Editing Homology (biology) (section)

===In cladistics===
{{further|Cladistics}}
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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>