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quences gene phylogeny as red and blue branches within grey species phylogeny top an ancestral gene duplication produces two paralogs histone h1 1 and 1 2 a speciation event produces orthologs in the two daughter species human and chimpanzee bottom in a separate species e coli a gene has a similar function histone like nucleoid structuring protein but has a separate evolutionary origin and so is an analog 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 or lateral gene transfer event xenologs 1 homology among dna rna or proteins is typically inferred from their nucleotide or amino acid sequence similarity significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence alignments of multiple sequences are used to indicate which regions of each sequence are homologous identity similarity and conservation edit a sequence alignment of mammalian histone proteins sequences are the middle 120 180 amino acid residues of the proteins residues that are conserved across all sequences are highlighted in grey the key below denotes conserved sequence conservative mutations semi conservative mutations and non conservative mutations 2 the term percent homology is often used to mean sequence similarity that is the percentage of identical residues percent identity or the percentage of residues conserved with similar physicochemical properties percent similarity e g leucine and isoleucine is usually used to quantify the homology based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation homology is the conclusion 3 the term percent homology is a misnomer sequences are either homologous or not 3 4 as with morphological and anatomical structures sequence similarity might occur because of convergent evolution or as with shorter sequences by chance meaning that they are not homologous homologous sequence regions are also called conserved this is not to be confused with conservation in amino acid sequences where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties partial homology can occur where a segment of the compared sequences has a shared origin while the rest does not such partial homology may result from a gene fusion event beyond sequence similarity edit proteins are known to conserve their tertiary structure more strongly than their amino acid sequences two distantly related proteins can have minimal or even undetectable sequence similarity yet have highly similar folds that can be compared via structural alignment examples of these proteins used to be only discovered by experimental structural determination methods modern protein structure prediction methods such as alphafold2 allow possible homologs to be identified without wet lab work 5 rna is also known to conserve tertiary structure more strongly than primary structure rna secondary structure prediction was found to be helpful in human to mouse comparison 6 orthology edit top an ancestral gene duplicates to produce two paralogs genes a and b a speciation event produces orthologs in the two daughter species bottom in a separate species an unrelated gene has a similar function gene c but has a separate evolutionary origin and so is an analog homologous sequences are orthologous if they are inferred to be 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 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 the molecular evolutionist walter fitch 7 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 genetic engineering significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes 8 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 9 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 citation needed databases of orthologous genes and de novo orthology inference tools edit given their tremendous importance for biology and bioinformatics orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences these resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons and those that use phylogenetic methods sequence comparison methods were first pioneered in the cogs database in 1997 10 these methods have been extended and automated in twelve different databases the most advanced being aybrah analyzing yeasts by reconstructing ancestry of homologs 11 as well as these following databases right now some tools predict orthologous de novo from the input protein sequences might not provide any database among these tools are sonicparanoid and orthofinder eggnog 12 13 greenphyldb 14 15 for plants inparanoid 16 17 focuses on pairwise ortholog relationships ohnologs 18 19 is a repository of the genes retained from whole genome duplications in the vertebrate genomes including human and mouse oma 20 orthodb 21 appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree orthoinspector archived 2020 01 27 at the wayback machine 22 is a repository of orthologous genes for 4753 organisms covering the three domains of life orthologid 23 24 orthomam 25 26 27 for mammals orthomcl 28 29 roundup 30 sonicparanoid 31 32 is a graph based method that uses machine learning to reduce execution times and infer orthologs at the domain level tree based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees as implemented in databases and software tools such as loft 33 treefam 34 35 orthofinder 36 a third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees for example ensemblcompara genetrees 37 38 homologene 39 ortholuge 40 paralogy edit paralogous genes are genes that are related via duplication events in the last common ancestor lca of the species being compared they result from the mutation of duplicated genes during separate speciation events when descendants from the lca share mutated homologs of the original duplicated genes then those genes are considered paralogs 1 as an example in the lca one gene gene a may get duplicated to make a separate similar gene gene b those two genes will continue to get passed to subsequent generations during speciation one environment will favor a mutation in gene a gene a1 producing a new species with genes a1 and b then in a separate speciation event one environment will favor a mutation in gene b gene b1 giving rise to a new species with genes a and b1 the descendants genes a1 and b1 are paralogous to each other because they are homologs that are related via a duplication event in the last common ancestor of the two species 1 additional classifications of paralogs include alloparalogs out paralogs and symparalogs in paralogs alloparalogs are paralogs that evolved from gene duplications that preceded the given speciation event in other words alloparalogs are paralogs that evolved from duplication events that happened in the lca of the organisms being compared the example above is an example alloparalogy symparalogs are paralogs that evolved from gene duplication of paralogous genes in subsequent speciation events from the example above if the descendant with genes a1 and b underwent another speciation event where gene a1 duplicated the new species would have genes b a1a and a1b in this example genes a1a and a1b are symparalogs 1 vertebrate hox genes are organized in sets of paralogs each hox cluster hoxa hoxb etc is on a different chromosome for instance the human hoxa cluster is on chromosome 7 the mouse hoxa cluster shown here has 11 paralogous genes 2 are missing 41 paralogous genes 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 clustered across multiple chromosomes with the hoxa d clusters being the best studied 41 another example are the globin genes which encode myoglobin and hemoglobin and 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 citation needed it is often asserted that orthologs are more functionally similar than paralogs of similar divergence but several papers have challenged this notion 42 43 44 in collaborative work anton yuryev and co authors demonstrated that genome wide protein protein interaction networks contain a significantly higher frequency of self interacting proteins homodimers and interactions between paralogous proteins than would be expected by chance these findings suggest that duplicated genes and their protein products are not distributed randomly within interaction networks but instead retain structural and functional relationships shaped by evolutionary history 4 regulation edit paralogs are often regulated differently e g by having different tissue specific expression patterns see hox genes however they can also be regulated differently on the protein level for instance bacillus subtilis encodes two paralogues of glutamate dehydrogenase gudb is constitutively transcribed whereas rocg is tightly regulated in their active oligomeric states both enzymes show similar enzymatic rates however swaps of enzymes and promoters cause severe fitness losses thus indicating promoter enzyme coevolution characterization of the proteins shows that compared to rocg gudb s enzymatic activity is highly dependent on glutamate and ph 45 paralogous chromosomal regions edit sometimes large regions of chromosomes share gene content similar to other chromosomal regions within the same genome 46 they are well characterised in the human genome where they have been used as evidence to support the 2r hypothesis sets of duplicated triplicated and quadruplicated genes with the related genes on different chromosomes are deduced to be remnants from genome or chromosomal duplications a set of paralogy regions is together called a paralogon 47 well studied sets of paralogy regions include regions of human chromosome 2 7 12 and 17 containing hox gene clusters collagen genes keratin genes and other duplicated genes 48 regions of human chromosomes 4 5 8 and 10 containing neuropeptide receptor genes nk class homeobox genes and many more gene families 49 50 51 and parts of human chromosomes 13 4 5 and x containing the parahox genes and their neighbors 52 the major histocompatibility complex mhc on human chromosome 6 has paralogy regions on chromosomes 1 9 and 19 53 much of the human genome seems to be assignable to paralogy regions 54 ohnology edit a whole genome duplication event produces a genome with two ohnolog copies of each gene a speciation event produces orthologs of a gene in the two daughter species a horizontal gene transfer event from one species to another adds a xenolog of the gene to its genome a speciation event produces orthologs of a gene in the two daughter species subsequent hybridisation of those species generates a hybrid genome with a homoeolog copy of each gene from both species ohnologous genes are paralogous genes that have originated by a process of whole genome duplication the name was first given in honour of susumu ohno by ken wolfe 55 ohnologues are useful for evolutionary analysis because all ohnologues in a genome have been diverging for the same length of time since their common origin in the whole genome duplication ohnologues are also known to show greater association with cancers dominant genetic disorders and pathogenic copy number variations 56 57 58 59 60 examples edit in older literature paralogous genes are often misleadingly called isoforms or isozymes in the case of enzymes for example the 5 amp activated protein kinase ampk an enzyme which performs different roles in human cells has 3 subunits 61 α catalytic domain has two paralogous versions α1 and α2 which are encoded from prkaa1 and prkaa2 β regulatory domain has two paralogous versions β1 and β2 which are encoded from prkab1 and prkab2 γ regulatory domain has three paralogous versions γ1 γ2 and γ3 which are encoded from prkag1 prkag2 and prkag3 in human skeletal muscle the preferred form is α2β2γ1 61 but in the human liver the most abundant form is α1β2γ1 61 g actin despite its conserved nature it has a varying number of paralogs at least six in mammals creatine kinase the presence of which in the blood can be used as an aid in the diagnosis of myocardial ...