Difference between revisions of "Homology (biology)" - New World Encyclopedia
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| − | In biology, '''homology''' is any similarity between structures that is attributed to their shared ancestry. There are examples in different branches of biology. Anatomical structures that | + | In biology, '''homology''' is any similarity between structures that is attributed to their shared ancestry. There are examples in different branches of biology. Anatomical structures that are similar in different biological taxa ([[species]], [[genus|genera]], etc.) would be termed homologous if they evolved from the same structure in some ancestor. |
In [[genetics]], homology is measured by comparing [[protein]] or [[DNA]] sequences, and 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. Homologous chromosomes are non-identical [[chromosome]s] that can pair (synapse) during [[meiosis]], and are believed to share common ancestry. | In [[genetics]], homology is measured by comparing [[protein]] or [[DNA]] sequences, and 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. Homologous chromosomes are non-identical [[chromosome]s] that can pair (synapse) during [[meiosis]], and are believed to share common ancestry. | ||
| − | Similarity in structures between diverse organisms—such as the similiar skeletal structures of the forelimbs of humans, bats, | + | Similarity in structures between diverse organisms—such as the similiar skeletal structures (utilizing same bones) of the forelimbs of humans, bats, whales, birds, dogs, and alligators—provides evidence of [[evolution#theory of descent with modification|evolution by common descent]] (theory of descent with modification). There is substantial evidence that new forms do develop on the foundation of earlier stages. However, it would be incorrect to state that homology provides evidence of [[evolution]] because it would be circular reasoning, with homology defined as similarity due to shared ancestry. |
The word ''homologous'' derives from the [[ancient Greek]] ''ομολογειν'', 'to agree'. | The word ''homologous'' derives from the [[ancient Greek]] ''ομολογειν'', 'to agree'. | ||
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== Homology of structures in evolution == | == Homology of structures in evolution == | ||
| − | Shared ancestry can be [[evolution]]ary or developmental. Evolutionary ancestry means that structures evolved from some structure in a common ancestor; for example, the wings of [[bat]]s and the arms of [[human]]s are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in [[embryo]]nal development; the [[ovary|ovaries]] of female humans and the [[testicle]]s of male humans are homologous in this sense. | + | Shared ancestry can be [[evolution]]ary or developmental. Evolutionary ancestry means that structures evolved from some structure in a [[evolution#theory of descent with modification|common ancestor]]; for example, the wings of [[bat]]s and the arms of [[human]]s are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in [[embryo]]nal development; the [[ovary|ovaries]] of female humans and the [[testicle]]s of male humans are homologous in this sense. |
| − | Homology is different from [[analogy (biology)|analogy]]. | + | Homology is different from [[analogy (biology)|analogy]]. For example, the wings of [[insect]]s, the wings of [[bat]]s, and the wings of [[bird]]s are analogous but not homologous; this phenomenon is called "homoplasy". These similar structures evolved through different [[Developmental biology|development]]al pathways, in a process labelled as [[convergent evolution]]. |
== Homology of sequences in genetics == | == Homology of sequences in genetics == | ||
| − | Homology among | + | Homology among [[protein]]s and [[DNA]] is often concluded on the basis of sequence similarity, especially in bioinformatics. For example, in general, if two [[gene]]s have an almost identical DNA sequence, 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 (genetics)|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. | + | 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. |
| − | Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. | + | Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. |
Homology of sequences are of two types: orthologous and paralogous. | Homology of sequences are of two types: orthologous and paralogous. | ||
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=== Orthology === | === Orthology === | ||
| − | '''Orthologs''', or orthologous genes, are any | + | '''Orthologs''', or orthologous genes, are any [[gene]]s in different [[species]], that are similar to each other and are attributed to have 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 | + | 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 [[evolution]]ary 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 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. | + | Orthologous sequences provide useful information in [[taxonomy|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 === | === Paralogy === | ||
| − | Homologous sequences are '''paralogous''' if they were separated by a | + | 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. | + | 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. It is considered that 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 [[evolution|evolve]]. The genes [[Translation (genetics)|encoding]] [[myoglobin]] and [[hemoglobin]] are considered to be ancient paralogs. Similarly, the four known classes of hemoglobins ( | + | Paralogous sequences provide useful insight to the way genomes [[evolution|evolve]]. The genes [[Translation (genetics)|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 considered to be paralogs of each other. While each of these genes serve the same basic function of [[oxygen]] transport, they differ slightly in function: fetal hemoglobin (hemoglobin F) has a higher affinity to oxygen than adult hemoglobin. |
| − | Another example can be found in | + | Another example can be found in [[rodent]]s such as [[rat]]s and [[mice]]. Rodents have a pair of [[insulin]] genes considered to be paralogous, 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 | + | 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 [[chimpanzee]]s are considered 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. |
=== Xenology === | === Xenology === | ||
| − | Homologs resulting from | + | 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 (NCBI 2004). |
== Homologous chromosome sets == | == Homologous chromosome sets == | ||
| − | + | Homologous chromosomes are defined as non-identical [[chromosome]]s that can pair (synapse) during [[meiosis]] (King and Stansfield 1997). Except for the [[sex chromosome]]s, homologous chromosomes share significant sequence similarity across their entire length, typically contain the same sequence of [[gene]]s, 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 == | == References == | ||
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| − | == | + | * DePinna, M. C. C. 1991. Concepts and tests of homology in the cladistic paradigm. ''Cladistics'' 7: 367-394. |
| − | + | * Dewey, C., and L. Pachter. 2006. [http://hmg.oxfordjournals.org/cgi/content/abstract/15/suppl_1/R51?ijkey=wGrptPhAQdD87An&keytype=ref Evolution at the nucleotide level: The problem of multiple whole-genome alignment]. ''Human Molecular Genetics'' 15(Review Issue 1): R51-R56. Retrieved April 26, 2007. | |
| + | * Fitch, W. M. 2000. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=10782117 Homology: A personal view on some of the problems.] ''Trends Genet.'' 16(5): 227-31. Retrieved April 26, 2007. | ||
| + | * Gegenbaur, G. 1898. ''Vergleichende Anatomie der Wirbelthiere'' Leipzig. | ||
| + | * Haeckel, Е. 1866. ''Generelle Morphologie der Organismen.'' Bd 1-2. Вerlin. | ||
| + | * King, R. C., and W. D. Stansfield. 1997. ''A Dictionary of Genetics'', 5th ed. New York: Oxford University Press. ISBN 0195094417. | ||
| + | * National Center for Biotechnology Information (NCBI). 2004. [http://www.ncbi.nlm.nih.gov/About/primer/phylo.html Just the facts: A basic introduction to the science underlying NCBI resources: Systematics and molecular phylogenetics]. ''NCBI: A Science Primer''. Retrieved April 26, 2007. | ||
| + | * Owen, R. 1847. ''On the Archetype and Homologies of the Vertebrate Skeleton.'' London. | ||
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[[Category:Life sciences]] | [[Category:Life sciences]] | ||
{{credit|118780639}} | {{credit|118780639}} | ||
Revision as of 23:03, 26 April 2007
In biology, homology is any similarity between structures that is attributed to their shared ancestry. There are examples in different branches of biology. Anatomical structures that are similar in different biological taxa (species, genera, etc.) would be termed homologous if they evolved from the same structure in some ancestor.
In genetics, homology is measured by comparing protein or DNA sequences, and 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. Homologous chromosomes are non-identical [[chromosome]s] that can pair (synapse) during meiosis, and are believed to share common ancestry.
Similarity in structures between diverse organisms—such as the similiar skeletal structures (utilizing same bones) of the forelimbs of humans, bats, whales, birds, dogs, and alligators—provides evidence of evolution by common descent (theory of descent with modification). There is substantial evidence that new forms do develop on the foundation of earlier stages. However, it would be incorrect to state that homology provides evidence of evolution because it would be circular reasoning, with homology defined as similarity due to shared 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 labelled 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 two genes have an almost identical DNA sequence, 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.
Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences.
Homology of sequences are of two types: orthologous and paralogous.
Orthology
Orthologs, or orthologous genes, are any genes in different species, that are similar to each other and are attributed to have 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.
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. It is considered that 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 considered to be paralogs of each other. While each of these genes serve the same basic function of oxygen transport, they differ 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 insulin genes considered to be paralogous, 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 considered 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.
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 (NCBI 2004).
Homologous chromosome sets
Homologous chromosomes are defined as non-identical chromosomes that can pair (synapse) during meiosis (King and Stansfield 1997). 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.
ReferencesISBN links support NWE through referral fees
- DePinna, M. C. C. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7: 367-394.
- Dewey, C., and L. Pachter. 2006. Evolution at the nucleotide level: The problem of multiple whole-genome alignment. Human Molecular Genetics 15(Review Issue 1): R51-R56. Retrieved April 26, 2007.
- Fitch, W. M. 2000. Homology: A personal view on some of the problems. Trends Genet. 16(5): 227-31. Retrieved April 26, 2007.
- Gegenbaur, G. 1898. Vergleichende Anatomie der Wirbelthiere Leipzig.
- Haeckel, Е. 1866. Generelle Morphologie der Organismen. Bd 1-2. Вerlin.
- King, R. C., and W. D. Stansfield. 1997. A Dictionary of Genetics, 5th ed. New York: Oxford University Press. ISBN 0195094417.
- National Center for Biotechnology Information (NCBI). 2004. Just the facts: A basic introduction to the science underlying NCBI resources: Systematics and molecular phylogenetics. NCBI: A Science Primer. Retrieved April 26, 2007.
- Owen, R. 1847. On the Archetype and Homologies of the Vertebrate Skeleton. London.
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