Homology (biology): Difference between revisions

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In biology, homology is any similarity between structures that is due to their shared ancestry. 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 is measured by comparing protein or DNA sequences, and genes that share a high sequence identity or similarity support the hypothesis that they share a common ancestor and are therefore homologous. Sequence homology may also indicate common function. Homologous chromosomes are non-identical chromosomes that can pair (synapse) during meiosis, and are believed to share common ancestry.

The word homologous derives from the ancient Greek ομολογειν, 'to agree'.

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 humans 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. For example, the wings of insects, the wings of bats and the wings of birds are analogous but not homologous; this phenomenon is called "homoplasy". These similar structures evolved through different developmental pathways, in a process known as convergent evolution.

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 2 or more genes have highly similar DNA sequences, it is likely that they are homologous. But sequence similarity may arise from different ancestors: 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.

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.)

Homology of sequences are of two types: orthologous and paralogous. [2]

Orthology

Orthologs, or orthologous genes, are any genes in different species, that are similar to each other and originated from a common ancestor, regardless of their functions. Thus orthologs are separated by an evolutionary 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. The term "ortholog" was coined in 1970.

A second definition of orthologous has arisen to describe any genes with very similar functions in different species. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure. This expanded use of orthologous is often criticized for confusing the meaning of the word, and furthermore being theoretically unsound, as the idea of a "very similar function" requires arbitrary cutoffs for similarity, and it is not clear how similarity of function is to be measured in different organisms.

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 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.

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 S, and hemoglobin F) are 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.

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 ^[1]. 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.^[2]

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.^[3] 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.

References

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.
Mindell, D.P. and A. Meyer. 2001. "Homology evolving." Trends in Ecology and Evolution 16:434-440.

Notes

^ Ken Wolfe (2000) Robustness—it's not where you think it is. Nature Genetics May;25(1):3-4. [1]
^ NCBI Phylogenetics Factsheet
^ RC King and WD Stansfield (1997). A Dictionary of Genetics (5^th Edition ed.). Oxford University Press. {{cite book}}: |edition= has extra text (help)

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 '''Orthologs''', or orthologous genes, are any genes in different species, that are similar to each other and originated from a common ancestor, regardless of their functions.  Thus orthologs are separated by an evolutionary [[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.  The term "ortholog" was coined in 1970.
-A second definition of ''orthologous'' has arisen to describe any genes with very similar functions in different species. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure.
+A second definition of ''orthologous'' has arisen to describe any genes with very similar functions in different species. This differs from the original definition in that there is no statement about evolutionary relation, or similarity in sequence or structure. This expanded use of ''orthologous'' is often criticized for confusing the meaning of the word, and furthermore being theoretically unsound, as the idea of a "very similar function" requires arbitrary cutoffs for similarity, and it is not clear how similarity of function is to be measured in different organisms.
 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 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.