関: orthologue

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For use of the term 'homologous' in reference to chromosomes, see Homologous chromosomes.

The principle of homology: The biological derivation relationship (shown by colors) of the various bones in the forelimbs of four vertebrates is known as homology and was one of Darwin’s arguments in favor of evolution.

The concept of homology is fundamental to the field of comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Homology is evaluated strictly in an evolutionary context. That is, organs in two species are homologous only if the same structure was present in their last common ancestor. Organs as disparate as a bat's wing, a seal's flipper, a cat's limb and a human arm have a common underlying anatomy which was present in their last common ancestor and so therefore are homologous as forelimbs.

Forelimbs in mammals provide one example of homology.

Homologous^{[Etymology 1]} traits of organisms are therefore due to descent from a common ancestor. The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not present in the last common ancestor but rather evolved separately. An example of an analogous trait would be the wings of bats and birds, which evolved independently in each lineage separately after diverging from an ancestor without wings.

It is important to distinguish between different hierarchical levels of homology in order to make informative biological comparisons. In the above example, the bird and bat wings are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods.^[1] Homology can also be described at the level of the gene. In genetics homology can refer to both the gene (DNA) and the corresponding protein product.

1 Etymology
2 Anatomical homology
3 Homologous structures in other phyla
4 Homology between genders and forms
5 Homologies across phyla
6 Determining homology
7 Plants
8 Sequence homology
- 8.1 Orthology
- 8.2 Paralogy
- 8.3 Ohnology
- 8.4 Xenology
- 8.5 Gametology
9 See also
10 Notes
11 References
12 Further reading
13 External links

Etymology

The word homology, coined in about 1656, derives from the Greek homologos, where homo = agreeing, equivalent, same + logos = relation. In biology, two things are homologous if they bear the same relationship to one another, such as a certain bone in various forms of the "hand".

Ray Lankester defined the terms "homogeny", meaning homology due to inheritance from a common ancestor, and "homoplasty", meaning homology due to other factors.^[2]^[3]

Anatomical homology

The wings of pterosaurs (1), bats (2) and birds (3) are analogous as wings, but homologous as forelimbs.

Shared ancestry can be evolutionary or developmental. Evolutionary ancestry means that structures evolved from some structure in a common ancestor; for example, the wings of bats and the arms of primates are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in embryonal development; the ovaries of female humans and the testicles of male humans are homologous in this sense.

Homology is different from analogy, which describes the relation between characters that are apparently similar yet phylogenetically independent. The wings of a maple seed and the wings of an albatross are analogous but not homologous (they both allow the organism to travel on the wind, but they didn't both develop from the same structure). Analogy is commonly also referred to as homoplasy, which is further distinguished into parallelism, reversal, and convergence.^[4]

From the point of view of evolutionary developmental biology (evo-devo) where evolution is seen as the evolution of the development of organisms, Rolf Sattler emphasized that homology can also be partial. New structures can evolve through the combination of developmental pathways or parts of them. As a result, hybrid or mosaic structures can evolve that exhibit partial homologies. For example, certain compound leaves of flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and shoots.^[5]^[6]

Homologous structures in other phyla

Discussions of homology commonly limit themselves to the limbs of tetrapod vertebrates, occasionally touching on other structures, such as modified teeth as in whales and elephants. Homologies provide important insights into classification elsewhere in the animal kingdom, although some of them may be highly counterintuitive. For example, within the arthropods, Brusca and Brusca ^[7] provide the following homologies for the first 10 somites (embryonic segments) in several groups of arthropods, but add that "...the subject of head appendage homology among the arthropods is quite unsettled and highly controversial..."

Somite	Trilobite	Spider (Chelicerata)	Centipede (Uniramia)	Insect (Uniramia)	Shrimp (Crustacea)
1	antennae	chelicerae (jaws and fangs)	antennae	antennae	1st antennae
2	1st legs	pedipalps	-	-	2nd antennae
3	2nd legs	1st legs	mandibles	mandibles	mandibles (jaws)
4	3rd legs	2nd legs	1st 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

Homology between genders and forms

Main article: List of homologues of the human reproductive system

The term homology is sometimes applied to reproductive structures that share a common embryonic origin, but become spectacularly different between the two genders in the adult. Those listed below are some of the more commonly cited examples.

Male structure	Female structure	Notes
prostate	skene's gland	-
penis	clitoris	-
-	uterus	homologous to eggshell-depositing organs in reptiles and birds
bulbourethral gland	Bartholin's gland	-

Among insects, the stinger used by infertile female worker bees is a modified ovipositor.

Homologies across phyla

For more details on this topic, see Deep homology.

Determining homology

Systematists identify two forms of homology: primary homology is that implied by a researcher, who states a belief that two characters share an ancestry; secondary homology is implied by parsimony analysis, where a character that only occurs once on a tree is taken to be homologous.^[8]

Plants

Modifications of primary leaves, stems, and roots occur in many higher plants.

Examples:

Primary organs	Defensive structures	Storage structures
Leaves	Spines	swollen leaves as in succulents
Stems	Thorns	tubers such as the potato, rhizomes such as ginger, and the fleshy stems of cacti.
Roots	-	carrot, and root tubers such as sweet potatoes

Sequence homology

As with anatomical structures, homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs).^[9]

Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms "percent homology" and "sequence similarity" are often used interchangeably. As with anatomical structures, high sequence similarity might occur because of convergent evolution^{[citation needed]}, or, as with shorter sequences, because of chance. Such sequences are similar but not homologous. Sequence regions that are homologous are also called conserved. This is not to be confused with conservation in amino acid sequences in which the amino acid at a specific position has been substituted with a different one with functionally equivalent physicochemical properties. One can, however, refer to partial homology where a fraction of the sequences compared (are presumed to) share descent, while the rest does not. For example, partial homology may result from a gene fusion event.

A sequence alignment of two proteins, produced by ClustalW

Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. (See sequence clustering and sequence alignment.) Some specialized biological databases collect homologous sequences in animal genomes: HOVERGEN,^[10] HOMOLENS,^[11] HOGENOM.^[12]

Orthology

Homologous sequences are orthologous if they were 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. Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. The term "ortholog" was coined in 1970 by Walter Fitch.^[13]

For instance, the plant Flu regulatory protein is present both in Arabidopsis (multicellular higher plant) and Chlamydomonas (single cell green algae). The Chlamydomonas version is more complex: it crosses the membrane twice rather than once, contains additional domains and undergoes alternative splicing. However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of gene engineering. Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes,^[14] inherited from the shared ancestor.

Orthology is strictly defined in terms of ancestry. Given that the exact ancestry of genes in different organisms is difficult to ascertain due to gene duplication and genome rearrangement events, the strongest evidence that two similar genes are orthologous is usually found by carrying out phylogenetic analysis of the gene lineage. Orthologs often, but not always, have the same function.^[15]

Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. The pattern of genetic divergence can be used to trace the relatedness of organisms. Two organisms that are very closely related are likely to display very similar DNA sequences between two orthologs. Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied.

Several specialized biological databases provide tools to identify and analyze orthologous gene sequences. These resources employ approaches that can be generally classified into those that are based on all pairwise sequence comparisons (heuristic) and those that use phylogenetic methods. Sequence comparison methods were first pioneered by COGs,^[16] now extended and automatically enhanced by the eggNOG^[17] database. InParanoid^[18] focuses on pairwise ortholog relationships. OrthoDB^[19] appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree. Other databases that provide eukaryotic orthologs include OrthoMCL,^[20] OMA, Roundup,^[21] OrthoMaM^[22] for mammals, OrthologID^[23] and GreenPhylDB^[24] for plants.

Tree-based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in resources such as TreeFam^[25] and LOFT.^[26] A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example Ortholuge,^[27] EnsemblCompara GeneTrees^[28] and HomoloGene.^[29]

Paralogy

Homologous sequences are paralogous if they were separated by a gene duplication event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.

Paralogous genes often belong to the same species, but this is not necessary: for example, the hemoglobin gene of humans and the myoglobin gene of chimpanzees are paralogs. Paralogs can be split into in-paralogs (paralogous pairs that arose after a speciation event) and out-paralogs (paralogous pairs that arose before a speciation event). Between-species out-paralogs are pairs of paralogs that exist between two organisms due to duplication before speciation, whereas within-species out-paralogs are pairs of paralogs that exist in the same organism, but whose duplication event happened before speciation. Paralogs typically have the same or similar function, but sometimes do not: due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions.

Paralogous sequences provide useful insight into the way genomes evolve. The genes encoding myoglobin and hemoglobin are considered to be ancient paralogs. Similarly, the four known classes of hemoglobins (hemoglobin A, hemoglobin A2, hemoglobin B, and hemoglobin F) are paralogs of each other. While each of these proteins serves the same basic function of oxygen transport, they have already diverged slightly in function: fetal hemoglobin (hemoglobin F) has a higher affinity for oxygen than adult hemoglobin. Function is not always conserved, however. Human angiogenin diverged from ribonuclease, for example, and while the two paralogs remain similar in tertiary structure, their functions within the cell are now quite different.

It is often asserted that orthologs are more functionally similar than paralogs of similar divergence, but several papers have challenged this notion.^[30]^[31]^[32]

Ohnology

Ohnologous genes are paralogous genes that have originated by a process of whole-genome duplication (WGD). The name was first given in honour of Susumu Ohno by Ken Wolfe.^[33] Ohnologs/Ohnologues are interesting for evolutionary analysis because they all have been diverging for the same length of time since their common origin.

Xenology

Homologs resulting from horizontal gene transfer between two organisms are termed xenologs. Xenologs can have different functions, if the new environment is vastly different for the horizontally moving gene. In general, though, xenologs typically have similar function in both organisms.^[34]

Gametology

Gametology denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes. Gametologs result from the origination of genetic sex determination and barriers to recombination between sex chromosomes. Examples of gametologs include CHDW and CHDZ in birds.

Notes

^ from Greek ομολογειν, 'to agree'

References

^ Scotland, R. W. (2010). "Deep homology: A view from systematics". BioEssays : news and reviews in molecular, cellular and developmental biology 32 (5): 438–449. doi:10.1002/bies.200900175. PMID 20394064. edit
^ Bower, Frederick Orpen (1906). "Plant Morphology". Congress of Arts and Science: Universal Exposition, St. Louis, 1904. Houghton, Mifflin. p. 64.
^ Williams, David Malcolm; Forey, Peter L. (2004). Milestones in Systematics. CRC Press. p. 198. ISBN 0-415-28032-X.
^ Cf. Butler, A. B.: Homology and Homoplasty. In: Squire, Larry R. (Ed.): Encyclopedia of Neuroscience, Academic Press, 2009, pp. 1195–1199.
^ Sattler R (1984). "Homology — a continuing challenge". Systematic Botany 9 (4): 382–94. doi:10.2307/2418787. JSTOR 2418787.
^ Sattler, R. (1994). "Homology, homeosis, and process morphology in plants". In Hall, Brian Keith. Homology: the hierarchical basis of comparative biology. Academic Press. pp. 423–75. ISBN 0-12-319583-7.
^ Brusca, R.C. & Brusca, G.J. 1990. Invertebrates. Sinauer Associates, Sunderland.: [i]-xviii, 1-922., P. 669
^ Pinna, M. C. C. (1991). "Concepts and Tests of Homology in the Cladistic Paradigm". Cladistics 7 (4): 367–394. doi:10.1111/j.1096-0031.1991.tb00045.x. edit
^ Koonin EV (2005). "Orthologs, paralogs, and evolutionary genomics". Annu. Rev. Genet. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID 16285863.
^ HOVERGEN: Homologous Vertebrate Genes Database
Duret L, Mouchiroud D, Gouy M (June 1994). "HOVERGEN: a database of homologous vertebrate genes". Nucleic Acids Res. 22 (12): 2360–5. doi:10.1093/nar/22.12.2360. PMC 523695. PMID 8036164.
^ HOMOLENS: Homologous Sequences in Ensembl Animal Genomes
Penel S, Arigon AM, Dufayard JF et al. (2009). "Databases of homologous gene families for comparative genomics". BMC Bioinformatics 10: S3. doi:10.1186/1471-2105-10-S6-S3. PMC 2697650. PMID 19534752.
^ HOGENOM : Database of Complete Genome Homologous Genes Families
^ Fitch W. (1970). "Distinguishing homologous from analogous proteins". Syst Zool 19 (2): 99–113. doi:10.2307/2412448. PMID 5449325.
^ A Falciatore, L Merendino, F Barneche, M Ceol, R Meskauskiene, K Apel, JD Rochaix (2005). The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas. Genes & Dev, 19:176-187 [1]
^ Fang G, Bhardwaj N, Robilotto R, Gerstein MB. (2010). "Getting Started in Gene Orthology and Functional Analysis". In Troyanskaya, Olga. PLoS Comput Biol. 6 (3): e1000703. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041.
^ COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997). "A genomic perspective on protein families". Science 278 (5338): 631–7. doi:10.1126/science.278.5338.631. PMID 9381173.
^ eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P (January 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Res. 38 (Database issue): D190–5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.
^ Inparanoid: Eukaryotic Ortholog Groups
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer EL (January 2010). "InParanoid 7: new algorithms and tools for eukaryotic orthology analysis". Nucleic Acids Res. 38 (Database issue): D196–203. doi:10.1093/nar/gkp931. PMC 2808972. PMID 19892828.
^ OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs
Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV (January 2011). "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011". Nucleic Acids Res. 39 (Database issue): D283–8. doi:10.1093/nar/gkq930. PMC 3013786. PMID 20972218.
^ OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006). "OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups". Nucleic Acids Res. 34 (Database issue): D363–8. doi:10.1093/nar/gkj123. PMC 1347485. PMID 16381887.
^ Roundup
DeLuca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (2006). "Roundup: a multi-genome repository of orthologs and evolutionary distances". Bioinformatics 22 (16): 2044–2046. doi:10.1093/bioinformatics/btl286. PMID 16777906.
^ OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (2007). "OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics". BMC Evol. Biol. 7: 241. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139.
^ OrthologID
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (March 2006). "OrthologID: automation of genome-scale ortholog identification within a parsimony framework". Bioinformatics 22 (6): 699–707. doi:10.1093/bioinformatics/btk040. PMID 16410324.
^ GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (January 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Res. 36 (Database issue): D991–8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457.
^ TreeFam: Tree families database
Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R (January 2008). "TreeFam: 2008 Update". Nucleic Acids Res. 36 (Database issue): D283–8. doi:10.1093/nar/gkm1005. PMC 2238856. PMID 18056084.
^ TreeFam: Tree families database
van der Heijden RT, Snel B, van Noort V, Huynen MA (March 2007). "Orthology prediction at scalable resolution by phylogenetic tree analysis". BMC Bioinformatics 8: 83. doi:10.1186/1471-2105-8-83. PMC 1838432. PMID 17346331.
^ Fulton, DL; Li, YY, Laird, MR, Horsman, BG, Roche, FM, Brinkman, FS (2006-05-28). "Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics 7: 270. doi:10.1186/1471-2105-7-270. PMC 1524997. PMID 16729895.
^ Vilella, AJ; Severin, J, Ureta-Vidal, A, Heng, L, Durbin, R, Birney, E (2009 Feb). "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates". Genome Research 19 (2): 327–35. doi:10.1101/gr.073585.107. PMC 2652215. PMID 19029536.
^ Sayers, EW; Barrett, T, Benson, DA, Bolton, E, Bryant, SH, Canese, K, Chetvernin, V, Church, DM, DiCuccio, M, Federhen, S, Feolo, M, Fingerman, IM, Geer, LY, Helmberg, W, Kapustin, Y, Landsman, D, Lipman, DJ, Lu, Z, Madden, TL, Madej, T, Maglott, DR, Marchler-Bauer, A, Miller, V, Mizrachi, I, Ostell, J, Panchenko, A, Phan, L, Pruitt, KD, Schuler, GD, Sequeira, E, Sherry, ST, Shumway, M, Sirotkin, K, Slotta, D, Souvorov, A, Starchenko, G, Tatusova, TA, Wagner, L, Wang, Y, Wilbur, WJ, Yaschenko, E, Ye, J (2011 Jan). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 39 (Database issue): D38–51. doi:10.1093/nar/gkq1172. PMC 3013733. PMID 21097890.
^ Studer, Romain A.; Robinson-Rechavi (3/4/2009). "How confident can we be that orthologs are similar, but paralogs differ?". Trends in Genetics 25 (5): 210–216. doi:10.1016/j.tig.2009.03.004. PMID 19368988.
^ Nehrt, Nathan; Clark, Radivojac, Hahn (2011). "Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals". In Rzhetsky, Andrey. PLos CB 7 (6): e1002073. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233.
^ Eisen, Jonathan. "Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper".
^ Wolfe K (May 2000). "Robustness—it's not where you think it is". Nat. Genet. 25 (1): 3–4. doi:10.1038/75560. PMID 10802639.
^ NCBI Phylogenetics Factsheet

External links

Brigandt, Ingo (2011) "Essay: Homology" in: The Embryo Project Encyclopedia. ISSN: 1940-5030.

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