Homology (biology)

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The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by Charles Darwin as an argument in favor of evolution. Homology vertebrates-en.svg
The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by Charles Darwin as an argument in favor of evolution.

In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555.

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In developmental biology, organs that developed in the embryo in the same manner and from similar origins, such as from matching primordia in successive segments of the same animal, are serially homologous. Examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Male and female reproductive organs are homologous if they develop from the same embryonic tissue, as do the ovaries and testicles of mammals including humans.

Sequence homology between protein or DNA sequences is similarly defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions.

Homology remains controversial in animal behaviour, but there is suggestive evidence that, for example, dominance hierarchies are homologous across the primates.

History

Pierre Belon systematically compared the skeletons of birds and humans in his Book of Birds (1555). BelonBirdSkel.jpg
Pierre Belon systematically compared the skeletons of birds and humans in his Book of Birds (1555).

Homology was noticed by Aristotle (c. 350 BC), [2] and was explicitly analysed by Pierre Belon in his 1555 Book of Birds, where he systematically compared the skeletons of birds and humans. The pattern of similarity was interpreted as part of the static great chain of being through the mediaeval and early modern periods: it was not then seen as implying evolutionary change. In the German Naturphilosophie tradition, homology was of special interest as demonstrating unity in nature. [1] [3] In 1790, Goethe stated his foliar theory in his essay "Metamorphosis of Plants", showing that flower part are derived from leaves. [4] The serial homology of limbs was described late in the 18th century. The French zoologist Etienne Geoffroy Saint-Hilaire showed in 1818 in his theorie d'analogue ("theory of homologues") that structures were shared between fishes, reptiles, birds, and mammals. [5] When Geoffroy went further and sought homologies between Georges Cuvier's embranchements , such as vertebrates and molluscs, his claims triggered the 1830 Cuvier-Geoffroy debate. Geoffroy stated the principle of connections, namely that what is important is the relative position of different structures and their connections to each other. [3] The Estonian embryologist Karl Ernst von Baer stated what are now called von Baer's laws in 1828, noting that related animals begin their development as similar embryos and then diverge: thus, animals in the same family are more closely related and diverge later than animals which are only in the same order and have fewer homologies. von Baer's theory recognises that each taxon (such as a family) has distinctive shared features, and that embryonic development parallels the taxonomic hierarchy: not the same as recapitulation theory. [3] The term "homology" was first used in biology by the anatomist Richard Owen in 1843 when studying the similarities of vertebrate fins and limbs, defining it as the "same organ in different animals under every variety of form and function", [6] and contrasting it with the matching term "analogy" which he used to describe different structures with the same function. Owen codified 3 main criteria for determining if features were homologous: position, development, and composition. In 1859, Charles Darwin explained homologous structures as meaning that the organisms concerned shared a body plan from a common ancestor, and that taxa were branches of a single tree of life. [1] [7] [3]

Definition

Eupatorus gracilicornis Vol.jpg
The front wings of beetles have evolved into elytra, hard wing-cases.
Libellula depressa.jpg
Dragonflies have the ancient insect body plan with two pairs of wings.
Nephrotoma guestfalica.jpg
The hind wings of Dipteran flies such as this cranefly have evolved divergently to form small club-like halteres.
The two pairs of wings of ancestral insects are represented by homologous structures in modern insects — elytra, wings, and halteres.

The word homology, coined in about 1656, is derived from the Greek ὁμόλογος homologos from ὁμός homos "same" and λόγος logos "relation". [8] [9] [lower-alpha 1]

Similar biological structures or sequences in different taxa are homologous if they are derived from a common ancestor. Homology thus implies divergent evolution. For example, many insects (such as dragonflies) possess two pairs of flying wings. In beetles, the first pair of wings has evolved into a pair of hard wing covers, [12] while in Dipteran flies the second pair of wings has evolved into small halteres used for balance. [lower-alpha 2] [13]

Similarly, the forelimbs of ancestral vertebrates have evolved into the front flippers of whales, the wings of birds, the running forelegs of dogs, deer, and horses, the short forelegs of frogs and lizards, and the grasping hands of primates including humans. The same major forearm bones (humerus, radius, and ulna [lower-alpha 3] ) are found in fossils of lobe-finned fish such as Eusthenopteron . [14]

Homology vs. analogy

Sycamore maple fruits have wings analogous but not homologous to an insect's wings. Acer pseudoplatanus MHNT.BOT.2004.0.461.jpg
Sycamore maple fruits have wings analogous but not homologous to an insect's wings.

The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not present in their most recent common ancestor but rather evolved separately. For example, the wings of insects and birds evolved independently in widely separated groups, and converged functionally to support powered flight, so they are analogous. Similarly, the wings of a sycamore maple seed and the wings of a bird are analogous but not homologous, as they develop from quite different structures. [15] [16] A structure can be homologous at one level, but only analogous at another. Pterosaur, bird and bat wings are analogous as wings, but homologous as forelimbs because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods, and evolved in different ways in the three groups. Thus, in the pterosaurs, the "wing" involves both the forelimb and the hindlimb. [17] Analogy is called homoplasy in cladistics, and convergent or parallel evolution in evolutionary biology. [18] [19]

In cladistics

Specialised terms are used in taxonomic research. Primary homology is a researcher's initial hypothesis based on similar structure or anatomical connections, suggesting that a character state in two or more taxa share is shared due to common ancestry. Primary homology may be conceptually broken down further: we may consider all of the states of the same character as "homologous" parts of a single, unspecified, transformation series. This has been referred to as topographical correspondence. For example, in an aligned DNA sequence matrix, all of the A, G, C, T or implied gaps at a given nucleotide site are homologous in this way. Character state identity is the hypothesis that the particular condition in two or more taxa is "the same" as far as our character coding scheme is concerned. Thus, two Adenines at the same aligned nucleotide site are hypothesized to be homologous unless that hypothesis is subsequently contradicted by other evidence. Secondary homology is implied by parsimony analysis, where a character state that arises only once on a tree is taken to be homologous. [20] [21] As implied in this definition, many cladists consider secondary homology to be synonymous with synapomorphy, a shared derived character or trait state that distinguishes a clade from other organisms. [22] [23] [24]

Shared ancestral character states, symplesiomorphies, represent either synapomorphies of a more inclusive group, or complementary states (often absences) that unite no natural group of organisms. For example, the presence of wings is a synapomorphy for pterygote insects, but a symplesiomorphy for holometabolous insects. Absence of wings in non-pterygote insects and other organisms is a complementary symplesiomorphy that unites no group (for example, absence of wings provides no evidence of common ancestry of silverfish, spiders and annelid worms). On the other hand, absence (or secondary loss) of wings is a synapomorphy for fleas. Patterns such as these lead many cladists to consider the concept of homology and the concept of synapomorphy to be equivalent. [25] [24] Some cladists follow the pre-cladistic definition of homology of Haas and Simpson, [26] and view both synapomorphies and symplesiomorphies as homologous character states. [27]

In different taxa

pax6 alterations result in similar changes to eye morphology and function across a wide range of taxa. PAX6 Phenotypes Washington etal PLoSBiol e1000247.png
pax6 alterations result in similar changes to eye morphology and function across a wide range of taxa.

Homologies provide the fundamental basis for all biological classification, although some may be highly counter-intuitive. For example, deep homologies like the pax6 genes that control the development of the eyes of vertebrates and arthropods were unexpected, as the organs are anatomically dissimilar and appeared to have evolved entirely independently. [28] [29]

In arthropods

The embryonic body segments (somites) of different arthropod taxa have diverged from a simple body plan with many similar appendages which are serially homologous, into a variety of body plans with fewer segments equipped with specialised appendages. [30] The homologies between these have been discovered by comparing genes in evolutionary developmental biology. [28]

Hox genes in arthropod segmentation Arthropod segment Hox gene expression.svg
Hox genes in arthropod segmentation
Somite
(body
segment)
Trilobite
(Trilobitomorpha)
Acadoparadoxides sp 4343.JPG
Spider
(Chelicerata)
Araneus quadratus MHNT.jpg
Centipede
(Myriapoda)
Scolopendridae - Scolopendra cingulata.jpg
Insect
(Hexapoda)
Cerf-volant MHNT Dos.jpg
Shrimp
(Crustacea)
GarneleCrystalRed20.jpg
1antennae chelicerae (jaws and fangs)antennaeantennae1st antennae
21st legs pedipalps --2nd antennae
32nd legs1st legs mandibles mandiblesmandibles (jaws)
43rd legs2nd legs1st maxillae 1st maxillae1st maxillae
54th legs3rd legs2nd maxillae2nd maxillae2nd maxillae
65th legs4th legscollum (no legs)1st legs1st legs
76th legs-1st legs2nd legs2nd legs
87th legs-2nd legs3rd legs3rd legs
98th legs-3rd legs-4th legs
109th legs-4th legs-5th legs

Among insects, the stinger of the female honey bee is a modified ovipositor, homologous with ovipositors in other insects such as the Orthoptera, Hemiptera, and those Hymenoptera without stingers. [31]

In mammals

The three small bones in the middle ear of mammals including humans, the malleus, incus, and stapes, are today used to transmit sound from the eardrum to the inner ear. The malleus and incus develop in the embryo from structures that form jaw bones (the quadrate and the articular) in lizards, and in fossils of lizard-like ancestors of mammals. Both lines of evidence show that these bones are homologous, sharing a common ancestor. [32]

Among the many homologies in mammal reproductive systems, ovaries and testicles are homologous. [33]

Rudimentary organs such as the human tailbone, now much reduced from their functional state, are readily understood as signs of evolution, the explanation being that they were cut down by natural selection from functioning organs when their functions were no longer needed, but make no sense at all if species are considered to be fixed. The tailbone is homologous to the tails of other primates. [34]

In plants

Leaves, stems, and roots

In many plants, defensive or storage structures are made by modifications of the development of primary leaves, stems, and roots. Leaves are variously modified from photosynthetic structures to form the insect-trapping pitchers of pitcher plants, the insect-trapping jaws of Venus flytrap, and the spines of cactuses, all homologous. [35]

Primary organsDefensive structuresStorage structures
Leaves Spines Swollen leaves (e.g. succulents)
Stems Thorns Tubers (e.g. potato), rhizomes (e.g. ginger), fleshy stems (e.g. cacti)
Roots-Root tubers (e.g. sweet potato), taproot (e.g. carrot)

Certain compound leaves of flowering plants are partially homologous both to leaves and shoots, because their development has evolved from a genetic mosaic of leaf and shoot development. [36] [37]

Flower parts

The ABC model of flower development. Class A genes affect sepals and petals, class B genes affect petals and stamens, class C genes affect stamens and carpels. In two specific whorls of the floral meristem, each class of organ identity genes is switched on. ABC flower developement.svg
The ABC model of flower development. Class A genes affect sepals and petals, class B genes affect petals and stamens, class C genes affect stamens and carpels. In two specific whorls of the floral meristem, each class of organ identity genes is switched on.

The four types of flower parts, namely carpels, stamens, petals, and sepals, are homologous with and derived from leaves, as Goethe correctly noted in 1790. The development of these parts through a pattern of gene expression in the growing zones (meristems) is described by the ABC model of flower development. Each of the four types of flower parts is serially repeated in concentric whorls, controlled by a small number of genes acting in various combinations. Thus, A genes working alone result in sepal formation; A and B together produce petals; B and C together create stamens; C alone produces carpels. When none of the genes are active, leaves are formed. Two more groups of genes, D to form ovules and E for the floral whorls, complete the model. The genes are evidently ancient, as old as the flowering plants themselves. [4]

Developmental biology

The Cretaceous snake Pachyrhachis problematicus had hind legs (circled). Pachyrhachis problematicus 45.JPG
The Cretaceous snake Pachyrhachis problematicus had hind legs (circled).

Developmental biology can identify homologous structures that arose from the same tissue in embryogenesis. For example, adult snakes have no legs, but their early embryos have limb-buds for hind legs, which are soon lost as the embryos develop. The implication that the ancestors of snakes had hind legs is confirmed by fossil evidence: the Cretaceous snake Pachyrhachis problematicus had hind legs complete with hip bones (ilium, pubis, ischium), thigh bone (femur), leg bones (tibia, fibula) and foot bones (calcaneum, astragalus) as in tetrapods with legs today. [38]

Sequence homology

A multiple sequence alignment of mammalian histone H1 proteins. Alignment positions conserved across all five species analysed are highlighted in grey. Positions with conservative, semi-conservative, and non-conservative amino acid replacements are indicated. Histone Alignment.png
A multiple sequence alignment of mammalian histone H1 proteins. Alignment positions conserved across all five species analysed are highlighted in grey. Positions with conservative, semi-conservative, and non-conservative amino acid replacements are indicated.

As with anatomical structures, sequence 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 speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is typically inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution of a common ancestor. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. [40]

Homologous sequences are orthologous if they are descended from the same ancestral sequence separated by a speciation 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. The term "ortholog" was coined in 1970 by the molecular evolutionist Walter Fitch. [41]

Homologous sequences are paralogous if they were created by a duplication event within the genome. For gene duplication events, 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. They can shape the structure of whole genomes and thus explain genome evolution to a large extent. Examples include the Homeobox (Hox) genes in animals. These genes not only underwent gene duplications within chromosomes but also whole genome duplications. As a result, Hox genes in most vertebrates are spread across multiple chromosomes: the HoxA–D clusters are the best studied. [42]

Dominance hierarchy behaviour, as in these weeper capuchin monkeys, may be homologous across the primates. Weeper Capuchin 01 (cropped).JPG
Dominance hierarchy behaviour, as in these weeper capuchin monkeys, may be homologous across the primates.

In behaviour

It has been suggested that some behaviours might be homologous, based either on sharing across related taxa or on common origins of the behaviour in an individual's development; however, the notion of homologous behavior remains controversial, [43] largely because behavior is more prone to multiple realizability than other biological traits. For example, D. W. Rajecki and Randall C. Flanery, using data on humans and on nonhuman primates, argue that patterns of behaviour in dominance hierarchies are homologous across the primates. [44]

As with morphological features or DNA, shared similarity in behavior provides evidence for common ancestry. [45] The hypothesis that a behavioral character is not homologous should be based on an incongruent distribution of that character with respect to other features that are presumed to reflect the true pattern of relationships. This is an application of Willi Hennig's [46] auxiliary principle.

Notes

  1. The alternative terms "homogeny" and "homogenous" were also used in the late 1800s and early 1900s. However, these terms are now archaic in biology, and the term "homogenous" is now generally found as a misspelling of the term "homogeneous" which refers to the uniformity of a mixture. [10] [11]
  2. If the two pairs of wings are considered as interchangeable, homologous structures, this may be described as a parallel reduction in the number of wings, but otherwise the two changes are each divergent changes in one pair of wings.
  3. These are coloured in the lead image: humerus brown, radius pale buff, ulna red.

Related Research Articles

Cladistics Method of biological systematics in evolutionary biology

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.

Clade Group of a common ancestor and all descendants

A clade, also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, the equivalent Latin term cladus is often used in taxonomical literature.

Paraphyly Property of a group which includes only descendants of a common ancestor, but excludes at least one monophyletic subgroup

In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. In contrast, a monophyletic group includes a common ancestor and all of its descendants. The terms are commonly used in phylogenetics and in the tree model of historical linguistics. Paraphyletic groups are identified by a combination of synapomorphies and symplesiomorphies. If many subgroups are missing from the named group, it is said to be polyparaphyletic.

Cladogram Diagram used to show relations among groups of organisms with common origins

A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

Evolutionary developmental biology Field of research that compares the developmental processes of different organisms to infer the ancestral relationships

Evolutionary developmental biology is a field of biological research that compares the developmental processes of different organisms to infer how developmental processes evolved.

Convergent evolution Independent evolution of similar features

Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.

Comparative anatomy Study of similarities and differences in the anatomy of different species

Comparative anatomy is the study of similarities and differences in the anatomy of different species. It is closely related to evolutionary biology and phylogeny.

Vestigiality Evolution keeping organs no longer needed

Vestigiality is the retention, during the process of evolution, of genetically determined structures or attributes that have lost some or all of the ancestral function in a given species. Assessment of the vestigiality must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful, but if the lack of the feature provides no advantage, and its presence provides no disadvantage, the feature may not be phased out by natural selection and persist across species.

Polyphyly Set of organisms that do not share an immediate common ancestor

A polyphyletic group or assemblage is a set of organisms, or other evolving elements, that have been grouped together based on characteristics that do not imply that they share a common ancestor that is not also the common ancestor of many other taxa. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly.

Apomorphy and synapomorphy Two concepts on heritable traits

In phylogenetics, an apomorphy is a novel character or character state that has evolved from its ancestral form. A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.

Parallel evolution is the similar development of a trait in distinct species that are not closely related, but share a similar original trait in response to similar evolutionary pressure.

Sequence homology Shared ancestry between DNA, RNA or protein sequences

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).

Divergent evolution Accumulation of differences between closely related species populations, leading to speciation

Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, leading to speciation. Divergent evolution is typically exhibited when two populations become separated by a geographic barrier and experience different selective pressures that drive adaptations to their new environment. After many generations and continual evolution, the populations become less able to interbreed with one another. The American naturalist J. T. Gulick (1832–1923) was the first to use the term "divergent evolution", with its use becoming widespread in modern evolutionary literature. Classic examples of divergence in nature are the adaptive radiation of the finches of the Galapagos or the coloration differences in populations of a species that live in different habitats such as with pocket mice and fence lizards.

Hox genes, a subset of homeobox genes, are a group of related genes that specify regions of the body plan of an embryo along the head-tail axis of animals. Hox proteins encode and specify the characteristics of 'position', ensuring that the correct structures form in the correct places of the body. For example, Hox genes in insects specify which appendages form on a segment, and Hox genes in vertebrates specify the types and shape of vertebrae that will form. In segmented animals, Hox proteins thus confer segmental or positional identity, but do not form the actual segments themselves.

Plesiomorphy and symplesiomorphy Ancestral character or trait state shared by two or more taxa

In phylogenetics, a plesiomorphy and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.

The arthropod leg is a form of jointed appendage of arthropods, usually used for walking. Many of the terms used for arthropod leg segments are of Latin origin, and may be confused with terms for bones: coxa, trochanter, femur, tibia, tarsus, ischium, metatarsus, carpus, dactylus, patella.

Autapomorphy Distinctive feature, known as a derived trait, that is unique to a given taxon

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon. It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, first introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, autos "self"; ἀπό, apo "away from"; and μορφή, morphḗ = "shape".

Orphan genes, ORFans, or taxonomically restricted genes (TRGs) are genes that lack a detectable homologue outside of a given species or lineage. Most genes have known homologues. Two genes are homologous when they share an evolutionary history, and the study of groups of homologous genes allows for an understanding of their evolutionary history and divergence. Common mechanisms that have been uncovered as sources for new genes through studies of homologues include gene duplication, exon shuffling, gene fusion and fission, etc. Studying the origins of a gene becomes more difficult when there is no evident homologue. The discovery that about 10% or more of the genes of the average microbial species is constituted by orphan genes raises questions about the evolutionary origins of different species as well as how to study and uncover the evolutionary origins of orphan genes.

Deep homology Control of growth and differentiation by deeply conserved genetic mechanisms

In 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.

A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred. Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent. Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.

References

  1. 1 2 3 Panchen, A. L. (1999). "Homology—history of a concept". Novartis Found Symp. Novartis Foundation Symposia. 222: 5–18. doi:10.1002/9780470515655.ch2. ISBN   9780470515655. PMID   10332750.
  2. Panchen, A. L. (1999). "Homology—history of a concept". Novartis Foundation Symposium. Novartis Foundation Symposia. 222: 5–18, discussion 18–23. doi:10.1002/9780470515655.ch2. ISBN   9780470515655. PMID   10332750.
  3. 1 2 3 4 Brigandt, Ingo (23 November 2011). "Essay: Homology". The Embryo Project Encyclopedia.
  4. 1 2 Dornelas, Marcelo Carnier; Dornelas, Odair (2005). "From leaf to flower: Revisiting Goethe's concepts on the ¨metamorphosis¨ of plants". Brazilian Journal of Plant Physiology. 17 (4): 335–344. doi: 10.1590/S1677-04202005000400001 .
  5. Geoffroy Saint-Hilaire, Etienne (1818). Philosophie anatomique. Vol. 1: Des organes respiratoires sous le rapport de la détermination et de l'identité de leurs piecès osseuses. Vol. 1. Paris: J. B. Baillière.
  6. Owen, Richard (1843). Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals, Delivered at the Royal College of Surgeons in 1843. Longman, Brown, Green, and Longmans. pp. 374, 379.
  7. Sommer, R. J. (July 2008). "Homology and the hierarchy of biological systems". BioEssays. 30 (7): 653–658. doi:10.1002/bies.20776. PMID   18536034.
  8. Bower, Frederick Orpen (1906). "Plant Morphology". Congress of Arts and Science: Universal Exposition, St. Louis, 1904. Houghton, Mifflin. p. 64.
  9. Williams, David Malcolm; Forey, Peter L. (2004). Milestones in Systematics . CRC Press. p.  198. ISBN   978-0-415-28032-7.
  10. "homogeneous, adj.". OED Online. March 2016. Oxford University Press. http://www.oed.com/view/Entry/88045? (accessed April 09, 2016).
  11. "homogenous, adj.". OED Online. March 2016. Oxford University Press. http://www.oed.com/view/Entry/88055? (accessed April 09, 2016).
  12. Wagner, Günter P. (2014). Homology, Genes, and Evolutionary Innovation. Princeton University Press. pp. 53–54. ISBN   978-1-4008-5146-1. elytra have very little similarity with typical wings, but are clearly homologous to forewings. Hence butterflies, flies, and beetles all have two pairs of dorsal appendages that are homologous among species.
  13. Lipshitz, Howard D. (2012). Genes, Development and Cancer: The Life and Work of Edward B. Lewis. Springer. p. 240. ISBN   978-1-4419-8981-9. For example, wing and haltere are homologous, yet widely divergent, organs that normally arise as dorsal appendages of the second thoracic (T2) and third thoracic (T3) segments, respectively.
  14. "Homology: Legs and Limbs". UC Berkeley. Retrieved 15 December 2016.
  15. "Secret Found to Flight of 'Helicopter Seeds'". LiveScience. 11 June 2009. Retrieved 2 March 2017.
  16. Lentink, D.; Dickson, W. B.; van Leeuwen, J. L.; Dickinson, M. H. (12 June 2009). "Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds" (PDF). Science. 324 (5933): 1438–1440. Bibcode:2009Sci...324.1438L. doi:10.1126/science.1174196. PMID   19520959. S2CID   12216605.
  17. Scotland, R. W. (2010). "Deep homology: A view from systematics". BioEssays. 32 (5): 438–449. doi:10.1002/bies.200900175. PMID   20394064. S2CID   205469918.
  18. Cf. Butler, A. B.: Homology and Homoplasty. In: Squire, Larry R. (Ed.): Encyclopedia of Neuroscience, Academic Press, 2009, pp. 1195–1199.
  19. "Homologous structure vs. analogous structure: What is the difference?" . Retrieved 27 September 2016.
  20. de Pinna, M. C. C. (1991). "Concepts and Tests of homology in the cladistic paradigm". Cladistics. 7 (4): 367–394. CiteSeerX   10.1.1.487.2259 . doi:10.1111/j.1096-0031.1991.tb00045.x. S2CID   3551391.
  21. Brower, Andrew V. Z.; Schawaroch, V. (1996). "Three steps of homology assessment". Cladistics. 12 (3): 265–272. doi:10.1111/j.1096-0031.1996.tb00014.x. PMID   34920625. S2CID   85385271.
  22. Page, Roderick D.M.; Holmes, Edward C. (2009). Molecular Evolution: A Phylogenetic Approach. John Wiley & Sons. ISBN   978-1-4443-1336-9.
  23. Brower, Andrew V. Z.; de Pinna, Mario C. C. (24 May 2012). "Homology and errors". Cladistics. 28 (5): 529–538. doi:10.1111/j.1096-0031.2012.00398.x. PMID   34844384. S2CID   86806203.
  24. 1 2 Brower, Andrew V. Z.; de Pinna, M. C. C. (2014). "About Nothing". Cladistics. 30 (3): 330–336. doi:10.1111/cla.12050. PMID   34788975. S2CID   221550586.
  25. Patterson, C. (1982). "Morphological characters and homology". In K. A. Joysey; A. E. Friday (eds.). Problems of Phylogenetic Reconstruction. London and New York: Academic Press. pp. 21–74.
  26. Haas, O. and G. G. Simpson. 1946. Analysis of some phylogenetic terms, with attempts at redefinition. Proc. Amer. Phil. Soc.90:319-349.
  27. Nixon, K. C.; Carpenter, J. M. (2011). "On homology". Cladistics. 28 (2): 160–169. doi:10.1111/j.1096-0031.2011.00371.x. PMID   34861754. S2CID   221582887.
  28. 1 2 Brusca, R. C.; Brusca, G. J. (1990). Invertebrates . Sinauer Associates. p.  669.
  29. Carroll, Sean B. (2006). Endless Forms Most Beautiful. Weidenfeld & Nicolson. pp. 28, 66–69. ISBN   978-0-297-85094-6.
  30. Novartis Foundation; Hall, Brian (2008). Homology. John Wiley. p. 29. ISBN   978-0-470-51566-2.
  31. Shing, H.; Erickson, E. H. (1982). "Some ultrastructure of the honeybee (Apis mellifera L.) sting". Apidologie. 13 (3): 203–213. doi: 10.1051/apido:19820301 .
  32. "Homology: From jaws to ears — an unusual example of a homology". UC Berkeley. Retrieved 15 December 2016.
  33. Hyde, Janet Shibley; DeLamater, John D. (June 2010). "Chapter 5" (PDF). Understanding Human Sexuality (11th ed.). New York: McGraw-Hill. p. 103. ISBN   978-0-07-338282-1.
  34. Larson 2004, p. 112.
  35. "Homology: Leave it to the plants". University of California at Berkeley. Retrieved 7 May 2017.
  36. Sattler, R. (1984). "Homology — a continuing challenge". Systematic Botany. 9 (4): 382–394. doi:10.2307/2418787. JSTOR   2418787.
  37. Sattler, R. (1994). "Homology, homeosis, and process morphology in plants". In Hall, Brian Keith (ed.). Homology: the hierarchical basis of comparative biology. Academic Press. pp. 423–75. ISBN   978-0-12-319583-8.
  38. "Homologies: developmental biology". UC Berkeley. Retrieved 15 December 2016.
  39. "Clustal FAQ #Symbols". Clustal. Archived from the original on 24 October 2016. Retrieved 8 December 2014.
  40. Koonin, E. V. (2005). "Orthologs, Paralogs, and Evolutionary Genomics". Annual Review of Genetics. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID   16285863.
  41. Fitch, W. M. (June 1970). "Distinguishing homologous from analogous proteins". Systematic Zoology. 19 (2): 99–113. doi:10.2307/2412448. JSTOR   2412448. PMID   5449325.
  42. Zakany, Jozsef; Duboule, Denis (2007). "The role of Hox genes during vertebrate limb development". Current Opinion in Genetics & Development. 17 (4): 359–366. doi:10.1016/j.gde.2007.05.011. ISSN   0959-437X. PMID   17644373.
  43. Moore, David S (2013). "Importing the homology concept from biology into developmental psychology". Developmental Psychobiology. 55 (1): 13–21. doi:10.1002/dev.21015. PMID   22711075.
  44. Rajecki, D. W.; Flanery, Randall C. (2013). Lamb, M. E.; Brown, A. L. (eds.). Social Conflict and Dominance in Children: a Case for a Primate Homology. Advances in Developmental Psychology. Taylor and Francis. p. 125. ISBN   978-1-135-83123-3. Finally, much recent information on children's and nonhuman primates' behavior in groups, a conjunction of hard human data and hard nonhuman primate data, lends credence to our comparison. Our conclusion is that, based on their agreement in several unusual characteristics, dominance patterns are homologous in primates. This agreement of unusual characteristics is found at several levels, including fine motor movement, gross motor movement, and behavior at the group level.
  45. Wenzel, John W. 1992. Behavioral homology and phylogeny. Annual Review of Ecology and Systematics 23:361-381
  46. Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press

Further reading