Homology (biology)

From Wikipedia, the free encyclopedia

For use of the term 'homologous' in reference to chromosomes, see Homologous chromosomes.

The principle of homology: The biological derivation relationship (shown by colors) of the various bones in the forelimbs of four vertebrates is known as homology and was one of Darwins arguments in favor of evolution.

The concept of Homology is fundamental to the field of comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Homology is evaluated strictly in an evolutionary context. That is, organs in two species are homologous only if the same structure was present in their last common ancestor. Organs as disparate as a bat's wing, a seal's flipper, a cat's limb and a human arm have a common underlying anatomy which was present in their last common ancestor and so therefore are homologous as forelimbs.

Forelimbs in mammals provide one example of homology.

Homologous[Etymology 1] traits of organisms are therefore due to descent from a common ancestor. The opposite of homologous organs areanalogous organs which do similar jobs in two taxa that were not present in the last common ancestor but rather evolved separately. An example of an analogous trait would be the wings of bats

and birds, which evolved independently in each lineage separately after diverging from an ancestor without wings. It is important to distinguish between different hierarchical levels of homology in order to make informative biological comparisons. In the above example, the 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.[1] Homology can also be described at the level of the gene. In genetics homology can refer to both the gene (DNA) and the corresponding protein product.
Contents
[hide]

1 Etymology 2 Anatomical homology 3 Homologous structures in other phyla 4 Homology between genders and forms 5 Homologies across phyla 6 Determining homology 7 Plants 8 Sequence homology

o o o o o

8.1 Orthology 8.2 Paralogy 8.3 Ohnology 8.4 Xenology 8.5 Gametology

9 See also 10 Notes 11 References 12 Further reading 13 External links

[edit]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."

Ray Lankester defined the terms "homogeny", meaning homology due to inheritance from a common ancestor, and "homoplasty", meaning homology due to other factors.[2][3]

[edit]Anatomical

homology

The wings of pterosaurs (1), bats (2) and birds (3) are analogous as wings, but homologous as forelimbs.

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 primates 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, 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.[4] 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 flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and shoots.[5][6]

[edit]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 Brusca [7] 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..."

Somite Trilobite

Spider (Chelicerata)

Centipede (Uniramia)

Insect (Uniramia)

Shrimp (Crustacea)

antennae chelicerae (jaws and fangs) antennae

antennae

1st antennae

1st legs

pedipalps

2nd antennae

2nd legs 1st legs

mandibles

mandibles

mandibles (jaws)

3rd legs

2nd legs

1st maxillae

1st maxillae 1st maxillae

4th legs

3rd legs

2nd maxillae

2nd maxillae 2nd maxillae

5th legs

4th legs

collum (no legs) 1st legs

1st legs

6th legs

1st legs

2nd legs

2nd legs

7th legs

2nd legs

3rd legs

3rd legs

8th legs

3rd legs

4th legs

10

9th legs

4th legs

5th legs

[edit]Homology

between genders and forms

The term homology is sometimes applied to reproductive structures that share a common embryonic origin, but become spectacularly different between the two genders in the adult. Those listed below are some of the more commonly cited examples.

Male structure

Female structure

Notes

prostate

skene's gland

penis

clitoris

uterus

homologous to eggshell-depositing organs in reptiles and birds

bulbourethral gland Bartholin's gland -

Among insects, the stinger used by infertile female worker bees is a modified ovipositor.

[edit]Homologies

across phyla

For more details on this topic, see Deep homology.

[edit]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.[8]

[edit]Plants
Modifications of primary leaves, stems, and roots occur in many higher plants. Examples:

Primary organs

Defensive structures

Storage structures

Leaves

Spines

swollen leaves as in succulents

Stems

Thorns

tubers such as the potato, rhizomes such as ginger, and the fleshy stems of cacti.

Roots

carrot, and root tubers such as sweet potatoes

[edit]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 aspeciation event (orthologs) or a duplication event (paralogs).[9] 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[citation needed], 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.

A sequence alignment of two proteins, produced by ClustalW

Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. (See sequence clustering and sequence alignment.) Some specializedbiological databases collect homologous sequences in animal genomes: HOVERGEN,[10]HOMOLENS,[11] HOGENOM.[12]

[edit]Orthology
Homologous sequences are orthologous if they were 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. 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.[13]

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,[14]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 to ascertain 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.[15] 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,[16] now extended and automatically enhanced by the eggNOG[17] database. InParanoid[18] focuses on pairwise ortholog relationships. OrthoDB[19] 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,[20] OMA, Roundup,[21] OrthoMaM[22] for mammals, OrthologID[23] and GreenPhylDB[24] 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[25]and LOFT.[26] A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example Ortholuge,[27] EnsemblCompara GeneTrees[28] and HomoloGene.[29]