Muller’s ratchet of the Y chromosome with gene conversion

Muller’s ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller’s ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller’s ratchet to explore the evolution of the Y chromosome. The model assumes a non-recombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.

Mutation Edgotype Drives Fitness Effect in Human

Missense mutations are known to perturb protein-protein interaction networks (known as interactome networks) in different ways. However, it remains unknown how different interactome perturbation patterns (“edgotypes”) impact organismal fitness. Here, we estimate the fitness effect of missense mutations with different interactome perturbation patterns in human, by calculating the fractions of neutral and deleterious mutations that do not disrupt PPIs (“quasi-wild-type”), or disrupt PPIs either by disrupting the binding interface (“edgetic”) or by disrupting overall protein stability (“quasi-null”). We first map pathogenic mutations and common non-pathogenic mutations onto homology-based three-dimensional structural models of proteins and protein-protein interactions in human. Next, we perform structure-based calculations to classify each mutation as either quasi-wild-type, edgetic, or quasi-null. Using our predicted as well as experimentally determined interactome perturbation patterns, we estimate that >∼40% of quasi-wild-type mutations are effectively neutral and the remaining are mostly mildly deleterious, that >∼75% of edgetic mutations are only mildly deleterious, and that up to ∼75% of quasi-null mutations may be strongly detrimental. These estimates are the first such estimates of fitness effect for different network perturbation patterns in any interactome. Our results suggest that while mutations that do not disrupt the interactome tend to be effectively neutral, the majority of human PPIs are under strong purifying selection and the stability of most human proteins is essential to human life.

A method to delineate de novo missense variants across pathways prioritizes genes linked to autism

Genotype-phenotype relationships shape health and population fitness but remain difficult to predict and interpret. Here, we apply an evolutionary action method to de novo missense variants in whole-exome sequences of individuals with autism spectrum disorder (ASD) to unravel genes and pathways connected to ASD. Evolutionary action predicts the impact of missense variants on protein function by measuring the fitness effect based on phylogenetic distances and substitution odds in homologous gene sequences. By examining de novo missense variants in 2384 individuals with ASD (probands) compared to matched siblings without ASD, we found missense variants in 398 genes representing 23 pathways that were biased toward higher evolutionary action scores than expected by random chance; these pathways were involved in axonogenesis, synaptic transmission, and neurodevelopment. The predicted fitness impact of de novo and inherited missense variants in candidate genes correlated with the IQ of individuals with ASD, even for new gene candidates. Taking an evolutionary action method, we detected those missense variants most likely to contribute to ASD pathogenesis and elucidated their phenotypic impact. This approach could be applied to integrate missense variants across a patient cohort to identify genes contributing to a shared phenotype in other complex diseases.

Historical Contingency Causes Divergence in Adaptive Expression of the lac Operon

Populations of Escherichia coli selected in constant and fluctuating environments containing lactose often adapt by substituting mutations in the lacI repressor that cause constitutive expression of the lac operon. These mutations occur at a high rate and provide a significant benefit. Despite this, eight of 24 populations evolved for 8,000 generations in environments containing lactose contained no detectable repressor mutations. We report here on the basis of this observation. We find that, given relevant mutation rates, repressor mutations are expected to have fixed in all evolved populations if they had maintained the same fitness effect they confer when introduced to the ancestor. In fact, reconstruction experiments demonstrate that repressor mutations have become neutral or deleterious in those populations in which they were not detectable. Populations not fixing repressor mutations nevertheless reached the same fitness as those that did fix them, indicating that they followed an alternative evolutionary path that made redundant the potential benefit of the repressor mutation, but involved unique mutations of equivalent benefit. We identify a mutation occurring in the promoter region of the uspB gene as a candidate for influencing the selective choice between these paths. Our results detail an example of historical contingency leading to divergent evolutionary outcomes.

The evolutionary origin of the universal distribution of mutation fitness effect

An intriguing fact long defying explanation is the observation of a universal exponential distribution of beneficial mutations in fitness effect for different microorganisms. To explain this effect, we use a population model including mutation, directional selection, linkage, and genetic drift. The multiple-mutation regime of adaptation at large population sizes (traveling wave regime) is considered. We demonstrate analytically and by simulation that, regardless of the inherent distribution of mutation fitness effect across genomic sites, an exponential distribution of fitness effects emerges in the long term. This result follows from the exponential statistics of the frequency of the less-fit alleles, f, that we predict to evolve, in the long term, for both polymorphic and monomorphic sites. We map the logarithmic slope of the distribution onto the previously derived fixation probability and demonstrate that it increases linearly in time. Our results demonstrate a striking difference between the distribution of fitness effects observed experimentally for naturally occurring mutations, and the "inherent" distribution obtained in a directed-mutagenesis experiment, which can have any shape depending on the organism. Based on these results, we develop a new method to measure the fitness effect of mutations for each variable residue using DNA sequences sampled from adapting populations. This new method is not sensitive to linkage effects and does not require the one-site model assumptions.

Prioritization of antimicrobial targets by CRISPR-based oligo recombineering

SummaryNucleophilic amino acids are important in covalent drug development yet underutilized as antimicrobial targets. Over recent years, several chemoproteomic technologies have been developed to mine chemically-accessible residues via their intrinsic reactivity toward electrophilic probes. However, these approaches cannot discern which reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based Oligo Recombineering (CORe) platform to systematically prioritize reactive amino acids according to their contribution to protein function. Our approach directly couples protein sequence and function with biological fitness. Here, we profile the reactivity of >1,000 cysteines on ~700 proteins in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. We competitively compared the fitness effect of 370 codon switches at 74 cysteines and identify functional sites in a diverse range of proteins. In our proof of concept, CORe performed >800 times faster than a standard genetic workflow. Reactive cysteines decorating the ribosome were found to be critical for parasite growth, with subsequent target-based screening validating the apicomplexan translation machinery as a target for covalent ligand development. CORe is system-agnostic, and supports expedient identification, functional prioritization, and rational targeting of reactive sites in a wide range of organisms and diseases.

Fitness maps to a large-effect locus in introduced stickleback populations

Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.

Assessing environmental impact of pollen-mediated transgene flow.

Potential environmental impact caused by pollen-mediated transgene flow from commercially cultivated genetically engineered (GE) crops to their non-GE crop counterparts and to their wild and weedy relatives has aroused tremendous biosafety concerns worldwide. This chapter provides information on the concept and classification of gene flow, the framework of the environmental biosafety assessment caused by pollen-mediated gene flow, and relevant case studies about transgene flow and its environmental impact. In general, gene flow refers to the movement of genes or genetic materials from a plant population to other populations. Crop-to- crop transgene flow at a considerable frequency may result in transgene 'contamination' of non-GE crops, causing potential food/feed biosafety problems and regional or international trade disputes. Crop-to- wild/weedy transgene flow may bring about environmental impacts, such as creating more invasive weeds, threatening local populations of wild relative species, or affecting genetic diversity of wild relatives, if the incorporated transgene can normally express in the recipient wild/weedy plants and significantly alter the fitness of the wild/weedy plants and populations. It is therefore necessary to establish a proper protocol to assess the potential environmental impacts caused by transgene flow. Three steps are important for assessing potential environment impacts of transgene flow to wild/weedy relatives: (i) to accurately measure the frequencies of transgene flow: (ii) to determine the expression level of a transgene incorporated in wild/weedy populations; and (iii) to estimate the fitness effect (benefit or cost) conferred by expression of a transgene in wild/weedy populations. The recently reported case of non-random allele transmission into GE and non-GE hybrid lineages or experimental populations challenges the traditional method of estimating the fitness effect for the assessment of environmental impacts of transgene flow. Furthermore, case studies of transgenic mitigation (TM) strategies illustrate ways that may reduce the impacts of a transgene on wild/weedy populations if crop-to- wild/weedy transgene flow is not preventable, such as in the case of gene flow from crop rice to its co-occurring weedy rice.