Introducing desirable transgenes into insect populations using Y-linked meiotic drive - a theoretical assessment

The use of genetic drive mechanisms to replace native mosquito genotypes with individuals bearing antipathogen transgenes is a potential strategy for repressing insect transmission of human diseases such as malaria and dengue. Antipathogen transgenes have been developed and tested, but efficient gene drive mechanisms are lacking. Here we theoretically assess the feasibility of introducing antipathogen genes into wild Aedes aegypti populations by using a naturally occurring meiotic drive system. We consider the release of males having both a Y-linked meiotic drive gene and an X-linked drive-insensitive response allele to which an antipathogen gene is linked. We use mathematical models and computer simulations to determine how the post-introduction dynamics of the antipathogen gene are affected by specific genetic characteristics of the system. The results show that when the natural population is uniformly sensitive to the meiotic drive gene, the antipathogen gene may be driven close to fixation if the fitness costs of the drive gene, the insensitive response allele, and the antipathogen gene are low. However, when the natural population has a small proportion of an X-linked insensitive response allele or an autosomal gene that strongly reduces the effect of the drive gene, the antipathogen gene does not spread if it has an associated fitness cost. Our modeling results provide a theoretical foundation for further experimental tests.     

Simulating natural selection in landscape genetics

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially-explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal panmictic populations in an allopatric setting in their predictions of population structure and frequency of fixation of adaptive alleles. We explore initial applications of a spatially-explicit, individual-based evolutionary landscape genetics program that incorporates all factors--mutation, gene flow, genetic drift and selection--that affect the frequency of an allele in a population. We incorporate natural selection by imposing differential survival rates defined by local relative fitness values on a landscape. Selection coefficients thus can vary not only for genotypes, but also in space as functions of local environmental variability. This simulator enables coupling of gene flow (governed by resistance surfaces), with natural selection (governed by selection surfaces). We validate the individual-based simulations under Wright-Fisher assumptions. We show that under isolation-by-distance processes, there are deviations in the rate of change and equilibrium values of allele frequency. The program provides a valuable tool (cdpop v1.0; http://cel.dbs.umt.edu/software/CDPOP/) for the study of evolutionary landscape genetics that allows explicit evaluation of the interactions between gene flow and selection in complex landscapes.     

Semele: a killer-male, rescue-female system for suppression and replacement of insect disease vector populations

Two strategies to control mosquito-borne diseases, such as malaria and dengue fever, are reducing mosquito population sizes or replacing populations with disease-refractory varieties. We propose a genetic system, Semele, which may be used for both. Semele consists of two components: a toxin expressed in transgenic males that either kills or renders infertile wild-type female recipients and an antidote expressed in females that protects them from the effects of the toxin. An all-male release results in population suppression because wild-type females that mate with transgenic males produce no offspring. A release that includes transgenic females results in gene drive since females carrying the allele are favored at high population frequencies. We use simple population genetic models to explore the utility of the Semele system. We find that Semele can spread under a wide range of conditions, all of which require a high introduction frequency. This feature is desirable since transgenic insects released accidentally are unlikely to persist, transgenic insects released intentionally can be spatially confined, and the element can be removed from a population through sustained release of wild-type insects. We examine potential barriers to Semele gene drive and suggest molecular tools that could be used to build the Semele system.     

Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.     

Designing gene drives to limit spillover to non-target populations

The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene-drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives—field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications.     

A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na(+)) transporter, as being a major factor controlling natural variation in leaf Na(+) accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na(+) in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.     

Inverse Medea as a novel gene drive system for local population replacement: a theoretical analysis

One strategy to control mosquito-borne diseases, such as malaria and dengue fever, on a regional scale is to use gene drive systems to spread disease-refractory genes into wild mosquito populations. The development of a synthetic Medea element that has been shown to drive population replacement in laboratory Drosophila populations has provided encouragement for this strategy but has also been greeted with caution over the concern that transgenes may spread into countries without their consent. Here, we propose a novel gene drive system, inverse Medea, which is strong enough to bring about local population replacement but is unable to establish itself beyond an isolated release site. The system consists of 2 genetic components--a zygotic toxin and maternal antidote--which render heterozygous offspring of wild-type mothers unviable. Through population genetic analysis, we show that inverse Medea will only spread when it represents a majority of the alleles in a population. The element is best located on an autosome and will spread to fixation provided any associated fitness costs are dominant and to very high frequency otherwise. We suggest molecular tools that could be used to build the inverse Medea system and discuss its utility for a confined release of transgenic mosquitoes.     

Evading resistance to gene drives

Gene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.     

Selection in a subdivided population with local extinction and recolonization

In a subdivided population, local extinction and subsequent recolonization affect the fate of alleles. Of particular interest is the interaction of this force with natural selection. The effect of selection can be weakened by this additional source of stochastic change in allele frequency. The behavior of a selected allele in such a population is shown to be equivalent to that of an allele with a different selection coefficient in an unstructured population with a different size. This equivalence allows use of established results for panmictic populations to predict such quantities as fixation probabilities and mean times to fixation. The magnitude of the quantity N(e)s(e), which determines fixation probability, is decreased by extinction and recolonization. Thus deleterious alleles are more likely to fix, and advantageous alleles less likely to do so, in the presence of extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.     

The influence of local extinctions on the probability of fixation of chromosomal rearrangements

We investigated the influence of local extinctions in a subdivided population on the probability of fixation of an initially rare allele, for different migration rates. The selective regimes considered were strict underdominance, meiotic drive, and underdominance associated with meiotic drive. We show that local extinctions can increase the probability of fixation of initially rare alleles in underdominant loci for relatively high migration rates, even when both homozygotes have the same fitness. This increase is due to drift during founder events. On the contrary, local extinctions decrease the probability of fixation of alleles favoured by meiotic drive. For a locus where both meiotic drive and underdominance act, the effect of local extinctions depends on the relative strength of the two selective regimes and the initial frequency of the rare allele. For parameter values such that the rare allele is initially selected against, local extinctions decrease the probability of fixation for low migration rates while they cause an increase for moderate migration rates. When the parameter values are such that the rare allele should always be favoured by selection, local extinctions always decrease the probability of fixation. In this latter case, we show the existence of an optimal migration rate which maximizes the probability of fixation.     

Sperm competition and the dynamics of X chromosome drive: stability and extinction

Several empirical studies of sperm competition in populations polymorphic for a driving X chromosome have revealed that Sex-ratio males (those carrying a driving X) are at a disadvantage relative to Standard males. Because the frequency of the driving X chromosome determines the population-level sex ratio and thus alters male and female mating rates, the evolutionary consequences of sperm competition for sex chromosome meiotic drive are subtle. As the SR allele increases in frequency, the ratio of females to males also increases, causing an increase in the male mating rate and a decrease in the female mating rate. While the former change may exacerbate the disadvantage of Sex-ratio males during sperm competition, the latter change decreases the incidence of sperm competition within the population. We analyze a model of the effects of sperm competition on a driving X chromosome and show that these opposing trends in male and female mating rates can result in two coexisting locally stable equilibria, one corresponding to a balanced polymorphism of the SR and ST alleles and the second to fixation of the ST allele. Stochastic fluctuations of either the population sex ratio or the SR frequency can then drive the population away from the balanced polymorphism and into the basin of attraction for the second equilibrium, resulting in fixation of the SR allele and extinction of the population.     

Latitudinal cline in allele length provides evidence for selection in a circadian rhythm gene

Divergent natural selection across a heterogeneous landscape can drive the evolution of locally adapted populations in which phenotypic variation is fine‐tuned to the environment. At the molecular level, such processes can be inferred by identifying correlations between genetic variation and environmental variables. We demonstrate that allele length and allele frequency at a regulatory circadian rhythm gene, OtsClock1b, are highly correlated (R² = 0.86, P = 1.25 × 10^?5) with latitude (a surrogate for photoperiod) in kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka). Two OtsClock1b alleles were identified that differed in length by seven amino acids, with the frequency of the shorter allele increasing from 50% in southern British Columbia (49°N) to complete fixation in Alaska (62°N). No such associations were detected for neutral microsatellite loci. In addition, a kokanee population sampled from Kamchatka, Russia (55°N) fits within the North American latitudinal cline, suggesting that this pattern may be convergent across large longitudinal spatial scales. This correlation provides evidence that natural selection rather than demographic processes may drive the distribution of genetic variation at OtsClock1b in kokanee. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 869–877.     

MUTANT INVASIONS AND ADAPTIVE DYNAMICS IN VARIABLE ENVIRONMENTS

The evolution of natural organisms is ultimately driven by the invasion and possible fixation of mutant alleles. The invasion process is highly stochastic, however, and the probability of success is generally low, even for advantageous alleles. Additionally, all organisms live in a stochastic environment, which may have a large influence on what alleles are favorable, but also contributes to the uncertainty of the invasion process. We calculate the invasion probability of a beneficial, mutant allele in a monomorphic, large population subject to stochastic environmental fluctuations, taking into account density‐ and frequency‐dependent selection, stochastic population dynamics and temporal autocorrelation of the environment. We treat both discrete and continuous time population dynamics, and allow for overlapping generations in the continuous time case. The results can be generalized to diploid, sexually reproducing organisms embedded in communities of interacting species. We further use these results to derive an extended canonical equation of adaptive dynamics, predicting the rate of evolutionary change of a heritable trait on long evolutionary time scales.     

Analysis of CCR5Delta32 geographic distribution and its correlation with some climatic and geographic factors

We studied the possible effects of climatic-geographic factors on the world distribution of the mutant allele for the chemokine receptor gene CCR5, which has a 32-bp deletion (CCR5Delta32) preventing cell invasion by the primary transmitting strain of HIV-1. New data on CCR5 polymorphisms in Russian, Ukrainian, and Moldavian populations are presented. All available data on CCR5Delta32 frequencies in the Old World (number of populations n = 77) were used for construction of a geographical gene map to analyze possible correlations between allele frequencies and eight climatic-geographic parameters. A strong positive correlation was found between the allele frequency and latitude (r = 0.72), a strong negative correlation with annual radiation balance (r = -0.66), and a weaker negative correlation with longitude (r = -0.34). Partial correlations were calculated excluding the influence of latitude. The negative correlation between the allele frequency and annual radiation balance decreased (r = -0.42), but remained large and significant. We propose that the existence of correlations between the cline of CCR5Delta32 frequencies and climatic-geographic parameters provides evidence for a possible effect of either natural environmental factors or large-scale population movements on the distribution of this allele.     

Patterns of variation within and between Greek populations of Ceratitis capitata suggest extensive gene flow and latitudinal clines

Four natural Greek populations of Mediterranean fruit fly, Ceratitis capitata (Wiedemann), was studied for genetic variability at 25 enzyme loci. The comparison of polymorphism within and between populations shows two loci with high between-population heterozygosity (HT) and very high fixation index (F(ST)) values, suggesting the presence of balancing selection. The gradual decline of common allele frequency of the polymorphic loci tested indicated that latitudinal clines are present in Greece. Indirect estimates of gene flow based both on Wright's method (Nm*) and on the Slatkin's method (Nm*), which depends on the frequencies of rare alleles found in only one population, revealed a substantial amount of gene flow (Nm = 3.493 and Nm* = 3.197). These estimates of gene flow may well explain why the "introduced" Greek populations of C. capitata, in spite of their low genetic variability, display the same polymorphic loci. Gene flow in combination with natural selection and genetic drift may have played an important role to genetic differentiation in this species in Greece.     

Selection, subdivision and extinction and recolonization

In a subdivided population, the interaction between natural selection and stochastic change in allele frequency is affected by the occurrence of local extinction and subsequent recolonization. The relative importance of selection can be diminished by this additional source of stochastic change in allele frequency. Results are presented for subdivided populations with extinction and recolonization where there is more than one founding allele after extinction, where these may tend to come from the same source deme, where the number of founding alleles is variable or the founders make unequal contributions, and where there is dominance for fitness or local frequency dependence. The behavior of a selected allele in a subdivided population is in all these situations approximately the same as that of an allele with different selection parameters in an unstructured population with a different size. The magnitude of the quantity N(e)s(e), which determines fixation probability in the case of genic selection, is always decreased by extinction and recolonization, so that deleterious alleles are more likely to fix and advantageous alleles less likely to do so. The importance of dominance or frequency dependence is also altered by extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.     

Dieldrin and diazinon resistance in populations of the Australian sheep blowfly, Lucilia cuprina, from sheep-grazing areas and rubbish tips

Populations of L. cuprina collected from adjacent sheep-grazing areas and rubbish tips in Victoria (Mansfield and Warrnambool) and New South Wales (Lismore) were tested for resistance to the insecticides diazinon and dieldrin. Populations from sheep-grazing areas had a significantly higher diazinon Rop-1 allele frequency than those from adjacent tips with the Victorian populations being more resistant than those from Lismore. Victorian sheep and tip populations had similar gene frequencies at the dieldrin resistance locus, but the Rdl allele frequency was significantly greater in the population at the tip than in the population from the sheep-grazing area at Lismore. The Rdl allele is at a higher frequency in flies from the Lismore area than in Victorian populations. The results at both loci are explained by a balance of selection and gene flow between sheep and tip populations and by selective differences between geographical areas. The exceptionally high frequency of the dieldrin Rdl allele in populations at the Lismore tip may be partially explained by the use of dichlorvos for fly control. Dosage mortality curve and genetic analyses suggest that dichlorvos (an organophosphorus compound) may select at the dieldrin resistance locus. Possible mechanisms for this are discussed. The consequences of genetic differentiation between L. cuprina populations within a region for an autocidal control program are considered.     

Invasion of gene duplication through masking for maladaptive gene flow

Gene duplication can increase an organism's ability to mask the effect of deleterious alleles present in the population, but this is typically a small effect when the source of the genetic variation is mutation. Migration can introduce orders of magnitude more deleterious alleles per generation and may therefore be an important force acting on the structure of genomes. Using formal analytical methods, we study the invasion of haplotypes containing two copies of the resident allele, assuming that a single-locus equilibrium is already established in a continent-island model of migration. Provided that the immigrant allele can be completely masked by multiple functional gene copies, a new duplication will deterministically spread so long as duplicate haplotypes are, on average, fitter than single-copy haplotypes. When fitness depends on the number of immigrant allele copies and their masking ability then the threshold for invasion depends on the rate of immigration and the rate of recombination between the gene copies. Results from several special cases, including formation of protein dimers and Dobzhansky-Muller incompatibilities, suggest that duplications can invade in a wide range of selection regimes. We hypothesize that duplication in response to gene flow may provide an explanation for the high levels of polymorphism in gene copy number observed in natural populations.     

Selection and drift in subdivided populations: a straightforward method for deriving diffusion approximations and applications involving dominance, selfing and local extinctions

Population structure affects the relative influence of selection and drift on the change in allele frequencies. Several models have been proposed recently, using diffusion approximations to calculate fixation probabilities, fixation times, and equilibrium properties of subdivided populations. We propose here a simple method to construct diffusion approximations in structured populations; it relies on general expressions for the expectation and variance in allele frequency change over one generation, in terms of partial derivatives of a "fitness function" and probabilities of genetic identity evaluated in a neutral model. In the limit of a very large number of demes, these probabilities can be expressed as functions of average allele frequencies in the metapopulation, provided that coalescence occurs on two different timescales, which is the case in the island model. We then use the method to derive expressions for the probability of fixation of new mutations, as a function of their dominance coefficient, the rate of partial selfing, and the rate of deme extinction. We obtain more precise approximations than those derived by recent work, in particular (but not only) when deme sizes are small. Comparisons with simulations show that the method gives good results as long as migration is stronger than selection.     

Neofunctionalization of duplicated genes under the pressure of gene conversion

Neofunctionalization occurs when a neofunctionalized allele is fixed in one of duplicated genes. This is a simple fixation process if duplicated genes accumulate mutations independently. However, the process is very complicated when duplicated genes undergo concerted evolution by gene conversion. Our simulations demonstrate that the process could be described with three distinct stages. First, a newly arisen neofunctionalized allele increases in frequency by selection, but gene conversion prevents its complete fixation. These two factors (selection and gene conversion) that work in opposite directions create an equilibrium, and the time during which the frequency of the neofunctionalized allele drifts around the equilibrium value is called the temporal equilibrium stage. During this temporal equilibrium stage, it is possible that gene conversion is inactivated by mutations, which allow the complete fixation of the neofunctionalized allele. And then, permanent neofunctionalization is achieved. This article develops basic population genetics theories on the process to permanent neofunctionalization under the pressure of gene conversion. We obtain the probability and time that the frequency of a newly arisen neofunctionalized allele reaches the equilibrium value. It is also found that during the temporal equilibrium stage, selection exhibits strong signature in the divergence in the DNA sequences between the duplicated genes. The spatial distribution of the divergence likely has a peak around the site targeted by selection. We provide an analytical expression of the pattern of divergence and apply it to the human red- and green-opsin genes. The theoretical prediction well fits the data when we assume that selection is operating for the two amino acid differences in exon 5, which are believed to account for the major part of the functional difference between the red and green opsins.