format-version: 1.2 date: 21:07:2009 15:16 saved-by: jroux auto-generated-by: OBO-Edit 1.101 default-namespace: ontology_of_homology_and_related_concepts_in_biology namespace-id-rule: * HOM:$sequence(7,0,9999999)$ [Typedef] id: HOM:0000000 name: similarity def: "Relation between biological objects which resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator] synonym: "resemblance" RELATED [] synonym: "sameness" EXACT [] xref: ECO:0000041 "inferred from similarity" xref: SO:similar_to is_transitive: true [Typedef] id: HOM:0000001 name: homology def: "Similarity by evolutionary origin." [BGEE:curator] xref: SO:0000853 "homologous_region" is_transitive: true is_a: HOM:0000000 ! similarity [Typedef] id: HOM:0000002 name: homoplasy def: "Similarity resulting from independent evolution." [DOI:10.1016/j.jhevol.2006.11.010 "Hall BK (2007) Journal of Human Evolution 52: 473-479"] synonym: "analogy" RELATED [] is_a: HOM:0000000 ! similarity [Typedef] id: HOM:0000003 name: homocracy def: "Anatomical structures which are organised through the expression of homologous or identical patterning genes. The terms homologous and homocratic are not mutually exclusive." [DOI:10.1007/BF02814484 "Theissen G (2005) Birth, life and death of developmental control genes: New challenges for the homology concept. Theory in Biosciences 124:199-212", DOI:10.1007/s00427-003-0301-4 "Nielsen C and Martinez P (2003) Patterns of gene expression: homology or homocracy? Development Genes and Evolution 213: 149-154"] xref: ECO:0000075 "inferred from gene expression similarity" is_transitive: true is_a: HOM:0000000 ! similarity [Typedef] id: HOM:0000004 name: convergence def: "Similarity due to independent evolution with different underlying mechanisms or structures." [DOI:10.1016/j.jhevol.2006.11.010 "Hall BK (2007) Journal of Human Evolution 52: 473-479"] synonym: "analogy" RELATED [] is_a: HOM:0000002 ! homoplasy [Typedef] id: HOM:0000005 name: parallelism def: "(i) Similarity due to independent evolution with homologous underlying mechanisms or structures. (ii) A feature present in closely related organisms but not present continuously in all the members of the lineage." [DOI:10.1016/j.jhevol.2006.11.010 "Hall BK (2007) Journal of Human Evolution 52: 473-479"] synonym: "parallel evolution" EXACT [] is_a: HOM:0000002 ! homoplasy [Typedef] id: HOM:0000006 name: structural homology def: "Homology defined by similarity in structure." [ISBN:0123195837 "Lauder GV (1994) in Hall BK (Ed.) Homology: The Hierarchical Basis of Comparative Biology. Academic Press, p. 153"] xref: ECO:0000071 "inferred from morphological similarity" xref: MI:2163 "by homology" is_transitive: true is_a: HOM:0000001 ! homology [Typedef] id: HOM:0000007 name: historical homology def: "Similarity due to common descent." [DOI:10.1016/S0169-5347(97)01125-7 "Abouheif E (1997) Developmental genetics and homology: a hierarchical approach. Trends in Ecology & Evolution, 12 405-408.", ISBN:0123195837 "Rieppel O (1994) in Hall BK (Ed.), Homology: The Hierarchical Basis of Comparative Biology. Academic Press, p. 65"] 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:0000857 "homologous" xref: SO:homologous_to xref: TAO:homologous_to is_transitive: true is_a: HOM:0000001 ! homology [Typedef] id: HOM:0000008 name: biological homology def: "Structures that share a set of developmental constraints caused by locally acting self-regulatory mechanisms of differentiation. Individualized parts of the phenotype." [DOI:10.1016/S0169-5347(97)01125-7 "Abouheif E (1997) Developmental genetics and homology: a hierarchical approach. Trends in Ecology & Evolution, 12 405-408.", DOI:10.1146/annurev.es.20.110189.000411 "Wagner GP (1999) The Biological Homology Concept. Annual Review of Ecology and Systematics 20: 51-69"] 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_transitive: true is_a: HOM:0000001 ! homology [Typedef] id: HOM:0000009 name: reversal def: "Phenotypes similar to those seen in ancestors within the lineage." [DOI:10.1016/j.jhevol.2006.11.010 "Hall BK (2007) Journal of Human Evolution 52: 473-479"] synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] is_a: HOM:0000002 ! homoplasy [Typedef] id: HOM:0000010 name: syntenic homology def: "Similarity in content and organization between chromosomes." [MeSH:Synteny] synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 "syntenic" is_a: HOM:0000006 ! structural homology [Typedef] id: HOM:0000011 name: paralogy def: "The relationship of any two homologous characters arising from a duplication of the gene for that character. Relationship between genes which have diverged after a duplication event." [DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231.", PMID:5449325 "Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst. zool. 19(2): 99-113."] xref: SO:0000854 "paralogous_region" xref: SO:0000859 "paralogous" xref: SO:paralogous_to is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000012 name: syntenic paralogy def: "Relationship between sets of syntenic blocks derived from duplication of a common ancestral region." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y "Coulier F et al. (2000) MetaHox gene clusters. Journal of Experimental Zoology 288:345-351", DOI:10.1186/1471-213X-7-100 "Woolfe A et al. (2007) CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Developmental Biology 7:100"] synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] is_a: HOM:0000010 ! syntenic homology is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000013 name: syntenic orthology def: "Similarity in content and organization between chromosomes of different species." [DOI:10.1101/gr.6380007 "Pontius JU et al. (2007) Initial sequence and comparative analysis of the cat genome. Genome Research, 17: 1675-1689 ."] is_a: HOM:0000010 ! syntenic homology [Typedef] id: HOM:0000014 name: partial homology def: "Partial similarity with regard to selected structural parameters." [ISBN:0123195837 "Hillis DM (1994) in Hall BK (Ed.) Homology: The Hierarchical Basis of Comparative Biology. Academic Press, p. 348", ISBN:0123195837 "Sattler R (1994) in Hall BK (Ed.) Homology: The Hierarchical Basis of Comparative Biology. Academic Press, p. 425", ISBN:978-0471984931 "Hall BK (Ed.) (2000) HOMOLOGY : NOVARTIS FOUNDATION SYMPOSIUM 222. Wiley & Sons"] comment: Defined for molecules only. 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 [Typedef] id: HOM:0000015 name: protein structural homology def: "Homology detectable 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 "Rossmann MG and Argos P (1976) Exploring structural homology of proteins. Journal of Molecular Biology 105, 1:75-95"] xref: MeSH:Structural Homology\, Protein is_a: HOM:0000006 ! structural homology [Typedef] id: HOM:0000016 name: non functional homology def: "A relationship between 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 [Typedef] id: HOM:0000017 name: orthology def: "The relationship of any two homologous characters whose common ancestor lies in the cenancestor of the taxa from which the two sequences were obtained. Relationship between genes which have diverged after a speciation event. This term can be used also for anatomical structures." [DOI:10.1007/BF02814484 "Theissen G (2005) Birth, life and death of developmental control genes: New challenges for the homology concept. Theory in Biosciences 124:199-212", DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231.", PMID:5449325 "Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst. zool. 19(2): 99-113."] comment: The term is sometimes used for anatomical structures as well. 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 [Typedef] id: HOM:0000018 name: xenology def: "The relationship of any two homologous characters whose history, since their common ancestor, involves an interspecies (horizontal) transfer of the genetic material for at least one of those characters." [DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231.", DOI:10.1146/annurev.genet.39.073003.114725 "Koonin EV (2005) ORTHOLOGS, PARALOGS, AND EVOLUTIONARY GENOMICS. Annual Review of Genetics, 39: 309-338"] comment: The term is sometimes used for structures (e.g. in case of a symbiosis). is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000019 name: 1:1 homology def: "Relationship between two members that share no other homologs in the lineages considered." [BGEE:curator] synonym: "one-to-one homology" EXACT [] is_transitive: true is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000020 name: 1:1 orthology def: "Relationship of a gene to its ortholog if no duplication occured in the two lineages after the speciation event that created the orthologs." [DOI:10.1007/BF02814484 "Theissen G (2005) Birth, life and death of developmental control genes: New challenges for the homology concept. Theory in Biosciences 124:199-212", http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] synonym: "one-to-one orthology" EXACT [] is_transitive: true is_a: HOM:0000017 ! orthology is_a: HOM:0000019 ! 1:1 homology [Typedef] id: HOM:0000022 name: ohnology def: "Relationship between genes which have diverged after a whole genome duplication event." [DOI:10.1038/75560 "Wolfe K (2000) Robustness-it's not where you think it is. Nature Genetics 25, 3-4"] synonym: "homoeology" RELATED [] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000023 name: in-paralogy def: "Paralogy between genes resulting from a lineage-specific duplication subsequent to a given speciation event." [DOI:10.1146/annurev.genet.39.073003.114725 "Koonin EV (2005) ORTHOLOGS, PARALOGS, AND EVOLUTIONARY GENOMICS. Annual Review of Genetics, 39: 309-338"] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000024 name: out-paralogy def: "Paralogy between genes resulting from a duplication preceding a given speciation event." [DOI:10.1146/annurev.genet.39.073003.114725 "Koonin EV (2005) ORTHOLOGS, PARALOGS, AND EVOLUTIONARY GENOMICS. Annual Review of Genetics, 39: 309-338"] synonym: "alloparalogy" EXACT [] synonym: "outparalogy" EXACT [] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000025 name: pro-orthology def: "Relationship between a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occured in species B but not in species A." [DOI:10.1006/scdb.1999.0338 "Sharman AC (1999) Some new terms for duplicated genes. Seminars in Cell and Developmental Biology, 10, 5: 561-563", DOI:10.1038/nrg2099 "Wagner GP (2007) The developmental genetics of homology. Nature Reviews Genetics. 8, 6: 473-9"] is_a: HOM:0000034 ! 1:many orthology [Typedef] id: HOM:0000026 name: semi-orthology def: "Relationship between a gene in species A and its ortholog in species B, when duplications more recent than the species split have occured in species A but not in species B." [DOI:10.1006/scdb.1999.0338 "Sharman AC (1999) Some new terms for duplicated genes. Seminars in Cell and Developmental Biology, 10, 5: 561-563", DOI:10.1038/nrg2099 "Wagner GP (2007) The developmental genetics of homology. Nature Reviews Genetics. 8, 6: 473-9"] comment: The converse of pro-orthologous. is_a: HOM:0000034 ! 1:many orthology [Typedef] id: HOM:0000027 name: serial homology def: "Iterative homology where structures are arranged along the main body axis." [doi:10.1146/annurev.es.20.110189.000411 "Wagner GP (1999) The Biological Homology Concept. Annual Review of Ecology and Systematics 20: 51-69"] synonym: "homonomy" RELATED [] is_transitive: true is_a: HOM:0000066 ! iterative homology [Typedef] id: HOM:0000028 name: heterochronous homology def: "Changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [ISBN:978-0674639416 "Gould SJ (1985) Ontogeny and Phylogeny. Belknap Press of Harvard University Press"] synonym: "heterochrony" EXACT [] is_a: HOM:0000008 ! biological homology [Typedef] id: HOM:0000029 name: paedomorphorsis def: "Change in which the adults of a species retain traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis "Wikipedia 07/2009", ISBN:978-0674639416 "Gould SJ (1985) Ontogeny and Phylogeny. Belknap Press of Harvard University Press"] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] is_a: HOM:0000028 ! heterochronous homology [Typedef] id: HOM:0000030 name: peramorphosis def: "Change in which individuals of a species mature past adulthood and take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis "Wikipedia 07/2009"] is_a: HOM:0000028 ! heterochronous homology [Typedef] id: HOM:0000031 name: progenesis def: "Paedomorphosis produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis "Wikipedia 07/2009", ISBN:978-0674639416 "Gould SJ (1985) Ontogeny and Phylogeny. Belknap Press of Harvard University Press"] is_a: HOM:0000029 ! paedomorphorsis [Typedef] id: HOM:0000032 name: neoteny def: "Paedomorphosis produced by retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny "Wikipedia 07/2009", ISBN:978-0674639416 "Gould SJ (1985) Ontogeny and Phylogeny. Belknap Press of Harvard University Press"] synonym: "juvenilization" EXACT [] is_a: HOM:0000029 ! paedomorphorsis [Typedef] id: HOM:0000034 name: 1:many orthology def: "Relationship between orthologs in two species, when duplications more recent than the species split have occured in one species but not the other." [DOI:10.1038/415741a "Theissen G (2002) Orthology: Secret life of genes. Nature 415:741", http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] synonym: "co-orthology" RELATED [] synonym: "many:1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] is_a: HOM:0000017 ! orthology is_a: HOM:0000037 ! 1:many homology [Typedef] id: HOM:0000036 name: many:many homology def: "Relationship between two members of a larger set of homologs." [DOI:10.1093/molbev/msp002 "Raghupathy N and Durand D (2009) Gene Cluster Statistics with Gene Families. Mol Biol Evol. 26:957Ð968."] synonym: "many-to-many homology" EXACT [] is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000037 name: 1:many homology def: "Relationship between a structure that has no other homologs in the species in which it is defined, and several homologous structures which are found in another species." [BGEE:curator] synonym: "one-to-many homology" EXACT [] is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000042 name: apomorphy def: "Homology based on recent shared ancestry, characterizing a monophyletic group." [ISBN:978-0252068140 "Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana."] synonym: "synapomorphy" RELATED [] is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000043 name: plesiomorphy def: "Plesiomorphy is homology based on more distant ancestry than apomorphy." [ISBN:978-0252068140 "Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana."] synonym: "symplesiomorphy" RELATED [] is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000044 name: deep homology def: "Sharing of the genetic regulatory apparatus and master control genes that are used to build morphologically and phylogenetically disparate features. Used for structures in distantly related taxa." [DOI:10.1007/BF02814485 "Rutishauser R and Moline P (2005) Evo-devo and the search for homology (ÒsamenessÓ) in biological systems. Theory in Biosciences 124:213-241", DOI:10.1038/nature07891 "Shubin N, Tabin C and Carroll S (2009) Deep homology and the origins of evolutionary novelty, Nature, 457, 818-823"] synonym: "deep genetic homology" EXACT [] synonym: "homoiology" RELATED [] is_a: HOM:0000003 ! homocracy is_a: HOM:0000005 ! parallelism [Typedef] id: HOM:0000045 name: hemiplasy def: "Homology with 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 "Robinson TJ et al.(2008) Hemiplasy and homoplasy in the karyotypic phylogenies of mammals, PNAS, 105, 38: 14477-14481"] is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000046 name: gametology def: "Homology arising through lack of recombination and subsequent differentiation of sex chromosomes." [PMID:11110898 "Garc’a-Moreno J and Mindell DP (2000) Rooting a Phylogeny with Homologous Genes on Opposite Sex Chromosomes (Gametologs): A Case Study Using Avian CHD, Mol Biol Evol, 17: 1826-1832"] is_a: HOM:0000047 ! chromosomal homology [Typedef] id: HOM:0000047 name: chromosomal homology def: "Homology between the chromosomes that can pair (synapse) during meiosis." [ISBN:0195307615 "King RC and Stansfield WD (1997). A Dictionary of Genetics (5th Edition ed.). Oxford University Press"] xref: MeSH:Chromosome Pairing is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000048 name: many:many orthology def: "Relationship between orthologs in two species, when duplications more recent than the species split have occured in both species." [DOI:10.1038/415741a "Theissen G (2002) Orthology: Secret life of genes. Nature 415:741", http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] synonym: "co-orthology" RELATED [] synonym: "many-to-many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] is_a: HOM:0000017 ! orthology is_a: HOM:0000036 ! many:many homology [Typedef] id: HOM:0000049 name: within-species paralogy def: "Relationship between two genes of the same species that arose from a duplication event." [http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] is_transitive: true is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000050 name: between-species paralogy def: "Relationship between two genes of different species that arose from a duplication event." [http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000051 name: postdisplacement def: "Delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis "Wikipedia 07/2009"] synonym: "post-displacement" EXACT [] is_a: HOM:0000029 ! paedomorphorsis [Typedef] id: HOM:0000052 name: hypermorphosis def: "A form of peramorphosis which represents a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis "Wikipedia 07/2009", ISBN:978-0674639416 "Gould SJ (1985) Ontogeny and Phylogeny. Belknap Press of Harvard University Press"] is_a: HOM:0000030 ! peramorphosis [Typedef] id: HOM:0000053 name: synology def: "Xenology that arose, not by the transfer of a gene between two species, but by a hybridization of two species." [doi:10.1007/BF00173425 "Gogarten JP (1994) Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages. J Mol Evol, 39, 541-543", DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231."] is_a: HOM:0000018 ! xenology [Typedef] id: HOM:0000054 name: isoorthology def: "Orthology with retention of the ancestral function." [DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231."] xref: ECO:0000080 "inferred from phylogeny" is_a: HOM:0000017 ! orthology is_a: HOM:0000062 ! equivalogy [Typedef] id: HOM:0000055 name: tandem paralogy def: "Relationship between sequences which have diverged after a duplication event and are adjacent in a chromosome segment." [DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231.", ISBN:978-0878932665 "Graur D and Li WH (2000) Molecular evolution. (Sinauer Associates, Sunderland, MA)"] synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000057 name: latent homology def: "Latent homology is the situation in which the developmental basis for a structure seen in a descendant exists in the developmental program that produced a different structure in the ancestor. Used for structures in closely related taxa." [DOI:10.1007/BF02814485 "Rutishauser R and Moline P (2005) Evo-devo and the search for homology (ÒsamenessÓ) in biological systems. Theory in Biosciences 124:213-241", DOI:doi\:10.1016/j.jhevol.2006.11.010 "Hall BK (2007) Homoplasy and homology: Dichotomy or continuum? Journal of Human Evolution. 52:5, 473-479", ISBN:0199141118 "de Beer G (1971). Homology, an unsolved problem. London, Oxford University Press."] synonym: "apomorphic tendency" EXACT [] synonym: "cryptic homology" EXACT [] synonym: "homoiology" RELATED [] synonym: "homoplastic tendency" RELATED [] synonym: "underlying synapomorphy" EXACT [] is_a: HOM:0000005 ! parallelism is_a: HOM:0000058 ! syngeny [Typedef] id: HOM:0000058 name: syngeny def: "Syngeny is the relationship of a recognizably corresponding character that occurs in two or more taxa, or as a repeated unit within an individual, and has a shared generative basis, regardless of the phylogenetic distribution of the character." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R "Butler AB and Saidel WM (2000) Defining sameness: historical, biological, and generative homology. Bioessays 22, 9: 846-53"] comment: Cannot be used when orthologous patterning gene are organising 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 [Typedef] id: HOM:0000060 name: apparent orthology def: "Single copy paralogs arising from reciprocal gene loss. Genes that actually are paralogs but appear to be orthologous due to differential, lineage-specific gene loss." [DOI:10.1146/annurev.genet.39.073003.114725 "Koonin EV (2005) ORTHOLOGS, PARALOGS, AND EVOLUTIONARY GENOMICS. Annual Review of Genetics, 39: 309-338", http://www.ensembl.org/info/docs/compara/homology_method.html "Ensembl Compara documentation 07/2009"] synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "pseudoorthology" EXACT [] is_a: HOM:0000011 ! paralogy is_a: HOM:0000019 ! 1:1 homology [Typedef] id: HOM:0000061 name: pseudoparalogy def: "Homology between genes that come out as paralogs in a single-genome analysis but actually ended up in the given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [DOI:10.1146/annurev.genet.39.073003.114725 "Koonin EV (2005) ORTHOLOGS, PARALOGS, AND EVOLUTIONARY GENOMICS. Annual Review of Genetics, 39: 309-338"] is_a: HOM:0000018 ! xenology [Typedef] id: HOM:0000062 name: equivalogy def: "Set of genes that are believed to have the same molecular function and to be related to a common ancestor having that same function. This may include examples of paralogy and xenology." [DOI:10.1093/nar/gkl1043 "Selengut JD et al. (2007) TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acid Research, 35: D260-D264"] is_transitive: true is_a: HOM:0000007 ! historical homology is_a: HOM:0000065 ! functional equivalence [Typedef] id: HOM:0000063 name: interology def: "Relationship between orthologous pairs of interacting molecules in different organisms." [DOI:10.1101/gr.1774904 "Yu H et al. (2004) Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs. Genome Research 14:1107-1118.", DOI:10.1126/science.287.5450.116 "Walhout AJM et al. (2000) Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development. Science 287:116-122."] is_transitive: true is_a: HOM:0000007 ! historical homology [Typedef] id: HOM:0000065 name: functional equivalence def: "Anatomical structures or genes which are similar or interchangeable in function." [DOI:10.1007/BF02814484 "Theissen G (2005) Birth, life and death of developmental control genes: New challenges for the homology concept. Theory in Biosciences 124:199-212", DOI:10.1038/415741a "Theissen G (2002) Orthology: Secret life of genes. Nature 415:741"] synonym: "functional similarity" RELATED [] is_transitive: true is_a: HOM:0000000 ! similarity [Typedef] id: HOM:0000066 name: iterative homology def: "Homology between parts of the same organism." [doi:10.1146/annurev.es.20.110189.000411 "Wagner GP (1999) The Biological Homology Concept. Annual Review of Ecology and Systematics 20: 51-69"] is_transitive: true is_a: HOM:0000008 ! biological homology [Typedef] id: HOM:0000068 name: paraxenology def: "Duplicate or multiple xenology, differing from simple xenology by the presence of two or more copies of the foreign gene in the host genome." [PMID:3065587 "Patterson C (1988) Homology in classical and molecular biology. Mol Biol Evol 5:603-625"] is_a: HOM:0000018 ! xenology [Typedef] id: HOM:0000069 name: plerology def: "Extra similarity between paralogous sequences which implies a relationship between paralogs that is incongruent with that based on other paralogies. Usually due to gene conversion process." [DOI:10.1016/S0168-9525(00)02005-9 "Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16:227-231.", PMID:3065587 "Patterson C (1988) Homology in classical and molecular biology. Mol Biol Evol 5:603-625"] is_a: HOM:0000011 ! paralogy [Typedef] id: HOM:0000071 name: homotopy def: "Relationship between structures with the same or similar relative positions." [DOI:10.1007/BF02814484 "Theissen G (2005) Birth, life and death of developmental control genes: New challenges for the homology concept. Theory in Biosciences 124:199-212", DOI:10.1007/BF02814485 "Rutishauser R and Moline P (2005) Evo-devo and the search for homology (ÒsamenessÓ) in biological systems. Theory in Biosciences 124:213-241", ISBN:0123195837 "Sattler R (1994) in Hall BK (Ed.) Homology: The Hierarchical Basis of Comparative Biology. Academic Press, p. 429"] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. is_transitive: true is_a: HOM:0000006 ! structural homology [Typedef] id: HOM:0000072 name: homeosis def: "Relationship of an ectopic structure to the normally positioned structure." [DOI:10.1007/BF02814485 "Rutishauser R and Moline P (2005) Evo-devo and the search for homology (ÒsamenessÓ) in biological systems. Theory in Biosciences 124:213-241"] synonym: "heterotopy" RELATED [] is_a: HOM:0000008 ! biological homology inverse_of: HOM:0000071 ! homotopy [Typedef] id: HOM:0000073 name: homoeology def: "Homology of genes or chromosomes derived from allopolyploidy." [DOI:10.1073/pnas.0505156102 "Nomura T et al. (2005) Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat. Proc. Natl. Acad. Sci. 102, 45: 16490-16495"] is_a: HOM:0000022 ! ohnology is_a: HOM:0000053 ! synology [Typedef] id: HOM:0000074 name: paramorphism def: "Relationship between two structures when one originated as a duplicate of the other and co-opted the expression of genes involved in growth and patterning of the ancestral structure." [DOI:10.1046/j.1525-142x.2000.00054.x "Minelli A (2000) Limbs and tail as evolutionarily diverging duplicates of the main body axis. Evolution and Development, 2, 3:157-165"] synonym: "axis paramorphism" RELATED [] is_a: HOM:0000003 ! homocracy is_a: HOM:0000066 ! iterative homology [Typedef] id: HOM:0000075 name: regulogy def: "Relationship between orthologous pairs of transcription factors and downstream regulated genes in different organisms." [DOI:10.1101/gr.1774904 "Yu H et al. (2004) Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs. Genome Research 14:1107-1118."] is_transitive: true is_a: HOM:0000007 ! historical homology