Ohno's dilemma: Evolution of new genes under continuous selection

“cation among the duplicates through a secondary functional attribute of the gene product (Bergthorsson et al. 2007).”

“First, it does not involve an intragenomic duplication step, so it is distinct from neo-or sub-functionalization of paralogous gene copies [1, 2, 4].”

“…appears to be (Piatigorsky 2007) and its potential importance in duplicate gene retention (Wistow 1993; Hughes 1994; Lynch and Force 2000; Bergthorsson et al. 2007), one interesting avenue of research could involve study of how, evolutionarily (e.g., Johnston et al. 2007) and…”

“The authors propose that gene redundancy was explained by the IAD model, while the specialization of the current enzyme arose from the conflict between SA and BA enzymatic activities, as explained by the EAC model (Huang et al. 2012).”

“Mechanisms leading to gene duplication are considered to be essential for the development of novel genes (Lynch and Conery 2000; Demuth et al. 2006; Bergthorsson et al. 2007), and the presence of duplicated genes involved in physiological processes underlines its pivotal role (De Grassi et al.…”

“However, a problem with this scenario, known as ‘Ohno’s Dilemma’ (Bergthorsson et al. 2007), is the difficulty of explaining how gene”

“Ohno’s dilemma states that a gene product must have a useful function at all stages of its evolution to be acted upon by positive selection [30].”

“This difference in size between the two housekeeping gene families may have been caused by an ancient duplication event that led to the addition of a family of def paralogs (genes derived from ancient duplication events) (Bergthorsson et al. 2007; Näsvall et al. 2012).”

“…1977; Haack and Roth 1995; Reams et al. 2010), are often found during laboratory selection conditions (Riehle et al. 2001; Kno¨ppel et al. 2016), and play a role in shaping genome diversification and the evolution of new genes (Bergthorsson et al. 2007; N € asvall et al. 2012; Zhou et al. 2012).”

“This model suggests that selection pressures promote the mutational improvement of CHS copies and develop side functions to adapt to environmental conditions (Bergthorsson et al., 2007; Copley, 2020).”

“Gene/genome duplication is a driving force for evolution (Bergthorsson et al., 2007; Maere and Van De Peer, 2010) and this could be nicely exemplified by the well-studied PAX gene family, where many duplicates were preserved in the genome and obtained new functions and new domains of expression…”

“This divergence can lead to the evolution of new genes and functions (Ohno, 1970; Bergthorsson et al., 2007; Nasvall et al., 2012).”

“In a different scenario [12] most of a gene’s ancestral secondary functions are not carried out at an optimal rate; duplication would be beneficial from the start as it enhances these secondary functions.”

“There is also evidence for a mechanism where there is no “invention” of new gene function(s) or direct partitioning of ancestral functions, but rather amplification followed by improvement of extant weak or secondary functions in duplicate genes [8-10].”

“Selection for greater gene dosage would lead to the retention of both paralogs with roughly symmetric rates of sequence divergence [24], unless selection for greater dosage is on the gene’s lesser auxiliary activities, in which case we might also expect asymmetric rates of sequence divergence [45].”

“Although this contrasts with the prevailing Innovation–Amplification–Divergence (IAD) model for natural enzyme evolution (Bergthorsson et al., 2007), it may not be an exceptional scenario – rather, as previously argued by Newton et al.”

“Among all of these evolutionary mechanisms for generating novel genes, gene duplication is a significant contributor that facilitates organisms to adapt to dynamically changing environments [2, 3].”

“One explanation may be the additive function of some duplicates: duplications resulting in a phenotypic change might protect daughter genes from relaxed selection and ultimately pseudogenization, thereby promoting the fixation of new genes under the appropriate selective regimes [62,63].”

“…the experimentally validated innovation ‐ amplification ‐ diversification (IAD) model best illustrates the potential synergism between the fitness ‐ and evolva-bility enhancing effects of gene duplications (Andersson et al., 2015; Bergthorsson et al., 2007; Copley, 2020; Nasvall et al., 2012).”

“As an example, student drawings (typically generated through group activities) were photographed using the iPad’s camera and projected for all students to consider.”

“Some of the models (reviewed in [36]) developed in order to explain the retention of both genes following gene duplication, include the evolution of a new function in one of the duplicates, the division of ancestral functions among duplicates and the”

“it can lead to novel phenotypes including antibiotic resistance [7,8].”

“When an allele with gene duplication arises in a population, the allele could achieve fixation either in a neutral fashion (random drift) [21,22], or by the initial advantage for increased gene dosage [23,24,25].”

“In conclusion, our findings nicely fit the innovation amplification and divergence (IAD) model of evolution (Bergthorsson et al., 2007).”

“The lack of complete homology of mammalian SBDPs in salmon brain tissues may be related more to the evidence of genome duplication in the salmonids [29] and the loss of function due to redundancy [30], or adaptation for different functions.”

“The maintenance of large gene families in genomes is a heavily debated issue in both prokaryotes and eukaryotes [10].”

“A leading model for the development of new function in enzymes involves the amplification of genes that express low-level promiscuous activities, which can then develop mutations that alter and refine the new activity (32).”

“Central to the IAD model is the observation that gene duplication via unequal crossing over is more likely to occur than a point mutation ( 3 , 7 ).”

“Nevertheless, other more recent views, such as Bergthorsson and colleagues [30], argued that situations in which paralogs retain different parts of the ancestral function (subfunctionalization) cannot explain the origin of de novo adaptive phenotypes.”

“Selective pressures can be important in determining the evolutionary fate of duplicated genes [48,49].”

“suggests that these gene sequences may have arisen through innovation, amplification and divergence (Bergthorsson et al. 2007) of a what was once a single genetic locus.”

“…main gene, In this study, silencing the GbCHI01 , GbCHI05 , GbCHI06 and GbCHI09 genes directly affected ROS accumulation, indicating that the four CHI family genes may directly confer resistance to Fusarium wilt and activate other defense systems of cotton by regulating ROS metabolism (Figure 10).”

“Moreover, evolutionary innovation generally involves gene duplication rather than a static genome (Bergthorsson et al., 2007), a fact rarely emphasized in most genetics or molecular biology textbooks.”

“In contrast, its paralogous gene MYB13, which was selectively constrained, with extremely low ω, was suggested to preserve ancestral function [52].”

“The high supply rate of genetically and functionally redundant gene copies might be especially advantageous when the environment imposes immediate selection for increased gene dosage and gene expression [1].”

“…a distinct function, reflected in anticodons that recognize a variety of different codon blocks, is likely to be low given that for duplicated genes the usual fate is pseudogenization, meaning that the acquisition of a new function via novel mutations is very rare (Bergthorsson et al. 2007).”

“The innovation-amplificationdivergence (IAD) model posits that selection acts on weak promiscuous activities present in existing proteins (19).”

“The amplification model supported by this article has already be proposed as a means of evolving new genes (17) and has been experimentally shown to be capable of generating a novel genetic function within as few as 3,000 cell generations (18).”

“The Innovation - Amplification - Divergence (IAD) model describes an evolutionary scenario by which a gene encoding a new function can arise ( 2 , 24 ) ( Fig.”

“Some duplicates benefit an organism by simply increasing the expression of a low-efficiency enzyme (Bergthorsson et al. 2007; Kondrashov and Kondrashov 2006).”

“Many models of protein functional evolution require gene duplication and posit the existence of multifunctional/promiscuous ancestors [57–61].”

“Moreover, neofunctionalization is not the only possible scenario of divergence after duplication [8-13].”

“This classical model has been criticized and alternative models postulated (Hughes 1994; Force et al. 1999; Bergthorsson et al. 2007).”

“Gene copy number variation enables two ways of escaping from the evolutionary tradeoff between two conflicting selection pressures (Francino 2005; Bergthorsson et al. 2007; Deng et al. 2010; N€asvall et al. 2012): 1) The extra gene copies can allow for higher expression, which provides more of both the original and th…”

“In [12], the duplication rate is assumed to be 10 per gene per generation, null functional mutation rate is on the order of 10 per gene per generation, and new functions arise at a rate of 10 per gene per generation.”

“While selective pressure maintaining the duplication should counter the inactivation of one of the VapD copies (a challenge known as Ohno’s dilemma [64]), in the absence of selection, one copy of VapD would quickly accumulate deleterious mutations leading to VapW.”

“Significance & Implications Where it has been previously assumed that activity is the driving factor for the evolution of conotoxins [4,15,18,19], we propose that the evolutionary pressures acting on the venom components of cone snails involve an interplay of production/ folding efficiency, activity at the target rece…”

“In molecular evolution, for example, gene duplicationisregardedastheprimarymechanisminvolvedinthecreationofbiological information ( Roth et al. 2007 ).”

“The Innovation-AmplificationDivergence (IAD) model (Bergthorsson et al. 2007) (fig.”

“The implication of altered duplicates on such responses (to different stresses) still deserves further research, but some light has been shed on how duplicates were selected, preserved, and still able to innovate following Ohno’s dilemma [71,72].”

“They include the “mutations during non-functionality” model (MDN) 15 ; the “Duplication-Degeneration-Complementation” model (DDC) 3 , the “Escape from Adaptive Conflict” model (EAC) 4, 14 , and the “Innovation-Amplification-Divergence” model (IAD) 8, 13 .”

“The function and components ofmanyGRNs are conserved in evolution based in the innovation, amplification and divergence theory (Bergthorsson et al., 2007; Romero-Campero et al., 2013).”

“Less often, duplicated genes could also gain novel functions, which would promote their retention (Bergthorsson et al., 2007).”

“The fate of duplicated genes varies, and new gene copies can either disappear or diverge to acquire new functions and to form a new family of homologs [1, 2].”

“divergence [42], where paralogs partially retain their secondary functions.”

“complex organism [32], thereby increasing the probability that a duplicated variant will offer further survival benefits [33, 34].”

“Second, the presence of the second copy of a gene may allow the accumulation of beneficial mutations (29, 30).”