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In biology, '''homology''' is commonly defined as any similarity between structures that is attributed to their shared ancestry. There are examples in different levels of organization. Entire 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, and partial sequences in [[DNA]] or [[protein]] would be similarly labeled if common ancestry was the cause.
 
In biology, '''homology''' is commonly defined as any similarity between structures that is attributed to their shared ancestry. There are examples in different levels of organization. Entire 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, and partial sequences in [[DNA]] or [[protein]] would be similarly labeled if common ancestry was the cause.
  

Revision as of 21:24, 3 April 2008

In biology, homology is commonly defined as any similarity between structures that is attributed to their shared ancestry. There are examples in different levels of organization. Entire 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, and partial sequences in DNA or protein would be similarly labeled if common ancestry was the cause.

This is a redefinition from the classical understanding of the term, which predates Darwin's theory of evolution, being coined by Richard Owen in the 1840s. Historically, homology was defined as similarity in structure and position, such as the pattern of bones in a bat's wing and those in a porpoise's flipper (Wells, 2000). Conversely, the term analogy signified functional similarity, such as the wings of a bird and those of a butterfly.

Similarity in structures between diverse organisms—such as the similar 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 evidence that new forms develop on the foundation of earlier stages. However, it would be incorrect to state that homology, as presently defined, 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 term homology is also used in a non-evolutionary sense in terms of homologous chromosomes, meaning a pair of non-identical chromosomes from a diploid organism that can pair (synapse) during meiosis, or regions of chromosomes with the same set of genes.

Homology of Structures in Evolution

The principle of homology illustrated by the adaptive radiation of the forelimb of mammals. All conform to the basic pentadactyl pattern but are modified for different usages. The third metacarpal is shaded throughout; the shoulder is crossed-hatched.

Homology in the classical sense, as similarity in structure and position of anatomical features between different organisms, was important evidence used by Darwin. However, it has now been redefined as structures that trace to common ancestors. Mayr (1982) states:

After 1859 there has been only one definition of homologous that makes biological sense... Attributes of two organisms are homologous when they are derived from an equivalent characteristics of the common ancestor.

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 labeled as convergent evolution.

Wells (2000) notes that homology as now defined can no longer be used as evidence for evolution because of circular reasoning. Furthermore, he finds even retaining the pre-Darwinian definition of homology as structural similarity problematic because of such factors as the lack of correspondence between homology and development pathways, since there are examples of similar structures in adult forms where ancestry is assumed that actually are products of radically different development processes. Likewise, he notes that some assumed homologous structures trace to different genes.

Homology of Sequences in Genetics

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 chromosomes that can pair (synapse) during meiosis, and are believed to share common ancestry.

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.

There are two types of homology of sequences: 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 serves 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.

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