Homology (biology)
Encyclopedia
Homology forms the basis of organization for comparative biology
. In 1843, Richard Owen
defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying structure of bones and muscles. Owen reasoned that there must be a common structural plan for all vertebrates, as well as for each class of vertebrates.
Homologousfrom Greek
ομολογειν, 'to agree' traits of organisms are due to sharing a common ancestor
, and such traits often have similar embryological origins and development. This is contrasted with analogous
traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately
. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology.
Whether or not a trait is homologous depends on both the taxonomic and anatomical levels at which the trait is examined. For example, the bird and bat wings are homologous as forearms in tetrapod
s. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapod
s. By definition, any homologous trait defines a clade
—a monophyletic
taxon
in which all the members have the trait (or have lost it secondarily); and all non-members lack it.
A homologous trait may be homoplasious – that is, it has evolved independently, but from the same ancestral structure – plesiomorphic – that is, present in a common ancestor but secondarily lost in some of its descendants – or (syn)apomorphic – present in an ancestor and all of its descendants.
A homologous trait is often called a homolog (also spelled homologue). In genetics, the term "homolog" is used both to refer to a homologous protein, and to the gene (DNA sequence) encoding it.
In biology, two things are homologous if they bear the same relationship to one another, such as a certain bone
in various forms of the "hand."
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 primate
s are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in embryo
nal development; the ovaries
of female humans and the testicle
s of male humans are homologous in this sense.
Homology is different from analogy
, which describes the relation between characters that are apparently similar yet phylogenetically independent. 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). Analogy is commonly also referred to as homoplasy, which is further distinguished into parallelism, reversal, and convergence.
From the point of view of evolutionary developmental biology
(evo-devo) 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 flower
ing plants are partially homologous both to leaves and shoots because they combine some traits of leaves and shoots.
provide the following homologies for the first 10 somites (embryonic segments) in several groups of arthropods, but add that "...the subject of head appendage homology among the arthropods is quite unsettled and highly controversial..."
Examples:
event (orthologs) or a duplication event
(paralogs).
Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms "percent homology" and "sequence similarity" are often used interchangeably. As with anatomical structures, high sequence similarity might occur because of convergent evolution
, or, as with shorter sequences, because of chance. 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. 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,
HOMOLENS,
HOGENOM.
event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. The term "ortholog" was coined in 1970 by Walter Fitch
.
For instance, the plant Flu regulatory protein is present both in Arabidopsis (multicellular higher plant) and Chlamydomonas (single cell green algae). The Chlamydomonas version is more complex: it crosses the membrane twice rather than once, contains additional domains and undergoes alternative splicing. However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of gene engineering. Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor.
Orthology is strictly defined in terms of ancestry. Given that the exact ancestry of genes in different organisms is difficult due to gene duplication
and genome rearrangement events, the strongest evidence that two similar genes are orthologous is usually found by carrying out phylogenetic analysis of the gene lineage. 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.
Several specialized biological databases provide tools to identify and analyze orthologous gene sequences. These resources employ approaches that can be generally classified into those that are based on all pairwise sequence comparisons (heuristic) and those that use phylogenetic methods. Sequence comparison methods were first pioneered by COGs, now extended and automatically enhanced by the eggNOG database. InParanoid focuses on pairwise ortholog relationships. OrthoDB
appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree. Other databases that provide eukaryotic orthologs include OrthoMCL, OMA
, Roundup, OrthoMaM for mammals,
OrthologID
and GreenPhylDB for plants.
Tree-based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in resources such as TreeFam and LOFT. A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example Ortholuge, EnsemblCompara GeneTrees and HomoloGene.
event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.
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. Paralogs can be split into in-paralogs, (paralogous pairs that arose after a speciation event), and out-paralogs (paralogous pairs that arose before a speciation event). Between species out-paralogs are pairs of paralogs that exist between two organisms due to duplication before speciation, whereas within species out-paralogs are pairs of paralogs that exist in the same organism, but whose duplication event happened before speciation. 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 into 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 proteins 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.
It is often asserted that orthologs are more functionally similar than paralogs of similar divergence, but several papers have challenged this notion .
s that have originated by a process of whole-genome duplication (WGD). The name was first given in honour of Susumu Ohno
by Ken Wolfe. Ohnologs are interesting for evolutionary analysis because they all have been diverging for the same length of time since their common origin.
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.
determination and barriers to recombination between sex chromosomes. Examples of gametologs include CHDW and CHDZ in birds.
Comparative biology
Comparative biology is a multidisciplinary approach to understanding organismic diversity that uses natural variation and disparity to elucidate phylogenetic history. Comparative biologists attempt to understand the diversity and complexity of life at all levels—from genes, to anatomy, to...
. In 1843, Richard Owen
Richard Owen
Sir Richard Owen, FRS KCB was an English biologist, comparative anatomist and palaeontologist.Owen is probably best remembered today for coining the word Dinosauria and for his outspoken opposition to Charles Darwin's theory of evolution by natural selection...
defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying structure of bones and muscles. Owen reasoned that there must be a common structural plan for all vertebrates, as well as for each class of vertebrates.
Ancient Greek
Ancient Greek is the stage of the Greek language in the periods spanning the times c. 9th–6th centuries BC, , c. 5th–4th centuries BC , and the c. 3rd century BC – 6th century AD of ancient Greece and the ancient world; being predated in the 2nd millennium BC by Mycenaean Greek...
ομολογειν, 'to agree' traits of organisms are due to sharing a common ancestor
Common descent
In evolutionary biology, a group of organisms share common descent if they have a common ancestor. There is strong quantitative support for the theory that all living organisms on Earth are descended from a common ancestor....
, and such traits often have similar embryological origins and development. This is contrasted with analogous
Analogy (biology)
An analogy is a trait or an organ that appears similar in two unrelated organisms. The cladistic term for the same phenomenon is homoplasy, from Greek for same form. Biological anologies are often the result of convergent evolution....
traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately
Convergent evolution
Convergent evolution describes the acquisition of the same biological trait in unrelated lineages.The wing is a classic example of convergent evolution in action. Although their last common ancestor did not have wings, both birds and bats do, and are capable of powered flight. The wings are...
. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology.
Whether or not a trait is homologous depends on both the taxonomic and anatomical levels at which the trait is examined. For example, the bird and bat wings are homologous as forearms in tetrapod
Tetrapod
Tetrapods are vertebrate animals having four limbs. Amphibians, reptiles, birds and mammals are all tetrapods; even snakes and other limbless reptiles and amphibians are tetrapods by descent. The earliest tetrapods evolved from the lobe-finned fishes in the Devonian...
s. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapod
Tetrapod
Tetrapods are vertebrate animals having four limbs. Amphibians, reptiles, birds and mammals are all tetrapods; even snakes and other limbless reptiles and amphibians are tetrapods by descent. The earliest tetrapods evolved from the lobe-finned fishes in the Devonian...
s. By definition, any homologous trait defines a clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
—a monophyletic
Monophyly
In common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of the members of the group. The term is synonymous with the uncommon term holophyly...
taxon
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
in which all the members have the trait (or have lost it secondarily); and all non-members lack it.
A homologous trait may be homoplasious – that is, it has evolved independently, but from the same ancestral structure – plesiomorphic – that is, present in a common ancestor but secondarily lost in some of its descendants – or (syn)apomorphic – present in an ancestor and all of its descendants.
A homologous trait is often called a homolog (also spelled homologue). In genetics, the term "homolog" is used both to refer to a homologous protein, and to the gene (DNA sequence) encoding it.
Etymology
The word homology, coined in about 1656, derives from the Greek homologos, where homo = agreeing, equivalent, same + logos = relation.In biology, two things are homologous if they bear the same relationship to one another, such as a certain bone
in various forms of the "hand."
Anatomical homology
Shared ancestry can be evolutionEvolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary or developmental. Evolutionary ancestry means that structures evolved from some structure in a common ancestor; for example, the wings of bat
Bat
Bats are mammals of the order Chiroptera "hand" and pteron "wing") whose forelimbs form webbed wings, making them the only mammals naturally capable of true and sustained flight. By contrast, other mammals said to fly, such as flying squirrels, gliding possums, and colugos, glide rather than fly,...
s and the arms of primate
Primate
A primate is a mammal of the order Primates , which contains prosimians and simians. Primates arose from ancestors that lived in the trees of tropical forests; many primate characteristics represent adaptations to life in this challenging three-dimensional environment...
s are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in embryo
Embryo
An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...
nal development; the ovaries
Ovary
The ovary is an ovum-producing reproductive organ, often found in pairs as part of the vertebrate female reproductive system. Ovaries in anatomically female individuals are analogous to testes in anatomically male individuals, in that they are both gonads and endocrine glands.-Human anatomy:Ovaries...
of female humans and the testicle
Testicle
The testicle is the male gonad in animals. Like the ovaries to which they are homologous, testes are components of both the reproductive system and the endocrine system...
s of male humans are homologous in this sense.
Homology is different from analogy
Analogy (biology)
An analogy is a trait or an organ that appears similar in two unrelated organisms. The cladistic term for the same phenomenon is homoplasy, from Greek for same form. Biological anologies are often the result of convergent evolution....
, which describes the relation between characters that are apparently similar yet phylogenetically independent. The wings of a maple
Maple
Acer is a genus of trees or shrubs commonly known as maple.Maples are variously classified in a family of their own, the Aceraceae, or together with the Hippocastanaceae included in the family Sapindaceae. Modern classifications, including the Angiosperm Phylogeny Group system, favour inclusion in...
seed and the wings of an albatross
Albatross
Albatrosses, of the biological family Diomedeidae, are large seabirds allied to the procellariids, storm-petrels and diving-petrels in the order Procellariiformes . They range widely in the Southern Ocean and the North Pacific...
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). Analogy is commonly also referred to as homoplasy, which is further distinguished into parallelism, reversal, and convergence.
From the point of view of evolutionary developmental biology
Evolutionary developmental biology
Evolutionary developmental biology is a field of biology that compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved...
(evo-devo) where evolution is seen as the evolution of the development of organisms, Rolf Sattler
Rolf Sattler
Rolf Sattler, Ph.D., D.Sc. , F.L.S., F.R.S.C., is a Canadian plant morphologist, biologist, philosopher, and educator. He is considered one of the most significant contributors to the field of plant morphology. His contributions are not only empirical but involved also a revision of the most...
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
Mosaic (disambiguation)
Mosaic is decorative art involving small pieces of glass, stone, or other material.Mosaic may also refer to:- Art :* Mosaic , a jewelled enameled Easter egg made under the supervision of the Russian jeweller Peter Carl Fabergé in 1914...
structures can evolve that exhibit partial homologies. For example, certain compound leaves of flower
Flower
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants . The biological function of a flower is to effect reproduction, usually by providing a mechanism for the union of sperm with eggs...
ing plants are partially homologous both to leaves and shoots because they combine some traits of leaves and shoots.
Homologous structures in other phyla
Discussions of homology commonly limit themselves to the limbs of tetrapod vertebrates, occasionally touching on other structures, such as modified teeth as in whales and elephants. Homologies provide important insights into classification elsewhere in the animal kingdom, although some of them may be highly counterintuitive. For example, within the arthropods, Brusca and Bruscaprovide the following homologies for the first 10 somites (embryonic segments) in several groups of arthropods, but add that "...the subject of head appendage homology among the arthropods is quite unsettled and highly controversial..."
| Somite Somite A somite is a division of the body of an animal. In vertebrates this is mainly discernible in the embryo stage; in arthropods it is a characteristic of a hypothetical ancestor.- In vertebrates :... |
Trilobite Trilobite Trilobites are a well-known fossil group of extinct marine arthropods that form the class Trilobita. The first appearance of trilobites in the fossil record defines the base of the Atdabanian stage of the Early Cambrian period , and they flourished throughout the lower Paleozoic era before... |
Spider (Chelicerata Chelicerata The subphylum Chelicerata constitutes one of the major subdivisions of the phylum Arthropoda, and includes horseshoe crabs, scorpions, spiders and mites... ) |
Centipede (Uniramia Uniramia S. M. Manton's polyphyletic Arthropod hypothesis with Uniramia as one of three Phyla.Uniramia is a group within the arthropods. In the past this group included the Onychophora, which are now considered a separate category. The group is currently used in a narrower sense.Uniramia is one of three... ) |
Insect (Uniramia Uniramia S. M. Manton's polyphyletic Arthropod hypothesis with Uniramia as one of three Phyla.Uniramia is a group within the arthropods. In the past this group included the Onychophora, which are now considered a separate category. The group is currently used in a narrower sense.Uniramia is one of three... ) |
Shrimp (Crustacea Crustacean Crustaceans form a very large group of arthropods, usually treated as a subphylum, which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill and barnacles. The 50,000 described species range in size from Stygotantulus stocki at , to the Japanese spider crab with a leg span... ) |
|---|---|---|---|---|---|
| 1 | antennae | chelicerae Chelicerae The chelicerae are mouthparts of the Chelicerata, an arthropod subphylum that includes arachnids, Merostomata , and Pycnogonida . Chelicerae are pointed appendages which are used to grasp food, and are found in place of the chewing mandibles most other arthropods have... (jaws and fangs) |
antennae | antennae | 1st antennae |
| 2 | 1st legs | pedipalps | - | - | 2nd antennae |
| 3 | 2nd legs | 1st legs | mandibles | mandibles | mandibles (jaws) |
| 4 | 3rd legs | 2nd legs | 1st maxillae | 1st maxillae | 1st maxillae |
| 5 | 4th legs | 3rd legs | 2nd maxillae | 2nd maxillae | 2nd maxillae |
| 6 | 5th legs | 4th legs | collum (no legs) | 1st legs | 1st legs |
| 7 | 6th legs | - | 1st legs | 2nd legs | 2nd legs |
| 8 | 7th legs | - | 2nd legs | 3rd legs | 3rd legs |
| 9 | 8th legs | - | 3rd legs | - | 4th legs |
| 10 | 9th legs | - | 4th legs | - | 5th legs |
Determining homology
Systematists identify two forms of homology: primary homology is that implied by a researcher, who states a belief that two characters share an ancestry; secondary homology is implied by parsimony analysis, where a character that only occurs once on a tree is taken to be homologous.Plants
Modifications of primary leaves, stems, and roots occur in many higher plants.Examples:
| Primary organs | Defensive structures | Storage structures |
|---|---|---|
| Leaves | Spines Thorns, spines, and prickles In botanical morphology, thorns, spines, and prickles are hard structures with sharp, or at least pointed, ends. In spite of this common feature, they differ in their growth and development on the plant; they are modified versions of different plant organs, stems, stipules, leaf veins, or hairs... |
swollen leaves as in succulents |
| Stems | Thorns Thorns, spines, and prickles In botanical morphology, thorns, spines, and prickles are hard structures with sharp, or at least pointed, ends. In spite of this common feature, they differ in their growth and development on the plant; they are modified versions of different plant organs, stems, stipules, leaf veins, or hairs... |
tubers such as the potato, rhizomes such as ginger, and the fleshy stems of cacti Cactus A cactus is a member of the plant family Cactaceae. Their distinctive appearance is a result of adaptations to conserve water in dry and/or hot environments. In most species, the stem has evolved to become photosynthetic and succulent, while the leaves have evolved into spines... . |
| Roots | - | carrot, and root tubers such as sweet potatoes |
Sequence Homology
As with anatomical structures, homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciationSpeciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...
event (orthologs) or a duplication event
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
(paralogs).
Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms "percent homology" and "sequence similarity" are often used interchangeably. As with anatomical structures, high sequence similarity might occur because of convergent evolution
Convergent evolution
Convergent evolution describes the acquisition of the same biological trait in unrelated lineages.The wing is a classic example of convergent evolution in action. Although their last common ancestor did not have wings, both birds and bats do, and are capable of powered flight. The wings are...
, or, as with shorter sequences, because of chance. Such sequences are similar but not homologous. Sequence regions that are homologous are also called conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
. This is not to be confused with conservation in amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequences in which the amino acid at a specific position has been substituted with a different one with functionally equivalent physicochemical properties. 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.
Sequence clustering
In bioinformatics, sequence clustering algorithms attempt to group sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" or protein origin.For proteins, homologous sequences are typically grouped into families...
and sequence alignment
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
.) Some specialized biological databases collect homologous sequences in animal genomes:
HOVERGEN,
HOMOLENS,
HOGENOM.
Orthology
Homologous sequences are orthologous if they were separated by a speciationSpeciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...
event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the last common ancestor. The term "ortholog" was coined in 1970 by Walter Fitch
Walter M. Fitch
Walter M. Fitch . Until his death he was professor of molecular evolution at the University of California, Irvine. He was also a member of the National Academy of Sciences, the American Philosophical Society, and the American Association for the Advancement of Science, and was a Foreign Member of...
.
For instance, the plant Flu regulatory protein is present both in Arabidopsis (multicellular higher plant) and Chlamydomonas (single cell green algae). The Chlamydomonas version is more complex: it crosses the membrane twice rather than once, contains additional domains and undergoes alternative splicing. However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of gene engineering. Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor.
Orthology is strictly defined in terms of ancestry. Given that the exact ancestry of genes in different organisms is difficult due to gene duplication
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
and genome rearrangement events, the strongest evidence that two similar genes are orthologous is usually found by carrying out phylogenetic analysis of the gene lineage. 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.
Several specialized biological databases provide tools to identify and analyze orthologous gene sequences. These resources employ approaches that can be generally classified into those that are based on all pairwise sequence comparisons (heuristic) and those that use phylogenetic methods. Sequence comparison methods were first pioneered by COGs, now extended and automatically enhanced by the eggNOG database. InParanoid focuses on pairwise ortholog relationships. OrthoDB
OrthoDB
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny...
appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree. Other databases that provide eukaryotic orthologs include OrthoMCL, OMA
Orthologous MAtrix
OMA is a database of orthologs extracted from available complete genomes.The orthology predictions of OMA are available in several forms:* OMA Pairs: for a given gene, a list of predicted orthologs in other species is provided....
, Roundup, OrthoMaM for mammals,
OrthologID
and GreenPhylDB for plants.
Tree-based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in resources such as TreeFam and LOFT. A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example Ortholuge, EnsemblCompara GeneTrees and HomoloGene.
Paralogy
Homologous sequences are paralogous if they were separated by a gene duplicationGene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.
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. Paralogs can be split into in-paralogs, (paralogous pairs that arose after a speciation event), and out-paralogs (paralogous pairs that arose before a speciation event). Between species out-paralogs are pairs of paralogs that exist between two organisms due to duplication before speciation, whereas within species out-paralogs are pairs of paralogs that exist in the same organism, but whose duplication event happened before speciation. 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 into the way genomes evolve
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
. The genes encoding
Translation (genetics)
In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...
myoglobin
Myoglobin
Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells. The only time myoglobin is found in the...
and hemoglobin
Hemoglobin
Hemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates, with the exception of the fish family Channichthyidae, as well as the tissues of some invertebrates...
are considered to be ancient paralogs. Similarly, the four known classes of hemoglobins (hemoglobin A
Hemoglobin A
Hemoglobin A or adult hemoglobin is the most common human hemoglobin tetramer, comprising over 97% of the total red cell hemoglobin. It consists of two alpha chains and two beta chains ....
, hemoglobin A2
Hemoglobin A2
Hemoglobin A2 is a normal variant of hemoglobin A that consists of two alpha and two delta chains and is found in small quantity in normal human blood. Hemoglobin A2 may be increased in beta thalassemia or to people who are heterozygous to beta thalassemia gene....
, hemoglobin B, and hemoglobin F
Fetal hemoglobin
Fetal hemoglobin, or foetal haemoglobin, is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old...
) are paralogs of each other. While each of these proteins 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
Angiogenin
Angiogenin also known as ribonuclease 5 is a protein that in humans is encoded by the ANG gene. Angiogenin is a potent stimulator of new blood vessel formation...
diverged from ribonuclease
Ribonuclease
Ribonuclease is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 and 3.1 classes of enzymes.-Function:All organisms studied contain...
, for example, and while the two paralogs remain similar in tertiary structure, their functions within the cell are now quite different.
It is often asserted that orthologs are more functionally similar than paralogs of similar divergence, but several papers have challenged this notion .
Ohnology
Ohnologous genes are paralogous geneGene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s that have originated by a process of whole-genome duplication (WGD). The name was first given in honour of Susumu Ohno
Susumu Ohno
was an Asian American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.- Biography :Susumu Ohno was born of Japanese parents in Seoul, Korea, on February 1, 1928. The second of five children, he was the son of the minister of education of the...
by Ken Wolfe. 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 transferHorizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
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.
Gametology
Gametology denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes. Gametologs result from the origination of genetic sexSex
In biology, sex is a process of combining and mixing genetic traits, often resulting in the specialization of organisms into a male or female variety . Sexual reproduction involves combining specialized cells to form offspring that inherit traits from both parents...
determination and barriers to recombination between sex chromosomes. Examples of gametologs include CHDW and CHDZ in birds.
See also
- CladisticsCladisticsCladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants . For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade...
- Deep homologyDeep homologyIn evolutionary developmental biology, the concept of deep homology is used to describe cases where growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species....
- List of homologues of the human reproductive system
- OrthoDBOrthoDBOrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny...
- Orthologous MAtrix (OMA)Orthologous MAtrixOMA is a database of orthologs extracted from available complete genomes.The orthology predictions of OMA are available in several forms:* OMA Pairs: for a given gene, a list of predicted orthologs in other species is provided....
- TreeFamTreefamTreeFam is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families....
- Protein homologyProtein homologyProtein homology is biological homology between proteins, meaning that the proteins are derived from a common "ancestor". The proteins may be in different species, with the ancestral protein being the form of the protein that existed in the ancestral species...