Editing Homology (biology)

{{short description|Shared ancestry between a pair of structures or genes in different taxa}}
{{good article}}
[[File:Homology vertebrates-en.svg<!-- This image, Homology vertebrates-en.svg, is referred to in the text! Please don't change it without also updating the text with something equally or more suitable. -->|thumb|300px|The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by [[Charles Darwin]] as an argument in favor of [[evolution]].]]
In [[biology]], '''homology''' is similarity in [[anatomical]] structures or [[genes]] between [[organism]]s of different [[taxa]] due to shared [[ancestry]], ''regardless'' of current functional differences. [[Evolutionary biology]] explains homologous structures as retained [[heredity]] from a [[common descent|common ancestor]] after having been subjected to [[adaptation (biology)|adaptive]] modifications for different purposes as the result of [[natural selection]].

The term was first applied to biology in a non-evolutionary context by the anatomist [[Richard Owen]] in 1843. Homology was later explained by [[Charles Darwin]]'s theory of evolution in 1859, but had been observed before this from [[Aristotle's biology]] onwards, and it was explicitly analysed by [[Pierre Belon]] in 1555. A common example of homologous structures is the [[forelimb]]s of [[vertebrates]], where the [[bat wing development|wings of bats]] and [[origin of avian flight|birds]], the [[arm]]s of [[primate]]s, the front [[flipper (anatomy)|flippers]] of [[whale]]s, and the [[foreleg]]s of [[quadrupedalism|four-legged]] vertebrates like [[horse]]s and [[crocodilian]]s are all derived from the same ancestral [[tetrapod]] structure.

In [[developmental biology]], organs that developed in the [[embryo]] in the same manner and from similar origins, such as from matching [[primordium|primordia]] in successive segments of the same animal, are [[serial homology|serially homologous]]. Examples include the legs of a [[centipede]], the [[insect mouthparts|maxillary and labial palps]] of an [[insect]], and the [[spinous process]]es of successive [[vertebrae]] in a vertebrate's [[vertebral column|backbone]]. Male and female [[sex organ]]s are homologous if they develop from the same embryonic tissue, as do the [[ovaries]] and [[testicle]]s of [[mammal]]s, including [[human]]s. {{Citation needed|date=December 2022}}

[[Sequence homology]] between [[protein]] or [[DNA sequence]]s is similarly defined in terms of shared ancestry. Two segments of [[DNA]] can have shared ancestry because of either a [[speciation]] event ([[Sequence homology#Orthology|orthologs]]) or a [[Gene duplication|duplication event]] ([[Sequence homology#Paralogy|paralogs]]). Homology among proteins or DNA is inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by [[divergent evolution]] from a common ancestor. [[Sequence alignment|Alignments]] of multiple sequences are used to discover the homologous regions.

Homology remains controversial in [[ethology|animal behaviour]], but there is suggestive evidence that, for example, [[dominance hierarchies]] are homologous across the [[primates]].

==History==
[[File:BelonBirdSkel.jpg|thumb|upright=1.35|[[Pierre Belon]] systematically compared the skeletons of birds and humans in his ''Book of Birds'' (1555).<ref name="Panchen 1999"/>]]

Homology was noticed by [[Aristotle's biology|Aristotle]] (c. 350 BC),<ref name="Panchen 1999">{{cite book | last=Panchen | first=A. L. | title= Novartis Foundation Symposium 222 - Homology| chapter=Homology — History of a Concept | series=Novartis Foundation Symposia | volume=222 | year=1999 | pmid=10332750 | pages=5–18; discussion 18–23| doi=10.1002/9780470515655.ch2 | isbn=9780470515655 }}</ref> and was explicitly analysed by [[Pierre Belon]] in his 1555 ''Book of Birds'', where he systematically compared the skeletons of birds and humans. The pattern of similarity was interpreted as part of the static [[great chain of being]] through the [[mediaeval]] and [[early modern]] periods: it was not then seen as implying evolutionary change. In the German ''[[Naturphilosophie]]'' tradition, homology was of special interest as demonstrating unity in nature.<ref name=Panchen1999>{{cite book |last=Panchen |first=A. L. |title=Novartis Foundation Symposium 222 - Homology |chapter=Homology — History of a Concept |journal=Novartis Foundation Symposium |series=Novartis Foundation Symposia |date=1999 |volume=222 |pages=5–18 |doi=10.1002/9780470515655.ch2 |pmid=10332750|isbn=9780470515655 }}</ref><ref name=Brigandt/> In 1790, [[Goethe]] stated his [[foliar theory]] in his essay "Metamorphosis of Plants", showing that flower parts are derived from leaves.<ref name=Dornelas>{{cite journal |doi=10.1590/S1677-04202005000400001 |title=From leaf to flower: Revisiting Goethe's concepts on the ¨metamorphosis¨ of plants |year=2005 |last1=Dornelas |first1=Marcelo Carnier |last2=Dornelas |first2=Odair |journal=Brazilian Journal of Plant Physiology |volume=17 |issue=4|pages=335–344 |doi-access=free }}</ref> The [[serial homology]] of limbs was described late in the 18th century. The French zoologist [[Étienne Geoffroy Saint-Hilaire]] showed in 1818 in his ''theorie d'analogue'' ("theory of homologues") that structures were shared between fishes, reptiles, birds and mammals.<ref>{{cite book |last=Geoffroy Saint-Hilaire |first=Étienne |author-link=Étienne Geoffroy Saint-Hilaire |url=https://www.biodiversitylibrary.org/item/18524#page/6/mode/1up |title=Philosophie anatomique. Vol. 1: Des organes respiratoires sous le rapport de la détermination et de l'identité de leurs piecès osseuses |date=1818 |publisher=J. B. Baillière |volume=1 |location=Paris}}</ref> When Geoffroy went further and sought homologies between [[Georges Cuvier]]'s ''[[embranchement]]s'', such as vertebrates and molluscs, his claims triggered the 1830 [[Cuvier–Geoffroy debate]]. Geoffroy stated the principle of connections, namely that what is important is the relative position of different structures and their connections to each other.<ref name="Brigandt">{{cite web |last=Brigandt |first=Ingo |title=Essay: Homology |url=https://embryo.asu.edu/pages/essay-homology |website=The Embryo Project Encyclopedia |date=23 November 2011}}</ref> [[Embryologist]] [[Karl Ernst von Baer]] stated what are now called [[von Baer's laws]] in 1828, noting that related animals begin their development as similar embryos and then diverge: thus, animals in the same [[family (biology)|family]] are more closely related and diverge later than animals which are only in the same [[order (biology)|order]] and have fewer homologies. Von Baer's theory recognises that each [[taxon]] (such as a family) has distinctive shared features, and that embryonic development parallels the taxonomic hierarchy: not the same as [[recapitulation theory]].<ref name="Brigandt"/> The term "homology" was first used in biology by the anatomist [[Richard Owen]] in 1843 when studying the similarities of vertebrate [[fin]]s and limbs, defining it as the "same organ in different animals under every variety of form and function",<ref>{{cite book |last=Owen |first=Richard |author-link=Richard Owen |url=https://www.biodiversitylibrary.org/item/29826#page/5/mode/1up |title=Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals, Delivered at the Royal College of Surgeons in 1843 |date=1843 |publisher=Longman, Brown, Green, and Longmans |pages=374, 379}}</ref> and contrasting it with the matching term "analogy" which he used to describe different structures with the same function. Owen codified three main criteria for determining if features were homologous: position, development and composition. In 1859, [[Charles Darwin]] explained homologous structures as meaning that the organisms concerned shared a [[body plan]] from a common ancestor, and that taxa were branches of a single [[tree of life (biology)|tree of life]].<ref name=Panchen1999/><ref name="Brigandt"/><ref>{{cite journal |last=Sommer |first=R. J. |date=July 2008 |title=Homology and the hierarchy of biological systems |journal=BioEssays |volume=30 |issue=7 |pages=653–658 |doi=10.1002/bies.20776 |pmid=18536034}}</ref>

==Definition==
{{multiple image
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| image1            = Eupatorus gracilicornis Vol.jpg
| caption1          = The front wings of [[beetle]]s<!-- such as this [[Eupatorus gracilicornis|five-horned rhinoceros beetle]]--> have evolved into [[elytron|elytra, hard wing-cases]].
| image2            = Libellula depressa.jpg
| caption2          = [[Dragonflies]]<!-- like this ''[[Libellula depressa]]''--> have the ancient insect body plan with two pairs of wings.
| image3            = Nephrotoma guestfalica.jpg
| caption3          = The hind wings of [[flies]] such as this [[cranefly]] have [[divergent evolution|evolved divergently]] to form small club-like [[haltere]]s.
| footer_align      = <!-- left (default), center, right -->
| footer            = The two pairs of wings of ancestral insects are represented by homologous structures in modern insects—elytra, wings and halteres.
}}

The word homology, coined in about 1656, is derived from the [[Ancient Greek|Greek]] ὁμόλογος {{transliteration|grc|homologos}} from ὁμός {{transliteration|grc|homos}} 'same' and λόγος {{transliteration|grc|logos}} 'relation'.<ref>{{cite book |last=Bower |first=Frederick Orpen |author-link=Frederick Orpen Bower |title=Congress of Arts and Science: Universal Exposition, St. Louis, 1904 |publisher=Houghton, Mifflin |year=1906 |page=64 |chapter=Plant Morphology |chapter-url=https://books.google.com/books?id=Xe4ZAQAAIAAJ&pg=PA64}}</ref><ref>{{cite book |title=Milestones in Systematics |url=https://archive.org/details/milestonessystem00will |url-access=limited |first1=David Malcolm |last1=Williams |first2=Peter L. |last2=Forey |publisher=CRC Press |year=2004 |isbn=978-0-415-28032-7 |page=[https://archive.org/details/milestonessystem00will/page/n109 198]}}</ref>{{efn|The alternative terms "homogeny" and "homogenous" were also used in the late 1800s and early 1900s. However, these terms are now archaic in biology, and the term "homogenous" is now generally found as a misspelling of the term "[[Homogeneous (chemistry)|homogeneous]]" which refers to the uniformity of a mixture.<ref>"homogeneous, adj.". OED Online. March 2016. Oxford University Press. http://www.oed.com/view/Entry/88045? (accessed 9 April 2016).</ref><ref>"homogenous, adj.". OED Online. March 2016. Oxford University Press. http://www.oed.com/view/Entry/88055? (accessed 9 April 2016).</ref>}}

Similar biological structures or sequences in different [[taxon|taxa]] are homologous if they are derived from a [[common descent|common ancestor]]. Homology thus implies [[divergent evolution]]. For example, many [[insect]]s (such as [[dragonflies]]) possess two pairs of flying [[wing (insect)|wings]]. In [[beetle]]s, the first pair of wings has evolved into a pair of [[elytron|hard wing covers]],<ref>{{cite book |last=Wagner |first=Günter P. |title=Homology, Genes, and Evolutionary Innovation |url=https://books.google.com/books?id=g7vzAgAAQBAJ&pg=PA53 |year=2014 |publisher=Princeton University Press |isbn=978-1-4008-5146-1 |pages=53–54 |quote=elytra have very little similarity with typical wings, but are clearly homologous to forewings. Hence butterflies, flies, and beetles all have two pairs of dorsal appendages that are homologous among species.}}</ref> while in [[Diptera]]n flies the second pair of wings has evolved into small [[halteres]] used for balance.{{efn|If the two pairs of wings are considered as interchangeable, homologous structures, this may be described as a parallel reduction in the number of wings, but otherwise the two changes are each divergent changes in one pair of wings.}}<ref>{{cite book |last=Lipshitz |first=Howard D. |title=Genes, Development and Cancer: The Life and Work of Edward B. Lewis |url=https://books.google.com/books?id=8g4GCAAAQBAJ&pg=PA240 |year=2012 |publisher=Springer |isbn=978-1-4419-8981-9 |page=240 |quote=For example, wing and haltere are homologous, yet widely divergent, organs that normally arise as dorsal appendages of the second thoracic (T2) and third thoracic (T3) segments, respectively.}}</ref>

Similarly, the forelimbs of ancestral [[vertebrate]]s have evolved into the front flippers of [[whale]]s, the wings of [[bird]]s, the running forelegs of [[dog]]s, [[deer]] and [[horse]]s, the short forelegs of [[frog]]s and [[lizard]]s, and the grasping [[hand]]s of [[primate]]s including humans. The same major forearm bones ([[humerus]], [[Radius (bone)|radius]] and [[ulna]]{{efn|These are coloured in the lead image: humerus brown, radius pale buff, ulna red.}}) are found in fossils of [[lobe-finned fish]] such as ''[[Eusthenopteron]]''.<ref>{{cite web|title=Homology: Legs and Limbs|url=http://evolution.berkeley.edu/evolibrary/article/0_0_0/homology_02|publisher=UC Berkeley|access-date=15 December 2016}}</ref>

===Homology vs. analogy===
[[File:Acer pseudoplatanus MHNT.BOT.2004.0.461.jpg|thumb|upright=0.7|[[Sycamore maple]] fruits have wings [[Convergent evolution|analogous]] but not homologous to an insect's wings.]]
{{further|Convergent evolution}}

The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not [[Phylogenetic tree|present in their most recent common ancestor]] but, rather, [[convergent evolution|evolved separately]]. For example, the [[insect wing|wings of insects]] and birds evolved independently in [[Phylum|widely separated groups]], and converged functionally to support powered [[flight]], so they are analogous. Similarly, the wings of a [[sycamore maple]] seed and the wings of a bird are analogous but not homologous, as they develop from quite different structures.<ref>{{cite web |title=Secret Found to Flight of 'Helicopter Seeds' |url=http://www.livescience.com/3672-secret-flight-helicopter-seeds.html |publisher=LiveScience |access-date=2 March 2017 |date=11 June 2009}}</ref><ref>{{cite journal |last1=Lentink, D. |last2=Dickson, W. B. |last3=van Leeuwen, J. L. |last4=Dickinson, M. H. |title=Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds |journal=Science |date=12 June 2009 |volume=324 |issue=5933 |pages=1438–1440 |doi=10.1126/science.1174196 |pmid=19520959 |bibcode=2009Sci...324.1438L |s2cid=12216605 |url=http://authors.library.caltech.edu/14781/2/Lentink2009p4415Science_supp.pdf }}</ref> A structure can be homologous at one level, but only analogous at another. [[Pterosaur]], [[Bird flight|bird]] and [[bat wing]]s are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of [[tetrapod]]s, and evolved in different ways in the three groups. Thus, in the pterosaurs, the "wing" involves both the forelimb and the hindlimb.<ref name=Scotland2010>{{Cite journal | last=Scotland | first=R. W. | title=Deep homology: A view from systematics | doi=10.1002/bies.200900175 | journal=BioEssays | volume=32 | issue=5 | pages=438–449 | year=2010 | pmid=20394064| s2cid=205469918 }}</ref> Analogy is called [[homoplasy]] in [[cladistics]], and [[convergent evolution|convergent or parallel evolution]] in evolutionary biology.<ref>Cf. Butler, A. B.: ''Homology and Homoplasty.'' In: Squire, Larry R. (Ed.): ''Encyclopedia of Neuroscience'', Academic Press, 2009, pp. 1195–1199.</ref><ref>{{cite web |url=http://explainry.com/difference-between/homologous-analogous-structures/ |title=Homologous structure vs. analogous structure: What is the difference? |access-date=27 September 2016}}</ref>

===In cladistics===
{{further|Cladistics}}
<!--much of this added by [[User:ABrower]] in 2018-->

Specialised terms are used in taxonomic research. Primary homology is a researcher's initial hypothesis based on similar structure or anatomical connections, suggesting that a character state in two or more taxa share is shared due to common ancestry. Primary homology may be conceptually broken down further: we may consider all of the states of the same character as "homologous" parts of a single, unspecified, transformation series. This has been referred to as topographical correspondence. For example, in an aligned DNA sequence matrix, all of the A, G, C, T or implied gaps at a given nucleotide site are homologous in this way. Character state identity is the hypothesis that the particular condition in two or more taxa is "the same" as far as our character coding scheme is concerned. Thus, two Adenines at the same aligned nucleotide site are hypothesized to be homologous unless that hypothesis is subsequently contradicted by other evidence. Secondary homology is implied by [[parsimony analysis]], where a character state that arises only once on a tree is taken to be homologous.<ref name="de Pinna1991">{{cite journal |last=de Pinna |first=M. C. C. |title=Concepts and Tests of homology in the cladistic paradigm |year=1991|journal=Cladistics |volume=7 |issue=4 |pages=367–394 |doi=10.1111/j.1096-0031.1991.tb00045.x |citeseerx=10.1.1.487.2259 |s2cid=3551391}}</ref><ref>{{cite journal |last1=Brower |first1=Andrew V. Z. |last2=Schawaroch |first2=V. |year=1996 |title=Three steps of homology assessment |journal=Cladistics |volume=12 |issue=3 |pages=265–272|doi=10.1111/j.1096-0031.1996.tb00014.x |pmid=34920625 |s2cid=85385271 }}</ref> As implied in this definition, many [[cladistics|cladists]] consider secondary homology to be synonymous with [[synapomorphy]], a shared derived character or [[Phenotypic trait|trait]] state that distinguishes a [[clade]] from other organisms.<ref name="PageHolmes2009">{{cite book |last1=Page |first1=Roderick D.M. |last2=Holmes |first2=Edward C. |title=Molecular Evolution: A Phylogenetic Approach |url=https://books.google.com/books?id=p2lWhjuK8m8C |date=2009 |publisher=[[John Wiley & Sons]] |isbn=978-1-4443-1336-9}}</ref><ref name="Brower de Pinna pp. 529–538">{{cite journal |last1=Brower |first1=Andrew V. Z. |last2=de Pinna |first2=Mario C. C. |title=Homology and errors |journal=Cladistics |volume=28 |issue=5 |date=24 May 2012 |doi=10.1111/j.1096-0031.2012.00398.x |pages=529–538|pmid=34844384 |s2cid=86806203 |doi-access=free }}</ref><ref name="Brower&dePinna2014">{{cite journal |last1=Brower |first1=Andrew V. Z. |last2=de Pinna |first2=Mario C. C. |date=2014 |title=About Nothing |journal=Cladistics |volume=30 |issue=3 |pages=330–336 |doi=10.1111/cla.12050 |pmid=34788975 |s2cid=221550586}}</ref>

Shared ancestral character states, symplesiomorphies, represent either synapomorphies of a more inclusive group, or complementary states (often absences) that unite no natural group of organisms. For example, the presence of wings is a synapomorphy for pterygote insects, but a symplesiomorphy for holometabolous insects. Absence of wings in non-pterygote insects and other organisms is a complementary symplesiomorphy that unites no group (for example, absence of wings provides no evidence of common ancestry of silverfish, spiders and annelid worms). On the other hand, absence (or secondary loss) of wings is a synapomorphy for fleas. Patterns such as these lead many cladists to consider the concept of homology and the concept of synapomorphy to be equivalent.<ref name="Brower&dePinna2014"/><ref>{{cite book |last=Patterson |first=C. |year=1982 |chapter=Morphological characters and homology |pages=21–74 |editor1=K. A. Joysey |editor2=A. E. Friday |title=Problems of Phylogenetic Reconstruction |publisher=Academic Press |location=London and New York}}</ref> Some cladists follow the pre-cladistic definition of homology of Haas and Simpson,<ref>Haas, O. and G. G. Simpson. 1946. Analysis of some phylogenetic terms, with attempts at redefinition. ''Proc. Amer. Phil. Soc.'' '''90''':319-349.</ref> and view both synapomorphies and symplesiomorphies as homologous character states.<ref>{{cite journal |last1=Nixon, K. C. |last2=Carpenter, J. M. |year=2011 |title=On homology |journal=Cladistics |volume=28 |issue=2 |pages=160–169 |doi=10.1111/j.1096-0031.2011.00371.x |pmid=34861754 |s2cid=221582887 |doi-access=free }}</ref>

==In different taxa==
[[File:PAX6 Phenotypes Washington etal PLoSBiol e1000247.png|thumb|''[[pax6]]'' alterations result in similar changes to eye morphology and function across a wide range of taxa.]]

Homologies provide the fundamental basis for all biological classification, although some may be highly counter-intuitive. For example, [[deep homology|deep homologies]] like the ''[[pax6]]'' genes that control the development of the eyes of vertebrates and arthropods were unexpected, as the organs are anatomically dissimilar and appeared to have evolved entirely independently.<ref name=Brusca/><ref>{{cite book |last=Carroll |first=Sean B. |author-link=Sean B. Carroll |title=Endless Forms Most Beautiful |title-link=Endless Forms Most Beautiful (book) |date=2006 |publisher=Weidenfeld & Nicolson |isbn=978-0-297-85094-6 |pages=28, 66–69}}</ref>

{{anchor|In arthropods}}

===In arthropods===
{{further|Arthropod leg}}

The embryonic body segments ([[somite]]s) of different [[arthropod]] taxa have diverged from a simple body plan with many similar appendages which are serially homologous, into a variety of body plans with fewer segments equipped with specialised appendages.<ref>{{cite book |last=Hall |first=Brian |title=Homology |url=https://books.google.com/books?id=vptaNfbkd8sC&pg=PA29 |date=2008 |publisher=John Wiley |isbn=978-0-470-51566-2 |page=29}}</ref> The homologies between these have been discovered by comparing [[gene]]s in [[evolutionary developmental biology]].<ref name=Brusca>{{cite book |last1=Brusca |first1=R. C. |last2=Brusca |first2=G. J. |year=1990 |title=Invertebrates |url=https://archive.org/details/invertebrates0000brus |url-access=registration |publisher=Sinauer Associates |page=[https://archive.org/details/invertebrates0000brus/page/669 669]}}</ref>

[[File:Arthropod segment Hox gene expression.svg|thumb|upright=1.3|[[Hox gene]]s in [[arthropod]] [[Segmentation (biology)|segmentation]]
]]

{| class="wikitable"
|-
! [[Somite]]<br/>(body<br/>segment)
! [[Trilobite]]<br/>([[Trilobitomorpha]])<br/>[[File:202003 Trilobite.svg|50px]]
! [[Spider]]<br/>([[Chelicerata]])<br/>[[File:202201 Common house spider.svg|50px]]
! [[Centipede]]<br/>([[Myriapoda]])<br/>[[File:Scolopendra subspinipes japonica (no background).png|80px]]
! [[Insect]]<br/>([[Hexapoda]])<br/>[[File:202101 Chrysodeixis eriosoma.svg|50px]]
! [[Shrimp]]<br/>([[Crustacea]])<br/>[[File:202112 Japanese tiger prawn.svg|50px]]
|-
| 1
| antennae
| [[chelicerae]] (jaws and fangs)
| antennae
| antennae
| 1st antennae
|-
| 2
| 1st legs
| [[pedipalps]]
| -
| -
| 2nd antennae
|-|
| 3
| 2nd legs
| 1st legs
| [[Mandible (arthropod mouthpart)|mandibles]]
| mandibles
| mandibles (jaws)
|-
| 4
| 3rd legs
| 2nd legs
| 1st [[Maxilla (arthropod mouthpart)|maxillae]]
| 1st maxillae
| 1st maxillae
|-
| 5
| 4th legs
| 3rd legs
| 2nd maxillae
| 2nd maxillae
| 2nd maxillae
|-
| 6
| 5th legs
| 4th legs
| collum (no legs)
| 1st legs
| 1st legs
|-
| 7
| 6th legs
| -
| 1st legs
| 2nd legs
| 2nd legs
|-
| 8
| 7th legs
| -
| 2nd legs
| 3rd legs
| 3rd legs
|-
| 9
| 8th legs
| -
| 3rd legs
| -
| 4th legs
|-
| 10
| 9th legs
| -
| 4th legs
| -
| 5th legs
|-
|}

Among insects, the [[stinger]] of the female [[honey bee]] is a modified [[ovipositor]], homologous with ovipositors in other insects such as the [[Orthoptera]], [[Hemiptera]] and those [[Hymenoptera]] without stingers.<ref>{{cite journal |last1=Shing |first1=H. |last2=Erickson |first2=E. H. |title=Some ultrastructure of the honeybee (''Apis mellifera'' L.) sting |journal=Apidologie |date=1982 |volume=13 |issue=3 |pages=203–213 |url=https://hal.archives-ouvertes.fr/hal-00890568/document |doi=10.1051/apido:19820301|doi-access=free }}</ref>

{{anchor|In mammals}}

===In mammals===
{{further|Comparative anatomy}}

The three small bones in the [[middle ear]] of mammals including humans, the [[malleus]], [[incus]] and [[stapes]], are today used to transmit sound from the [[eardrum]] to the [[inner ear]]. The malleus and incus develop in the embryo from structures that form jaw bones (the quadrate and the articular) in lizards, and in fossils of lizard-like ancestors of mammals. Both lines of evidence show that these bones are homologous, sharing a common ancestor.<ref>{{cite web |title=Homology: From jaws to ears — an unusual example of a homology|url=http://evolution.berkeley.edu/evolibrary/article/homology_06|publisher=UC Berkeley |access-date=15 December 2016}}</ref>

Among the many [[List of related male and female reproductive organs|homologies in mammal reproductive systems]], [[ovaries]] and [[testicle]]s are homologous.<ref name="Hyde2010">{{cite book |last1=Hyde |first1=Janet Shibley |author-link1=Janet Shibley Hyde |title=Understanding Human Sexuality |last2=DeLamater |first2=John D. |author-link2=John DeLamater |date=June 2010 |publisher=[[McGraw-Hill]] |isbn=978-0-07-338282-1 |edition=11th |place=New York |page=103 |chapter=Chapter 5 |chapter-url=http://highered.mcgraw-hill.com/sites/dl/free/0072986360/238525/hyd86360_ch05.pdf}}</ref>

Rudimentary organs such as the human [[coccyx|tailbone]], now much reduced from their functional state, are readily understood as signs of [[evolution]], the explanation being that they were cut down by [[natural selection]] from functioning organs when their functions were no longer needed, but make no sense at all if species are considered to be fixed. The tailbone is homologous to the tails of other primates.<ref>{{cite book |last=Larson |first=Edward J. |author-link=Edward Larson |title=Evolution: The Remarkable History of Scientific Theory |publisher=Modern Library |year=2004 |isbn=978-0-679-64288-6 |url-access=registration |url=https://archive.org/details/evolutionremarka00lars |page=112}}</ref>

{{anchor|In plants}}

===In plants===
====Leaves, stems and roots====
In many plants, defensive or storage structures are made by modifications of the development of primary [[leaves]], [[plant stem|stems]] and [[root]]s. Leaves are variously modified from [[photosynthetic]] structures to form the insect-trapping pitchers of [[pitcher plants]], the insect-trapping jaws of the [[Venus flytrap]], and the spines of [[cacti]], all homologous.<ref>{{cite web |title=Homology: Leave it to the plants |url=http://evolution.berkeley.edu/evolibrary/article/homology_01 |publisher=University of California at Berkeley |access-date=7 May 2017}}</ref>

{| class="wikitable"
|-
! Primary organs
! Defensive structures
! Storage structures
|-
| Leaves
| [[Thorns, spines, and prickles|Spines]]
| Swollen leaves (e.g. [[succulents]])
|-
| Stems
| [[Thorns, spines, and prickles|Thorns]]
| Tubers (e.g. [[potato]]), rhizomes (e.g. [[ginger]]), fleshy stems (e.g. [[cacti]])
|-
| Roots
| -
| Root tubers (e.g. [[sweet potato]]), taproot (e.g. [[carrot]])
|}

Certain [[compound leaf|compound leaves]] of flowering plants are partially homologous both to leaves and shoots, because their [[evolutionary developmental biology|development has evolved]] from a [[mosaic (genetics)|genetic mosaic]] of leaf and shoot development.<ref>{{cite journal |last=Sattler, R. |title=Homology — a continuing challenge |journal=Systematic Botany |volume=9 |pages=382–394 |year=1984 |doi=10.2307/2418787 |issue=4 |jstor=2418787}}</ref><ref>{{cite book |last=Sattler, R. |chapter=Homology, homeosis, and process morphology in plants |editor=Hall, Brian Keith |title=Homology: the hierarchical basis of comparative biology |publisher=Academic Press |year=1994 |pages=423–75 |isbn=978-0-12-319583-8 }}</ref>

<gallery mode="packed">
File:EurAshLeaf.jpg|One [[pinnate]] leaf of [[European ash]]
File:Detail on a palm frond (8297623365).jpg|Detail of [[palm (plant)|palm]] leaf
File:Ocotillothron02262006.JPG|Leaf [[petiole (botany)|petioles]] adapted as [[Thorns, spines, and prickles|spines]] in ''[[Fouquieria splendens]]''
File:Musa acuminata Gran Canaria 2.JPG|The very large leaves of the banana, ''[[Musa acuminata]]''
File:Split Aloe.jpg|Succulent water [[storage organ|storage]] leaf of ''[[Aloe]]''
File:Venus Flytrap showing trigger hairs.jpg|Insect-trapping leaf of a [[Venus flytrap]]
File:Nepenthes muluensis.jpg|Insect-trapping leaf of [[pitcher plant]]
File:Onions 002.jpg|Food storage leaves in an [[onion]] [[bulb]]
</gallery>

====Flower parts====
[[File:ABC flower developement.svg|thumb|The [[ABC model of flower development]]. Class A genes affect [[sepal]]s and [[petal]]s, class B genes affect [[petal]]s and [[stamen]]s, class C genes affect stamens and [[carpel]]s. In two specific whorls of the floral [[meristem]], each class of organ identity genes is switched on.]]
{{further|ABC model of flower development}}

The four types of flower parts, namely [[carpel]]s, [[stamen]]s, [[petal]]s and [[sepal]]s, are homologous with and derived from leaves, as [[Goethe]] correctly noted in 1790. The development of these parts through a pattern of [[gene expression]] in the growing zones ([[meristem]]s) is described by the [[ABC model of flower development]]. Each of the four types of flower parts is serially repeated in concentric whorls, controlled by a small number of genes acting in various combinations. Thus, A genes working alone result in sepal formation; A and B together produce petals; B and C together create stamens; C alone produces carpels. When none of the genes are active, leaves are formed. Two more groups of genes, D to form [[ovule]]s and E for the floral whorls, complete the model. The genes are evidently ancient, as old as the [[flowering plant]]s themselves.<ref name="Dornelas"/>

==Developmental biology==
[[File:Eupodophis at Royal Belgian Institute of Natural Sciences, Brussels.jpg|thumb|The [[Cretaceous]] snake ''[[Eupodophis]]'' had hind legs (circled).]]

[[Developmental biology]] can identify homologous structures that arose from the same tissue in [[embryogenesis]]. For example, adult [[snake]]s have no legs, but their early embryos have limb-buds for hind legs, which are soon lost as the embryos develop. The implication that the ancestors of snakes had hind legs is confirmed by [[fossil]] evidence: the [[Cretaceous]] snake ''[[Pachyrhachis problematicus]]'' had hind legs complete with hip bones ([[ilium (bone)|ilium]], [[pubis (bone)|pubis]], [[ischium]]), thigh bone ([[femur]]), leg bones ([[tibia]], [[fibula]]) and foot bones ([[calcaneum]], [[Talus bone|astragalus]]) as in tetrapods with legs today.<ref>{{cite web |title=Homologies: developmental biology |url=http://evolution.berkeley.edu/evolibrary/article/lines_07 |publisher=UC Berkeley |access-date=15 December 2016}}</ref>

{{anchor|Orthology}}
{{anchor|Paralogy}}
{{anchor|Paralogous genes}}

==Sequence homology==
<!-- This section is linked from [[Primary structure]] -->
{{main|Sequence homology}}
{{further|Deep homology|Evolutionary developmental biology}}
[[File:Histone Alignment.png|thumb|300px|left|A multiple [[sequence alignment]] of mammalian [[histone H1]] proteins. [[Conserved sequence|Alignment positions conserved]] across all five species analysed are highlighted in grey. Positions with [[Conservative replacement|conservative]], semi-conservative and [[segregating site|non-conservative]] amino acid replacements are indicated.<ref>{{cite web|url=http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#23|website=Clustal|title=Clustal FAQ #Symbols|access-date=8 December 2014|archive-url=https://web.archive.org/web/20161024045656/http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#23|archive-date=24 October 2016|url-status=dead}}</ref>]]

As with anatomical structures, [[sequence homology]] between [[protein]] or [[DNA sequence]]s is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a [[speciation]] event ([[Sequence homology#Orthology|orthologs]]) or a [[Gene duplication|duplication event]] ([[Sequence homology#Paralogy|paralogs]]). Homology among proteins or DNA is typically inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution of a common ancestor. [[Sequence alignment|Alignments]] of multiple sequences are used to indicate which regions of each sequence are homologous.<ref>{{cite journal |last=Koonin, E. V. |title=Orthologs, Paralogs, and Evolutionary Genomics |journal=Annual Review of Genetics |volume=39 |pages=309–38 |year=2005 |pmid=16285863 |doi=10.1146/annurev.genet.39.073003.114725|url=https://zenodo.org/record/1234975 }}</ref>

Homologous sequences are orthologous if they are descended from the same ancestral sequence separated by a [[speciation]] event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be ''orthologous''. The term "ortholog" was coined in 1970 by the [[molecular evolution]]ist [[Walter M. Fitch|Walter Fitch]].<ref name="Fitch WM 99–113">{{cite journal |last=Fitch, W. M. |title=Distinguishing homologous from analogous proteins |journal=Systematic Zoology |volume=19 |issue=2 |pages=99–113 |date=June 1970 |pmid=5449325 |doi=10.2307/2412448|jstor=2412448 }}</ref>

Homologous sequences are paralogous if they were created by a duplication event within the genome. For [[gene duplication]] events, if a gene in an organism is duplicated, the two copies are paralogous. They can shape the structure of whole genomes and thus explain genome evolution to a large extent. Examples include the [[Homeobox]] ([[Hox gene|Hox]]) genes in animals. These genes not only underwent gene duplications within [[chromosome]]s but also [[Genome evolution|whole genome duplications]]. As a result, Hox genes in most vertebrates are spread across multiple chromosomes: the HoxA–D clusters are the best studied.<ref name=Zakany>{{Cite journal |last1=Zakany |first1=Jozsef |last2=Duboule |first2=Denis |date=2007 |title=The role of Hox genes during vertebrate limb development |journal=Current Opinion in Genetics & Development |volume=17 |issue=4 |pages=359–366 |doi=10.1016/j.gde.2007.05.011|issn=0959-437X |pmid=17644373}}</ref>

Some sequences are homologous, but they have diverged so much that their sequence similarity is not sufficient to establish homology. However, many proteins have retained very similar structures, and [[structural alignment]] can be used to demonstrate their homology.<ref>{{Cite journal |last1=Holm |first1=Liisa |last2=Laiho |first2=Aleksi |last3=Törönen |first3=Petri |last4=Salgado |first4=Marco |date=2022-11-23 |title=DALI shines a light on remote homologs: one hundred discoveries |journal=Protein Science |volume=32 |issue=1 |pages=e4519 |language=en |doi=10.1002/pro.4519 |pmid=36419248 |pmc=9793968 |issn=0961-8368}}</ref>

==In behaviour==
{{main|Homology (psychology)}}

It has been suggested that some [[Ethology|behaviours]] might be homologous, based either on sharing across related taxa or on common origins of the behaviour in an individual's development; however, the notion of homologous behavior remains controversial,<ref>{{cite journal |last=Moore |first=David S. |year=2013 |title=Importing the homology concept from biology into developmental psychology |journal=Developmental Psychobiology |volume=55 |issue=1 |pages=13–21 |doi=10.1002/dev.21015 |pmid=22711075}}</ref> largely because behavior is more prone to [[multiple realizability]] than other biological traits. For example, D. W. Rajecki and Randall C. Flanery, using data on humans and on nonhuman [[primates]], argue that patterns of behaviour in [[dominance hierarchies]] are homologous across the primates.<ref>{{cite book |last1=Rajecki |first1=D. W. |url=https://books.google.com/books?id=DtDGBQAAQBAJ&pg=PT125 |title=Social Conflict and Dominance in Children: a Case for a Primate Homology |last2=Flanery |first2=Randall C. |work=Advances in Developmental Psychology |publisher=Taylor and Francis |year=2013 |isbn=978-1-135-83123-3 |editor-last1=Lamb |editor-first1=M. E. |page=125 |quote=Finally, much recent information on children's ''and'' nonhuman primates' behavior in groups, a conjunction of hard human data and hard nonhuman primate data, lends credence to our comparison. Our conclusion is that, based on their agreement in several unusual characteristics, dominance patterns are homologous in primates. This agreement of unusual characteristics is found at several levels, including fine motor movement, gross motor movement, and behavior at the group level. |editor-last2=Brown |editor-first2=A. L.}}</ref>

[[File:Weeper Capuchin 01 (cropped).JPG|thumb|upright=1.2<!--format for low image-->|[[Dominance hierarchy]] behaviour, as in these [[weeper capuchin]] monkeys, may be homologous across the [[primates]].]]

As with morphological features or DNA, shared similarity in behavior provides evidence for common ancestry.<ref>Wenzel, John W. 1992. Behavioral homology and phylogeny. ''Annual Review of Ecology and Systematics'' 23:361-381</ref> The hypothesis that a behavioral character is not homologous should be based on an incongruent distribution of that character with respect to other features that are presumed to reflect the true pattern of relationships. This is an application of Willi Hennig's<ref>Hennig, W. 1966. ''Phylogenetic Systematics''.  University of Illinois Press</ref> [[Willi Hennig|auxiliary principle]].

==Notes==
{{notelist}}

==See also==
* [[Analogy (biology)]]
* [[Primitive (phylogenetics)]]

==References==
{{reflist|30em}}

==Further reading==

* Brigandt, Ingo (2011) [http://embryo.asu.edu/handle/10776/1754 "Essay: Homology."] In: ''The Embryo Project Encyclopedia''. {{ISSN|1940-5030}}. [http://embryo.asu.edu/handle/10776/1754 http://embryo.asu.edu/handle/10776/1754]
* {{cite book |last=Carroll |first=Sean B. |author-link=Sean B. Carroll |title=Endless Forms Most Beautiful |title-link=Endless Forms Most Beautiful (book) |publisher=W.W. Norton & Co |location=New York |year=2006 |isbn=978-0-297-85094-6 |ref=none}}
* {{cite book |last=Carroll |first=Sean B. |author-link=Sean B. Carroll |title=The making of the fittest: DNA and the ultimate forensic record of evolution |publisher=W.W. Norton & Co |location=New York |year=2006 |isbn=978-0-393-06163-5 |ref=none}}
* {{cite journal |last=DePinna |first=M.C. |title=Concepts and tests of homology in the cladistic paradigm |journal=Cladistics |volume=7 |pages=367–94 |year=1991 |doi=10.1111/j.1096-0031.1991.tb00045.x |issue=4 |citeseerx=10.1.1.487.2259 |s2cid=3551391 |ref=none}}
* {{cite journal |last1=Dewey |first1=C.N. |first2=L. |author2-link=Lior Pachter |last2=Pachter |title=Evolution at the nucleotide level: the problem of multiple whole-genome alignment |journal=Human Molecular Genetics |volume=15 |issue=Spec No 1 |pages=R51–R56 |date=April 2006 |pmid=16651369 |doi=10.1093/hmg/ddl056 |doi-access=free |ref=none}}
* {{cite journal |last=Fitch |first=W.M. |title=Homology a personal view on some of the problems |journal=Trends in Genetics |volume=16 |issue=5 |pages=227–31 |date=May 2000 |pmid=10782117 |doi=10.1016/S0168-9525(00)02005-9 |ref=none}}
* {{cite book |last=Gegenbaur |first=G. |title=Vergleichende Anatomie der Wirbelthiere&nbsp;... |location=Leipzig |year=1898 |ref=none}}
* {{cite book |last=Haeckel |first=Еrnst |author-link=Ernst Haeckel |title=Generelle Morphologie der Organismen |url=https://archive.org/details/bub_gb_wghbAAAAQAAJ |location=Bd 1-2. Вerlin |year=1866 |ref=none}}
* {{cite journal |last1=Kuzniar |first1=A. |last2=van Ham |first2=R.C. |last3=Pongor |first3=S. |last4=Leunissen |first4=J.A. |title=The quest for orthologs: finding the corresponding gene across genomes |journal=Trends Genet. |volume=24 |issue=11 |pages=539–551 |date=November 2008 |pmid=18819722 |doi=10.1016/j.tig.2008.08.009 |ref=none}}
* {{cite journal |last1=Mindell |first1=D.P. |last2=Meyer |first2=A. |title=Homology evolving |journal=Trends in Ecology and Evolution |volume=16 |pages=434–40 |year=2001 |url=http://euplotes.biology.uiowa.edu/web/IBS593/week4/Homologyevolving.pdf |archive-url=https://web.archive.org/web/20100627024721/http://euplotes.biology.uiowa.edu/web/IBS593/week4/Homologyevolving.pdf |url-status=dead |archive-date=2010-06-27 |doi=10.1016/S0169-5347(01)02206-6 |issue=8 |bibcode=2001TEcoE..16..434M |ref=none}}
* {{cite book |last=Owen |first=Richard |author-link=Richard Owen |title=On the archetype and homologies of the vertebrate skeleton |url=https://archive.org/details/onarchetypeandh01owengoog |location=London |year=1847 |publisher=John van Voorst, Paternoster Row. |ref=none}}

== External links ==
* {{commons-inline}}

{{Evolution}}
{{fins, limbs and wings}}

{{Use dmy dates|date=April 2017}}

{{DEFAULTSORT:Homology (Biology)}}
[[Category:Evolutionary biology concepts]]
[[Category:Phylogenetics]]
[[Category:Comparative anatomy]]