Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil

Field-based recombinase polymerase amplification and lab-based qPCR assays for detection of Helicoverpa armigera

Helicoverpa armigera (Hübner) is a major crop pest native to Europe, Asia, Australia, and Africa which has recently invaded South America and has caused billions of dollars in agricultural losses. Because of challenges in differentiating between H. armigera and Helicoverpa zea (Boddie), a closely related species native to North and South America, genetic tests have previously been developed to detect H. armigera DNA in pooled samples of moth legs. In this study, a field-based recombinase polymerase amplification (RPA) assay using a lateral flow strip and a qPCR melt curve assay were developed for specific detection of H. armigera DNA in pooled moth samples. In addition, a crude DNA extraction protocol for whole moths was developed to allow rapid preparation of DNA samples. The RPA field test was able to detect ≥ 10 pg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of 999 H. zea equivalents. The qPCR assay was able to detect ≥ 100 fg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of up to 99,999 H. zea equivalents. Both RPA and qPCR assays detected H. armigera in the crude DNA extracted in the field from a pool of one H. armigera moth and 999 H. zea moths. These newly developed molecular assays to detect H. armigera will contribute to large-scale surveillance programs of H. armigera.

Complex multiple introductions drive fall armyworm invasions into Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda is thought to have undergone a rapid 'west-to-east' spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations in this study were overwhelmingly C- and R-strain hybrids (n = 252/262). SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved 'bridgehead populations' in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the 'African origin spread' nor the 'Myanmar source population to China' hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.

Baseline Susceptibility and Cross-Resistance of HearNPV in Helicoverpa armigera (Lepidoptera: Noctuidae) in Brazil

The marked adoption of bioinsecticides in Brazilian agriculture in recent years is, at least partially, explained by the increasingly higher levels of insect pest resistance to synthetic insecticides. In particular, several baculovirus-based products have been registered in the last 5 years, including Helicoverpa armigera nucleopolyhedrovirus (HearNPV: Baculoviridae: Alphabaculovirus (Armigen^®)). Understanding the susceptibility of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) to HearNPV is an important step toward development of robust Integrated Pest Management (IPM) and Insect Resistance Management programs (IRM) aimed at managing this serious insect pest. In this study, droplet feeding bioassays were used to characterize the baseline susceptibility to HearNPV (Armigen^®) in H. armigera populations collected from major soybean and cotton-growing regions in Brazil. We defined and validated a diagnostic concentration for susceptibility monitoring of H. armigera populations to HearNPV. Additionally, cross-resistance between HearNPV and the insecticides flubendiamide and indoxacarb was evaluated by testing HearNPV in a susceptible strain and in resistant strains of H. armigera to these insecticides. A low interpopulation variation of H. armigera to HearNPV was detected. The LC₅₀ values ranged from 1.5 × 10⁵ to 1.1 × 10⁶ occlusion bodies (OBs) per mL (7.3-fold variation). The mortality rate at the identified diagnostic concentration of 6.3 × 10⁸ OBs/mL, based on the calculated LC₉₉, ranged from 98.6 to 100% in populations of H. armigera collected from 2018 to 2020. No cross-resistance was detected between HearNPV and flubendiamide or indoxacarb. These results suggest that HearNPV (Armigen^®) can be an effective tool in IPM and IRM programs to control H. armigera in Brazil.

Genetic Variation and Population Structure of the Old World Bollworm Helicoverpa armigera (Hübner, 1808) (Lepidoptera: Noctuidae) in Ethiopia

Helicoverpa armigera is one of the most destructive insect pests of economically valuable crops in the world. Despite its economic importance, the population genetic structure of this insect remains unexplored in Ethiopia. To investigate the genetic diversity and population structure of H. armigera, we sampled 170 individuals from 15 populations throughout Ethiopia. We sequenced a fragment of the mitochondrial cytochrome b (cyt b) gene and five exon-primed intron-crossing (EPIC) markers. Twenty cyt b haplotypes with low-to-moderate haplotype diversity (mean Hd = 0.537) and high nucleotide diversity (mean Pi = 0.00339) were identified. The most frequently observed and widely distributed cyt b haplotype was designated as Hap_1 (67.058%), which is identical to sequences found across the globe. Tajima's D and Fu's F for the cyt b data were negative, supporting a model of population expansion. Within populations, a mean of 2.493 alleles/locus was recorded across the five EPIC loci, ranging from 1.200 to 3.600 alleles/locus. The highest mean effective number of alleles/population was 2.369 and the lowest was 1.178. The mean observed heterozygosity (HO) of the five loci (0-0.289; mean 0.104 ± 0.020) was lower than the expected heterozygosity (HE) (0.095-0.523; mean 0.258 ± 0.028). AMOVA detected significant genetic structure with 61% of the total molecular genetic variation of EPIC genotypes occurring between populations, suggesting a considerable degree of differentiation among populations. STRUCTURE analyses clustered the H. armigera populations into three distinct population groups but very low isolation by distance (R2 = 0.0132, P < 0.05).

Genetic diversity and demographic history of the Old World Bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae), in Ethiopia inferred from mitochondrial gene sequences

The Old World bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae), is a globally distributed agricultural and horticultural insect pest. Despite the economic importance of this insect in Ethiopia, its genetic diversity and demographic history are poorly understood. We examined the nucleotide variation of the mitochondrial cytochrome c oxidase subunit I (COI) gene fragment of 74 H. armigera individuals from six collection sites in Ethiopia. We recorded 15 COI haplotypes in H. armigera, ten globally shared and five exclusive to Ethiopia (HaET15, HaET14, HaET10, HaET7, and HaET4). Haplotype HaET1 was the most widely geographically distributed and frequent (71.62%). Analysis of molecular variance (AMOVA) revealed a high and significant level of variation within H. armigera populations (θ_ST = −0.0135). Negative values of the neutrality test and nonsignificant index of mismatch distribution supported the demographic expansion of H. armigera populations in Ethiopia; furthermore, this was also supported by the nonsignificant values of the sum of squared deviations (SSD) and raggedness index (r). The high genetic variation and population expansion of H. armigera have immense implications for devising locally adapted management strategies in area‐wide integrated pest management IPM programs. However, a comprehensive study of H. armigera genetic diversity and population structure using various molecular markers is needed for future confirmation.

Global population genomic signature of Spodoptera frugiperda (fall armyworm) supports complex introduction events across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by its chronological detection across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range. 870 high-quality nuclear single nucleotide polymorphic DNA markers identified five distinct New World population clusters, broadly reflecting FAW native geographical ranges and the absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinning the pest’s global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated the potential of population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

This population genomics study identifies the complex multiple introduction history of Spodoptera frugiperda (fall armyworm) from the Americas, into Africa and Asia. This provides new insight into the ‘east-to-west’ directionality of gene flow, and suggests ample genomic exchange at the nuclear level.

Helicoverpa armigera and Helicoverpa zea hybridization: constraints, heterosis, and implications for pest management

BACKGROUND

The invasion of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) into the New World has made it possible for this pest to hybridize with a native American species, H. zea (Boddie), under natural conditions. We investigated the viability and development of hybrids of these two Helicoverpa species. We reared the parental species and evaluated crosses between H. armigera males and H. zea females and vice versa, two intercrosses between hybrids, and eight backcrosses between hybrids and parental species. We estimated the length of immature stages, fecundity, survival, sex ratio, and heterosis.

RESULTS

Although hybridization occcurred, with heterosis during the development of immatures, reproductive incompatibilities also were observed between the parental species and between hybrids from subsequent crosses. The interspecific crosses between hybrids and backcrosses confirmed the possibility of introgression events and their perpetuation in field populations. The results indicate that hybridization events are favored at high population levels, while at low population levels the 'species identities' will be maintained.

CONCLUSIONS

The possibility of interspecific gene flow and its perpetuation through successive crosses and backcrosses suggests several recommenations for management. Populations of both species should be maintained at an equilibrium level to reduce the chance of interspecific crosses, which are presumably more likely to occur during pest outbreaks. The existence of hybridization and resistance to different active pesticide ingredients should be monitored. All practices related to managing the resistance of these pests to chemical and biological insecticides should be systematized to reduce the chance of selecting for resistant individuals.

Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm

The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned into 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultra-dense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta, and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of GO categories related to climate adaptation, feeding behavior and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.

Determinants of Insecticide Resistance Evolution: Comparative Analysis Among Heliothines

It is increasingly clear that pest species vary widely in their propensities to develop insecticide resistance. This review uses a comparative approach to analyze the key pest management practices and ecological and biochemical or genetic characteristics of the target that contribute to this variation. We focus on six heliothine species, three of which, Helicoverpa armigera, Heliothis virescens, and Helicoverpa zea, have developed resistances to many pesticide classes. The three others, Helicoverpa punctigera, Helicoverpa assulta, and Helicoverpa gelotopoeon, also significant pests, have developed resistance to very few pesticide classes. We find that host range and movement between alternate hosts are key ecological traits that influence effective selection intensities for resistance. Operational issues are also critical; area-wide, cross-pesticide management practices that account for these ecological factors are key to reducing selection intensity. Without such management, treatment using broad-spectrum chemicals serves to multiply the effects of host plant preference, preadaptive detoxification ability, and high genetic diversity to create a pesticide treadmill for the three high-propensity species.Without rigorous ongoing management, such a treadmill could still develop for newer, more selective chemistries and insecticidal transgenic crops.

Assay Optimization Can Equalize the Sensitivity of Real-Time PCR with ddPCR for Detection of Helicoverpa armigera (Lepidoptera: Noctuidae) in Bulk Samples

Simple Summary

Invasive species are a constant threat to agriculture throughout the world against which early detection is one of the primary defenses. The Old World bollworm is one of the most important invasive agricultural pests in the world. While historically absent from the Americas, this species was first found in South America in 2013 and poses an ongoing threat of spreading into North America. Surveys are conducted each year, which result in hundreds or thousands of traps that must be screened for this species. Unfortunately, the most common non-target is the native corn earworm, which is nearly identical morphologically to the Old World bollworm and cannot be easily separated. Molecular methods have been developed to screen these trap samples, but the required equipment is expensive and not commonly available. This study details improvements to current molecular methods that will allow for screening of bulk trap samples using standard laboratory instruments and protocols. The ability to perform these methods in nearly any molecular biology lab will greatly enhance our ability to detect and exclude this important pest.

Abstract

Helicoverpa armigera (Hübner) is one of the most important agricultural pests in the world. This historically Old World species was first reported in Brazil in 2013 and has since spread throughout much of South America and into the Caribbean. Throughout North America, H. armigera surveys are ongoing to detect any incursions. Each trap is capable of capturing hundreds of native Helicoverpa zea (Boddie). The two species cannot be separated without genitalic dissection or molecular methods. A ddPCR assay is currently used to screen large trap samples, but this equipment is relatively uncommon and expensive. Here, we optimized a newly designed assay for accurate and repeatable detection of H. armigera in bulk samples across both ddPCR and less costly, and more common, real-time PCR methods. Improvements over previously designed assays were sought through multiple means. Our results suggest bulk real-time PCR assays can be improved through changes in DNA extraction and purification, so that real-time PCR can be substituted for ddPCR in screening projects. While ddPCR remains a more sensitive method for detection of H. armigera in bulk samples, the improvements in assay design, DNA extraction, and purification presented here also enhance assay performance over previous protocols.

An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae)

An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30–99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages:•

The resulting protocol is an easy-to-use time-saving method.

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This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products.

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DNA purity estimations reveal A260:A280 ratios above 1.9.

Who Is Dermanyssus gallinae? Genetic Structure of Populations and Critical Synthesis of the Current Knowledge

Despite the economic and animal welfare importance of the Poultry Red Mite Dermanyssus gallinae, its genetic structure has been studied in a scattered way so far. The prophylaxis and control of such a globally distributed ectoparasite can be significantly improved by understanding its genetic population structure (composition in species and intraspecific variants). The present study aims to establish a rigorous framework for characterizing the neutral genetic structure of D. gallinae based on a literature review combined with an integrative analysis of the data available in GenBank on population-level nucleotide sequence diversity supplemented by a new dataset. The integrative analysis was conducted on sequence data extracted from GenBank coupled with new sequences of two fragments of the mitochondrial gene encoding Cytochrome Oxidase I (CO1) as well as of an intron of the nuclear gene encoding Tropomyosin (Tpm) from several PRM populations sampled from European poultry farms. Emphasis was placed on using the mitochondrial gene encoding CO1 on which the main universal region of DNA barcoding in animals is located. The species D. gallinae sensu lato is a species complex, encompassing at least two cryptic species, i.e., not distinguishable by morphological characters: D. gallinae sensu stricto and D. gallinae L1. Only D. gallinae s.s. has been recorded among the populations sampled in poultry farms worldwide. Current knowledge suggests they are structured in three mitochondrial groups (haplogroups A, B, and C). Haplogroup A is cosmopolitan, and the other two present slightly contrasted distributions (B rather in the northern part of Europe, C most frequently found in the southern part). Recent data indicate that a dynamic geographic expansion of haplogroup C is underway in Europe. Our results also show that NUMT (nuclear mitochondrial DNA) pseudogenes have generated artifactual groups (haplogroups E and F). It is important to exclude these artifact groups from future analyses to avoid confusion. We provide an operational framework that will promote consistency in the analysis of subsequent results using the CO1 fragment and recommendations for future analyses.

HearNPV susceptibility in Helicoverpa armigera and Helicoverpa punctigera strains resistant to Bt toxins Cry1Ac, Cry2Ab, and Vip3Aa

Genetically engineered crops expressing insecticidal toxins from Bacillus thuringiensis (Bt) have improved the management of targeted lepidopteran pests and reduced the use of insecticide sprays. These benefits explain an increasing adoption of Bt crops worldwide, intensifying the selection pressure on target species and the risk of resistance. Nucleopolyhedroviruses (NPVs) are effective bioinsecticides against numerous important lepidopteran pests. If Bt-resistant insects are shown to be susceptible to NPVs then these bioinsecticides could be a valuable component of Insecticide Resistance Management (IRM) strategies for Bt crops. We assessed the effectiveness of a Helicoverpa nucleopolyhedrovirus (HearNPV) against several different Bt-resistant strains. Utilising a droplet feeding bioassay we confirmed susceptibility to HearNPV in Helicoverpa punctigera and Helicoverpa armigera larvae resistant to the Bt toxins Cry1Ac, Cry2Ab, and Vip3A. Dual resistant H. punctigera, (Cry1Ac/Cry2Ab, and Cry2Ab/Vip3A) and dual resistant H. armigera (Cry2Ab/Vip3A) were also susceptible to HearNPV. Regardless of their specific resistance profile, Bt-resistant larvae displayed statistically similar lethal concentration (LC₅₀) and lethal time (LT₅₀) responses to HearNPV when compared to Bt-sensitive control insects. These results indicate that Bt-resistant H. armigera and H. punctigera are not cross-resistant to HearNPV. Consequently, the use of HearNPV against these pests may be a valuable tool to an IRM strategy for controlling Bt-resistant populations.

Helicoverpa armigera Harm 1 Haplotype Predominates in the Heliothinae (Lepidoptera: Noctuidae) Complex Infesting Tomato Crops in Brazil

Tomato (Solanum lycopersicum L.) is a natural host for the Helicoverpa-Chloridea (Lepidoptera: Noctuidae: Heliothinae) pest complex. The species Helicoverpa armigera (Hübner) was responsible for significant yield losses in several crops after its detection in Brazil. The morphology of its larval stage resembles common Heliothinae species, making pest control decisions difficult. The overall lack of studies on the Heliothinae associated with tomatoes in Brazil and the establishment of H. armigera in the country plus their recent outbreaks supported our investigation about the relative importance of the insects from the Helicoverpa-Chloridea complex in this vegetable crop. A nationwide survey was carried out across fresh-market and processing tomato fields. Molecular analyses targeting a segment of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene and their sequence analyses indicated the presence of a pest complex, comprising the introduced species H. armigera and the indigenous species, Helicoverpa zea (Boddie), and Chloridea virescens (Fabricius). The Harm 1 haplotype of H. armigera was identified as the predominant Heliothinae pest infesting fresh-market tomatoes. The New World species Chloridea subflexa (Guenée) as well as the exotic Solanaceae-specific species Helicoverpa assulta (Guenée) were not found in our survey. Additional larvae surveys in processing tomato fields during 2013/2014 in Central Brazil also indicated H. armigera as the most abundant Heliothinae species (95%) together with H. zea (4.75%) and C. virescens (0.25%). The occurrence of distinct Helicoverpa species (which are potentially capable of interbreeding) indicates that novel crop management strategies will be necessary in order to minimize damages caused by this pest complex in tomatoes.

Host plant use of Helicoverpa spp. (Lepidoptera: Noctuidae) in the Brazilian agricultural landscape

BACKGROUND

The Old-World bollworm, Helicoverpa armigera (Hübner), was recently documented attacking cotton and soybean plants in Brazil; however, restricted basic knowledge on host plant interactions and landscape use in Brazil have limited the effectiveness of control measures. In this study, we evaluated the suitability of different crops commonly cultivated in Brazil as hosts for H. armigera and H. zea, and examined their contribution to the establishment and size of H. armigera and H. zea field populations. We also estimated the proportions of H. armigera and H. zea moths that used cotton, noncotton C₃ plants, and C₄ plants as hosts in four regions in Brazil through the length of the cropping season.

RESULTS

Viability of H. armigera larvae was highest on cotton (46.1%), followed by millet (39.5%), sorghum (31.2%), soybean (24.2%), and maize (21.1%). Noncotton C₃ hosts served as the major source of H. armigera moths in all regions evaluated, and C₄ hosts were a source of H. armigera mainly in regions where winter maize is typically cultivated. H. armigera moths that used cotton plants as natal hosts were observed during the reproductive stage of the crop mainly in the state of Bahia. Only C₄ host plants were a consistent source of H. zea moths, primarily when maize was in the reproductive stage. H. armigera individuals were the main species infesting cotton and soybean fields while H. zea individuals were the main species infesting maize ears.

CONCLUSIONS

Regional differences in the host use and population dynamics of H. armigera among the regions evaluated may be attributed to variation in alternative host utilization (crops, noncrops, and weeds) and the possible occurrence of facultative diapause and or migration.

Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in Brazil: the Big Outbreak Monitored by Light Traps

The first detection of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in Brazil pointed to a gloomy future for South American agriculture in the 2012/2013 harvest, and insecticide sales increased exponentially during 2013 and 2014. However, after this outbreak, the population of this insect returned to manageable levels. This study documents data on H. armigera moth collection using light traps during the outbreak in two locations: (a) western region of the state of Bahia, including population levels of H. armigera and main noctuid pests during the big outbreak (February and March 2013); (b) Federal District, including monthly data for five growing seasons (July 2012-June 2017). During the outbreak, an average of 527.3 moths were collected per trap (cotton crop, March) in the western region of Bahia each night, while the maximum average in the Federal District was 75.4 moths (January). The number of moths decreased in the following growing seasons, and in October 2016, the maximum number was 2.8 moths per trap. Aspects related to the variations of H. armigera and Helicoverpa zea (Boddie) populations, including the study of phenology and relationship with climatic factors and Oceanic Niño Index, were analyzed and discussed. All aspects are approached to contribute to the management of lepidopteran pests, especially H. armigera, in the productive systems of the Brazilian Cerrado.

Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths

Hybridization between invasive and native species has raised global concern, given the dramatic increase in species range shifts and pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact between sister lineages of local and invasive species provides a natural laboratory to understand the factors that determine introgression and the maintenance or loss of species barriers. Here, we characterize the early evolutionary outcomes following secondary contact between invasive Helicoverpa armigera and native H. zea in Brazil. We carried out whole-genome resequencing of Helicoverpa moths from Brazil in two temporal samples: during the outbreak of H. armigera in 2013 and 2017. There is evidence for a burst of hybridization and widespread introgression from local H. zea into invasive H. armigera coinciding with H. armigera expansion in 2013. However, in H. armigera, the admixture proportion and the length of introgressed blocks were significantly reduced between 2013 and 2017, suggesting selection against admixture. In contrast to the genome-wide pattern, there was striking evidence for adaptive introgression of a single region from the invasive H. armigera into local H. zea, including an insecticide resistance allele that increased in frequency over time. In summary, despite extensive gene flow after secondary contact, the species boundaries are largely maintained except for the single introgressed region containing the insecticide-resistant locus. We document the worst-case scenario for an invasive species, in which there are now two pest species instead of one, and the native species has acquired resistance to pyrethroid insecticides through introgression.

Arthropod Invasions Versus Soybean Production in Brazil: A Review

Soybean production in Brazil has been markedly affected by invasions of non-native arthropod species that feed on the crop, severely impacting biodiversity, food security, health, and economic development. Data on soybean production losses and increase in insecticide usage over the last two decades have not been explored in association with past invasion events, and the dynamics underlying the recent blitz of invasive species into Brazil remain largely unclear. We provide a review of arthropod invasions in the Brazilian soybean agroecosystem since 1990, indicating that the introductions of Bemisia tabaci (Gennadius) MEAM1 (Hemiptera: Aleyrodidae), Tetranychus urticae (Koch) (Acari: Tetranychidae), and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) are likely correlated with periods of increase in insecticide usage for soybean production. Using these three cases as examples, we review factors that could lead to increased likelihood of future invasions by particular pests, outlining four possible criteria to evaluate potential invasiveness of non-native arthropods: likelihood of entry, likelihood of establishment, biological features of the species, and availability of control measures. Spodoptera litura (F.) (Lepidoptera: Noctuidae) and Aphis glycines (Matsumura) (Hemiptera: Sternorrhynca) are examples of highly damaging soybean pests, related to one or more of these factors, that could be introduced into Brazil over the next years and which could lead to problematic scenarios. Melanagromyza sojae (Zehnter) (Diptera: Agromyzidae) also meets these criteria and has successfully invaded and colonized Brazilian soybean fields in recent years. Our review identifies current issues within soybean pest management in Brazil and highlights the need to adopt management measures to offset future costs and minimize lost revenue.

Comparative Toxicity of Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) to Selected Insecticides

Until recently, the Old World bollworm (OWB) Helicoverpa armigera (Hübner) and the corn earworm Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) were geographically isolated. Both species are major pests of agricultural commodities that are known to develop insecticide resistance, and they now coexist in areas where H. armigera invaded the Americas. This is the first study to compare the susceptibility of the two species to conventional insecticides. The susceptibility of third instar H. armigera and H. zea larvae to indoxacarb, methomyl, spinetoram, and spinosad was determined using a diet-overlay bioassay in a quarantine laboratory in Puerto Rico. Mortality was assessed at 48 h after exposure for up to eight concentrations per insecticide. Spinetoram exhibited the highest acute toxicity against H. armigera, with a median lethal concentration (LC50) of 0.11 µg a.i./cm2, followed by indoxacarb and spinosad (0.17 µg a.i./cm2 for both) and methomyl (0.32 µg a.i./cm2). Spinetoram was also the most toxic to H. zea (LC50 of 0.08 µg a.i./cm2), followed by spinosad (0.17 µg a.i./cm2) and methomyl (0.18 µg a.i./cm2). Indoxacarb was the least toxic to H. zea, with an LC50 of 0.21 µg a.i./cm2. These findings could serve as a comparative reference for monitoring the susceptibility of H. armigera and H. zea to indoxacarb, methomyl, spinetoram, and spinosad in Puerto Rico, and may facilitate the detection of field-selected resistance for these two species and their potential hybrids in areas recently invaded by H. armigera.

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.

Influence of Temperature and Precipitation Anomaly on the Seasonal Emergence of Invasive Bark Beetles in Subtropical South America

Several invasive bark beetle species have caused major economic and ecological losses in South America. Accurate predictions of beetle emergence times will make control efforts more efficient and effective. To determine whether bark beetle emergence can be predicted by season, temperature, or precipitation, we analyzed trapping records for three introduced pest species of bark beetles in Uruguay. We used trigonometric functions as seasonal predictors in generalized linear models to account for purely seasonal effects, while testing for effects of temperature and precipitation. Results show that all three beetle species had strong but unique seasonal emergence patterns and responded differently to temperature and precipitation. Cyrtogenius luteus (Blandford) emerged in summer and increased with precipitation but was not affected by temperature. Hylurgus ligniperda (Fabricius) emerged in winter and increased with temperature but was not affected by precipitation. Orthotomicus erosus (Wollaston) had a primary emergence in spring, and a smaller emergence in early summer, but showed no significant relationship with temperature or precipitation. This study shows that the emergence of these bark beetle species in Uruguay is influenced by seasonality more than by temperature and precipitation fluctuations. It also shows how seasonality can be easily incorporated into models to make more accurate predictions about pest population dynamics.

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

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.

One maternal lineage leads the expansion of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae) in the New and Old Worlds

The bronze bug, Thaumastocoris peregrinus, an Australian native insect, has become a nearly worldwide invasive pest in the last 16 years and has been causing significant damage to eucalypts (Myrtaceae), including Eucalyptus spp. and Corymbia spp. Its rapid expansion leads to new questions about pathways and routes that T. peregrinus used to invade other continents and countries. We used mtDNA to characterize specimens of T. peregrinus collected from 10 countries where this species has become established, including six recently invaded countries: Chile, Israel, Mexico, Paraguay, Portugal, and the United States of America. We then combined our mtDNA data with previous data available from South Africa, Australia, and Europe to construct a world mtDNA network of haplotypes. Haplotype A was the most common present in all specimens of sites sampled in the New World, Europe, and Israel, however from Australia second more frequently. Haplotype D was the most common one from native populations in Australia. Haplotype A differs from the two major haplotypes found in South Africa (D and G), confirming that at least two independent invasions occurred, one from Australia to South Africa, and the other one from Australia to South America (A). In conclusion, Haplotype A has an invasion success over many countries in the World. Additionally, analyzing data from our work and previous reports, it is possible to suggest some invasive routes of T. peregrinus to predict such events and support preventive control measures.

Multiple incursion pathways for Helicoverpa armigera in Brazil show its genetic diversity spreading in a connected world

The Old World cotton bollworm Helicoverpa armigera was first detected in Brazil with subsequent reports from Paraguay, Argentina, Bolivia, and Uruguay. This pattern suggests that the H. armigera spread across the South American continent following incursions into northern/central Brazil, however, this hypothesis has not been tested. Here we compare northern and central Brazilian H. armigera mtDNA COI haplotypes with those from southern Brazil, Uruguay, Argentina, and Paraguay. We infer spatial genetic and gene flow patterns of this dispersive pest in the agricultural landscape of South America. We show that the spatial distribution of H. armigera mtDNA haplotypes and its inferred gene flow patterns in the southwestern region of South America exhibited signatures inconsistent with a single incursion hypothesis. Simulations on spatial distribution patterns show that the detection of rare and/or the absence of dominant mtDNA haplotypes in southern H. armigera populations are inconsistent with genetic signatures observed in northern and central Brazil. Incursions of H. armigera into the New World are therefore likely to have involved independent events in northern/central Brazil, and southern Brazil/Uruguay-Argentina-Paraguay. This study demonstrates the significant biosecurity challenges facing the South American continent, and highlights alternate pathways for introductions of alien species into the New World.

Chromosomal deletions mediated by CRISPR/Cas9 in Helicoverpa armigera

Helicoverpa armigera, cotton bollworm, is one of the most disastrous pests worldwide, threatening various food and economic crops. Functional genomic tools may provide efficient approaches for its management. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, dependent on a single guide RNA (sgRNA), has been used to induce indels for targeted mutagenesis in cotton bollworm. However, genomic deletions may be more desirable to disrupt the function of noncoding genes or regulatory sequences. By injecting two sgRNAs with Cas9 protein targeting different exons, we obtained predictable genomic deletions of several hundred bases. We achieved this type of modification with different combinations of sgRNA pairs, including HaCad and HaABCC2. Our finding indicated that CRISPR/Cas9 can be used as an efficient tool to engineer genomes with chromosomal deletion in H. armigera.

Diversity analysis reveals genetic homogeneity among Indian populations of legume pod borer, Maruca vitrata (F.)

Legume pod borer, Maruca vitrata, has lately emerged as one of the major insect pests of pigeonpea causing considerable crop losses. Thus, efficient management of M. vitrata is an important component for sustained pigeonpea productivity for which information on insect diversity could be useful. Present study was undertaken to evaluate the diversity in M. vitrata populations collected from major pigeonpea growing areas of India using molecular markers, Cytochrome C Oxidase subunit 1 (cox1) and Translational Elongation Factor-1α (tef-1α). Genomic DNA from larvae of different populations was extracted; 709 bp and 550 bp fragments of cox1 and tef-1α were PCR-amplified, cloned and sequenced. Comparison of sequences of different populations using multiple sequence alignment did not show any differences in cox1 and tef-1α sequences within the Indian populations. However, further analysis based upon cox1 sequences has revealed moderate nucleotide diversity (π = 0.26174) among Indian and global M. vitrata populations, whereas nucleotide diversity within Indian populations is nonsignificant (π = 0.00226). Additionally, phylogenetic analysis of cox1 sequences grouped all the Indian populations into one cluster while that of global were completely separate indicating a different ancestral background. This is a maiden attempt for diversity assessment of Indian M. vitrata populations that established them to be genetic homologs with different ancestral background.

Invasion origin, rapid population expansion, and the lack of genetic structure of cotton bollworm (Helicoverpa armigera) in the Americas

In 2013, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) was officially declared as present in Brazil and, after two years, the species was detected in the Caribbean and North America. Information on genetic features and accurate distribution of pests is the basis for agricultural protection policies. Furthermore, such knowledge is imperative to develop control strategies, understand the geographical range, and genetic patterns of this species in the Americas. Here, we carried out the widest sampling of H. armigera in the South American continent and Puerto Rico, after we estimated the diversity, demographic parameters, and genetic structure. The Internal Transcribed Spacer 1 (ITS1) nuclear marker was used to investigate the presence of putative hybrids between H. armigera and H. zea, and they were observed at a frequency of 1.5%. An ABC analysis, based in COI gene fragment, suggested Europe as the origin of South America specimens of H. armigeraand following a movement northward through the Caribbean. Three mtDNA genes and three nDNA markers revealed high genetic diversity distributed without the defined population structure of H. armigera in South America. Most of the genetic variation is within populations with a multidirectional expansion of H. armigera among morphoclimatic regions. High genetic diversity, rapid population expansion, and hybridization have implications for pest management since they suggest that adaptive alleles are spread through wide areas in South America that favor rapid local adaptation of H. armigera to new and disturbed environments (e.g., in agricultural areas).

Escalating insecticide resistance in Australian grain pests: contributing factors, industry trends and management opportunities

Insecticide resistance is an ever-increasing problem that threatens food production globally. Within Australia, the grain industry has a renewed focus on resistance due to diminishing chemical options available to farmers and the increasing prevalence and severity of resistance encountered in the field. Chemicals are too often used as the major tool for arthropod pest management, ignoring the potent evolutionary forces from chemical selection pressures that lead to resistance. A complex array of factors (biological, social, economic, political, climatic) have contributed to current trends in insecticide usage and resistance in the Australian grain industry. We review the status of insecticide resistance and provide a context for how resistance is currently managed. We discuss emerging technologies and research that could be applied to improve resistance management. This includes generating baseline sensitivity data for insecticides before they are launched, developing genetic diagnostics for the full complement of known resistances, expanding resistance monitoring programs, and utilizing new technologies. Additional benefits are likely to be achieved through a combination of industry awareness and engagement, risk modeling, adoption of integrated pest management tactics, greater collaboration between industry stakeholders, and policy changes around chemical use and record keeping. The Australian grain context provides lessons for other agricultural industries. © 2018 Society of Chemical Industry.

Mitochondrial DNA genomes of five major Helicoverpa pest species from the Old and New Worlds (Lepidoptera: Noctuidae)

Five species of noctuid moths, Helicoverpa armigera, H. punctigera, H. assulta, H. zea, and H. gelotopoeon, are major agricultural pests inhabiting various and often overlapping global distributions. Visual identification of these species requires a great deal of expertise and misidentification can have repercussions for pest management and agricultural biosecurity. Here, we report on the complete mitochondrial genomes of H. assulta assulta and H. assulta afra, H. gelotopoeon, H. punctigera, H. zea, and H. armigera armigera and H. armigera conferta' assembled from high-throughput sequencing data. This study significantly increases the mitogenome resources for these five agricultural pests with sequences assembled from across different continents, including an H. armigera individual collected from an invasive population in Brazil. We infer the phylogenetic relationships of these five Helicoverpa species based on the 13 mitochondrial DNA protein-coding genes (PCG's) and show that two publicly available mitogenomes of H. assulta (KP015198 and KR149448) have been misidentified or incorrectly assembled. We further consolidate existing PCR-RFLP methods to cover all five Helicoverpa pest species, providing an updated method that will contribute to species differentiation and to future monitoring efforts of Helicoverpa pest species across different continents. We discuss the value of Helicoverpa mitogenomes to assist with species identification in view of the context of the rapid spread of H. armigera in the New World. With this work, we provide the molecular resources necessary for future studies of the evolutionary history and ecology of these species.

Going global - genomic insights into insect invasions

The spread of invasive insect pests is becoming an increasing problem for agriculture globally. We discuss a number of invasive insects, already of major economic significance that have recently expanded their range to become truly global threats. These include the noctuid moths Helicoverpa and Spodoptera, whose caterpillars have long been among the worst pests in their native Old and New World habitats, respectively, and the whitefly Bemisia, a major vector of plant virus diseases. Importantly, genomic resources for these species have recently become available, allowing research to move beyond the restrictions imposed by earlier approaches limited to a single or few mitochondrial and nuclear markers, to employ genome-wide genotyping and resequencing protocols. These studies have shown hybridisation within the various species complexes, identified regions under selection in agricultural environments, and enable monitoring of genes important as biosecurity risks through introgression into established populations free of the genes. In all cases studied, global trade has emerged as the probable cause of insect spread, making it ever more important that biosecurity protocols and agencies work with researchers to make the most effective use of emerging genomic resources and tools.

Movement Ecology of Pest Helicoverpa: Implications for Ongoing Spread

The recent introduction and spread of Helicoverpa armigera throughout South America highlight the invasiveness and adaptability of moths in the Helicoverpa genus. Long-range movement in three key members, H. armigera, H. zea, and H. punctigera, occurs by migration and international trade. These movements facilitate high population admixture and genetic diversity, with important economic, biosecurity, and control implications in today's agricultural landscape. This is particularly true for the spread of resistance alleles to transgenic crops expressing Bacillus thuringiensis (Bt) toxins that are planted over vast areas to suppress Helicoverpa spp. The ability to track long-distance movement through radar technology, population genetic markers, and/or long-distance dispersal modeling has advanced in recent years, yet we still know relatively little about the population trajectories or migratory routes in Helicoverpa spp. Here, we consider how experimental and theoretical approaches can be integrated to fill key knowledge gaps and assist management practices.

Detection of sister-species in invasive populations of the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Uganda

The fall armyworm (FAW) Spodoptera frugiperda (J. E. Smith) is a species native to the Americas. This polyphagous lepidopteran pest was first reported in Nigeria and the Democratic Republic of São Tomé and Principe in 2016, but its presence in eastern Africa has not been confirmed via molecular characterisation. In this study, FAW specimens from western and central Uganda were identified based on the partial mtDNA COI gene sequences, with mtDNA COI haplotypes matching those identified in Nigeria and São Tomé. In this study, we sequence an additional partial mtDNA Cyt b gene and also the partial mtDNA COIII gene in Ugandan FAW samples. We detected identical mitochondrial DNA haplotypes for both the mtDNA Cyt b and COI partial genes, while combining the mtDNA COI/Cyt b haplotypes and mtDNA COIII haplotypes enabled a new maternal lineage in the Ugandan corn-preferred FAW samples to be identified. Our results suggested that the African incursions of S. frugiperda involved at least three maternal lineages. Recent full genome, phylogenetic and microsatellite analyses provided evidence to support S. frugiperda as likely consisted of two sympatric sister species known as the corn-preferred and rice-preferred strains. In our Ugandan FAW populations, we identified the presence of mtDNA haplotypes representative of both sister species. It is not known if both FAW sister species were originally introduced together or separately, and whether they have since spread as a single population. Further analyses of additional specimens originally collected from São Tomé, Nigeria and throughout Africa would be required to clarify this issue. Importantly, our finding showed that the genetic diversity of the African corn-preferred FAW species is higher than previously reported. This potentially contributed to the success of FAW establishment in Africa. Furthermore, with the additional maternal lineages detected, there is likely an increase in paternal lineages, thereby increasing the diversity of the African FAW population. Knowledge of the FAW genetic diversity will be needed to assess the risks of introducing Bt-resistance traits and to understand the FAW incursion pathways into the Old World and its potential onward spread. The agricultural implications of the presence of two evolutionary divergent FAW lineages (the corn and the rice lineage) in the African continent are further considered and discussed.

Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa

Helicoverpa armigera is a major agricultural and horticultural pest that recently spread from its historical distribution throughout much of the Old World to the Americas, where it is already causing hundreds of millions of dollars in damage every year. The species is notoriously quick to generate and disseminate pesticide resistance throughout its range and has a wider host range than the native Helicoverpa zea. Hybridization between the two species increases the opportunity for novel, agriculturally problematic ecotypes to emerge and spread through the Americas.

Within the mega-pest lineage of heliothine moths are a number of polyphagous, highly mobile species for which the exchange of adaptive traits through hybridization would affect their properties as pests. The recent invasion of South America by one of the most significant agricultural pests, Helicoverpa armigera, raises concerns for the formation of novel combinations of adaptive genes following hybridization with the closely related Helicoverpa zea. To investigate the propensity for hybridization within the genus Helicoverpa, we carried out whole-genome resequencing of samples from six species, focusing in particular upon H. armigera population structure and its relationship with H. zea. We show that both H. armigera subspecies have greater genetic diversity and effective population sizes than do the other species. We find no signals for gene flow among the six species, other than between H. armigera and H. zea, with nine Brazilian individuals proving to be hybrids of those two species. Eight had largely H. armigera genomes with some introgressed DNA from H. zea scattered throughout. The ninth resembled an F1 hybrid but with stretches of homozygosity for each parental species that reflect previous hybridization. Regions homozygous for H. armigera-derived DNA in this individual included one containing a gustatory receptor and esterase genes previously associated with host range, while another encoded a cytochrome P450 that confers insecticide resistance. Our data point toward the emergence of novel hybrid ecotypes and highlight the importance of monitoring H. armigera genotypes as they spread through the Americas.

Phylogeography of Diaphorina citri (Hemiptera: Liviidae) and its primary endosymbiont, 'Candidatus Carsonella ruddii': an evolutionary approach to host-endosymbiont interaction

BACKGROUND

In insects, little is known about the co-evolution between their primary endosymbionts and hosts at the intraspecific level. This study examined co-diversification between the notorious agricultural pest Diaphorina citri and its primary endosymbionts (P-endosymbiont), 'Candidatus Carsonella ruddii' at the population level.

RESULTS

Maximum likelihood, haplotype network, principal components and Bayesian clustering identified three lineages for D. citri and its P-endosymbiont: a Western clade containing individuals from Pakistan, Bhutan (Phuentsholing), Vietnam (Son La), USA, Myanmar and China (Ruili, Yunnan); a Central clade, with accessions originating from Southwest China, Bhutan (Tsirang) and Bangladesh; and an Eastern clade containing individuals from Southeast Asia, and East and South China. A more diverse genetic structure was apparent in the host mitochondrial DNA than their P-endosymbionts; however, the two sets of data were strongly congruent.

CONCLUSION

This study provides evidence for the co-diversification of D. citri and its P-endosymbiont during the migration from South Asia to East and Southeast Asia. We also suggest that the P-endosymbiont may facilitate investigations into the genealogy and migration history of the host. The biogeography of D. citri and its P-endosymbiont indicated that D. citri colonized and underwent a secondary dispersal from South Asia to East and Southeast Asia. © 2018 Society of Chemical Industry.

Genome-Wide Characterization of DNA Methylation in an Invasive Lepidopteran Pest, the Cotton Bollworm Helicoverpa armigera

The genes and genomes of insect pests are shaped by the wide array of selective forces encountered in their environments. While the molecular adaptations that evolve are beginning to be understood at the genomic and transcriptomic level, they have been less well characterized at an epigenetic level. Here, we present a genome-wide map of DNA methylation at single-nucleotide resolution for the cotton bollworm moth, Helicoverpa armigera, a globally invasive pest of agriculture. We show that methylation is almost identical in the larvae and adults of H. armigera and that, through whole-genome bisulfite sequencing (WGBS), at the most ∼0.9% of CpG sites in this species are methylated. We find that DNA methylation occurs primarily in exons, is positively correlated with gene expression, and that methylated genes are enriched for cellular "housekeeping" roles. H. armigera has an exceptional capacity for long-range migration. To explore the role of methylation in influencing the migratory phenotype of H. armigera, we performed targeted bisulfite sequencing on selected loci from 16 genes that were differentially expressed between adult moths exhibiting distinct flight performance in behavioral assays. While most CpG sites in these genes were not methylated between flight phenotypes, we identified hypermethylation in a demethylase (KDM4) that targets lysine-specific histone modifications, which are strongly associated with transcription and methylation. The H. armigera methylome provides new insights into the role of DNA methylation in a noctuid moth and is a valuable resource for further research into the epigenetic control of adaptive traits in this important pest.

High frequency of CYP337B3 gene associated with control failures of Helicoverpa armigera with pyrethroid insecticides in Brazil

Control failures with the use of pyrethroid insecticides have been reported frequently for populations of Helicoverpa armigera (Hübner) in Brazil, since its detection in 2013. Here, we confirmed and investigated the metabolic mechanisms of pyrethroid resistance in H. armigera populations from Brazil. Mortality of H. armigera populations was lower than 50% at the highest dose (10μg a.i./3rd instar larva) of the pyrethroids deltamethrin and fenvalerate in dose-response bioassays. Very low mortality (10 to 40%) was obtained at a diagnostic dose of 10μg a.i./larva for each pyrethroid in H. armigera populations collected from different agricultural regions in Brazil, from 2013 to 2016. In synergist bioassays, when larvae were treated with PBO synergist, the mortality of all populations tested was 100%. The frequency of the cytochrome P450 CYP337B3 gene was above 0.95 in all populations of H. armigera. We found only fourteen heterozygous H. armigera out of 497 individuals tested for this gene subfamily. Our results indicated that H. armigera populations from Brazil have different degrees of susceptibility to deltamethrin and fenvalerate, but all populations can be considered tolerant to pyrethroid insecticides. The chimeric P450 CYP337B3 enzyme is one of the main mechanisms of pyrethroid resistance in Brazilian H. armigera populations.

CRISPR/Cas9 mediated genome editing of Helicoverpa armigera with mutations of an ABC transporter gene HaABCA2 confers resistance to Bacillus thuringiensis Cry2A toxins

High levels of resistance to Bt toxin Cry2Ab have been identified to be genetically linked with loss of function mutations of an ABC transporter gene (ABCA2) in two lepidopteran insects, Helicoverpa armigera and Helicoverpa punctigera. To further confirm the causal relationship between the ABCA2 gene (HaABCA2) and Cry2Ab resistance in H. armigera, two HaABCA2 knockout strains were created from the susceptible SCD strain with the CRISPR/Cas9 genome editing system. One strain (SCD-A2KO1) is homozygous for a 2-bp deletion in exon 2 of HaABCA2 created by non-homologous end joining (NHEJ). The other strain (SCD-A2KO2) is homozygous for a 5-bp deletion in exon 18 of HaABCA2 made by homology-directed repair (HDR), which was produced to mimic the r2 resistance allele of a field-derived Cry2Ab-resistant strain from Australia. Both knockout strains obtained high levels of resistance to both Cry2Aa (>120-fold) and Cry2Ab (>100-fold) compared with the original SCD strain, but no or very limited resistance to Cry1Ac (<4-fold). Resistance to Cry2Ab in both knockouts is recessive, and genetic complementary tests confirmed Cry2Ab resistance alleles are at the same locus (i.e. HaABCA2) for the two strains. Brush border membrane vesicles (BBMVs) of midguts from both knockout strains lost binding with Cry2Ab, but maintained the same binding with Cry1Ac as the SCD strain. In vivo functional evidence from this study demonstrates knockout of HaABCA2 confers high levels of resistance to both Cry2Aa and Cry2Ab, confirming that HaABCA2 plays a key role in mediating toxicity of both Cry2Aa and Cry2Ab against H. armigera.

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

BACKGROUND

Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests.

RESULTS

We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes.

CONCLUSIONS

The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

ModelFinder: fast model selection for accurate phylogenetic estimates

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.