Patterns of infestation, dispersion, and gene flow in Rhyzopertha dominica based on population genetics and ecological modeling

Doctor of PhilosophyDepartment of EntomologyJames F. CampbellThomas W. PhillipsMovement is a fundamental feature of animals that impacts processes across multiple scales in space and time. Due to the heterogeneous and fragmented nature of habitats that make up landscapes, movement is not expected to be random in all instances, and an increase in fitness is an expected consequence for those that can optimize movement to find valuable and scarce recourses. I studied the movement of Rhyzopertha dominica (Coleoptera: Bostrichidae), one of the most important pests of stored grain worldwide, within and between resource patches. At a fine spatial scale, I identified factors that contribute to overall and upward movement in the grain mass. Three-week-old insects tented to stay closer to the surface than one or two-week-old insects. Females tended to be more active and to explore more than males. I also found that males tended to stay closer to the surface than females and that might be related to the ability to attract females from outside the patch since there was no significant difference regarding female’s attraction within the grain patch. Interaction with feeding sites or other individuals of the same sex creates positive feedback and a more clumped spatial pattern of feeding and foraging behavior. On the other hand, interaction with individuals of different sex creates negative feedback and a more random or overdispersed pattern. At a broad spatial scale, I studied the long-term consequence of R. dominica movement on the development of population structure within the U.S. To evaluate population structure, I used reduced representation of the genome followed by direct sequencing of beetles collected from different locations across the U.S where wheat or rice is produced and stored. Ecoregions were more important in explaining structure of R. dominica populations than crop type. I also found significant isolation by distance; however, model selection primarily elected grain production and movement variables to explain population differentiation and diversity. Understanding animal movement is essential to establishing relationships between distribution and surrounding landscape, and this knowledge can improve conservation and management strategies

Diatraea saccharalis history of colonization in the Americas: The case for human-mediated dispersal

The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.Fil: Francischini, Fabricio J. B.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Cordeiro, Erick M. G.. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; BrasilFil: Campos, Jaqueline B. de. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Alves Pereira, Alessandro. Universidade Estadual de Campinas; BrasilFil: Gomes Viana, João Paulo. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Wu, Xing. University of Illinois; Estados UnidosFil: Wei, Wei. University of Illinois; Estados UnidosFil: Brown, Patrick. University of Illinois; Estados UnidosFil: Joyce, Andrea. University of California; Estados UnidosFil: Murúa, María Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Fogliata, Sofia Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Clough, Steven J.. University of Illinois; Estados Unidos. United States Department of Agriculture; Estados UnidosFil: Zucchi, María Inmaculada. Universidade Estadual de Campinas; Brasi

Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae

Abstract: The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host–plant associations, uncovering the widespread co‐option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.Peer reviewedFinal Published versio

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Isolation by Distance, Source-Sink Population Dynamics and Dispersal Facilitation by Trade Routes: Impact on Population Genetic Structure of a Stored Grain Pest

Population genetic structure of agricultural pests can be impacted not only by geographic distance and the broader ecological and physical barriers but also by patterns related to where crops are produced and how they are moved after harvest. Stored-product pests, for instance, specialize in exploiting grains such as wheat and rice from on-farm storage through transportation to final processing at often geographically distant locations; therefore human-aided movement may impact their dispersal. Although stored product insects are associated with stored grain, they can also exploit resources in the surrounding environments so different ecological regions where the grain is grown and stored may also influence population structure. Here we used 1,156 SNP markers to investigate how geographic distance, ecological and agricultural variables can impact the genetic structure and gene flow of the stored food pest beetle Rhyzopertha dominica. We found a substantial degree of admixture between weakly structured populations in the US. Ecological regions were more important in explaining R. dominica population structure than crop type, suggesting insect movement between wheat and rice grain distribution channels. We have also found a significant correlation between the genetic and geographical distance (i.e., isolation by distance). However, our modeling approach combining the ecological and management variables has highlighted the importance of the volume of grain received by a location in the dispersal dynamics of the pest. The first-generation migrant analysis offered additional supported to movement over great distances that are likely associated with grain movement. Our data suggest that a multitude of factors play small but significant parts in the movement dynamics of the pest. The beetles can take advantage of the source-sink dynamic of grain movement in the US, but also engage in a high rate of movement at the local scale. Understanding population structure for R. dominica will provide insights into the potential for local processes of adaptation and broader patterns of movement that will impact management programs and the potential for spread of resistance genes

Hybridization and introgression between Helicoverpa armigera and H. zea: an adaptational bridge

Abstract Background Invasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native pest, and even more so when they can hybridize and produce fertile progeny. The global pest Helicoverpa armigera was first detected in Brazil in 2013 and generated a wave of speculations about the possibility of hybridization with the native sister taxon Helicoverpa zea. In the present study, we used genome-wide single nucleotide polymorphisms from field-collected individuals to estimate hybridization between H. armigera and H. zea in different Brazilian agricultural landscapes. Results The frequency of hybridization varied from 15 to 30% depending on the statistical analyses. These methods showed more congruence in estimating that hybrids contained approximately 10% mixed ancestry (i.e. introgression) from either species. Hybridization also varied considerably depending on the geographic locations where the sample was collected, forming a ‘mosaic’ hybrid zone where introgression may be facilitated by environmental and landscape variables. Both landscape composition and bioclimatic variables indicated that maize and soybean cropland are the main factors responsible for high levels of introgression in agricultural landscapes. The impact of multiple H. armigera incursions is reflected in the structured and inbred pattern of genetic diversity. Conclusions Our data showed that the landscape composition and bioclimatic variables influence the introgression rate between H. armigera and H. zea in agricultural areas. Continuous monitoring of the hybridization process in the field is necessary, since agricultural expansion, climatic fluctuations, changing composition of crop species and varieties, and dynamic planting seasons are some factors in South America that could cause a sudden alteration in the introgression rate between Helicoverpa species. Introgression between invasive and native pests can dramatically impact the evolution of host ranges and resistance management

Diversity, genetic structure, and population genomics of the tropical tree centrolobium tomentosum in remnant and restored Atlantic forests

The rapid pace of deforestation and fragmentation that took place in the Brazilian Atlantic Forest and other global hotspots for biodiversity conservation has motivated ecosystem restoration efforts. The genetic viability of restored tree populations and their potential to conserve genetic diversity remains, however, unclear. Here, we assessed the genetic viability and potential to conserve the genetic diversity of restored populations of Centrolobium tomentosum, a native legume tree, in the Brazilian Atlantic Forest, based on a genotyping by sequencing (GBS). We have successfully generated a total of 2877 single nucleotide polymorphism (SNP) markers across the whole C. tomentosum genome. Surprisingly, restoration sites presented overall higher levels of genetic diversity compared to natural remnant areas and negative inbreeding coefficient (FIS), mainly in juveniles’ trees from newer restored areas, indicating an excess of heterozygotes probably due to the founding event. The most likely number of genetic clusters found was two (K = 2), suggesting that diverse seed sources were used to produce seedlings for restoration. Clear signs of gene flow from restored to natural remnants areas had also been detected when diversity values of adults and juveniles were contrasted. Even though we did not find any clear relation of the genetic diversity and landscape composition, the low percentage of forest and high levels of fragmentation are likely reducing patch connectivity in some areas. LOSITAN detected 88 SNP outliers under positive selection, but analysis with Bayescan failed to support this evidence. In conclusion, our post hoc evaluation of restored tree populations indicated that the old restored area is stable and new areas have great potential to contribute to conserving genetic diversity and increasing the chances of the natural populations to persist over time20510731085CNPQ - Conselho Nacional de Desenvolvimento Científico e TecnológicoFAPESP – Fundação de Amparo à Pesquisa Do Estado De São Paulo310446/2015-5; 304817/2015-52011/50296-8; 2017/02393-0; 2015/06349-0; 2015/15536-9; 2014/01364-

Patterns of genome-wide variation, population differentiation and SNP discovery of the red banded stink bug (piezodorus guildinii)

Unravelling the details of range expansion and ecological dominance shifts of insect pests has been challenging due to the lack of basic knowledge about population structure, gene flow, and most importantly, how natural selection is affecting the adaptive process. Piezodous guildinii is an emerging pest of soybean in the southern region of the United States, and increasingly important in Brazil in recent years. However, the reasons P. guildinii is gradually becoming more of a problem are questions still mostly unanswered. Here, we have genotyped P. guildinii samples and discovered 1,337 loci containing 4,083 variant sites SNPs that were used to estimate genetic structure and to identify gene candidates under natural selection. Our results revealed the existence of a significant genetic structure separating populations according to their broad geographic origin, i.e., U.S. and Brazil, supported by AMOVA (F-GT = 0.26), STRUCTURE, PCA, and F-ST analyses. High levels of gene flow or coancestry within groups (i.e., within countries) can be inferred from the data, and no spatial pattern was apparent at the finer scale in Brazil. Samples from different seasons show more heterogeneous compositions suggesting mixed ancestry and a more complex dynamic. Lastly, we were able to detect and successfully annotated 123 GBS loci (10.5%) under positive selection. The gene ontology (GO) analysis implicated candidate genes under selection with genome reorganization, neuropeptides, and energy mobilization. We discuss how these findings could be related to recent outbreaks and suggest how new efforts directed to better understand P. guildinii population dynamics9CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP202001/2015-62017/02393-0FAPESP (Brazil)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2017/02393-0]; National Council for Scientific and Technological Development (CNPq)National Council for Scientific and Technological Development (CNPq) [202001/2015-6]; Sao Paulo Research Foundation (FAPESP, Portuguese: Fundacao de Amparo a Pesquisa do Estado de Sao Paulo)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP); Brazilian National Council for Scientific and Technological Development (CNPq, Portuguese: Conselho Nacional de Desenvolvimento Cientifico e Tecnologico)National Council for Scientific and Technological Development (CNPq); FAPESPFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP