Computer modeling of joint selection response of MGE patterns and a polygenic system]

Using computer simulation, selection response of three genome patterns--polygenes, mobile genetic elements (MGEs), and labels of identity by origin (LIOs)--were studied. In each generation of selection, variability of each pattern type was described by on UPGMA tree. Stringent positive truncation selection on an additive polygenic trait and recombination between segments of the genetic map were considered. MGEs were classified into three groups: modifiers (enhancers) of the polygenic expression, markers, and independent copies. It was shown that at generations 30 to 40, 95-96% and 70-80% of respectively enforced and non-enforced active polygenic alleles were fixed (2-3% and 16-17% lost). In all generations, Hkn < or = Dkn of the length of the maximal route along the tree. At the same time, modifier MGEs were fixed for 85-88% (lost for 11-12%); marker MGEs, for 60-70 (lost for 21-25%); and independent copies, for 30-40 (lost for 50-60%). The behavior of independent MGE copies was generally consistent with the predictions of the genetic drift theory, modifier MGEs behaved similarly to the modified polygenes, and marker MGEs exhibited intermediate properties. The LIO patterns showed rapid homozygotization: their variability dropped dramatically between generations 10 and 30. In F50, the final consensus pattern of polygenes included 16 out of 18 enforced and 18 out of 21 non-enforced polygenic alleles. The fixation/loss ratios were 16:3 for modifier MGEs, 15:6 for marker MGEs, and 25:28 (with 7 polymorphic) for independent copies. The LIO consensus pattern contained 13 out of 100 original markers, which formed 26 fragments of one to ten map segments in size; 21 fragments contained active polygenic alleles, and 14 of them had also modifier MGEs. Recombinational shuffling of patterns was not completed. In the course of selection, active polygenic alleles take along adjacent segments, including those containing modifier MGEs and markers. These constitute the conservative part of all consensus patterns while the remaining segments are random.     

Truncation family selection and nonsystematic inbreeding leads to a rapid fixation of a pattern of mobile genetic elements in a computer model

A computer simulation model of the population dynamics of a polygenic system and a pattern of mobile genetic elements (MGEs) under directional truncation selection for a quantitative trait was developed. Modifier MGEs were shown to be rapidly and adaptively fixed (or lost) together with the modified polygenes. Marker MGEs and independent MGE copies were fixed and lost just as rapidly but in a random manner. Using specific marking of initial haploid genomes and direct computing of the mean proportion of identical encounters at each locus in each generation, it was shown that the mean nonselective inbreeding coefficient F(n) dramatically increases in the course of selection, reaching values 0.7-0.9 in 15-20 generations. As a result, adaptive homozygotization of polygenes and modifier MGEs and random homozygotization of marker MGEs, independent MGE copies, and all other genes of the genome occurs. These results confirm the hypothesis on the "champion" polygene pattern advanced earlier to explain the data of selection experiments.     

Response of the MGE 412 pattern to truncation selection of a quantitative trait in an isogenic line of drosophila after severe heat shock (SHS)

Positive and negative selection on the total length of two fragments of an interrupted longitudinal wing vein in an isogenic line of Drosophila melanogaster was accompanied by changes in the genomic localization pattern of MGE 412. Strong truncation selection was conducted in the population of effective size Ne = 160 for 50 generations. Twenty-six out of 35 polymorphic HHS-induced segments of MGE localization behaved as independent copies and markers, whereas 9 segments proved to be selective. The second group included "hot" segments of HHS transposition induction (43B, 97E, etc.). Thus, final consensus patterns of induced MGE transpositions have a random and an adaptive component in generation 50 of positive and negative selection. Selective patterns probably include modifier MGEs, which generate induced genetic regulatory variation of polygenes controlling the selected quantitative trait in the isogenic line after HHS.     

Computer Simulation of Concerted Evolution of Patterns of Polygenes, Transposable Elements, and Origin Identity Labels: Negative Selection

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.     

Negative selection and computer models of the joint evolution of the patterns of polygenes,transposable elements,and origin identity labels

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.     

Computer system for simulating population dynamic patterns of polygenes and mobile genetic elements upon truncation selection for a quantitative trait

A computer system was developed for simulation of population dynamics of interacting polygene patterns and mobile genetic elements (MGEs) under selection for a quantitative trait. The system is stochastic (Monte Carlo) and takes into account the main sources of random change in the patterns (recombinations, transpositions, excisions), genetic drift, and determined trends of selection and other genetic processes in a finite population. Using this model, it is possible to analyze the dynamics of many population parameters that cannot be experimentally estimated: frequencies of polygenic alleles, proportions of adaptive and random fixations, average heterozygosities of polygenes and MGEs, coefficient of inbreeding, heritability, etc. In addition, the model can be used to test various hypotheses on polygene-MGE interaction.     

A method to optimize selection on multiple identified quantitative trait loci

A mathematical approach was developed to model and optimize selection on multiple known quantitative trait loci (QTL) and polygenic estimated breeding values in order to maximize a weighted sum of responses to selection over multiple generations. The model allows for linkage between QTL with multiple alleles and arbitrary genetic effects, including dominance, epistasis, and gametic imprinting. Gametic phase disequilibrium between the QTL and between the QTL and polygenes is modeled but polygenic variance is assumed constant. Breeding programs with discrete generations, differential selection of males and females and random mating of selected parents are modeled. Polygenic EBV obtained from best linear unbiased prediction models can be accommodated. The problem was formulated as a multiple-stage optimal control problem and an iterative approach was developed for its solution. The method can be used to develop and evaluate optimal strategies for selection on multiple QTL for a wide range of situations and genetic models.     

Arrested development of the rabbit stomach worm Obeliscoides cuniculi: Manipulation of the ability to arrest through processes of selection

Through a process of selection in an isolate of O. cuniculi, the propensity for arrested development in response to cold treatment was increased from 15 to over 90% in five generations. In subsequent generations, the propensity for arrest remained high so long as selection pressure was maintained. The selected high arresting isolate exhibited a corresponding increase in ability to arrest without prior cold treatment of infective larvae. In the absence of selection for arrest, this isolate reverted to one with a lower propensity for arrest. These results indicate that arrested development has a genetic basis.

A hypothesis was developed which proposed that continuous variation in the rate of development is controlled by polygenes and that a worm will exhibit arrested developmet if its genotype has an enrichment of alleles for slow growth at the various polygenic loci.     

Computer Simulation of the Joint Evolution of the Patterns of Polygenes, Transposable Elements, and Origin Identity Labels: Stabilizing Selection

A computer model of the populations dynamics of the patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of stabilizing selection for an additive quantitative trait (with the target value being 0.4 of the maximum) was analyzed. It was demonstrated that the final plateaus of the trait value and the frequencies of the active values of polygenes are reached rapidly, namely, within five to seven generations (the effective selection period). The inbreeding coefficient during this period also grows rapidly and then gradually increases eventually reaching 0.7. The inbreeding coefficient reaches plateau (at 1.0) only in generations 300–350, which suggests the effect of gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. By generation 100 of selection, the final patterns of TEs and OILs were not formed completely. Fixations and losses, especially those of the OIL pattern, were delayed. In general, however, the population heterogeneity with respect to the patterns studied does not stabilize. This heterogeneity decreases the case of stabilizing selection, although more slowly than in the cases of positive and negative selections.     

Selection against genetic defects in conservation schemes while controlling inbreeding

We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (ΔF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1–2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on ΔF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained ΔF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of ΔF is very important.     

An Experimental Test of the Relationship between Genetic Variation and Environmental Variation in Tribolium Flour Beetles

The hypothesis that a component of genetic variation for polygenic fitness traits is maintained by environmental heterogeneity was tested using an experimental system involving two species of flour beetles, Tribolium castaneum and T. confusum. Replicated populations of each species from a number of environmental treatments were analyzed for various fitness components following almost 60 generations of natural selection. Environmental differences consisted of flours of cereals commonly invaded by natural populations of these insects.—Tests for adaptation to environments were based on experiments in which populations were reared factorially on each flour, such that population treatment x flour interactions could be detected. Measurements were made of survival, growth rate, larval weight, pupal weight, developmental time, fecundity of individuals at low density and fecundity and cannibalism at high density in both fresh and conditioned media.—Flour differences were found to have significant effects on most traits. Evidence for significant genetic variation and significant genotype x environment interaction was also found. However, no evidence could be found to support the hypothesis that genetic variation was maintained by environmental heterogeneity in food resources. The absence of adaptation to the experimental treatments despite the presence of genetic variation in fitness components suggests that pleiotropy may assume an important role in determining net fitness values of polygenes.     

The Evolution of Recombination: Removing the Limits to Natural Selection

One of the oldest hypotheses for the advantage of recombination is that recombination allows beneficial mutations that arise in different individuals to be placed together on the same chromosome. Unless recombination occurs, one of the beneficial alleles is doomed to extinction, slowing the rate at which adaptive mutations are incorporated within a population. We model the effects of a modifier of recombination on the fixation probability of beneficial mutations when beneficial alleles are segregating at other loci. We find that modifier alleles that increase recombination do increase the fixation probability of beneficial mutants and subsequently hitchhike along as the mutants rise in frequency. The strength of selection favoring a modifier that increases recombination is proportional to λ(2)Sδr/r when linkage is tight and λ(2)S(3)δ r/N when linkage is loose, where λ is the beneficial mutation rate per genome per generation throughout a population of size N, S is the average mutant effect, r is the average recombination rate, and δr is the amount that recombination is modified. We conclude that selection for recombination will be substantial only if there is tight linkage within the genome or if many loci are subject to directional selection as during periods of rapid evolutionary change.     

Evolutionarily stable mutation rate in a periodically changing environment

Evolution of mutation rate controlled by a neutral modifier is studied for a locus with two alleles under temporally fluctuating selection pressure. A general formula is derived to calculate the evolutionarily stable mutation rate μ(ess) in an infinitely large haploid population, and following results are obtained. (I) For any fluctuation, periodic or random: (1) if the recombination rate r per generation between the modifier and the main locus is 0, μ(ess) is the same as the optimal mutation rate μ(op) which maximizes the long-term geometric average of population fitness; and (2) for any r, if the strength s of selection per generation is very large, μ(ess) is equal to the reciprocal of the average number T of generations (duration time) during which one allele is persistently favored than the other. (II) For a periodic fluctuation in the limit of small s and r, μ(ess)T is a function of sT and rT with properties: (1) for a given sT, μ(ess)T decreases with increasing rT; (2) for sT </= 1, μ(ess)T is almost independent of sT, and depends on rT as μ(ess)T & 1.6 for rT << 1 and μ(ess)T & 6/rT for rT >> 1; and (3) for sT >/= 1, and for a given rT, μ(ess)T decreases with increasing sT to a certain minimum less than 1, and then increases to 1 asymptotically in the limit of large sT. (III) For a fluctuation consisting of multiple Fourier components (i.e., sine wave components), the component with the longest period is the most effective in determining μ(ess) (low pass filter effect). (IV) When the cost c of preventing mutation is positive, the modifier is nonneutral, and μ(ess) becomes larger than in the case of neutral modifier under the same selection pressure acting at the main locus. The value of c which makes μ(ess) equal to μ(op) of the neutral modifier case is calculated. It is argued that this value gives a critical cost such that, so long as the actual cost exceeds this value, the evolution rate at the main locus must be smaller than its mutation rate μ(ess).     

Genetic control of in vitro shoot regeneration from leaf explants inSolanum chacoense Bitt.

Although the heritable nature of plant tissue culture responses is now well documented in many species, only a few studies have been conducted to elucidate complete inheritance patterns. Genetic control of in vitro shoot regeneration from leaf explants was investigated inSolanum chacoense using parental, F₁ and F₂ generations. Broad-sense heritability estimates were high for frequency (percentage) of responsive leaf explants (61–83%) and number of shoots regenerated per responsive explant (53–75%). Consistent with high heritability estimates, a hypothesis involving three genes could be formulated to explain the variability in the response observed in this study. This model implies that homozygous recessive alleles at any two (out of three) loci are required for the highest response, i.e., more than two shoots per explant in more than 40% of the explants. The presence of homozygous recessive alleles at any one of the three loci produces an intermediate response, i.e., fewer than 40% of the explants regenerating fewer than two shoots per explant, and a dominant allele at all the three loci results in non-responsiveness. Additional minor modifier genes, each with a small effect, would also be required to account for the variable intensity of regeneration within groups. Such a relatively simple genetic control of in vitro regenerability suggests that incorporation of this trait should be easy in potato improvement programmes.     

Population dynamics of the additive polygenic system under truncation selection]

Common features of the equations describing dynamics of the additive polygenic system under truncation selection are summarized. A combination of parameters playing the role of the effective selective pressure on the ith polygenic locus was revealed. The product of mean relative fitnesses of the individual polygenic loci, [formula: see text], was shown to play the role of relative mean fitness of the polygenic population. This value depends on the measurable parameters of the character distribution in the population: [formula: see text]. It was shown that under the constant population number during truncation selection, the characteristic of the best genotype increases, [formula: see text]; which is also a product of the frequencies of preferable genotypes at individual polygenic loci. This value plays the role of the proportion of the number of the best ("champion") genotype in the population. In fact, this is the champion genotype polygene consensus pattern frequency, which a priori indicates the possibility of the champion pattern fixation. The analogue of Haldane's dilemma for the polygenic system which restrict the number of polygenes simultaneously subjected to adaptive evolution [formula: see text] was obtained for the case of constant effective population number (Ne = const).     

The average frequency of private alleles in a partially isolated population

An analytic model is developed to explore the relationship between gene flow, selection, and genetic drift. We assume that a single copy of a mutant allele appears in a finite, partially isolated population and allow for the effects of immigration, genic selection, and mutation on the frequency of the mutant. Our concern is with the distribution of the mutant's frequency before it either is lost from the population or emigrates. Before either of these events, the allele will be a “private allele” and would be found in only one of several populations in a larger collection. Slatkin [(1985) Evolution 39, 53–65] found several simple properties of private alleles in his simulations. We use the method developed by Karlin and Tavaré [(1980) Genet. Res. 37, 33–46; (1981a), Theor. Pop. Biol. 19, 187–214; (1981b) Theor. Pop. Biol. 19, 215–229] for a model similar to ours to obtain a diffusion equation with a “killing term” and obtain the mean and variance of the mutant's frequency and its expected frequency in samples of a specified size. There is only fair agreement between the analytic results from this model and those from Slatkin's (loc. cit.) simulations. The rescaling method used to obtain the results indicates that if emigration is relatively frequent, the distribution of rare alleles is governed largely by the balance between genetic drift and emigration, with selection, mutation, and immigration playing a lesser role.     

An Experimental Test of Adaptive Introgression in Locally Adapted Populations of Splash Pool Copepods

As species struggle to keep pace with the rapidly warming climate, adaptive introgression of beneficial alleles from closely related species or populations provides a possible avenue for rapid adaptation. We investigate the potential for adaptive introgression in the copepod, Tigriopus californicus, by hybridizing two populations with divergent heat tolerance limits. We subjected hybrids to strong heat selection for 15 generations followed by whole-genome resequencing. Utilizing a hybridize evolve and resequence (HER) technique, we can identify loci responding to heat selection via a change in allele frequency. We successfully increased the heat tolerance (measured as LT₅₀) in selected lines, which was coupled with higher frequencies of alleles from the southern (heat tolerant) population. These repeatable changes in allele frequencies occurred on all 12 chromosomes across all independent selected lines, providing evidence that heat tolerance is polygenic. These loci contained genes with lower protein-coding sequence divergence than the genome-wide average, indicating that these loci are highly conserved between the two populations. In addition, these loci were enriched in genes that changed expression patterns between selected and control lines in response to a nonlethal heat shock. Therefore, we hypothesize that the mechanism of heat tolerance divergence is explained by differential gene expression of highly conserved genes. The HER approach offers a unique solution to identifying genetic variants contributing to polygenic traits, especially variants that might be missed through other population genomic approaches.     

Structural basis for inhibition of the type I-F CRISPR–Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14

CRISPR–Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins are produced by MGEs to counteract CRISPR–Cas systems and can be used to regulate genome editing by CRISPR techniques. Here, we report the cryo-EM structures of three type I-F Acr proteins, AcrIF4, AcrIF7 and AcrIF14, bound to the type I-F CRISPR–Cas surveillance complex (the Csy complex) from Pseudomonas aeruginosa. AcrIF4 binds to an unprecedented site on the C-terminal helical bundle of Cas8f subunit, precluding conformational changes required for activation of the Csy complex. AcrIF7 mimics the PAM duplex of target DNA and is bound to the N-terminal DNA vise of Cas8f. Two copies of AcrIF14 bind to the thumb domains of Cas7.4f and Cas7.6f, preventing hybridization between target DNA and the crRNA. Our results reveal structural detail of three AcrIF proteins, each binding to a different site on the Csy complex for inhibiting degradation of MGEs.     

Statistical genetic considerations for maintaining germ plasm collections

One objective of the regeneration of genetic populations is to maintain at least one copy of each allele present in the original population. Genetic diversity within populations depends on the number and frequency of alleles across all loci. The objectives of this study on outbreeding crops are: (1) to use probability models to determine optimal sample sizes for the regeneration for a number of alleles at independent loci; and (2) to examine theoretical considerations in choosing core subsets of a collection. If we assume that k-1 alleles occur at an identical low frequency of p₀ and that the k^th allele occurs at a frequency of 1-[(k-1)p₀], for loci with two, three, or four alleles, each with a p₀ of 0.05, 89–110 additional individuals are required if at least one allele at each of 10 loci is to be retained with a 90% probability; if 100 loci are involved, 134–155 individuals are required. For two, three, or four alleles, when p₀ is 0.03 at each of 10 loci, the sample size required to include at least one of the alleles from each class in each locus is 150–186 individuals; if 100 loci are involved, 75 additional individuals are required. Sample sizes of 160–210 plants are required to capture alleles at frequencies of 0.05 or higher in each of 150 loci, with a 90–95% probability. For rare alleles widespread throughout the collection, most alleles with frequencies of 0.03 and 0.05 per locus will be included in a core subset of 25–100 accessions.     

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell–cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing “arms race.” Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic’s effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell–cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated.