Homology (biology)

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The word homologous is from the Ancient Greek for 'agree'- ομολογειν, eg. homologous chromosomes 'agree' with each other.

In genetics, homology is measured by comparing protein or DNA sequences. Two homologous genes share a high sequence identity or similarity, supporting the hypothesis that they share a common ancestor. Sequence homology may also indicate common function. Sequence regions that are homologous may also be called conserved. Homologous sequences can be classified into two subtypes: orthologous or paralogous.

In evolutionary biology, Homology is used to describe structures that are alike due to common ancestry.

1 Homology of structures in evolution
2 Homology of sequences in genetics
- 2.1 Orthology
- 2.2 Paralogy
3 Homologous chromosome sets
4 Literature
5 Notes
6 See also

[edit] Homology of structures in evolution

In biology, two or more structures are said to be homologous if they are alike because of shared ancestry. This could be evolutionary ancestry, meaning that the structures evolved from some structure in a common ancestor (the wings of bats and the arms of humans are homologous in this sense), or developmental ancestry, meaning that the 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; for instance, the wings of insects, the wings of bats and the wings of birds are analogous but not homologous, this phenomenon is known as homoplasy. These similar structures evolved through different developmental pathways, in a process known as convergent evolution.

[edit] 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 genes have an almost identical DNA sequence, it is likely that they are homologous. However, it may be that the sequence similarity did not arise from their sharing a common ancestor; short sequences may be similar by chance, or 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.

The phrase "percent homology", as sometimes used by those outside the fields of evolutionary biology or bioinformatics, is incorrect. The phrases "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.

Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. (See sequence clustering and sequence alignment.)

[edit] Orthology

Homology of sequences can be of two types: orthologous or paralogous.

The term "ortholog" was coined in 1970 to describe two similar genes in two different species that originated from a common ancestor. Despite this common origin, the genes need not necessarily have the same function. Homologous sequences are orthologous if they were separated by a speciation event: if a gene exists in a species, and that species diverges into two species, then the divergent copies of this gene in the resulting species are orthologous.

A second definition of orthologous has arisen to describe any two genes in two different species with very similar functions. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure.

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

[edit] 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 pair of sequences that are orthologous to each other are called orthologs, a pair that are paralogous are called paralogs. Orthologs will typically have the same or similar function. This is not always true for paralogs: 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 S, and hemoglobin F) are all paralogs of each other. While each of these genes serve the same basic function of oxygen transport, they have already diverged slightly in function: fetal hemoglobin (hemoglobin F) has a higher affinity to oxygen than adult hemoglobin.

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.

[edit] Homologous chromosome sets

Homologous chromosomes are non-identical chromosomes that can pair (synapse) during meiosis.^[1] 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 homologs 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.

[edit] Literature

Fitch, W.M. 2000. Homology: a personal view on some of the problems. Trends Genet. 16(5):227-31.
Dewey, C and Pachter L. "Evolution at the Nucleotide Level: The Problem of Whole-Genome Multiple Alignment" Human Molecular Genetics 15:R51-R56.
Haeckel, Е. Generelle Morphologie der Organismen. Bd 1-2. Вerlin, 1866.
Gegenbaur, G. Vergleichende Anatomie der Wirbelthiere... Leipzig, 1898.
Owen, R. On the archetype and homologies of the vertebrate skeleton. London, 1847.
DePinna, M.C.C. 1991. "Concepts and tests of homology in the cladistic paradigm." Cladistics 7: 367-394.