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Register a new userNeutral networks of genotypes: Evolution behind the curtain
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Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of On the origin of species by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and selection within the framework of a formal theory, able eventually to predict the dynamics and fate of evolving populations. However, a large body of empirical evidence collected over the last decades strongly suggests that some of the assumptions of those classical models necessitate a deep revision. The viability of organisms is not dependent on a unique and optimal genotype. The discovery of huge sets of genotypes (or neutral networks) yielding the same phenotype --in the last term the same organism--, reveals that, most likely, very different functional solutions can be found, accessed and fixed in a population through a low-cost exploration of the space of genomes. The evolution behind the curtain may be the answer to some of the current puzzles that evolutionary theory faces, like the fast speciation process that is observed in the fossil record after very long stasis periods.
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The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most apparent genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked recurrent deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1,000 Genomes project (Abecasis et al. 2012) and detect signatures of pervasive positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as the presence of unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to show that the observed signatures require a high rate of strongly adaptive substitutions in the vicinity of the amino acid changes. We further demonstrate that the observed signatures of positive selection correlate more strongly with the presence of regulatory sequences, as predicted by ENCODE (Gerstein et al. 2012), than the positions of amino acid substitutions. Our results establish that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson (King and Wilson 1975) that adaptive divergence is primarily driven by regulatory changes.
This paper develops a quasispecies model that incorporates the SOS response. We consider a unicellular, asexually replicating population of organisms, whose genomes consist of a single, double-stranded DNA molecule, i.e. one chromosome. We assume that repair of post-replication mismatched base-pairs occurs with probability $ lambda $, and that the SOS response is triggered when the total number of mismatched base-pairs exceeds $ l_S $. We further assume that the per-mismatch SOS elimination rate is characterized by a first-order rate constant $ kappa_{SOS} $. For a single fitness peak landscape where the master genome can sustain up to $ l $ mismatches and remain viable, this model is analytically solvable in the limit of infinite sequence length. The results, which are confirmed by stochastic simulations, indicate that the SOS response does indeed confer a fitness advantage to a population, provided that it is only activated when DNA damage is so extensive that a cell will die if it does not attempt to repair its DNA.
This paper develops a mathematical model describing the influence that conjugation-mediated Horizontal Gene Transfer (HGT) has on the mutation-selection balance in an asexually reproducing population of unicellular, prokaryotic organisms. It is assumed that mutation-selection balance is reached in the presence of a fixed background concentration of antibiotic, to which the population must become resistant in order to survive. We analyze the behavior of the model in the limit of low and high antibiotic-induced first-order death rate constants, and find that the highest mean fitness is obtained at low rates of bacterial conjugation. As the rate of conjugation crosses a threshold, the mean fitness decreases to a minimum, and then rises asymptotically to a limiting value as the rate of conjugation becomes infinitely large. However, this limiting value is smaller than the mean fitness obtained in the limit of low conjugation rate. This dependence of the mean fitness on the conjugation rate is fairly small for the parameter ranges we have considered, and disappears as the first-order death rate constant due to the presence of antibiotic approaches zero. For large values of the antibiotic death rate constant, we have obtained an analytical solution for the behavior of the mean fitness that agrees well with the results of simulations. The results of this paper suggest that conjugation-mediated HGT has a slightly deleterious effect on the mean fitness of a population at mutation-selection balance. Therefore, we argue that HGT confers a selective advantage by allowing for faster adaptation to a new or changing environment. The results of this paper are consistent with the observation that HGT can be promoted by environmental stresses on a population.
Despite numerous mass extinctions in the Phanerozoic eon, the overall trend in biodiversity evolution was not blocked and the life has never been wiped out. Almost all possible catastrophic events (large igneous province, asteroid impact, climate change, regression and transgression, anoxia, acidification, sudden release of methane clathrate, multi-cause etc.) have been proposed to explain the mass extinctions. However, we should, above all, clarify at what timescale and at what possible levels should we explain the mass extinction? Even though the mass extinctions occurred at short-timescale and at the species level, we reveal that their cause should be explained in a broader context at tectonic timescale and at both the molecular level and the species level. The main result in this paper is that the Phanerozoic biodiversity evolution has been explained by reconstructing the Sepkoski curve based on climatic, eustatic and genomic data. Consequently, we point out that the P-Tr extinction was caused by the tectonically originated climate instability. We also clarify that the overall trend of biodiversification originated from the underlying genome size evolution, and that the fluctuation of biodiversity originated from the interactions among the earths spheres. The evolution at molecular level had played a significant role for the survival of life from environmental disasters.
This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating genomes, whose only source of genetic variation is due to copying errors during replication. We consider a time-dependent, single-fitness-peak landscape where the master sequence changes by a single point mutation every time $ tau $. We are able to analytically solve for the evolutionary dynamics of the population in the point-mutation limit. In particular, our model provides an analytical expression for the fraction of mutators in the dynamic fitness landscape that agrees well with results from stochastic simulations.
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