Biology subjects

Gould, F.

Publications and source records attributed to Gould, F..

11 recordsLinked to original sources

bioRxiv2022

Development of the First High-Density Linkage Map in the Maize Weevil, Sitophilus zeamais

The maize weevil, Sitophilus zeamais, is a worldwide pest that disproportionately affects subsistence farmers in developing countries. Damage from this pest threatens food security in these communities as widely available and effective control methods are lacking. With advances over the last decade in the development of advanced genetic pest management techniques, addressing pest issues at the ecosystem level as opposed to the farm level may be a possibility. However, pest species selected for genetic management techniques require a well-characterized genome and few genomic tools have been developed for maize weevil. Here, we have measured the genome size and developed the first genetic linkage map for this species. The genome size was determined using flow cytometry as 682 Mb and 674 Mb for females and males, respectively. The linkage map contains 11 linkage groups, which correspond to the 10 autosomes and 1 X-chromosome found in the species and it contains 1,121 SNPs. This linkage map will be useful for assembling a complete genome for maize weevil.

genetics↗

bioRxiv2022

Population genetic structure of the maize weevil, Sitophilus zeamais, in southern Mexico

The maize weevil, Sitophilus zeamais, is a ubiquitous pest of maize and other cereal crops worldwide and remains a threat to food security in subsistence communities. Few population genetic studies have been conducted on the maize weevil, but those that exist have shown that there is very little genetic differentiation between geographically dispersed populations and that it is likely the species has experienced a recent range expansion within the last few hundred years. While the previous studies found little genetic structure, they relied primarily on mitochondrial and nuclear microsatellite markers for their analyses. It is possible that more fine-scaled population genetic structure exists due to local population dynamics, the biological limits of natural species dispersal, and the isolated nature of subsistence farming communities. In contrast to previous studies, here, we utilized genome-wide single nucleotide polymorphism data to evaluate the genetic population structure of the maize weevil from the southern and coastal Mexican states of Oaxaca and Chiapas. Our study is the first to find significant genetic population structure in the maize weevil. Here, we show that although there continues to be gene flow between populations of maize weevil, that fine-scale genetic structure exists. It is possible that this structure is shaped by the movement and trade of maize by humans in the region, by geographic barriers to gene flow, or a combination of factors.

genetics↗

bioRxiv2021

A critical assessment of the detailed Aedes aegypti simulation model Skeeter Buster 2 using field experiments of indoor insecticidal control in Iquitos, Peru

The importance of mosquitoes in human pathogen transmission has motivated major research efforts into mosquito biology in pursuit of more effective vector control measures. Aedes aegypti is a particular concern in tropical urban areas, where it is the primary vector of numerous flaviviruses, including the yellow fever, Zika, and dengue viruses. With an anthropophilic habit, Ae. aegypti prefers houses, human blood meals, and ovipositioning in water-filled containers. We hypothesized that this relatively simple ecological niche should allow us to predict the impacts of insecticidal control measures on mosquito populations. To do this, we use Skeeter Buster 2 (SB2), a stochastic, spatially explicit, mechanistic model of Ae. aegypti population biology. SB2 builds on Skeeter Buster, which reproduced equilibrium dynamics of Ae. aegypti in Iquitos, Peru. Our goal was to predict the response of mosquito populations to perturbations by indoor insecticidal spraying and widespread destructive insect surveys. To evaluate SB2, we conducted two field experiments in Iquitos, Peru: a smaller pilot study in 2013 (S-2013) followed by a larger experiment in 2014 (L-2014). Here, we compare model predictions with (pre-viously reported) empirical results from these experiments. In both simulated and empirical populations, repeated spraying yielded substantial yet temporary reductions in adult densities. The proportional effects of spraying were broadly comparable between simulated and empirical results, but we found noteworthy differences. In particular, SB2 consistently over-estimated the proportion of nulliparous females and the proportion of containers holding immature mosquitoes. We also observed less temporal variation in simulated surveys of adult abundance relative to corresponding empirical observations. Our results indicate the presence of ecological heterogeneities or sampling processes not effectively represented by SB2. Although additional empirical research could further improve the accuracy and precision of SB2, our results under-score the importance of non-linear dynamics in the response of Ae. aegypti populations to perturbations, and suggest general limits to the fine-grained predictability of its population dynamics over space and time.

ecology↗

bioRxiv2020

Genome evolution in an agricultural pest following adoption of transgenic crops

Replacement of synthetic insecticides with transgenic crops for pest management has been both economically and environmentally beneficial. These benefits have often eroded as pests evolved resistance to transgenic crops, but a broad understanding of the timing and complexity of adaptive changes which lead to field-evolved resistance in pest species is lacking. Wild populations of Helicoverpa zea, a major lepidopteran crop pest and the target of transgenic Cry toxin-expressing cotton and corn, have recently evolved widespread, damaging levels of resistance. Here, we quantified patterns of genomic change in wild H. zea collected between 2002 and 2017 when adoption rates of Cry-expressing crops expanded in North America. Using a combination of genomic approaches, we identified significant temporal changes in allele frequency throughout the genomes of field-collected H. zea. Many of these changes occurred concurrently with increasingly damaging levels of resistance to Cry toxins between 2012 and 2016, in a pattern consistent with polygenic selection. Surprisingly, none of the eleven previously described Cry resistance genes showed signatures of selection in wild H. zea. Furthermore, we observed evidence of a very strong selective sweep in one region of the H. zea genome, yet this strongest change was not additively associated with Cry resistance. This first, whole genome analysis of field-collected specimens to study evolution of Cry resistance demonstrates the potential and need for a more holistic approach to examining pest adaptation to changing agricultural practices. Significance StatementEvolution of pest resistance to management approaches in agricultural landscapes is common and results in economic losses. Early detection of pest resistance evolution prior to significant crop damage would benefit the agricultural community. It has been hypothesized that new genomic approaches could track molecular signals of emerging resistance problems and trigger efforts to pre-empt widespread damage. We tested this hypothesis by quantifying genomic changes in the pest Helicoverpa zea over a 15 year period concurrent with commercialization and subsequent loss of efficacy of transgenic Bt-expressing crops. Our results demonstrate the complex nature of evolution in agricultural ecosystems and provide insight into the potential for and pitfalls associated with use of genomic approaches for resistance monitoring. We discuss approaches for improvement.

evolutionary biology↗

bioRxiv2020

Mathematical modeling of genetic pest management through female lethality with independently segregating alleles

Many novel genetic approaches are under development to combat insect pests. One genetic strategy aims to suppress or locally eliminate a species through large, repeated releases of genetically engineered strains that render female offspring unviable under field conditions. Strains with this female-killing (FK) characteristic have been developed either with all of the molecular components in a single construct or with the components in two constructs inserted at independently assorting loci. Strains with two constructs are typically considered to be only of value as research tools and for producing solely male offspring in rearing factories which are subsequently sterilized by radiation before release. A concern with the two-construct strains is that once released, the two constructs would become separated and therefore non-functional. The only FK strains that have been released in the field without sterilization are single-construct strains. Here, we use a population genetics model with density dependence to evaluate the relative effectiveness of female killing approaches based on single- and two-construct arrangements. We find that, in general, the single-construct arrangement results in slightly faster population suppression, but the two-construct arrangement can eventually cause stronger suppression and cause local elimination with a smaller release size. Based on our results, there is no a priori reason that males carrying two independently segregating constructs need to be sterilized prior to release. In some cases, a fertile release would be more efficient for population suppression.Competing Interest StatementThe authors have declared no competing interest.View Full Text

evolutionary biology↗

bioRxiv2019

Locally Fixed Alleles: A method to localize gene drive to island populations

Invasive species pose a major threat to biodiversity on islands. While successes have been achieved using traditional removal methods, such as toxicants aimed at rodents, these approaches have limitations and various off-target effects on island ecosystems. Gene drive technologies designed to eliminate a population provide an alternative approach, but the potential for drive-bearing individuals to escape from the target release area and impact populations elsewhere is a major concern. Here we propose the \"Locally Fixed Alleles\" approach as a novel means for localizing elimination by a drive to an island population that exhibits significant genetic isolation from neighboring populations. Our approach is based on the assumption that in small island populations of rodents, genetic drift will lead to multiple genomic alleles becoming fixed. In contrast, multiple alleles are likely to be maintained in larger populations on mainlands. Utilizing the high degree of genetic specificity achievable using homing drives, for example based on the CRISPR/Cas9 system, our approach aims at employing one or more locally fixed alleles as the target for a gene drive on a particular island. Using mathematical modeling, we explore the feasibility of this approach and the degree of localization that can be achieved. We show that across a wide range of parameter values, escape of the drive to a neighboring population in which the target allele is not fixed will at most lead to modest transient suppression of the non-target population. While the main focus of this paper is on elimination of a rodent pest from an island, we also discuss the utility of the locally fixed allele approach for the goals of population suppression or population replacement. Our analysis also provides a threshold condition for the ability of a gene drive to invade a partially resistant population.

evolutionary biology↗

bioRxiv2018

Tethered homing gene drives: a new design for spatially restricted population replacement and suppression

Optimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the potential unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in face of gene flow. We present a new gene drive system, Tethered Homing (TH), with improved capacity for localized population alteration, especially for population suppression. The TH drive is based on driving a payload gene using a homing construct that is anchored to a spatially restricted gene drive. We use a proof of principle mathematical model to show the dynamics of a TH drive that uses engineered underdominance as an anchor. This system is composed of a split homing drive and a two-locus engineered underdominance drive linked to one part of the split drive (the Cas endonuclease). In addition to improved localization, the TH system offers the ability to gradually adjust the genetic load in a population after the initial alteration, with minimal additional release effort.

bioengineering↗

bioRxiv2017

Efficacy of Aedes aegypti control by indoor Ultra Low Volume (ULV) insecticide spraying in Iquitos, Peru

BackgroundAedes aegypti is a primary vector of dengue, chikungunya, Zika, and urban yellow fever viruses. Indoor, ultra low volume (ULV) space spraying with pyrethroid insecticides is the main approach used for Ae. aegypti emergency control in many countries. Given the widespread use of this method, the lack of large-scale experiments or detailed evaluations of municipal spray programs is problematic.\n\nMethodology/Principal FindingsTwo experimental evaluations of non-residual, indoor ULV pyrethroid spraying were conducted in Iquitos, Peru. In each, a central sprayed sector was surrounded by an unsprayed buffer sector. In 2013, spray and buffer sectors included 398 and 765 houses, respectively. Spraying reduced the mean number of adults captured per house by ~83 percent relative to the pre-spray baseline survey. In the 2014 experiment, sprayed and buffer sectors included 1,117 and 1,049 houses, respectively. Here, the sprayed sectors number of adults per house was reduced ~64 percent relative to baseline. Parity surveys in the sprayed sector during the 2014 spray period indicated an increase in the proportion of very young females. We also evaluated impacts of a 2014 citywide spray program by the local Ministry of Health, which reduced adult populations by ~60 percent. In all cases, adult densities returned to near-baseline levels within one month.\n\nConclusions/SignificanceOur results demonstrate that densities of adult Ae. aegypti can be reduced by experimental and municipal spraying programs. The finding that adult densities return to approximately pre-spray densities in less than a month is similar to results from previous, smaller scale experiments. Our results demonstrate that ULV spraying is best viewed as having a short-term entomological effect. The epidemiological impact of ULV spraying will need evaluation in future trials that measure capacity of insecticide spraying to reduce disease transmission.

epidemiology↗

bioRxiv2017

Invasion and migration of self-limiting gene drives: a comparative analysis

Recent advances in research on gene drives have produced genetic constructs that could theoretically spread a desired gene (payload) into all populations of a species, with a single release in one place. This attribute has advantages, but also comes with risks and ethical concerns. There has been a call for research on gene drive systems that are spatially and/or temporally self-limiting. Here we use a population genetics model to compare the expected characteristics of three spatially self-limiting gene drive systems: one-locus underdominance, two-locus underdominance, and daisy-chain drives. We find large differences between these gene drives in the minimum release size required for successfully driving a payload into a population. The daisy-chain system is the most efficient, requiring the smallest release, followed by the two-locus underdominance system, and then the one-locus underdominance system. However, when the target population exchanges migrants with a non-target population, the gene drives requiring smaller releases suffer from higher risks of unintended spread. For payloads that incur relatively low fitness costs (up to 30%), a simple daisy-chain drive is practically incapable of remaining localized, even with migration rates as low as 0.5% per generation. The two-locus underdominance system can achieve localized spread under a broader range of migration rates and of payload fitness costs, while the one-locus underdominance system largely remains localized. We also find differences in the extent of population alteration and in the permanence of the alteration achieved by the three gene drives. The two-locus underdominance system does not always spread the payload to fixation, even after successful drive, while the daisy-chain system can, for a small set of parameter values, achieve a temporally-limited spread of the payload. These differences could affect the suitability of each gene drive for specific applications. Note: This manuscript has been accepted for publication in the journal Evolutionary Applications and is pending publication. We suggest that any reference to or quotation of this article should be made with this recognition.

bioengineering↗

bioRxiv2017

Evaluating Strategies For Reversing CRISPR-Cas9 Gene Drives

A gene drive biases inheritance of a gene so that it increases in frequency within a population even when the gene confers no fitness benefit. There has been renewed interest in environmental releases of engineered gene drives due to recent proof of principle experiments with the CRISPR-Cas9 system as a drive mechanism. Release of modified organisms, however, is controversial, especially when the drive mechanism could theoretically alter all individuals of a species. Thus, it is desirable to have countermeasures to reverse a drive if a problem arises. Several genetic mechanisms for limiting or eliminating gene drives have been proposed and/or developed, including synthetic resistance, reversal drives, and immunizing reversal drives. While predictions about efficacy of these mechanisms have been optimistic, we lack detailed analyses of their expected dynamics. We develop a discrete time model for population genetics of a drive and proposed genetic countermeasures. Efficacy of drive reversal varies between countermeasures. For some parameter values, the model predicts unexpected behavior including polymorphic equilibria and oscillatory dynamics. The timing and number of released individuals containing a genetic countermeasure can substantially impact outcomes. The choice among countermeasures by researchers and regulators will depend on specific goals and population parameters of target populations.

evolutionary biology↗

bioRxiv2017

Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously express proteins derived Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation to this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other host plants, or 3) loss of resistance to previously used management practices including insecticides. Here we begin to address the question of whether such changes occurred in H. virescens populations between the years 1997 and 2012. As part of our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD-seq enabled genome scan to identify loci with significant allele frequency changes over the 15 year period after Bt crops became widespread in the agricultural landscape. Confirmation that a known genetic change at a previously described H. virescens target of selection was detectable in our genome scan increased our confidence in this methodology. We quantified the strength of selection required to elicit the observed allele frequency changes at loci under selection. Potential contributions of genes near the loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.

evolutionary biology↗