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