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直系同源与旁系同源  

2012-05-09 15:16:05|  分类: 进化与系统学 |  标签: |举报 |字号 订阅

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http://en.wikipedia.org/wiki/Homology_%28biology%29

http://www.plob.org/2012/06/19/2271.html

Homology (biology)

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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 Darwin’s arguments in favor of evolution.

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.

Forelimbs in mammals provide one example of homology.

Homologous[Etymology 1] 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 tetrapods. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods.[1] 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.[1]

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.[1]

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.

Contents

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]

Anatomical homology

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

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]

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)
1 antennae chelicerae (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

Homologies across phyla

See Deep homology.

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]

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

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 speciation 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, 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 specialized biological databases collect homologous sequences in animal genomes: HOVERGEN,[10] HOMOLENS,[11] HOGENOM.[12]

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 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]

Paralogy

Homologous sequences are paralogous if they were separated by a gene duplication event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.

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 after 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 [30] [31] [32] .

Ohnology

Ohnologous genes are paralogous genes that have originated by a process of whole-genome duplication (WGD). The name was first given in honour of Susumu Ohno by Ken Wolfe.[33] Ohnologs/Ohnologues 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 transfer between two organisms are termed xenologs. Xenologs can have different functions, if the new environment is vastly different for the horizontally moving gene. In general, though, xenologs typically have similar function in both organisms.[34]

Gametology

Gametology denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes. Gametologs result from the origination of genetic sex determination and barriers to recombination between sex chromosomes. Examples of gametologs include CHDW and CHDZ in birds.



Orthology vs. Paralogy

         同源有两种不同的情况即垂直方向的(orthology)与水平方向的(paralogy)。
【直系同源】
         直系同源(orthology)是比较基因组学中最重要的定义。直系同源的定义是:
  (1)在进化上起源于一个始祖基因并垂直传递(vertical descent)的同源基因;
  (2)分布于两种或两种以上物种的基因组;
  (3)功能高度保守乃至于近乎相同,甚至于其在近缘物种可以相互替换;
  (4)结构相似;
  (5)组织特异性与亚细胞分布相似。 
         在这些条件中,垂直传递和功能相同是最重要的。如多种抗药性基因,在细菌、果蝇、河豚鱼、小鼠、人类的基因组中都存在,其结构相似,功能都与多种药物的抗性有关。直系同源基因的鉴定是比较基因组的研究线索和内容,直系同源的存在是基因组进化的重要证据, 因此对直系同源的定义与条件的掌握甚为严格。鉴定直系同源的实际操作标准(practical criteria)为:
         如基因组Ⅰ中的A基因与基因组Ⅱ中的A‘基因被认为是直系同源,则要求:
  (1)A‘的产物比任何在基因组Ⅱ中所发现的其它基因产物都更相似于A产物;
  (2)A‘与A的相似程度比在任何一个亲缘关系较远的基因组中的任一基因都要高;
  (3)A编码的蛋白与A‘编码的蛋白要从头到尾都能并排比较, 即含有相似以至于相同的模序(motif)。
【旁系同源】
        旁系同源(paralogy)基因是指同一基因组(或同系物种的基因组)中,由于始祖基因的加倍而横向(horizontal)产生的几个同源基因。
        直系与旁系的共性是同源,都源于各自的始祖基因。

其区别在于:

 Orthologuous means proteins that have the same function in different species and that may or may not have arisen from a common ancestor.

Paralogous means genes that have arisen from a common ancestor and are present in the same genome. Pararolgue may or may not have the same function.Ortho same function different species, para common ancestor one species.

在进化起源上,直系同源是强调在不同基因组中的垂直传递,旁系同源则是在同一基因组中的横向 加倍;在功能上,直系同源要求功能高度相似,而旁系同源在定义上对功能上没有严格要求,可能相似,但也可能并不相似(尽管结构上具一定程度的相似),甚至 于没有功能(如基因家族中的假基因)。旁系同源的功能变异可能是横向加倍后的重排变异或进化上获得了另一功能, 其功能相似也许只是机械式的相关(mechanistically related),或非直系同源基因取代新产生的非亲缘或远缘蛋白在不同物种具有相似的功能。在真细菌与古细菌的基因组中,30%~50%的基因属旁系同 源,在真核基因组的比例更高(Koonin  EV  and  Galperin MY,1997)。
       相似与同源,直系与旁系需要在定义上加以明确,但实际应用中很难截然分开。 与别的常用术语也很难明确界定。 但基因家族或多基因家族(gene  family, multigene family)的原来的定义较侧重于结构,因而一个直系基因可以与几个旁系基因同属于一个基因家族。在这一定义上,旁系同源可以说是一个基因家族中的其他成员(Huynen et al, 1997)。
        随着不同物种全基因组序列的阐明,上述概念愈见重要并更明确。从已知的 7 个物种的全基因组序列比较,如所有的保守基因都据同源关系而加以分类(Tatusov  RL  et  al.,1997),可归纳出 720 个直系同源簇(clusters  of orthologous groups,COG),每一 COG 由一个直系同源蛋白或存在于至少 3 个种系(lineage)的直系的旁系同源组(orthologous sets of paralogs)组成。而基因家族又因大批基因及产物序列而赋予新的内容, 这对于扩大对生物过程的认识与操作基因的能力有很大的意义(Henikoff et al.,1997)。

  

1.直向同源基因

  直向同源基因(orthologous gene)又译为“垂直同源基因”、“正同源基因” 或“定向进化同源基因”、“直系同源基因”,是指从同一祖先垂直进化而来的基因。或者说,一个祖先物种分化产生两种新物种,那么这两种新物种共同具有的由 这个祖先物种继承下来的基因就称为直向同源基因。直向同源基因通常是编码生命必需的酶、辅酶或关键性的调控蛋白的基因,具有功能保守,进化缓慢,变化速度 可覆盖整个进化历史,且序列变化速度与进化距离相当等特征。大多数直向同源基因功能相同或相近,调控途径也相似, 因此在基因组序列的注释中,是最可靠的选择,例如人α一珠蛋白基因与小鼠α一珠蛋白基因。   
2.横向同源基因   横向同源基因(paralogous gene)又译为“旁系同源基因”、“并系同源基因”或“平行进化同源基因”,是指由于基因重复而产生的同源基因例如人γ一珠蛋白基因和β一珠蛋白基因。 基因重复后,进化选择压力变小、其中一条基因丢失或发生沉默都是促使横向同源基因分化产生新特性或新功能的原因。然而,虽然某些横向同源基因转录区序列相 似度不高,但它们的操纵子却仍然具有较高的保守度。值得注意的是,横向同源基因并不局限于同一物种内,不同物种中由于始祖基因的复制而分化的基因也称横向 同源基因,如鼠α一珠蛋白和鸡β一珠蛋白基因。   
3.异源同源基因   异源同源基因(xenologous gene)是由于基因在不同物种间的横向转移(horizontal transfer)而产生的。异源同源基因在原核生物中研究比较多。最近研究表明,异源同源基因的原位取代xenolo—gous gene displacement in situ)是细菌进化的强大推动力。另外,在比较真核基因组和原核生物基因组时发现,小部分脊椎动物基因在细菌中有同源序列,而在其他真核生物中却没有发 现同源序列。一种解释认为,这些基因从细菌直接水平地转移到脊椎动物的祖先,也是异源同源基因;另外一种解释则认为,是由于其他的真核生物丢失了这些基 因。   基因的直向同源、横向同源或异源同源关系见图1。如图1所示,祖先物种通过两次物种分化形成 ABC三个物种;伴随物种分化而进行的两次基因重复共形成A1、B1、B2、C1、C2、C3等6个基因。显然,C2与C3互为横向同源;B1与C1互为 直向同源;AB1与其他6个基因互为异源同源。然而,B1和B2、B2和C1又是什么关系呢?在这个问题上曾引起争议。我们从图中可以看出,B1和B2、 B2和C1的分离是由于第一次基因重复而产生的,套用定义,可得出B1和B2、B2和C1互为横向同源。同理,B1和C2/C3、C1和C2/C3也互为 横向同源。类似的,根据直向同源基因的定义,B2和C2/C3、A1和所有B基因及C基因互为直向同源。   以上只是根据基本定义进行的大致的归分。然而,在研究亲缘关系较远的物种时,物种分化和基因重 复的嵌套发生使研究具有很大的复杂性和困难度。这时,笼统的划分直系同源和旁系同源关系并不足以解决问题,我们需要一个更为精确的分类。在图1中,为了区 别于B1和C1的简单的直向同源关系,把B2和C2/C3的同源称为“共生直向同源”co—ortholog)或“横向同源基因家族谱系特异性扩充” (1ineage—specific expansion ofparalogous family)。为了区分C2和C3、B1和C2/C3这两种同源关系,可以根据物种分化和基因重复的发生的先后次序,把横向同源基因又分为内横向同源基 因(inparalog)和外横向同源基因(outparalog)。在物种分化之后产生横向同源基因的称“内横向同源基因”;在物种分化之前产生横向同 源基因的称“外横向同源基因”。 “内横向同源基因”和“外横向同源基因” 只是一种相对的划分,取决于所研究的系统和选作标准的某特定分化事件。图1中,若以第二次物种分化为准线,则C2和C3的分离发生在物种分化之后,因此它 们互为内横向同源基因;B1和C2/C3的分离发生在物种分化之前, 因此B1和C2/C3互为外横向同源基因。
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