Gene Duplication

During development, gene duplication events produced paralogs, or a set of genes derived from duplication within the genome of a species.

From: Vitamins and Hormones , 2020

Species Trees, Inference of

S. Edwards , in Encyclopedia of Evolutionary Biological science, 2016

Gene Duplication and the Multispecies Coalescent

Gene duplication is too an important source of genomic information for inference of species trees and genome history ( Figure1; Rasmussen and Kellis, 2012; Boussau et al., 2013; Szollsi et al., 2014; Wu et al., 2014). Factor duplication and loss can be considered a specific instance of more general birth–death models, which can account for births (speciation, factor duplication, and HGT) too as losses (species extinction, factor loss) (Szollsi et al., 2014). Powerful models now exist for estimating the history of multigene families given a species tree through coalescent processes also as gene duplication and loss (Rasmussen and Kellis, 2012). Such methods are increasingly useful for more accurately defining orthologs, paralogs, and the history of cistron duplication and loss in genomes. Although non covered in detail in this article, such models are a useful complement to methods for inferring the history of species themselves.

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Factor Duplication and Speciation

Tiratha R. Singh , Ankush Bansal , in Encyclopedia of Bioinformatics and Computational Biology, 2019

Conclusion

Gene duplication and speciation are two prominent mechanisms for finding clues for evolution. Phylogenetic analysis helps researchers to sympathize the bequeathed association of species or sequence of their interest. Gene duplication events, exon shuffling, and speciation have a stiff role in the process of evolution and to study convergence and deviation from ancestral data. This commodity provides descriptive information about basic concepts of phylogeny that may help students and researchers to become aware of terminologies used in cistron duplication and speciation analysis. It is presented in a way where basic to advanced level data is existence compiled on the diverse topics and it is estimated that this information will serve as comprehensive data to students, kinesthesia members, and researchers working in this area. It reflects how bioinformatics can shape a computational pipeline for the analysis of biological information in an evolutionary scenario and will assistance the evolutionary biologists likewise to implement bioinformatics at some level for further exploration of bones principles.

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Fundamentals of Molecular Development*

Supratim Choudhuri , in Bioinformatics for Beginners, 2014

two.three.four.1.A Factor Duplication and the 2R Hypothesis

Cistron duplication creates paralogs. Susumu Ohno'south seminal book Evolution past Factor Duplication (1970) xiii popularized the concept that gene duplication plays an of import role in evolution. By comparing the genome size of different groups of non-vertebrate chordates and vertebrates, Ohno argued that the complexity of vertebrate genomes during development was achieved past whole-genome duplications in the lineage leading to vertebrates. Analysis of orthologous genes (orthologs g ) showed that compared to urochordates (e.chiliad. ocean squirts), the genomes of jawless vertebrates, such as lamprey and hagfish, contain at to the lowest degree two orthologs and the genomes of mammals contain three or more orthologs. Ohno proposed that the ancestors of reptiles, birds, and mammals had experienced at to the lowest degree one tetraploid evolution either at the stage of fish or at the stage of amphibians. Since the plow of the millennium, the modern version of Ohno'south hypothesis, known as the two rounds (2R) hypothesis, has resurfaced and gained popularity. There are disagreements regarding the stages of development when genome duplications took place. The most popular version of the 2R hypothesis proposes that ane circular of genome duplication took place at the root of the vertebrate lineage—that is, after the emergence of urochordates—followed by another around the time Agnatha (jawless vertebrates, e.chiliad. lamprey and hagfish) and Gnathostomata (jawed vertebrates) split—that is, earlier the radiation of jawed vertebrates. fourteen–16 There are, yet, debates about the 2R hypothesis, only that is beyond the scope of this department.

Ohno considered whole-genome duplication to exist more important as an evolutionary mechanism than individual gene duplication, but gene duplication is now known to exist a major machinery for the creation of novel genetic material and an important driver of genome evolution. Genome sequencing shows that gene duplication is prevalent in all three domains of life (Bacteria, Archaea, Eukarya). In multicellular eukaryotes, including humans, ~40–60% genes have been produced through duplication, depending on the species. Several publications have reported on the charge per unit of factor duplication in various eukaryotic species, but the results vary significantly. For example, based on observations from the genomic databases for several eukaryotic species, Lynch and Conery estimated that in eukaryotes the average rate of gene duplication is approximately 0.01 per gene per million years (i.e. the probability of duplication of a eukaryotic gene is at least 1% per 1000000 years h,i ). 17,eighteen Even so, Cotton and Page estimated a factor duplication rate that is one order of magnitude lower than the estimate of Lynch and Conery. xix Many duplicated genes are inactivated by accumulating degenerative mutations and become pseudogenes. Gene duplication tin result from unequal crossing over, retrotransposon insertion, segmental duplication, and chromosomal (whole-genome) duplication.

If the rate of cistron duplication is assumed to exist somewhere in between the ii estimates cited higher up, so it becomes close to the rate of fixed nucleotide substitutions, especially in poly peptide-coding genes. Using data from human and rodents, and assuming 80 1000000 years as the time of divergence between the two lineages, the average stock-still nucleotide exchange rate in poly peptide-coding genes was calculated to be 0.74 per nonsynonymous site and 3.51 per synonymous site per billion (xnine) years. twenty However, such average estimates could still vary significantly in different species.

Unequal crossing over unremarkably generates tandem duplication, which could involve the entire cistron or part of a cistron. Figure 2.three shows duplication of a section of the factor through unequal crossing over. Duplication of the entire gene involves duplication of the introns also as the regulatory sequences. The insertion of processed (retrotransposed) pseudogenes can too introduce genetic variability to the genome, particularly if the retrotransposed pseudogenes recruit new promoters and become functional. Some expressed pseudogenes regulate the mRNA expression of the normal gene. For case, Makorin1-p1 in mice is a transcribed pseudogene, which regulates the expression of the normal factor Makorin1. 21 Pseudogenes are of ii main types: (I) duplicated (nonprocessed) and (Two) retrotransposed (processed). Duplicated pseudogenes ascend from genomic Dna duplication or unequal crossing over. They retain the original exon–intron system of the functional gene (hence nonprocessed), but their protein-coding potential is lost because of the loss of transcription regulatory elements, such as promoters or enhancers, or mutations disrupting the ORF, such as frameshifts or premature stop codons. In contrast, processed pseudogenes outcome from retrotransposition—that is, they arise from reverse transcription of mRNA into complementary Deoxyribonucleic acid (cDNA) followed by the integration of the cDNA into the genome. As a outcome, processed pseudogenes lack introns and promoter, and they typically incorporate the poly(A) tail. Because they are retrotransposed, they are flanked by straight repeats. Processed pseudogenes are usually nonfunctional unless they are integrated under the influence of an active promoter, or recruit new promoters over fourth dimension to become functional. Some other blazon of pseudogene is known as the unitary pseudogene. A unitary pseudogene is a regular cistron that has lost the protein-coding potential because of spontaneous mutation in the coding region; so it is neither duplicated nor retrotransposed. Because about pseudogenes are nonfunctional, they are not under choice pressure and are free to accumulate further mutations and increasingly diverge from the parent sequence from which they were derived. Pseudogenes accept been identified in all known genomes, just their numbers greatly vary. For example, the estimated number of pseudogenes is x,000–20,000 in humans, but only 110 in Drosophila. 22

Human genome sequencing has revealed the widespread occurrence of segmental duplications, which often involve blocks of 1–200-kb (or longer) sequences that take been copied from one region of the genome and integrated into another region. Hence, segmental duplications create paralogous loci. The duplicated regions represent low-re-create repeats and have >90% identity. Such potent sequence identity suggests that they are relatively recent in origin. The finished sequence of the human being genome reported almost 5.3% of the genome as segmental duplications.

Chromosomal (whole-genome) duplication is idea to arise past the breakdown of the normal mitotic or meiotic procedure. If chromosomes duplicate but do not split up (chromosomal non-disjunction) and are maintained in the same cell, a diploid gamete is produced. Fertilization of a diploid gamete by a normal haploid gamete would produce a triploid organism. The aforementioned mechanism tin can produce tetraploidy and fifty-fifty college ploidy. In add-on to the to a higher place machinery of polyploidy, termed autopolyploidy, genome duplication and polyploidy can too be produced by hybridization of two related species that produce viable offspring. Such polyploidy is called allopolyploidy, and allopolyploids produce a various set of gametes. During evolution, whole-genome duplication resulting in polyploidy occurred frequently in plants but infrequently in animals.

The evolutionary fate of duplicated genes involves either acquiring new function or becoming nonfunctional. In most cases, the duplicated genes are free to larn degenerative mutations and become pseudogenes (pseudogenization) because at that place are no functional constraints and the genes are not under choice pressure. Thus, pseudogenization is a neutral process. In order for the gene to escape pseudogenization and functional death, selection pressure level must strength the duplicated gene to drift towards fixation through neofunctionalization. Gene duplication followed by neofunctionalization of the duplicated gene provides an important mechanism for the genome to diverge both structurally and functionally. Neofunctionalization involves acquiring new function by the duplicated gene at the expense of the bequeathed function—that is, the duplicated gene acquires a part that was not nowadays in the bequeathed gene. For example, the type III antifreeze protein (AFPIII) cistron in the Antarctic zoarcid fish evolved from a sialic acrid synthase (SAS) cistron afterward duplication, deviation, and neofunctionalization. The SAS is an old cytoplasmic enzyme present in microbes through vertebrates, whereas AFPIIIs are secreted plasma proteins that bind to invading ice crystals and arrest ice growth to forestall fish from freezing. The SAS gene possesses both sialic acid synthase and rudimentary ice-binding activities. Following duplication, the N-terminal SAS domain was deleted and replaced by a nascent signal peptide needed for the extracellular consign of the mature protein. Further optimization of the C-terminal domain's ice-binding ability through amino acid changes led to the development of AFPIII every bit a neofunctionalized secreted protein capable of not-colligative freezing-bespeak depression. 23 Another example is the retinoic acid receptor (RAR) gene. Mammals accept three RAR paralogs—RARα, β, and γ—created by genome duplications at the fourth dimension of origin of vertebrates. Using pharmacological ligands selective for specific paralogs, it was demonstrated that RARβ kept the bequeathed RAR role, whereas RARα and RARγ diverged both in ligand-binding capacity and in expression patterns. Therefore, neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates. 24 Many other examples of neofunctionalization have been reported in the literature.

Neofunctionalization does not always have to arise post-obit gene duplication. A beneficial mutation of the wild-type gene may create a mutant allele with new function. If the beneficial mutant allele is maintained by balancing option, the carrier (heterozygote) volition have increased fettle. If the beneficial mutant allele becomes the source of the duplicated gene, then the duplicated gene will be quickly fixed in the population by positive selection. 25

Another functional outcome of gene duplication and departure is subfunctionalization. Like pseudogenization, subfunctionalization is also a neutral process. Subfunctionalization occurs when the duplicated copies (paralogs) partition the attributes of the ancestral gene, such as function and/or expression. Following a duplication event, both paralogs feel a menstruation of relaxed option and accelerated evolution. This is because natural selection does not distinguish which paralog should be under selection and which paralog should be gratis from selective constraint. Thus, both genes might accumulate mutations that impair ancestral gene function. Under this status, each paralog may retain one role of the function (subfunction) of the ancestral gene. Alternatively, each individual paralog may lose its ability to substitute for the ancestral factor function, only together the ii paralogs may still be able to complement each other in producing bequeathed cistron role. Subfunctionalization has been proposed as an culling mechanism driving indistinguishable cistron retention in organisms with small constructive population sizes. 26 A model to explain the high retentiveness of duplicated genes through subfunctionalization was provided early on by the duplication–degeneration–complementation (DDC) model. 27 According to the DDC model, originally proposed in the context of cis-regulatory elements, subfunctionalization is driven entirely past degenerative mutations. Degenerative changes occur in regulatory sequences of both duplicated copies such that the expression pattern of the original cistron can only be accomplished when the 2 duplicated genes tin can complement each other. Therefore, degenerative mutations in the regulatory elements may increase the chance of indistinguishable gene retention. An implication of the DDC model is that the paralogs tin not accumulate aforementioned inactivating mutations that would interfere with their ability of complementation. A number of examples of subfunctionalization accept been reported in the literature. A common instance is the normal human hemoglobin, which is composed of ii α-chains and two β-chains (α2β2) encoded past α-globin and β-globin genes, respectively. The α- and β-globin genes are products of cistron duplication and subsequent subfunctionalization because they complement each other in producing normal functional hemoglobin. 28 An case of subfunctionalization in terms of differential expression of paralogs is that of the pax6a and pax6b genes in zebrafish; these paralogs arose following a whole-genome duplication consequence most 350 million years ago. The expression patterns of pax6a and pax6b have diverged from each other since the duplication event. Whereas pax6a is widely expressed in the brain compared to pax6b, but pax6b is expressed in the developing pancreas. Such differential expression of pax6b in brain and pancreas is due to the loss of a brain-specific downstream regulatory element but gain of an upstream pancreas enhancer element. 29 An instance of subfunctionalization has also been reported in Archaea. When Tocchini-Valentini and coworkers searched the genome of Sulfolobus solfataricus (Archaea; Crenarchaeota) for homologs j of Methanocaldococcus jannaschii (Archaea; Euryarchaeota) tRNA endonuclease, they found 2 paralogs of the tRNA endonuclease gene of M. jannaschii in the genome of the South. solfataricus. Characterization of these two paralogous cistron products revealed that both are required for tRNA endonuclease activity, each complementing the other for complete activeness. Detailed assay of the amino acid sequences of the ii proteins demonstrated that these two sequences had evolved by duplication of the ancestral sequence followed by deviation and subfunctionalization of the sequences. 30 Effigy 2.four shows the three fates of duplicated genes discussed here (pseudogenization, neofunctionalization, subfunctionalization) using cis-regulatory modules as targets of divergence.

Effigy ii.4. Three possible fates of duplicated genes: pseudogenization (nonfunctionalization), neofunctionalization, and subfunctionalization using cis-regulatory modules as targets of departure.

Duplicated genes are not under option pressure; hence, there are no functional constraints and a duplicated gene is free to acquire degenerative mutations and become a pseudogene. Sometimes, the conquering of new function by the duplicated factor (neofunctionalization) provides an important mechanism for the genome to diverge both structurally and functionally. The newly acquired function is non present in the ancestral factor. Subfunctionalization occurs when the duplicated copies (paralogs) partition the attributes of the ancestral gene, such equally office and/or expression. The figure shows that degenerative changes occurred in regulatory sequences of both paralogs such that the expression pattern of the original gene tin just be achieved when the 2 duplicated genes complement each other (see text for examples).

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The Origin of Evolutionarily Novel Genes and Evolution of New Functions and Structural Complexity in Multicellular Organisms

Andrei P. Kozlov , in Evolution by Tumor Neofunctionalization, 2014

9.2.2 Similarly to Gene Duplication and Retrotransposition Events, Tumors May Provide "Raw Material" for the Evolution of Complexity

Factor duplication provides "raw material" for the mutational process. The "extra" factor copies, functionally unnecessary to the organism, are used in genome evolution and the origin of novel genes. In a similar mode, tumors may provide "extra" cell masses, functionally unnecessary to the organism, which could be used in progressive evolution for the origin of evolutionary innovations and morphological novelties.

Although pathological to individual organisms, tumors still may play an evolutionary role. The analogy of tumors with mutational process in this respect has already been discussed above. Here I will refer to the illustration with the part of not-LTR retrotransposons in genome evolution. Every bit discussed above, non-LTR retrotransposons LINE-one, Alu and SVA played an important role in human genome evolution. Haig Kazazian called mobile elements the "drivers of genome evolution" [Kazazian, 2004]. At the same time, they cause many human genetic diseases past de novo insertions [Kazazian et al., 1988; Deininger and Batzer, 1999; Chen et al., 2005; Callinan and Batzer, 2006; Belancio et al., 2008]. The estimated retrotransposition rates of Alu, LINE-1 and SVA are very high – one in 21 births, 212 births and 916 births, respectively [Xing et al., 2009].

Similar to factor duplication and retrotransposons, tumors might provide the raw material – extra cell masses – for the evolution of multicellular organisms, i.e. they could exist "drivers" of the development of multicellularity merely as mobile elements were the drivers of genome evolution.

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Human Variability and the Origins and Evolution of Language

T.West. Deacon , in On Human Nature, 2017

Intragenomic Relaxed Selection

Gene duplication is a common occurrence in the evolution of genomes ( Ohno, 1970; Ohta, 1994; Van de Peer et al., 2001). It is probably the major source of new genes in the class of evolution. Information technology is also a major means past which cooperative poly peptide complexes arise in development (Orgel, 1977; Zhang, 2003). Multiple occurrences of cistron duplication over the course of evolution have produced "families" of structurally and functionally related genes. It may even exist the case that virtually "new" genes arise as members of a "lineage" of genes sharing a common ancestral gene (Walsh, 1995; Zhang, 2003).

During cistron duplication, a length of Dna is literally copied and spliced into the chromosome nearby, possibly as a issue of uneven crossover events during meiotic replication, viral factor insertion and excision, or some other intrinsic or extrinsic mechanism that modifies factor replication. The effect of such events is that a nucleotide sequence may be duplicated that contains intact regulatory and coding segments for production of a functional protein. The functional consequence is that there is at present two ways of producing the same poly peptide and its phenotypic issue. This back-up tin can relax selection on the duplicate gene'due south office. Thus, if i of two duplicated genes acquires mutations that dethrone its phenotypic part, information technology will not impact the reproduction of the organism (and that modified copy) so long as the other copy remains intact. Moreover, the now mutated factor can continue to acquire mutational changes, so long as its modified phenotypic effect is not somehow deleterious. Such mutations will thus exist effectively or near neutral.

The typical effect of this sort of neutrality with respect to pick tin can be described as a "random walk" away from the original function. The upshot is the accumulation of arbitrary sequence changes at the genetic level and a progressively degraded or dedifferentiated contribution to the phenotype. Presumably, persistent shielding from any option effects will eventually lead to complete loss of function, as in pseudogenes.

This has been the fate of a very large number of genes in the man genome, which were one time associated with a more astute olfactory sense (eg, Rouquier et al., 1998). Information technology is estimated that a typical mammal has on the order of 1300 genes encoding distinct olfactory receptor molecules. This number was radically reduced both in primate and in human evolution. The human species has had roughly lx% of these genes degrade to become pseudogenes (Gilad et al., 2003). This clearly reflects very weak, to nearly nonexistent, choice to maintain the numbers and diversity of these receptor molecules.

Just degradation to pseudogene status is not inevitable for gene duplicates. Because gene duplication tin can involve an already functional segment of Dna, slight degradations of its sequence may but incrementally change its phenotypic effects. The progressive degradation of functional specificity that is probable to result can, however, be seen as a sort of "exploration" of variants of the original function. For example, a single protein may require structural compromises to conform its multiple associations to other molecules, simply multiple variant forms may each evolve specificity for i or another of these relationships.

In other words, the duplication, relaxation of purifying pick, and random walk that results from cistron duplication tin provide a kind of exploration of the infinite of possible synergistic relationships that can issue from a sort of fractionation of existing functions. This is a recipe for increasing functional complication (Lynch and Conery, 2003).

If the prevalence of gene duplication in animal and establish genomes is any indication, the probability that a given duplication will consequence in a useful fragmentation of an original office is far from goose egg. Gene families, consisting of many paralogous genes (eg, derived from a common bequeathed gene), are widespread in complex organisms and are ofttimes responsible for similar or even synergistic phenotypic functions. To illustrate this, consider 2 well-known examples.

The first is the globin gene family unit, and specifically the hemoglobins. The hemoglobin protein complex contained in red blood cells comprises two varieties of the hemoglobin protein—alpha and beta hemoglobin—each produced by a singled-out hemoglobin cistron. Two blastoff- and ii beta-hemoglobin proteins fit together to form a tetrahedral complex made possible due to the complementary shapes of the molecular surfaces forming the interior of the tetramer with the fe-containing oxygen-bounden regions occupying the "corners" of the tetrahedron. These ii forms of hemoglobin arose from a gene duplication event, and the ancestral hemoglobin itself arose from duplication of an ancestral gene for both hemoglobin and myoglobin.

Changes that increased the stability of tetrameric bounden of the two hemoglobin variants announced to take been favored by natural selection with respect to ane another, probably because of the superior oxygen send capacity of the tetrahedral form. In other words, in their evolutionary random walks through dissimilar three-dimensional configurations, the two "sister" versions of hemoglobin retained their oxygen-bounden function while effectively "sampling" the consequences of this secondary feature of their molecular shape "explored" via sexual recombination.

This detail combination of alpha and beta hemoglobins is non, however, present at all stages of the mammalian life cycle. In the fetus of a placental mammal, boosted variant beta-hemoglobin forms are expressed, three of which are termed gamma, delta, and epsilon hemoglobin. These variants are expressed at dissimilar stages of gestation, and are each coded past a different variant indistinguishable of the beta course of the gene, with the unabridged family unit present in a continuous segment of chromosome 11. These beta-hemoglobin duplication events, which occurred during the course of placental mammal evolution, have as well given ascension to two pseudo-beta hemoglobin genes, which no longer produce a corresponding protein. The remaining four beta-hemoglobin genes are expressed at slightly dissimilar times during development in the order epsilon-gamma-delta-beta.

The functional value of this is related to the fetus's need to acquire oxygen from mother'south hemoglobin and yet nevertheless transfer it from blood to its own somatic cells despite changes in placentation and increasing trunk size. As a result, embryonic and fetal hemoglobin requires a different oxygen-bounden affinity over the class of gestation. At dissimilar stages of gestation, there will be a different optimal balance of hemoglobin affinities between mother and baby. The different beta-hemoglobin variants expressed during unlike phases of gestation enable the fetus to progressively adapt to this challenge, until at nativity beta hemoglobin becomes the predominant course produced. Analogous to the complementarity "discovered" due to alpha/beta duplication, these additional duplications of the beta-hemoglobin cistron led to synergies of timing and oxygen-bounden affinities that became subject to selection in the context of internal gestation.

In summary, spontaneous factor duplication results in functional back-up, thereby reducing the intensity of purifying selection on each duplicate. Relaxation of purifying selection allows variations to persist and accumulate in one duplicate while maintaining the original function in the other. If accumulated changes result in but modest degradation of the original functional specificity, at that place is a nonzero probability that pairings of duplicates volition occur that complement each other'due south functional differences resulting in synergistic effects.

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Biotransformation

J.R. Cashman , M.S. Motika , in Comprehensive Toxicology, 2010

4.05.3.three FMO Factor Organisation

Gene duplication of a common bequeathed gene that took identify long before the difference of mammals led to all members of the FMO cistron family. Therefore, in all mammalian species, orthologues of each FMO form should be found. The individual genes are on the aforementioned chromosomal arm of human chromosome 1 (Phillips et al. 1995). All FMOs share a similar pattern of intron–exon organization. FMO2, three, and 5 contain eight coding exons (2 through 9), and the size and boundaries of these are highly conserved. FMO also contains at to the lowest degree one noncoding exon (numbered 1) and man FMO1 and 4 contain an additional noncoding exon (numbered 0) (Dolphin et al. 1997; Ziegler 1991). FMOs one, two, 3, 4, and 6 are located in a 220-kb cluster of region 1q23–25 of human chromosome i (Hernandez et al. 2004). FMO5 is located outside this cluster in region 1q21.1. Approximately iv   Mb centromeric of the original FMO gene cluster is another cluster with five of the FMO pseudogenes. The pseudogene cluster presumably arose through a series of independent gene duplication events because the nucleotide sequences of members of the human pseudogene cluster (FMOs 7P–11P) are more similar to each other than to members of the known factor cluster (FMOs 1–iv and 6) (Gelb et al. 1997; Hernandez et al. 2004).

Selective pressures led to the development of FMOs with new and advantageous functions. Possibly, an ancestral FMO was important to detoxicate natural products. Later, equally humans were exposed to less of these materials, other more than region-specific issues placed selective force per unit area for molecular development (Cashman and Zhang 2006). Certain FMOs may have evolved to detoxicate specific toxins. Populations with a loftier prevalence of certain FMO variants probable serve every bit examples of evolutionary pressure. Individuals from the tropics possess FMO3 mutations with decreased functional activeness. Such FMO3 variants may have evolved to decrease metabolism of odorous trimethylamine (TMA), and then that TMA could be used equally a archaic volatile insecticide (Cashman and Zhang 2006; Cashman et al. 2003; Mitchell et al. 1997). Too, although most humans lack full-length FMO2, certain individuals of African or Latino descent express a functional FMO2 protein (Whetstine et al. 2000). Maybe, at one time, humans needed FMO2 to detoxicate certain materials that they were not exposed to later and FMO2 became nonvital and evolved to a nonfunctional pseudogene.

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The Evolution of The Human Encephalon: Apes and Other Ancestors

E.J. Vallender , in Evolution of Nervous Systems (2nd Edition), 2017

iv.07.2.1.ii Cistron Duplication

Cistron duplication has long been recognized equally a potential source of evolutionary novelty ( Ohno, 1970). Afterwards a duplication event occurs, the most mutual fate is simply for one of the genes to deteriorate into a pseudogene without any meaningful phenotypic effect. In some cases, however, the new paralog persists. In these cases, with two genes now effectively doing a single chore, evolutionary pressures are relaxed. This tin can lead to neofunctionalization, where one of the copies maintains its ancestral function while the other develops a new part, or subfunctionalization, where the two copies each accept on some, but not all, of the functions of the ancestral gene (Hughes, 1994; Force et al., 1999). In either case, there is a modify in the evolutionary pressures on the gene: a cistron that had been undergoing balancing selective pressures to maintain ii functions can now devote each of its copies to doing one of the functions "ameliorate" (subfunctionalization), or a new re-create of a gene that sees its original function taken care of by its paralog is free to "attempt new things" (neofunctionalization).

When this subfunctionalization or neofunctionalization occurs, the same evolutionary mechanisms that would apply to any single factor also occur. Protein sequence might change; regulatory sequences might be altered. The key gene that differentiates this machinery from more traditional evolutionary alter is the lessening of a negative constraint first. Usually genes are under strong selective pressures to maintain their existing functions, then whatsoever difference from this would likely be harmful; duplication events relieve this pressure and let more freedom for the genes to explore the fitness mural. Of grade, every bit mentioned previously, the about common event is that ane of the paralogs speedily "falls off" this landscape losing any functional relevance and leaving the other paralog to acquit on as before.

The all-time example of adaptive evolution following factor duplication in primates comes from studying the emergence of color vision (Hunt et al., 1998). In the last mutual ancestor of New and Erstwhile World monkeys and apes (Simiiformes), at that place were ii opsin genes, a "blue" opsin on an autosome and a "green" opsin on the 10 chromosome. After the deviation between the Platyrrhini and Catarrhini, a duplication of the "green" opsin occurred in the bequeathed catarrhine. Neofunctionalization followed and a new "red" opsin emerged, leading to trichromatic vision in Old Earth monkeys, apes, and humans. The shift likely contributed, at least in function, to the subsequent speciation consequence and to the movement into novel ecological niches (Dominy and Lucas, 2001).

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Evo-Devo: Regulatory and Protein-Coding Evolution in Plant Diversification

J.C. Preston , in Encyclopedia of Evolutionary Biology, 2016

Gene Duplications Tin Reduce Genetic Pleiotropy and Foster Phenotypic Novelty

Cistron duplication events in plants are a common occurrence. Single genes tin can exist replicated through the action of transposable elements, slippage during DNA replication, or unequal crossing during meiosis, whereas whole genomes tin can be duplicated via accidents in meiosis (autopolyploidization) or hybridization betwixt distinct taxa (allopolyploidization). The near common fate for duplicate genes is the functional conservation of ane paralog and not-functionalization of the other ( Rensing, 2014) (Figure 4(a)). Non-functionalization tin occur extremely quickly through epigenetic silencing of paralogs or homeologs (genes duplicated through allopolyploidy), possibly every bit an adaptation to combat factor dosage effects, or gradually over evolutionary time due to relaxed pick (Woodhouse et al., 2014). Less frequently, both functional paralogs can exist maintained in the genome, either through the process of sub-functionalization (where the descendent genes partition the functions of their parent) (Figure 4(b)), or neo-functionalization (where one gene evolves a new function) (Ohno, 1970) (Figure iv(c)).

Figure 4. Potential fates of duplicated genes. (a) One paralog becomes a non-functional pseudogene by acquiring deleterious mutations while the other retains the ancestral functions. (b) Both genes acquire deleterious mutations in different cis-regulatory and poly peptide-coding modules, thus partitioning the ancestral gene function through sub-functionalization. (c) 1 paralog acquires a novel advantageous mutation (orangish) that can lead to evolutionary innovation in plant grade, whereas the other paralog retains the ancestral functions.

Sub- and neo-functionalization of duplicate genes can occur through mutations in either protein coding or cis-regulatory regions of genes (Figure iv). Although sub-functionalization does not promote phenotypic modify per se, it tin substantially reduce genetic pleiotropy by constraining the impact of mutations to simply a subset of developmental functions carried out by the parental (pre-duplication) gene. In this instance, mutations in the coding regions of sub-functionalized genes tin can lead to evolutionary 'tinkering' of phenotypes (Carroll et al., 2001) rather than 'hopeful monsters' caused past and then-called macromutations (Goldschmidt, 1940). For instance, in snapdragon (Antirrhinum majus) a single amino acid change in combination with the rewiring of interacting poly peptide expression has been sufficient to convert the MADS-box gene FARINELLI (FAR) from a regulator of stamen and carpel develop (as is seen in its paralog PLENA (PLE)) to a regulator of stamen development alone (Airoldi et al., 2010).

There are numerous examples of neo-functionalized duplicate genes that have driven major developmental innovations in plants, including shoot apical meristems and flowers (Rensing, 2014). In the fewer instances where the underlying mutation for neo-functionalization has been determined, some are due to regulatory changes, some to protein-coding changes, and others both. For example, a unmarried amino acid commutation in the duplicated domestication gene TEOSINTE GLUME Compages 1 (TGA1) was responsible for converting the solidly encased kernels of teosinte to naked kernels in maize (Wang et al., 2005, 2015). Thus, protein-coding changes tin affect discrete phenotypes in plants, and are perhaps more important to the development of development than was once thought.

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The polyploid origins of crop genomes and their implications: A case study in legumes

Brian Nadon , Scott Jackson , in Advances in Agronomy, 2020

Abstract

Gene duplication and polyploidy are some of the most important, yet underappreciated, evolutionary forces that have shaped all flowering plants on earth, and the ingather plants that enable human economic activity are prime exemplars of duplication in action. Polyploidy involves an immediate doubling, tripling, or more of a genome, oftentimes followed by desperate chromosomal reorganization or a reduction back to diploidy, and has occurred many times in the history of most characterized establish genomes. Understanding how duplication shapes plant genomes is critical for understanding how to feed a growing and hungry global human being population. Of particular importance are legumes, one of the largest plant families on earth, often noted for their nitrogen fixation abilities and high nutritional value due to their protein content. Among these Papilionoid ( Faboideae) legume crops are alfalfa, soybean, peanut, and common bean. All of these have experienced polyploidy events somewhere in their history, some aboriginal (60   My or more) and some very recent (e.g., ~   10,000 years ago in peanut). The modes by which these polyploidies arose, whether from divergent genomes coming together (allopolyploidy), or identical or similar genomes duplicating (autopolyploidy), tin can affect their evolution, domestication, and improvement considerably, whether by generating new functional diversity or driving speciation. Appreciating the indelible mark polyploidy and duplication leave on these legume genomes will enable a better understanding of the molecular biology, breeding, and agronomy of these critical crops.

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Genes and Evolution

P. Balaresque , T.East. King , in Current Topics in Developmental Biology, 2016

6 Phenotypic Variation, Accommodation, and Duplication: Are Copy Number Genes an Easy Solution to Respond to Rapid Changes?

Gene duplication is one of the fundamental factors responsible for genetic innovation. Duplicated genes in eukaryotes are often related to metabolism (such as amylase genes above), stress responses, and cell decease ( Maere et al., 2005). In the human genome, the widespread presence of pocket-size and large-calibration copy number variant (CNV) has been shown in normal populations (Sebat et al., 2004; Sharp et al., 2005). Deletion and duplications are represented equally and occur in unstable genomic regions; nigh 70 different genes were shown to vary in CNVs (Sebat et al., 2004). There is a significant overrepresentation of genes associated with environmentally regulated function and immunity, suggesting an adaptive advantage of dosage imbalance in these regions (Conrad & Antonarakis, 2007). Among these genes, nosotros can cite genes involved in (i) various ecology perceptions, such every bit olfactory genes (OR); (two) variable power to digest/metabolize new food sources, such as amylase genes (AMY); (iii) responses to drugs, such as the cytochrome P-450 isoform genes (CYP2) responsible for the biotransformation of 40% of all drugs; and (four) responses to pathogens, such as the DFB4 and CCL3L1 genes influencing the susceptibility to HIV-1 infection (Gonzalez et al., 2005). Considering many of these genes have been positively selected in humans (Nguyen, Webber, & Ponting, 2006), these CNV genes could play a key role in recent human phenotypic adaptations and might been seen as a cardinal mechanism of adaptation (discussed in Kondrashov, 2012).

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https://world wide web.sciencedirect.com/science/commodity/pii/S0070215316300011