8b59e185b01511/synonym/ee0f23e7dd7ddbf69de58c0abba12e5b |publisher=Catalogue of Life |access-date=11 March 2017 |url-status=live |archive-url=https://web.archive.org/web/20170312194754/http://www.catalogueoflife.org/col/details/species/id/e3b90576561f93a8ac8b59e185b01511/synonym/ee0f23e7dd7ddbf69de58c0abba12e5b |archive-date=12 March 2017 |df=dmy-all }}

{{main|Lumpers and splitters}}

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 corroborated 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 species names are discovered to apply to the same species, the older species name is given priority and usually retained, and the newer name considered as a junior synonym, a process called synonymy. 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 recognising differences or commonalities between organisms.{{cite journal |last=Simpson |first=George Gaylord |author-link=George Gaylord Simpson |title=The Principles of Classification and a Classification of Mammals |journal=Bulletin of the American Museum of Natural History |volume=85 |page=23 |year=1945}}{{cite journal |last=Chase |first=Bob |title=Upstart Antichrist |journal=History Workshop Journal |volume=60 |issue=1 |date=2005 |pages=202–206|doi=10.1093/hwj/dbi042|s2cid=201790420 }} The circumscription of taxa, considered a taxonomic decision at the discretion of cognizant specialists, is not governed by the Codes of Zoological or Botanical Nomenclature, in contrast to the PhyloCode, and contrary to what is done in several other fields, in which the definitions of technical terms, like geochronological units and geopolitical entities, are explicitly delimited.{{cite journal |last1=Laurin |first1=Michel |title=The PhyloCode: The logical outcome of millennia of evolution of biological nomenclature? |journal=Zoologica Scripta |date=23 July 2023 |volume=52 |issue=6 |pages=543–555 |doi=10.1111/zsc.12625 |s2cid=260224728 |language=en |issn=0300-3256|url=https://hal.science/hal-04225307v1/file/Laurin%202023%20Logical%20outcome%20Zool.%20Scr%20hal.pdf }}

{{main|Sensu}}

The nomenclatural codes that guide the naming of species, including the ICZN for animals and the ICN for plants, do not make rules for defining the boundaries of the species. Research can change the boundaries, also known as circumscription, based on new evidence. Species may then need to be distinguished by the boundary definitions used, and in such cases the names may be qualified with sensu stricto ("in the narrow sense") to denote usage in the exact meaning given by an author such as the person who named the species, while the antonym sensu lato ("in the broad sense") denotes a wider usage, for instance including other subspecies. Other abbreviations such as "auct." ("author"), and qualifiers such as "non" ("not") may be used to further clarify the sense in which the specified authors delineated or described the species.{{cite web |last=Wilson |first=Philip |title=sensu stricto, sensu lato |url=http://www.treeterms.co.uk/definitions/sensu-stricto-sensu-lato |website=AZ of tree terms |date=2016 |access-date=9 January 2018 |url-status=live |archive-url=https://web.archive.org/web/20180110054734/http://www.treeterms.co.uk/definitions/sensu-stricto-sensu-lato |archive-date=10 January 2018 |df=dmy-all }}{{cite web |title=Glossary: sensu |url=http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?booksection=glossary&nfv=true |publisher=International Commission on Zoological Nomenclature |access-date=9 January 2018 |url-status=live |archive-url=https://web.archive.org/web/20170802164704/http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?booksection=glossary&nfv=true |archive-date=2 August 2017 |df=dmy-all }}

{{anchor|Reproductive species}}

{{anchor|Isolation species}}

{{anchor|Biological Species Concept}}

Species are subject to change, whether by evolving into new species, exchanging genes with other species, merging with other species or by becoming extinct.{{sfn|Zachos|2016|pp=77–96}}

{{main|Speciation}}

The evolutionary process by which biological populations of sexually-reproducing organisms evolve to become distinct or reproductively isolated as species is called speciation.{{cite journal |last=Cook |first=Orator F. |author-link=Orator F. Cook |date=30 March 1906 |title=Factors of species-formation |journal=Science |volume=23 |issue=587 |pages=506–507 |doi=10.1126/science.23.587.506 |pmid=17789700|bibcode=1906Sci....23..506C |url=https://zenodo.org/record/1447954 }}{{cite journal |last=Cook |first=Orator F. |author-link=Orator F. Cook |date=November 1908 |title=Evolution Without Isolation |journal=The American Naturalist |volume=42 |issue=503 |pages=727–731 |doi=10.1086/279001|bibcode=1908ANat...42..727C |s2cid=84565616 }} Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book The Origin of Species.{{cite journal |last=Via |first=Sara |date=16 June 2009 |title=Natural selection in action during speciation |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=106 |issue=Suppl 1 |pages=9939–9946 |doi=10.1073/pnas.0901397106 |pmc=2702801 |pmid=19528641 |df=dmy-all |bibcode=2009PNAS..106.9939V |doi-access=free }} 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.{{cite journal |last1=Barton |first1=N. H. |title=What role does natural selection play in speciation? |journal=Philosophical Transactions of the Royal Society B |date=June 2010 |volume=365 |issue=1547 |doi=10.1098/rstb.2010.0001 |pmid=20439284 |pmc=2871892 |pages=1825–1840}} A different mechanism, phyletic speciation, involves one lineage gradually changing over time into a new and distinct form (a chronospecies), without increasing the number of resultant species.{{cite journal |last1=Mayr |first1=Ernst |author-link=Ernst Mayr |title=Speciation and Macroevolution |journal=Evolution |volume=36 |issue=6 |year=1982 |pages=1119–1132 |doi=10.1111/j.1558-5646.1982.tb05483.x |pmid=28563569 |s2cid=27401899 |doi-access=free }}

{{main|Horizontal gene transfer}}

File:Tree Of Life (with horizontal gene transfer).svgs between widely separated species complicate the phylogeny of bacteria.]]

Horizontal gene transfer between organisms of different species, either through hybridisation, 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, and weakening the concept of a bacterial species.{{cite journal |last=Pennisi |first=Elizabeth |author-link=Elizabeth Pennisi |page=335 |volume=334–335 |journal=Science |year=2004 |title=Researchers Trade Insights about Gene Swapping |url=http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf |archive-url=https://web.archive.org/web/20060218071130/http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf |archive-date=18 February 2006 |df=dmy-all}}{{cite journal |doi=10.1016/j.tig.2004.02.004 |pmid=15041172 |url=http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf |title=Cladogenesis, coalescence and the evolution of the three domains of life |journal=Trends in Genetics|volume=20 |issue=4 |pages=182–187 |year=2004 |last1=Zhaxybayeva |first1=Olga |last2=Peter Gogarten |first2=J. |url-status=live |archive-url=https://web.archive.org/web/20090326181517/http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf |archive-date=26 March 2009 |df=dmy-all}}{{cite journal |doi=10.1111/bij.12872 |title=Speciation through the looking-glass |journal=Biological Journal of the Linnean Society |volume=120 |issue=2 |pages=480–488 |year=2017 |last1=Vaux |first1=Felix |last2=Trewick |first2=Steven A. |last3=Morgan-Richards |first3=Mary |doi-access=free }}

Louis-Marie Bobay and Howard Ochman suggest, based on analysis of the genomes of many types of bacteria, that they can often be grouped "into communities that regularly swap genes", in much the same way that plants and animals can be grouped into reproductively isolated breeding populations. Bacteria may thus form species, analogous to Mayr's biological species concept, consisting of asexually reproducing populations that exchange genes by homologous recombination.{{cite journal |last=Venton |first=Danielle |title=Highlight: Applying the Biological Species Concept across All of Life |journal=Genome Biology and Evolution |volume=9 |issue=3 |year=2017 |pages=502–503 |doi=10.1093/gbe/evx045|pmid=28391326 |pmc=5381533 }}{{cite journal |last1=Bobay |first1=Louis-Marie |last2=Ochman |first2=Howard |title=Biological Species Are Universal across Life's Domains |journal=Genome Biology and Evolution |volume=9 |issue=3 |year=2017 |pages=491–501 |doi=10.1093/gbe/evx026|pmid=28186559 |pmc=5381558 }}

{{further|Extinction|Extinction event}}

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 Ordovician, Devonian, 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.{{cite book |editor1-last=Kunin |editor1-first=W. E. |editor2-last=Gaston |editor2-first=Kevin |title=The Biology of Rarity: Causes and consequences of rare–common differences |url=https://books.google.com/books?id=4LHnCAAAQBAJ&pg=PA110 |date=1996 |publisher=Springer |isbn=978-0-412-63380-5 |url-status=live |archive-url=https://web.archive.org/web/20150905164104/https://books.google.com/books?id=4LHnCAAAQBAJ&pg=PA110&lpg=PA110&dq |archive-date=5 September 2015 |df=dmy-all }}{{cite book |last1=Stearns |first1=Beverly Peterson |last2=Stearns |first2=Stephen C. |title=Watching, from the Edge of Extinction |location=New Haven, London |url=https://books.google.com/books?id=0BHeC-tXIB4C&q=99%20percent |year=2000 |publisher=Yale University Press |isbn=978-0-300-08469-6 |page=preface x |df=dmy-all }} Another form of extinction is through the assimilation of one species by another through hybridization. The resulting single species has been termed as a "compilospecies".{{sfn|Zachos|2016|p=82}}

Biologists and conservationists need to categorise and identify organisms in the course of their work. Difficulty assigning organisms reliably to a species constitutes a threat to the validity of research results, for example making measurements of how abundant a species is in an ecosystem moot. Surveys using a phylogenetic species concept reported 48% more species and accordingly smaller populations and ranges than those using nonphylogenetic concepts; this was termed "taxonomic inflation",{{cite journal |doi=10.1111/jzs.12088 |title=Taxonomic inflation, the Phylogenetic Species Concept and lineages in the Tree of Life – a cautionary comment on species splitting |journal=Journal of Zoological Systematics and Evolutionary Research |volume=53 |issue=2 |pages=180–184 |year=2015 |last1=Zachos |first1=Frank E.|doi-access=free }} which could cause a false appearance of change to the number of endangered species and consequent political and practical difficulties.{{cite journal |first1=Paul-Michael |last1=Agapow |first2=Olaf R. P. |last2=Bininda-Emonds |author3-link=Keith A. Crandall |first3=Keith A. |last3=Crandall |first4=John L. |last4=Gittleman |first5=Georgina M. |last5=Mace |first6=Jonathon C. |last6=Marshall |first7=Andy |last7=Purvis |journal=The Quarterly Review of Biology |volume=79 |issue=2 |year=2004 |pages=161–179 |title=The Impact of Species Concept on Biodiversity Studies |url=http://www.efn.uncor.edu/departamentos/divbioeco/divveg1/micologia/practico%20micologia/trabajo%20de%20campo/2-The%20impact%20of%20species%20concept%20on%20biodiversity%20studies.%20Agapow%20et%20al.%20(2004).pdf |doi=10.1086/383542 |pmid=15232950 |jstor=10.1086/383542 |url-status=live |archive-url=https://web.archive.org/web/20180111110303/http://www.efn.uncor.edu/departamentos/divbioeco/divveg1/micologia/practico%20micologia/trabajo%20de%20campo/2-The%20impact%20of%20species%20concept%20on%20biodiversity%20studies.%20Agapow%20et%20al.%20(2004).pdf |archive-date=11 January 2018 |df=dmy-all |citeseerx=10.1.1.535.2974 |s2cid=2698838 }} Some observers claim that there is an inherent conflict between the desire to understand the processes of speciation and the need to identify and to categorise.{{cite journal |last=Hey |first=Jody |date=July 2001 |title=The mind of the species problem |journal=Trends in Ecology and Evolution |volume=16 |issue=7 |pages=326–329 |doi=10.1016/S0169-5347(01)02145-0 |pmid=11403864}}

Conservation laws in many countries make special provisions to prevent species from going extinct. Hybridization zones between two species, one that is protected and one that is not, have sometimes led to conflicts between lawmakers, land owners and conservationists. One of the classic cases in North America is that of the protected northern spotted owl which hybridises with the unprotected California spotted owl and the barred owl; this has led to legal debates.{{cite book |chapter-url=http://digitalcommons.unl.edu/usgsstaffpub/708 |title=The Endangered Species Act at Thirty, Volume 2: Conserving Biodiversity in Human-Dominated Landscapes |last1=Haig |first1=Susan M. |last2=Allendorf |first2=F.W. |publisher=Island Press |year=2006 |editor1-last=Scott |editor1-first=J. Michael |place=Washington |pages=150–163 |chapter=Hybrids and Policy |editor2-last=Goble |editor2-first=D. D. |editor3-first=Frank W. |editor3-last=Davis |url-status=live |archive-url=https://web.archive.org/web/20180207144821/https://digitalcommons.unl.edu/usgsstaffpub/708/ |archive-date=7 February 2018 |df=dmy-all }}

It has been argued, that since species are not comparable, simply counting them is not a valid measure of biodiversity; alternative measures of phylogenetic biodiversity have been proposed.{{cite journal |last1=Faith |first1=Daniel P. |title=Conservation evaluation and phylogenetic diversity |journal=Biological Conservation |date=1 January 1992 |volume=61 |issue=1 |pages=1–10 |doi=10.1016/0006-3207(92)91201-3 |bibcode=1992BCons..61....1F |issn=0006-3207}}{{cite journal |last1=Vane-Wright |first1=R. I. |last2=Humphries |first2=C. J. |last3=Williams |first3=P. H. |date=1991 |title=What to protect? – systematics and the agony of choice |journal=Biological Conservation |volume=55 |issue=3 |pages=235–254 |doi=10.1016/0006-3207(91)90030-D|bibcode=1991BCons..55..235V }}

{{main|Aristotle's biology}}

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. More importantly, in Aristotle's works, the terms γένος (génos) and εἶδος (eidos) are relative; a taxon that is considered an eidos in a given context can be considered a génos in another, and be further subdivided into eide (plural of eidos).{{cite book |last1=Pellegrin |first1=Pierre |title=Aristotle's classification of animals: biology and the conceptual unity of the Aristotelian corpus |date=1986 |publisher=Univ. of California Pr |location=Berkeley, Calif. |isbn=0-520-05502-0 |page=xiv + 235}}{{cite journal |last1=Laurin |first1=Michel |last2=Humar |first2=Marcel |title=Phylogenetic signal in characters from Aristotle's History of Animals |journal=Comptes Rendus Palevol |date=10 January 2022 |issue=1 |doi=10.5852/cr-palevol2022v21a1 |s2cid=245863171 |language=fr|doi-access=free }} His approach remained influential until the Renaissance,{{cite book |last=Leroi |first=Armand Marie |author-link=Armand Marie Leroi |title=The Lagoon: How Aristotle Invented Science |title-link=Aristotle's Lagoon |publisher=Bloomsbury |date=2014 |isbn=978-1-4088-3622-4 |pages=88–90}} and still, to a lower extent, today.{{cite journal |last1=Rigato |first1=Emanuele |last2=Minelli |first2=Alessandro |title=The great chain of being is still here |journal=Evolution: Education and Outreach |date=28 June 2013 |volume=6 |issue=1 |page=18 |doi=10.1186/1936-6434-6-18 |url=http://www.evolution-outreach.com/content/6/1/18 |issn=1936-6434 |doi-access=free }}

{{Main|Great chain of being}}

File:John Ray from NPG.jpg believed that species breed true and do not change, even though variations exist.]]

File:Carl von Linné.jpg created the binomial system for naming 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, an English naturalist, was the first to attempt a biological definition of species in 1686, as follows:

{{blockquote|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.{{cite book |last=Ray |first=John |author-link=John Ray |title=Historia plantarum generalis, Tome I, Libr. I |date=1686 |page=Chap. XX, page 40}}, quoted in {{cite book |last=Mayr |first=Ernst |year=1982 |title=The growth of biological thought: diversity, evolution, and inheritance |url=https://archive.org/details/growthofbiologic00mayr |url-access=registration |publisher=Belknap Press |page=[https://archive.org/details/growthofbiologic00mayr/page/256 256]|isbn=978-0-674-36445-5 }}}}

In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics, and not simply based upon differences.{{cite book |last1=Davis |first1=P. H. |last2=Heywood |first2=V. H. |year=1973 |title=Principles of Angiosperm Taxonomy |location=Huntington, NY |publisher=Robert E. Krieger Publishing Company |page=17 }} Like many contemporary systematists,{{cite book |last1=Magnol |first1=Petrus |title=Prodromus historiae generalis plantarum in quo familiae plantarum per tabulas disponuntur |date=1689 |publisher=Pech |page=79 |url=https://books.google.com/books?id=RShVAAAAcAAJ&dq=Prodromus+historiae+generalis+plantarum+in+quo+familiae+plantarum+per+tabulas+disponuntur&pg=PA1 |language=la}}{{cite book |last1=Tournefort |first1=Joseph Pitton de |title=Elemens de botanique, ou Methode pour connoître les plantes. I. [Texte.] / . Par Mr Pitton Tournefort... [T. I-III] |date=1694 |publisher=L'Imprimerie Royale |location=Paris |page=562 |url=https://gallica.bnf.fr/ark:/12148/btv1b8454361d/f9.item |language=en}}{{cite book |last1=Jussieu |first1=Antoine-Laurent de |title=Antonii Laurentii de Jussieu ... Genera plantarum secundum ordines naturales disposita: juxta methodum in horto regio Parisiensi exaratam, anno M.DCC.LXXIV.. |date=1789 |publisher=Apud viduam Herissant, typographum, viâ novâ B.M. sub signo Crucis Aureæ. Et Theophilum Barrois, ad ripam Augustinianorum. |page=498 |url=https://books.google.com/books?id=ctEsqqV0LHoC&dq=Genera+plantarum+secundum+ordines+naturales+disposita+juxta+methodum+in+horto+regio+parisiensi+exaratam%2C+anno+1774&pg=PA1 |language=la}} he established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships.{{Cite book |first1=James L. |last1=Reveal |first2=James S. |last2=Pringle |title=Flora of North America |year=1993 |chapter=7. Taxonomic Botany and Floristics |publisher=Oxford University Press |isbn=978-0-19-505713-3 |pages=160–161}}{{Cite book |first=George Gaylord |last=Simpson |author-link=George Gaylord Simpson |year=1961 |title=Principles of Animal Taxonomy |publisher=Columbia University Press |pages=56–57}} At the time, however, it was still widely believed that there was no organic connection between species (except, possibly, between those of a given genus), no matter how similar they appeared. This view was influenced by European scholarly and religious education, which held that the taxa had been created 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.{{cite journal |last=Mahoney |first=Edward P. |title=Lovejoy and the Hierarchy of Being |journal=Journal of the History of Ideas |volume=48 |issue=2 |pages=211–230 |doi=10.2307/2709555 |jstor=2709555 |year=1987 }}

In viewing evidence of hybridisation, Linnaeus recognised that species were not fixed and could change; he did not consider that new species could emerge and maintained a view of divinely fixed species that may alter through processes of hybridisation or acclimatisation.{{cite web |title=Carl Linnaeus (1707–1778) |url=http://www.ucmp.berkeley.edu/history/linnaeus.html |publisher=UCMP Berkeley |access-date=24 January 2018 |url-status=live |archive-url=https://web.archive.org/web/20110430160025/http://www.ucmp.berkeley.edu/history/linnaeus.html |archive-date=30 April 2011 |df=dmy-all }} 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.{{cite book |last=Gould |first=Stephen Jay |author-link=Stephen Jay Gould |title=The Structure of Evolutionary Theory |year=2002 |publisher=Belknap Harvard |location=Harvard |isbn=978-0-674-00613-3 |pages=[https://archive.org/details/structureofevolu00goul/page/170 170–197] |title-link=The Structure of Evolutionary Theory }}

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.{{cite book |last=Bowler |first=Peter J. |author-link=Peter J. Bowler |year=2003 |title=Evolution: The History of an Idea |edition=3rd |location=Berkeley, CA |publisher=University of California Press |isbn=978-0-520-23693-6 |pages=[https://archive.org/details/evolutionhistory0000bowl_n7y8/page/177 177–223 and passim] |url=https://archive.org/details/evolutionhistory0000bowl_n7y8/page/177 }} 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, writing:

{{blockquote|I look at the term species 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.{{cite book |last=Menand |first=Louis |title=The Metaphysical Club: A Story of Ideas in America |year=2001 |publisher=Farrar, Straus and Giroux |isbn=978-0-374-70638-8 |pages=[https://archive.org/details/metaphysicalclub00mena/page/123 123–124] |title-link=The Metaphysical Club: A Story of Ideas in America }}}}

{{Div col |colwidth = 18em }}

• Cline
• Encyclopedia of Life
• Endangered species
• Global biodiversity
• Lists of animal species
• Lists of plant species
• Outline of zoology
• Systematics
• Speciation
• History of speciation
• Pseudospeciation

{{Div col end}}

{{Clear}}

{{reflist}}

{{refbegin}}

• {{cite book |editor1-last=Claridge |editor1-first=M. F. |editor2-last=Dawah |editor2-first=H. A. |editor3-last=Wilson |editor3-first=M. R. |publisher=Chapman & Hall |title=Species: The Units of Biodiversity |year=1997 |isbn=978-0-412-63120-7}}
• {{cite book |editor1-last=Wheeler |editor1-first=Quentin |editor1-link=Quentin D. Wheeler |editor2-last=Meier |editor2-first=Rudolf |title=Species Concepts and Phylogenetic Theory: A Debate |publisher=Columbia University Press |year=2000 |isbn=978-0-231-10143-1 }}
• {{cite book |last=Zachos |first=Frank E. |title=Species Concepts in Biology: Historical Development, Theoretical Foundations and Practical Relevance |publisher=Springer |year=2016 |isbn=978-3-319-44964-7 }}

{{refend}}

{{Wikiquote}}

• [https://species.wikimedia.org/wiki/Main_Page Wikispecies] – The free species directory that anyone can edit from the Wikimedia Foundation
• [http://www.barcodinglife.org/ Barcoding of species]
• [http://www.catalogueoflife.org/ Catalogue of Life]
• [https://web.archive.org/web/20061211145046/http://www.finitesite.com/dandelion/Linnaeus.HTML European Species Names in Linnaean, Czech, English, German and French]
• [https://web.archive.org/web/20140407073920/http://plato.stanford.edu-online-documents-archive.info/entries/species/ "Species" entry] at the Stanford Encyclopedia of Philosophy
• [http://visualtaxa.redgolpe.com/ VisualTaxa]

{{Speciation}}

{{Taxonomic ranks}}

{{Evolution}}

{{Evolutionary psychology}}

{{Authority control}}

Category:Bacterial nomenclature

Category:Biological concepts

Category:Biology terminology

Category:Botanical nomenclature

Category:Plant taxonomy

rank24