format-version: 1.2 data-version: releases/2015-01-07 date: 02:12:2009 15:16 default-namespace: homology_and_related_concepts_in_biology namespace-id-rule: * HOM:$sequence(7,0,9999999)$ ontology: hom [Term] id: HOM:0000000 name: similarity def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator] synonym: "correspondence" RELATED [DOI:10.1007/BF02814479] synonym: "resemblance" RELATED [] synonym: "sameness" EXACT [] xref: ECO:0000041 "inferred from similarity" xref: SO:similar_to [Term] id: HOM:0000001 name: homology def: "Similarity that results from common evolutionary origin." [DOI:10.1002/bies.950180611, DOI:10.1002/jmor.1051730307, DOI:10.1007/BF02814480] comment: This broad definition encompasses all the working definitions proposed so far in the literature. is_a: HOM:0000000 ! similarity disjoint_from: HOM:0000002 ! homoplasy [Term] id: HOM:0000002 name: homoplasy def: "Similarity that results from independent evolution." [DOI:10.1016/j.jhevol.2006.11.010] synonym: "analogy" RELATED [] is_a: HOM:0000000 ! similarity [Term] id: HOM:0000003 name: homocracy def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [DOI:10.1007/BF02814484, DOI:10.1007/s00427-003-0301-4, DOI:10.1186/1742-9994-2-15] comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. xref: ECO:0000075 "inferred from gene expression similarity" is_a: HOM:0000000 ! similarity [Term] id: HOM:0000004 name: convergence def: "Homoplasy that involves different underlying mechanisms or structures." [DOI:10.1016/j.jhevol.2006.11.010] comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] is_a: HOM:0000002 ! homoplasy [Term] id: HOM:0000005 name: parallelism def: "Homoplasy that involves homologous underlying mechanisms or structures." [DOI:10.1016/j.jhevol.2006.11.010] comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] is_a: HOM:0000002 ! homoplasy [Term] id: HOM:0000006 name: structural homology def: "Homology that is defined by similarity with regard to selected structural parameters." [DOI:10.1016/j.jhevol.2006.11.014, DOI:10.1146/annurev.es.20.110189.000411, ISBN:0123195837] synonym: "idealistic homology" RELATED [] xref: ECO:0000071 "inferred from morphological similarity" xref: MI:2163 "by homology" is_a: HOM:0000001 ! homology [Term] id: HOM:0000007 name: historical homology def: "Homology that is defined by common descent." [DOI:10.1016/S0169-5347(97)01125-7, ISBN:0123195837] synonym: "cladistic homology" EXACT [] synonym: "homology" BROAD [] synonym: "phylogenetic homology" EXACT [] synonym: "taxic homology" EXACT [] synonym: "true homology" RELATED [] xref: ECO:0000080 "inferred from phylogeny" xref: RO_proposed_relation:homologous_to xref: SO:0000330 "conserved_region" xref: SO:0000853 "homologous_region" xref: SO:0000857 "homologous" xref: SO:homologous_to xref: TAO:homologous_to is_a: HOM:0000001 ! homology [Term] id: HOM:0000008 name: biological homology def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [DOI:10.1016/S0169-5347(97)01125-7, DOI:10.1146/annurev.es.20.110189.000411] comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. synonym: "transformational homology" RELATED [] xref: ECO:0000067 "inferred from developmental similarity" is_a: HOM:0000001 ! homology [Term] id: HOM:0000009 name: reversal def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [DOI:10.1016/j.jhevol.2006.11.010] synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] is_a: HOM:0000002 ! homoplasy [Term] id: HOM:0000010 name: syntenic homology def: "Structural homology that is detected by similarity in content and organization between chromosomes." [MeSH:Synteny] synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 "syntenic" xref: SO:0005858 "syntenic_region" is_a: HOM:0000006 ! structural homology [Term] id: HOM:0000011 name: paralogy def: "Historical homology that involves genes that diverged after a duplication event." [DOI:10.1016/S0168-9525(00)02005-9, DOI:10.1146/annurev.genet.39.073003.114725, PMID:5449325] xref: SO:0000854 "paralogous_region" xref: SO:0000859 "paralogous" xref: SO:paralogous_to is_a: HOM:0000007 ! historical homology disjoint_from: HOM:0000017 ! orthology [Term] id: HOM:0000012 name: syntenic paralogy def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, DOI:10.1186/1471-213X-7-100] synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] is_a: HOM:0000010 ! syntenic homology is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000013 name: syntenic orthology def: "Syntenic homology that involves chromosomes of different species." [DOI:10.1101/gr.6380007] is_a: HOM:0000010 ! syntenic homology [Term] id: HOM:0000014 name: partial homology def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [ISBN:0123195837, ISBN:978-0471984931] synonym: "fractional homology" EXACT [] synonym: "mixed homology" RELATED [] synonym: "modular homology" RELATED [] synonym: "partial correspondence" RELATED [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] is_a: HOM:0000006 ! structural homology [Term] id: HOM:0000015 name: protein structural homology def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [DOI:10.1016/0022-2836(76)90195-9] xref: MeSH:Structural Homology\, Protein is_a: HOM:0000006 ! structural homology [Term] id: HOM:0000016 name: non functional homology def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [SO:non_functional_homolog_of] synonym: "pseudogene" BROAD [] xref: SO:non_functional_homolog_of is_a: HOM:0000006 ! structural homology disjoint_from: HOM:0000062 ! equivalogy [Term] id: HOM:0000017 name: orthology def: "Historical homology that involves genes that diverged after a speciation event." [DOI:10.1007/BF02814484, DOI:10.1016/S0168-9525(00)02005-9, DOI:10.1146/annurev.genet.39.073003.114725, PMID:5449325] comment: The term is sometimes also used for anatomical structures. xref: ECO:00000060 "inferred from sequence orthology" xref: SO:0000855 "orthologous_region" xref: SO:0000858 "orthologous" xref: SO:orthologous_to is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000018 name: xenology def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [DOI:10.1016/S0168-9525(00)02005-9, DOI:10.1146/annurev.genet.39.073003.114725] comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000019 name: 1 to 1 homology def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000020 name: 1 to 1 orthology def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [DOI:10.1007/BF02814484, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] is_a: HOM:0000017 ! orthology is_a: HOM:0000019 ! 1 to 1 homology [Term] id: HOM:0000021 name: allogeny def: "Relationship between recognizably corresponding characters that occurs in two or more taxa and have different generative bases." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R] synonym: "generative homoplasy" EXACT [] is_obsolete: true [Term] id: HOM:0000022 name: ohnology def: "Paralogy that results from a whole genome duplication event." [DOI:10.1038/75560] synonym: "homoeology" RELATED [] is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000023 name: in-paralogy def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [DOI:10.1146/annurev.genet.39.073003.114725] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] is_a: HOM:0000011 ! paralogy disjoint_from: HOM:0000024 ! out-paralogy [Term] id: HOM:0000024 name: out-paralogy def: "Paralogy that results from a duplication preceding a given speciation event." [DOI:10.1146/annurev.genet.39.073003.114725] synonym: "alloparalogy" EXACT [] synonym: "outparalogy" EXACT [] is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000025 name: pro-orthology def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [DOI:10.1006/scdb.1999.0338, DOI:10.1038/nrg2099] is_a: HOM:0000034 ! 1 to many orthology [Term] id: HOM:0000026 name: semi-orthology def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [DOI:10.1006/scdb.1999.0338, DOI:10.1038/nrg2099] comment: The converse of pro-orthologous. is_a: HOM:0000034 ! 1 to many orthology [Term] id: HOM:0000027 name: serial homology def: "Iterative homology that involves structures arranged along the main body axis." [DOI:10.1146/annurev.es.20.110189.000411] synonym: "homonomy" RELATED [] is_a: HOM:0000066 ! iterative homology [Term] id: HOM:0000028 name: heterochronous homology def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [ISBN:978-0674639416] synonym: "heterochrony" EXACT [] is_a: HOM:0000008 ! biological homology [Term] id: HOM:0000029 name: paedomorphorsis def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, ISBN:978-0674639416] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] is_a: HOM:0000028 ! heterochronous homology disjoint_from: HOM:0000030 ! peramorphosis [Term] id: HOM:0000030 name: peramorphosis def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis] is_a: HOM:0000028 ! heterochronous homology [Term] id: HOM:0000031 name: progenesis def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, ISBN:978-0674639416] is_a: HOM:0000029 ! paedomorphorsis [Term] id: HOM:0000032 name: neoteny def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, ISBN:978-0674639416] synonym: "juvenilization" EXACT [] is_a: HOM:0000029 ! paedomorphorsis [Term] id: HOM:0000033 name: mimicry def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http:\://en.wikipedia.org/wiki/Mimicry] is_a: HOM:0000004 ! convergence created_by: admin creation_date: 2009-07-30T11:28:41Z [Term] id: HOM:0000034 name: 1 to many orthology def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [DOI:10.1038/415741a, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "1:many orthology" EXACT [] synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] is_a: HOM:0000017 ! orthology is_a: HOM:0000037 ! 1 to many homology [Term] id: HOM:0000036 name: many to many homology def: "Historical homology that involves two members of a larger set of homologs." [DOI:10.1093/molbev/msp002] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000037 name: 1 to many homology def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000042 name: apomorphy def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [ISBN:978-0252068140] synonym: "synapomorphy" RELATED [] is_a: HOM:0000007 ! historical homology disjoint_from: HOM:0000043 ! plesiomorphy [Term] id: HOM:0000043 name: plesiomorphy def: "Historical homology that is based on distant shared ancestry." [ISBN:978-0252068140] comment: This term is usually contrasted to apomorphy. synonym: "symplesiomorphy" RELATED [] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000044 name: deep homology def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [DOI:10.1007/BF02814485, DOI:10.1038/nature07891] comment: Used for structures in distantly related taxa. synonym: "deep genetic homology" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] is_a: HOM:0000003 ! homocracy is_a: HOM:0000005 ! parallelism [Term] id: HOM:0000045 name: hemiplasy def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [DOI:10.1073/pnas.0807433105] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000046 name: gametology def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [PMID:11110898] is_a: HOM:0000047 ! chromosomal homology [Term] id: HOM:0000047 name: chromosomal homology def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [ISBN:0195307615] xref: MeSH:Chromosome Pairing is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000048 name: many to many orthology def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [DOI:10.1038/415741a, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "co-orthology" RELATED [] synonym: "many-to-many orthology" EXACT [] synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] is_a: HOM:0000017 ! orthology is_a: HOM:0000036 ! many to many homology [Term] id: HOM:0000049 name: within-species paralogy def: "Paralogy that involves genes from the same species." [http://www.ensembl.org/info/docs/compara/homology_method.html] is_a: HOM:0000011 ! paralogy disjoint_from: HOM:0000050 ! between-species paralogy [Term] id: HOM:0000050 name: between-species paralogy def: "Paralogy that involves genes from different species." [http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes have diverged before a speciation event. is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000051 name: postdisplacement def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis] synonym: "post-displacement" EXACT [] is_a: HOM:0000029 ! paedomorphorsis [Term] id: HOM:0000052 name: hypermorphosis def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, ISBN:978-0674639416] is_a: HOM:0000030 ! peramorphosis [Term] id: HOM:0000053 name: synology def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [DOI:10.1007/BF00173425, DOI:10.1016/S0168-9525(00)02005-9] is_a: HOM:0000018 ! xenology [Term] id: HOM:0000054 name: isoorthology def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [DOI:10.1016/S0168-9525(00)02005-9] xref: ECO:0000080 "inferred from phylogeny" is_a: HOM:0000017 ! orthology is_a: HOM:0000062 ! equivalogy [Term] id: HOM:0000055 name: tandem paralogy def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [DOI:10.1016/S0168-9525(00)02005-9, ISBN:978-0878932665] synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000057 name: latent homology def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [DOI:10.1007/BF02814485, DOI:10.1016/j.jhevol.2006.11.010, DOI:10.1186/1742-9994-2-15, ISBN:0199141118] comment: Used for structures in closely related taxa. synonym: "apomorphic tendency" EXACT [] synonym: "cryptic homology" EXACT [] synonym: "homoiology" RELATED [] synonym: "homoplastic tendency" RELATED [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] is_a: HOM:0000005 ! parallelism is_a: HOM:0000058 ! syngeny [Term] id: HOM:0000058 name: syngeny def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, DOI:10.1186/1742-9994-2-15] comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. synonym: "generative homology" EXACT [] is_a: HOM:0000003 ! homocracy [Term] id: HOM:0000060 name: apparent orthology def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [DOI:10.1146/annurev.genet.39.073003.114725, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "pseudoorthology" EXACT [] is_a: HOM:0000019 ! 1 to 1 homology is_a: HOM:0000050 ! between-species paralogy [Term] id: HOM:0000061 name: pseudoparalogy def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [DOI:10.1146/annurev.genet.39.073003.114725] comment: These genes may come out as paralogs in a single-genome analysis. is_a: HOM:0000018 ! xenology [Term] id: HOM:0000062 name: equivalogy def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [DOI:10.1093/nar/gkl1043] comment: This may include examples of orthology, paralogy and xenology. is_a: HOM:0000007 ! historical homology is_a: HOM:0000065 ! functional equivalence [Term] id: HOM:0000063 name: interology def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [DOI:10.1101/gr.1774904, DOI:10.1126/science.287.5450.116] is_a: HOM:0000007 ! historical homology [Term] id: HOM:0000065 name: functional equivalence def: "Similarity that is characterized by interchangeability in function." [DOI:10.1007/BF02814484, DOI:10.1038/415741a] synonym: "functional similarity" RELATED [] is_a: HOM:0000000 ! similarity [Term] id: HOM:0000066 name: iterative homology def: "Biological homology that involves parts of the same organism." [DOI:10.1146/annurev.es.20.110189.000411] is_a: HOM:0000008 ! biological homology [Term] id: HOM:0000068 name: paraxenology def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [PMID:3065587] synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] is_a: HOM:0000018 ! xenology [Term] id: HOM:0000069 name: plerology def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [PMID:3065587] comment: This phenomenon is usually due to gene conversion process. is_a: HOM:0000011 ! paralogy [Term] id: HOM:0000071 name: homotopy def: "Structural homology that involves structures with the same or similar relative positions." [DOI:10.1007/BF02814484, DOI:10.1007/BF02814485, ISBN:0123195837] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. is_a: HOM:0000006 ! structural homology disjoint_from: HOM:0000072 ! homeosis [Term] id: HOM:0000072 name: homeosis def: "Biological homology that involves an ectopic structure and the normally positioned structure." [DOI:10.1007/BF02814485, DOI:10.1016/j.cell.2008.06.030] synonym: "heterotopy" RELATED [] is_a: HOM:0000008 ! biological homology [Term] id: HOM:0000073 name: homoeology def: "Synology that results from allopolyploidy." [DOI:10.1073/pnas.0505156102] comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. is_a: HOM:0000022 ! ohnology is_a: HOM:0000053 ! synology [Term] id: HOM:0000074 name: paramorphism def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [DOI:10.1007/s10441-007-9023-8, DOI:10.1046/j.1525-142x.2000.00054.x] synonym: "axis paramorphism" RELATED [] is_a: HOM:0000003 ! homocracy is_a: HOM:0000066 ! iterative homology [Term] id: HOM:0000075 name: regulogy def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [DOI:10.1101/gr.1774904] is_a: HOM:0000007 ! historical homology