Homology

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In evolutionary biology, homology refers to any similarity between characteristics of organisms that is due to their shared ancestry. The word homologous derives from the ancient Greek ομολογειν, 'to agree'. There are examples in different branches of biology. Anatomical structures that perform the same function in different biological species and evolved from the same structure in some ancestor species are homologous. In genetics, homology refers to a similarity of DNA sequences. The DNA sequences are usually similar, not identical. DNA sequences in the same cell can be similar, and DNA in different organisms can be similar. DNA codes with similar sequences are presumed to have a common ancestry. Homologous chromosomes are chromosomes with the same genes and similar sequences. Homology is important in reproduction because pairs of homologous chromosomes line up together during meiosis.

The concept of homology is contrasted with that of analogy, which refers to two tructures that perform the same or similar function by a similar mechanism but evolved separately. Hence, similar structures may have evolved through different pathways, a process known as convergent evolution, or may be homologous.

Homology of structures in evolution

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. 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). This is called homoplasy. But structures can be homologous and analogous. The wings of a bat and a bird are homologous, in that they both developed from the pectoral fins of fish[citation needed]. They are also analogous, in that the forelimbs of the ancestors of birds and of bats developed into organs of a similar new function independently. Thus evolution can be initially divergent, giving rise to homologous structures, and subsequently convergent, causing the structures to become analogous again.

From the point of view of evolutionary developmental biology (evo-dev) 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 to leaves and shoots because they combine some traits of leaves and shoots[1][2]

Homology of sequences in genetics

Homology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics. For example, in general, if two or more genes have highly similar DNA sequences, it is likely that they are homologous. But sequence similarity may also arise without common ancestry: short sequences may be similar by chance, and sequences may be similar because both were selected to bind to a particular protein, such as a transcription factor. 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.

The phrase "percent homology" is sometimes used but is incorrect. "Percent identity" or "percent similarity" should be used to quantify the similarity between the biomolecule sequences. For two naturally occurring sequences, percent identity is a factual measurement, whereas homology is a hypothesis supported by evidence. 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.

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[3], HOMOLENS[4], HOGENOM[5].

Homologous sequences are of two types: orthologous and paralogous.[6]

Orthology

Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that are similar to each other because they originated from a common ancestor. The term "ortholog" was coined in 1970 by Walter Fitch.

The strongest evidence that two similar genes are orthologous is the result of a phylogenetic analysis of the gene lineage. Genes that are found within one clade are orthologs, descended from a common ancestor. Orthologs often, but not always, have the same function.

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.

Some other specialized biological databases provide tools to identify and collect orthologous sequences: OrthoMCL[7] for eukaryotes, OrthoMaM[8] for mammals, OrthologID[9] and GreenPhylDB[10] for plants.

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.

A set of sequences that are paralogous are called paralogs of each other. 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 to 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 genes 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.

Another example can be found in rodents such as rats and mice. Rodents have a pair of paralogous insulin genes, although it is unclear if any divergence in function has occurred.

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. This is a common problem in bioinformatics: when genomes of different species have been sequenced and homologous genes have been found, one can not immediately conclude that these genes have the same or similar function, as they could be paralogs whose function has diverged.

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.[11] Ohnologs 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.[12]

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.

Homologous chromosome sets

Homologous chromosomes are non-identical chromosomes that can pair (synapse) during meiosis.[13] Except for the sex chromosomes, homologous chromosomes share significant sequence similarity across their entire length, typically contain the same sequence of genes, and pair up to allow for proper disjunction during meiosis. The chromosomes can also undergo cross-over at this stage. There may be some variations between genes on homologues giving rise to alternate forms or alleles. Sex chromosomes have a shorter region of sequence similarity. Based on the sequence similarity and our knowledge of biology, it is believed that they are paralogous.

References

  1. Sattler R (1984). "Homology — a continuing challenge". Systematic Botany 9 (4): 382–94. doi:10.2307/2418787.
  2. Sattler, R. (1994). "Homology, homeosis, and process morphology in plants", in Hall, Brian Keith: Homology: the hierarchical basis of comparative biology. Academic Press, 423–75. ISBN 0-12-319583-7. 
  3. 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. PMID 8036164.
  4. 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 (Suppl 6): S3. doi:10.1186/1471-2105-10-S6-S3. PMID 19534752.
  5. HOGENOM : Database of Complete Genome Homologous Genes Families
  6. Koonin EV (2005). "Orthologs, paralogs, and evolutionary genomics". Annu. Rev. Genet. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID 16285863.
  7. 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. PMID 16381887.
  8. 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. PMID 18053139.
  9. 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.
  10. 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. PMID 17986457.
  11. Wolfe K (May 2000). "Robustness—it's not where you think it is". Nat. Genet. 25 (1): 3–4. doi:10.1038/7556010.1038/75560. PMID 10802639.
  12. NCBI Phylogenetics Factsheet
  13. RC King and WD Stansfield (1997). A Dictionary of Genetics, 5th, Oxford University Press. ISBN 0-19-509442-5. 

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