Molecular genetics and genomics generate new insights into invertebrate pest invasions

Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand

Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under-studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome-wide single nucleotide polymorphisms (SNPs), generating genotyping-by-sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.

Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China

The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.

From chip to SNP: Rapid development and evaluation of a targeted capture genotyping-by-sequencing approach to support research and management of a plaguing rodent

The management of invasive species has been greatly enhanced by population genetic analyses of multilocus single-nucleotide polymorphism (SNP) datasets that provide critical information regarding pest population structure, invasion pathways, and reproductive biology. For many applications there is a need for protocols that offer rapid, robust and efficient genotyping on the order of hundreds to thousands of SNPs, that can be tailored to specific study populations and that are scalable for long-term monitoring schemes. Despite its status as a model laboratory species, there are few existing resources for studying wild populations of house mice (Mus musculus spp.) that strike this balance between data density and laboratory efficiency. Here we evaluate the utility of a custom targeted capture genotyping-by-sequencing approach to support research on plaguing house mouse populations in Australia. This approach utilizes 3,651 hybridization capture probes targeting genome-wide SNPs identified from a sample of mice collected in grain-producing regions of southeastern Australia genotyped using a commercially available microarray platform. To assess performance of the custom panel, we genotyped wild caught mice (N = 320) from two adjoining farms and demonstrate the ability to correctly assign individuals to source populations with high confidence (mean >95%), as well as robust kinship inference within sites. We discuss these results in the context of proposed applications for future genetic monitoring of house mice in Australia.

Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys

Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we used genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated single nucleotide polymorphisms (SNPs) located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has probably evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such traits, highlighting the need for future sustainable and targeted management strategies.

Temporal sampling and network analysis reveal rapid population turnover and dynamic migration pattern in overwintering regions of a cosmopolitan pest

Genetic makeup of insect pest is informative for source-sink dynamics, spreading of insecticide resistant genes, and effective management. However, collecting samples from field populations without considering temporal resolution and calculating parameters related to historical gene flow may not capture contemporary genetic pattern and metapopulation dynamics of highly dispersive pests. Plutella xylostella (L.), the most widely distributed Lepidopteran pest that developed resistance to almost all current insecticides, migrates heterogeneously across space and time. To investigate its real-time genetic pattern and dynamics, we executed four samplings over two consecutive years across Southern China and Southeast Asia, and constructed population network based on contemporary gene flow. Across 48 populations, genetic structure analysis identified two differentiated insect swarms, of which the one with higher genetic variation was replaced by the other over time. We further inferred gene flow by estimation of kinship relationship and constructed migration network in each sampling time. Interestingly, we found mean migration distance at around 1,000 km. Such distance might have contributed to the formation of step-stone migration and migration circuit over large geographical scale. Probing network clustering across sampling times, we found a dynamic P. xylostella metapopulation with more active migration in spring than in winter, and identified a consistent pattern that some regions are sources (e.g., Yunnan in China, Myanmar and Vietnam) while several others are sinks (e.g., Guangdong and Fujian in China) over 2 years. Rapid turnover of insect swarms and highly dynamic metapopulation highlight the importance of temporal sampling and network analysis in investigation of source-sink relationships and thus effective pest management of P. xylostella, and other highly dispersive insect pests.

Past and recent farming degrades aquatic insect genetic diversity

Recent declines in once-common species are triggering concern that an environmental crisis point has been reached. Yet, the lack of long abundance time series data for most species can make it difficult to attribute these changes to anthropogenic causes, and to separate them from normal cycles. Genetic diversity, on the other hand, is sensitive to past and recent environmental changes, and reflects a measure of a populations' potential to adapt to future stressors. Here, we consider whether patterns of genetic diversity among aquatic insects can be linked to historical and recent patterns of land use change. We collated mitochondrial cytochrome c oxidase subunit I (COI) variation for >700 aquatic insect species across the United States, where patterns of agricultural expansion and intensification have been documented since the 1800s. We found that genetic diversity was lowest in regions where cropland was historically (pre-1950) most extensive, suggesting a legacy of past environmental harm. Genetic diversity further declined where cropland has since expanded, even after accounting for climate and sampling effects. Notably though, genetic diversity also appeared to rebound where cropland has diminished. Our study suggests that genetic diversity at the community level can be a powerful tool to infer potential population declines and rebounds over longer time spans than is typically possible with ecological data. For the aquatic insects that we considered, patterns of land use many decades ago appear to have left long-lasting damage to genetic diversity that could threaten evolutionary responses to rapid global change.

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

Background

An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle’s mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation.

Results

High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles.

Conclusions

The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08628-z.

Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China

Increasing damage of pests in agriculture and forestry can arise both as a consequence of changes in local species and through the introduction of alien species. In this study, we used population genetics approaches to examine population processes of two pests of the tree‐of‐heaven trunk weevil (TTW), Eucryptorrhynchus brandti (Harold) and the tree‐of‐heaven root weevil (TRW), E. scrobiculatus (Motschulsky) on the tree‐of‐heaven across their native range of China. We analyzed the population genetics of the two weevils based on ten highly polymorphic microsatellite markers. Population genetic diversity analysis showed strong population differentiation among populations of each species, with F_ST ranges from 0.0197 to 0.6650 and from −0.0724 to 0.6845, respectively. Populations from the same geographic areas can be divided into different genetic clusters, and the same genetic cluster contained populations from different geographic populations, pointing to dispersal of the weevils possibly being human‐mediated. Redundancy analysis showed that the independent effects of environment and geography could account for 93.94% and 29.70% of the explained genetic variance in TTW, and 41.90% and 55.73% of the explained genetic variance in TRW, respectively, indicating possible impacts of local climates on population genetic differentiation. Our study helps to uncover population genetic processes of these local pest species with relevance to control methods.

Selection of genome-wide SNPs for pooled allelotyping assays useful for population monitoring

Parasitic worms are serious pests of humans, livestock and crops worldwide. Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution. The evolution of chemical resistance, ecological changes, and pest dispersal have allowed an increasing number of pests to become difficult to control with current management methods. Their lifestyle limits the use of ecological and individual-based management of populations. There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies. This study presents a multi-locus, equal-representation, whole genome pooled SNPs selection approach as a monitoring tool for the ovine nematode parasite Haemonchus contortus. The SNP selection method used two reference genomes of different quality, then validated these SNPs against a high-quality recent genome assembly. From over 11 million high-quality SNPs identified, 334 SNPs were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools. As a proof-of-concept, 21 Australian H. contortus populations with various phenotypes and genotypes were screened. This analysis confirmed the overall low-level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance. The analysis showed that 66% of the SNPs were necessary for stability in assessing population genetic patterns, and SNP pairs did not show linkage according to allelic frequencies across the 21 populations. This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection. The SNP selection method could also be applied to other parasite species.

Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.

Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution

The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.

Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.

The evolutionary dynamics of biological invasions: A multi-approach perspective

Biological invasions, the establishment and spread of non-native species in new regions, can have extensive economic and environmental consequences. Increased global connectivity accelerates introduction rates, while climate and land-cover changes may decrease the barriers to invasive populations spread. A detailed knowledge of the invasion history, including assessing source populations, routes of spread, number of independent introductions, and the effects of genetic bottlenecks and admixture on the establishment success, adaptive potential, and further spread, is crucial from an applied perspective to mitigate socioeconomic impacts of invasive species, as well as for addressing fundamental questions on the evolutionary dynamics of the invasion process. Recent advances in genomics together with the development of geographic information systems provide unprecedented large genetic and environmental datasets at global and local scales to link population genomics, landscape ecology, and species distribution modeling into a common framework to study the invasion process. Although the factors underlying population invasiveness have been extensively reviewed, analytical methods currently available to optimally combine molecular and environmental data for inferring invasive population demographic parameters and predicting further spreading are still under development. In this review, we focus on the few recent insect invasion studies that combine different datasets and approaches to show how integrating genetic, observational, ecological, and environmental data pave the way to a more integrative biological invasion science. We provide guidelines to study the evolutionary dynamics of invasions at each step of the invasion process, and conclude on the benefits of including all types of information and up-to-date analytical tools from different research areas into a single framework.

Genetic structure and population demographics of Hypnoidus bicolor (Coleoptera: Elateridae) in the Canadian Prairies

BACKGROUND

Following banning of the pesticide lindane in most counties, wireworms (i.e., the soil-living larval stages of click beetles) have become major pests of a variety of economically important field crops. Hypnoidus bicolor is a common pest species in the Canadian Prairies. However, little is known about its life history, which impedes the development of effective integrated pest management (IPM) strategies. Population genetic approaches have the potential to assist in the development of IPM.

RESULTS

We sequenced a 622-bp fragment of the COX1 gene from 326 H. bicolor wireworm and click beetles collected from 13 localities on the Canadian Prairies. Two genetically distinct (>4.66% sequence divergence) clades were identified, suggesting that they may be part of a species complex. Clade A predominated and increased in prevalence the further east samples were collected, whereas the opposite was true for clade B. Clade B appears to be comprised of two mitochondrial DNA groups, however, one group was represented by only one haplotype. Both clades were characterized by uneven gene flow among populations with low levels of regional genetic structuring. Clade A appeared to have undergone population and range expansions, which may coincide with the advent of intensive agriculture practices in the prairies.

CONCLUSION

Knowledge of species composition and population structure is important for the development of effective IPM strategies but is often lacking for wireworms. Our study fills these knowledge gaps for a predominant pest species in the prairies, H. bicolor, by providing robust evidence for cryptic forms and characterizing its dispersal patterns and population dynamics. © 2021 Society of Chemical Industry.

Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

Local adaptation is particularly likely in invertebrate pests that typically have short generation times and large population sizes, but there are few studies on pest species investigating local adaptation and separating this process from contemporaneous and historical gene flow. Here, we use a population genomic approach to investigate evolutionary processes in the two most dominant spider mites in China, Tetranychus truncatus Ehara and Tetranychus pueraricola Ehara et Gotoh, which have wide distributions, short generation times, and large population sizes. We generated genome resequencing of 246 spider mites mostly from China, as well as Japan and Canada at a combined total depth of 3,133×. Based on demographic reconstruction, we found that both mite species likely originated from refugia in southwestern China and then spread to other regions, with the dominant T. truncatus spreading ~3,000 years later than T. pueraricola. Estimated changes in population sizes of the pests matched known periods of glaciation and reinforce the recent expansion of the dominant spider mites. T. truncatus showed a greater extent of local adaptation with more genes (76 vs. 17) associated with precipitation, including candidates involved in regulation of homeostasis of water and ions, signal transduction, and motor skills. In both species, many genes (135 in T. truncatus and 95 in T. pueraricola) also showed signatures of selection related to elevation, including G-protein-coupled receptors, cytochrome P450s, and ABC-transporters. Our results point to historical expansion processes and climatic adaptation in these pests which could have contributed to their growing importance, particularly in the case of T. truncatus.

Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths

The peach fruit moth (PFM), Carposina sasakii Matsumura, is a major phytophagous orchard pest widely distributed across Northeast Asia. Here, we report the chromosome-level genome for the PFM, representing the first genome for the family Carposinidae, from the lepidopteran superfamily Copromorphoidea. The genome was assembled into 404.83 Mb sequences using PacBio long-read and Illumina short-read sequences, including 275 contigs, with a contig N50 length of 2.62 Mb. All contigs were assembled into 31 linkage groups assisted by the Hi-C technique, including 30 autosomes and a Z chromosome. BUSCO analysis showed that 98.3% of genes were complete and 0.4% of genes were fragmented, while 1.3% of genes were missing in the assembled genome. In total, 21,697 protein-coding genes were predicted, of which 84.80% were functionally annotated. Because of the importance of diapause triggered by photoperiod in PFM, five circadian genes in the PFM as well as in the other related species were annotated, and potential genes related to diapause and photoperiodic reaction were also identified from transcriptome sequencing. In addition, manual annotation of detoxification gene families was undertaken and showed a higher number of glutathione S-transferase (GST) gene in PFM than in most other lepidopterans, in contrast to a lower number of uridine diphosphate (UDP)-glycosyltransferase (UGT) gene, carboxyl/cholinesterases (CCE) gene and cytochrome P450 monooxygenase (P450) gene, suggesting different detoxication pathways in this moth. The high-quality genome provides a resource for comparative evolutionary studies of this moth and its relatives within the context of radiations across Lepidoptera.

What Is the Spatial Extent of a Bemisia tabaci Population?

Effective pest management depends on basic knowledge about insect dispersal patterns and gene flow in agroecosystems. The globally invasive sweet potato whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is considered a weak flier whose life history nonetheless predisposes it to frequent dispersal, but the scale over which populations exchange migrants, and should therefore be managed, is uncertain. In this review, we synthesize the emergent literature on B. tabaci population genetics to address the question: What spatial scales define B. tabaci populations? We find that within-species genetic differentiation among sites is often low, and evidence of population structuring by host plant or geography is rare. Heterozygote deficits prevail among populations, indicating that migrants from divergent populations are frequently sampled together. Overall, these results suggest that there is high ongoing gene flow over large spatial extents. However, genetic homogeneity typical of recently invading populations could obscure power to detect real isolation among populations. Genome-wide data collected systematically across space and time could distinguish signatures of invasion history from those of ongoing gene flow. Characterizing the spatial extent of B. tabaci populations could reveal whether insecticide rotations can be tailored to specific commodities or if coordination across linked commodities and regions is justified.

Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis

Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.

Insect genomes: progress and challenges

In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.

Molecular characterization of black flies (Diptera: Simuliidae) in areas with pest outbreaks and simuliotoxicosis in Northeast Anatolia Region, Turkey

Accurate species identification provides the foundation for successful pest management and vector control of black flies. Accordingly, we examined the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of four morphologically and chromosomally identified species of black flies (Simulium vernumgroup sp., S. bergi Rubtsov, S. bezzii (Corti), and S. kiritshenkoi Rubtsov) in Northeast Anatolia Region of Turkey where simuliid pest problems and simuliotoxicosis cases have been reported among cattle. COI gene sequences of these species and closely related species available in GenBank were used to provide species-level diagnoses and infer relationships. Both subgenera (Nevermannia and Simulium) were monophyletic, and subclades generally corresponded with species groups. Intraspecific genetic divergence was 0.2-1.6%, whereas the mean interspecific genetic divergence among the four species was 11.2-14.5%. The COI analysis produced results congruent with morphological concepts of the nominal species S. bergi and S. bezzii. Probable misidentifications in GenBank were revealed, especially for species in the S. ornatum and S. vernum groups, complicating identification capability. Sequence variation in the COI barcode region also might not be adequate for species delineation and identification among some species in these two species groups.

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.

Intra-species variation and geographic differentiation among the populations of the quarantine agricultural pest leucinoides orbonalis (lepidoptera: Crambidae) in the global assemblage - a prospective of DNA barcoding

Leucinodes orbonalis Guenée is serious quarantine pest occurring globally, studies are needed to enlighten the genetic complexities associated with the species. India is considered to be the origin of the L. orbonalis, therefore availability of species records from this region enable to analyse the genetic differences and dispersal of the lineages. The results of the study reported 47 haplotypes in four clusters pertaining to their ancestral lineage. The transition/transversion bias (R) was observed to be higher with 1.238 and 1.312 in the first and third codon positions respectively. The overall intraspecies divergence was found to be 0.302. AMOVA revealed that the total variations were then as reported 67.15 among the south-east countries but our studies reported the total variation to be 77.25% (Germany, India, South east and Australia). F_ST and Mantel's test indicated that there was no correlation between the genetic variation and geographical distance. The overall haplotype diversity was 0.852, where the nucleotide diversity of H31 (0.00593) was highest and H1 (0.00087) was lowest. The genetic diversity indices Tajima D and Fu's Fs static for H1, H13 and H31 had negative values which possibly inferred for the bottle neck effect. The ML tree was constituted the branch length of 5.0157 with one out-group. The tree was formed with ten distinctive clades with the haplotypes congregated together based on similar genetic composition.

Biology, Ecology, and Control of Lasioderma serricorne (F.) (Coleoptera: Anobiidae): A Review

The cigarette beetle, Lasioderma serricorne(F.) (Coleoptera: Anobiidae), is an important pest in the food and tobacco industry in many regions of the world. Despite a great deal of research, control of this pest still relies on the use of phosphine fumigation, which is becoming less effective as the insect develops resistance to this compound. In addition, series of other nonchemical methods used to control the insect have given mixed and irregular results. This review summarizes and discusses information on important aspects of the biology and ecology of the cigarette beetle, and its control. The topics covered include a taxonomic discussion of the cigarette beetle, which includes a discussion of other anobiid species of economic importance. The mating behavior of the insect and conditions favorable for pest development were described. The review also includes a discussion of the life stages of the insect, its feeding habit, and economic damage. Important aspects of its chemical ecology and a discussion on the association between this species and its microorganisms, and major natural enemies, were presented. A summary of its flight behavior, including the factors governing flight initiation and temporal and seasonal flight activity were reviewed. Finally, the control methods currently used in the management of the insect were described. The review also identifies potential areas of further research on L. serricorne and gives an analysis of the control methods worthy of further investigation in the search for practical and sustainable methods for the management of this pest.

Patterns of genetic differentiation in Colorado potato beetle correlate with contemporary, not historic, potato land cover

Changing landscape heterogeneity can influence connectivity and alter genetic variation in local populations, but there can be a lag between ecological change and evolutionary responses. Temporal lag effects might be acute in agroecosystems, where land cover has changed substantially in the last two centuries. Here, we evaluate how patterns of an insect pest's genetic differentiation are related to past and present agricultural land cover change over a 150-year period. We quantified change in the amount of potato, Solanum tuberosum L., land cover since 1850 using county-level agricultural census reports, obtained allele frequency data from 7,408 single-nucleotide polymorphism loci, and compared effects of historic and contemporary landscape connectivity on genetic differentiation of Colorado potato beetle, Leptinotarsa decemlineata Say, in two agricultural landscapes in the United States. We found that potato land cover peaked in Wisconsin in the early 1900s, followed by rapid decline and spatial concentration, whereas it increased in amount and extent in the Columbia Basin of Oregon and Washington beginning in the 1960s. In both landscapes, we found small effect sizes of landscape resistance on genetic differentiation, but a 20× to 1,000× larger effect of contemporary relative to historic landscape resistances. Demographic analyses suggest population size trajectories were largely consistent among regions and therefore are not likely to have differentially impacted the observed patterns of population structure in each region. Weak landscape genetic associations might instead be related to the coarse resolution of our historical land cover data. Despite rapid changes in agricultural landscapes over the last two centuries, genetic differentiation among L. decemlineata populations appears to reflect ongoing landscape change. The historical landscape genetic framework employed in this study is broadly applicable to other agricultural pests and might reveal general responses of pests to agricultural land-use change.

Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure

Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme-associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an F ST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.

Biological and genetic features of introduced aphid populations in agroecosystems

In agroecosystems, introduced aphids that reproduce by obligate parthenogenesis (OP) show strong biased representation of a few genotypes (superclones), whereas species with cyclical parthenogenesis (CP) exhibit the opposite trend with many unique genotypes. We analyzed the biological and genetic features of 23 different aphid species introduced in different geographic areas and climates, finding putative superclones in about 60% of them. We have examined the proximal causes for aphid establishment and spread after their introduction, and found that OP, host availability, and phenotypic plasticity are among the main variables underpinning the ability of aphids to succeed in new geographic areas, which may explain the high potential for invasion in this group of pest insects.

Rapid evolution in insect pests: the importance of space and time in population genomics studies

Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems.

Rapid adaptation of invertebrate pests to climatic stress?

There is surprisingly little information on adaptive responses of pests and disease vectors to climatic stresses even though the short generation times and large population sizes associated with pests make rapid adaptation likely. Most evidence of adaptive differentiation has been obtained from geographic comparisons and these can directly or indirectly indicate rates of adaptation where historical data on invasions are available. There is very little information on adaptive shifts in pests detected through molecular comparisons even though the genomes of many pests are now available and can help to identify markers underlying adaptation. While the limited evidence available points to frequent rapid adaptation that can affect pest and disease vector control, constraints to adaptation are also evident and a predictive framework around the likelihood and limits of rapid adaptation is required.

Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

Background

Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades.

Results

First, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population.

Conclusions

Taken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.

Diversity of tortricid moths in apple orchards: evidence for a cryptic species of Grapholita (Lepidoptera: Tortricidae) from China

Understanding herbivore diversity both at the species and genetic levels is a key to effective pest management. We examined moth samples from multiple locations from a major apple growing region in China. For specimen collection, we used a pheromone trap designed to attract Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Surprisingly, we found a second species captured at high proportions. Its external morphology (e.g., male genitalia and forewing coloration) was the same as for Grapholita funebrana Treitschke (Lepidoptera: Tortricidae) specimens from Europe. However, the barcode sequence of the mitochondrial gene cytochrome oxidase I (COI) diverged markedly between specimens from China and Europe, and the genetic distance value between the specimens from the two regions as estimated using the Juke-Cantor (JC) model amounted to 0.067. These morphological and molecular findings together point to a cryptic species in G. funebrana from China. Further molecular analyses based on COI and COII genes revealed its extremely high genetic diversity, indicating that the origin of this species includes the sampling region. Moreover, molecular data suggest that this species passed through a recent population expansion. This is the first report on a cryptic species in G. funebrana, as well as the first report on its genetic diversity.

Phylogeography of the Wheat Stem Sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): Implications for Pest Management

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America, and damage resulting from this species has recently expanded southward. Current pest management practices are inadequate and uncertainty regarding geographic origin, as well as limited data on population structure and dynamics across North America impede progress towards more informed management. We examined the genetic divergence between samples collected in North America and northeastern Asia, the assumed native range of C. cinctus using two mitochondrial regions (COI and 16S). Subsequently, we characterized the structure of genetic diversity in the main wheat producing areas in North America using a combination of mtDNA marker and microsatellites in samples collected both in wheat fields and in grasses in wildlands. The strong genetic divergence observed between North American samples and Asian congeners, in particular the synonimized C. hyalinatus, did not support the hypothesis of a recent American colonization by C. cinctus. Furthermore, the relatively high genetic diversity both with mtDNA and microsatellite markers offered additional evidence in favor of the native American origin of this pest. The genetic diversity of North American populations is structured into three genetic clusters and these are highly correlated with geography. Regarding the recent southern outbreaks in North America, the results tend to exclude the hypothesis of recent movement of damaging wheat stem sawfly populations from the northern area. The shift in host plant use by local populations appears to be the most likely scenario. Finally, the significance of these findings is discussed in the context of pest management.

Analysis of Seasonal Risk for Importation of the Mediterranean Fruit Fly, Ceratitis capitata (Diptera: Tephritidae), via Air Passenger Traffic Arriving in Florida and California

The Mediterranean fruit fly, Ceratitis capitata (Wiedemann), is one of the most economically damaging pests in the world and has repeatedly invaded two major agricultural states in the United States, Florida and California, each time requiring costly eradication. The Mediterranean fruit fly gains entry primarily in infested fruit carried by airline passengers and, since Florida and California each receive about 13 million international passengers annually, the risk of Mediterranean fruit fly entering the United States is potentially very high. The risk of passengers bringing the pest into Florida or California from Mediterranean fruit fly-infested countries was determined with two novel models, one estimated seasonal variation in airline passenger number and the other defined the seasonal and spatial variability in Mediterranean fruit fly abundance. These models elucidated relationships among the risk factors for Mediterranean fruit fly introduction, such as amount of passenger traffic, routes traveled, season of travel, abundance of Mediterranean fruit fly in countries where flights departed, and risk of the pest arriving at destination airports. The risk of Mediterranean fruit fly being introduced into Florida was greatest from Colombia, Brazil, Panama, Venezuela, Argentina, and Ecuador during January-August, whereas primarily the risk to California was from Brazil, Panama, Colombia, and Italy in May-August. About three times more Mediterranean fruit flies were intercepted in passenger baggage at airports in Florida than California, although the data were compromised by a lack of systematic sampling and other limitations. Nevertheless, this study achieved the goal of analyzing available data on seasonal passenger flow and Mediterranean fruit fly population levels to determine when surveillance should be intensified at key airports in Florida and California.

Population structure and gene flow in the global pest, Helicoverpa armigera

Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages. Here, we integrate several end points derived from high-throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping-by-sequencing and whole-genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from diverse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field-caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.

Molecular evidence for multiple phylogenetic groups within two species of invasive spiny whiteflies and their parasitoid wasp

The invasive orange spiny whitefly (OSW) Aleurocanthus spiniferus has extended its distribution to non-native areas since the early 20th century. In a similar manner, the invasive tea spiny whitefly (TSW) A. camelliae has been expanding over East Asia in recent decades. In this study, the genetic diversity of OSW and TSW and of their important parasitoid wasp Encarsia smithi was investigated in China and Japan to enable more efficient biological control policies. We detected two phylogenetic groups (haplogroups A1 and A2) in OSW and three phylogenetic groups (haplotypes B1 and B2, and haplogroup B3) in TSW in China; however, only a single haplotype was detected in each whitefly species in Japan. Based on historical records and molecular data, OSW was considered to be native to China whereas TSW has probably expanded to China from a more southern location in the last 50 years; China appears to be the source region for OSW and TSW invading Japan. In E. smithi, two phylogenetic groups were detected in Japan: haplotype I, associated with OSW, and haplogroup II mostly associated with TSW, except in two locations. These data support the hypothesis that E. smithi parasitizing TSW in Japan did not originate from the existent population parasitizing OSW but was newly imported into Japan following the invasion of its host.

Species identification, host range and diversity of Cecidophyopsis mites (Acari: Trombidiformes) infesting Ribes in Latvia

Cecidophyopsis mites are important pests in all cultivation regions of Ribes causing bud galls and sterility. Despite their economic importance, the knowledge on Cecidophyopsis species infesting Ribes in various areas of the world is still deficient. The present study was carried out to identify Cecidophyopsis species occurring in Latvia on cultivated and wild Ribes, to assess their host range and gain insight into the genetic diversity of these insufficiently studied pests by use of multiplex PCR, rDNA sequences and morphological characters. Cecidophyopsis alpina, C. aurea, C. spicata and C. selachodon were detected to occur in all surveyed habitats. For the first time, C. alpina was identified on blackcurrants and redcurrants, and C. aurea on redcurrants, blackcurrants and alpine currants. The presence of C. ribis was not confirmed with molecular tools during this study. Phylogenetic analyses confirmed the presence of four Cecidophyopsis species identified by multiplex PCR. A close phylogenetic relatedness was found for C. aurea and C. alpina, and for C. ribis and C. spicata highlighting the necessity for additional studies. Our findings suggest a need to consider also other Cecidophyopsis species besides C. ribis in breeding programs for host resistance to mites.

Cryptic Biodiversity and the Origins of Pest Status Revealed in the Macrogenome of Simulium colombaschense (Diptera: Simuliidae), History's Most Destructive Black Fly

The European black fly Simulium (Simulium) colombaschense (Scopoli), once responsible for as many as 22,000 livestock deaths per year, is chromosomally mapped, permitting its evolutionary relationships and pest drivers to be inferred. The species is 12 fixed inversions removed from the standard sequence of the subgenus Simulium. Three of these fixed inversions, 38 autosomal polymorphisms, and a complex set of 12 X and 6 Y chromosomes in 29 zygotic combinations uniquely characterize S. colombaschense and reveal 5 cytoforms: 'A' in the Danube watershed, 'B' in Italy's Adige River, 'C' in the Aliakmonas River of Greece, 'D' in the Aoös drainage in Greece, and 'E' in the Belá River of Slovakia. 'C' and 'D' are reproductively isolated from one another, and 'B' is considered a cytotype of 'A,' the probable name bearer of colombaschense. The species status of 'E' cannot be determined without additional collections. Three derived polytene sequences, based on outgroup comparisons, place S. colombaschense in a clade of species composed of the S. jenningsi, S. malyschevi, and S. reptans species groups. Only cytoforms 'A' and 'B' are pests. Within the Simuliidae, pest status is reached through one of two principal pathways, both of which promote the production of large populations of blood-seeking flies: (1) colonization of the world's largest rivers (habitat specialization) or (2) colonization of multiple habitat types (habitat generalization). Evolutionary acquisition of the ability to colonize large rivers by an ancestor of the S. jenningsi-malyschevi-reptans clade set the scene for the pest status of S. colombaschense and other big-river members of the clade. In an ironic twist, the macrogenome of S. colombaschense reveals that the name associated with history's worst simuliid pest represents a complex of species, two or more of which are nonpests potentially vulnerable to loss of their limited habitat.

Population genetic differentiation of the black locust gall midge Obolodiplosis robiniae (Haldeman) (Diptera: Cecidomyiidae): a North American pest invading Asia

Obolodiplosis robiniae is native to North America and is an important introduced insect pest that forms leaf margin roll galls on species of genus Robinia (Fabaceae) in China. It was first detected in China in 2004, but subsequently spread and provoked local outbreaks. An analysis of a 676-bp sequence of the mitochondrial DNA cytochrome oxidase subunit I was conducted in 560 individuals from 28 populations, in order to (1) assess population genetic structuring and (2) explore possible explanations for the rapid spread and invasion success of O. robiniae. Yet, only four haplotypes were identified and the nucleotide diversity was low (π = 0.00005) and among the 560 specimens studied, only ten showed haplotypic variation involving no more than three substitutions. The result showed a low degree of genetic diversity among populations of the successful invasive gall midge, which suggested that the pest experienced a severe genetic bottleneck and a loss of genetic diversity after its introduction. The successful establishment and spread of O. robiniae in China is attributed to the wide distribution of its host plant, thus allowing ample opportunities for gene flow in the pest species, and to the advantageous life history characteristics of O. robiniae.

Population genetic structure of the predatory, social wasp Vespula pensylvanica in its native and invasive range

Invasive species cause extensive damage to their introduced ranges. Ocean archipelagos are particularly vulnerable to invasive taxa. In this study, we used polymorphic microsatellite markers to investigate the genetic structure of the social wasp Vespula pensylvanica in its native range of North America and its introduced range in the archipelago of Hawaii. Our goal was to gain a better understanding of the invasion dynamics of social species and the processes affecting biological invasions. We found that V. pensylvanica showed no significant genetic isolation by distance and little genetic structure over a span of 2000 km in its native range. This result suggests that V. pensylvanica can successfully disperse across large distances either through natural- or human-mediated mechanisms. In contrast to the genetic patterns observed in the native range, we found substantial genetic structure in the invasive V. pensylvanica range in Hawaii. The strong patterns of genetic differentiation within and between the Hawaiian Islands may reflect the effects of geographic barriers and invasion history on gene flow. We also found some evidence for gene flow between the different islands of Hawaii which was likely mediated through human activity. Overall, this study provides insight on how geographic barriers, invasion history, and human activity can shape population genetic structure of invasive species.

Development of polymorphic microsatellite markers of Obolodiplosis robiniae (Haldeman) (Diptera: Cecidomyiidae), a North American pest invading Asia

Microsatellite markers were developed for epidemiological studies on the black locust gall midge Obolodiplosis robiniae (Haldeman) (Diptera: Cecidomyiidae), a native North America pest introduced to Europe and Asia. Polymorphism at each locus was tested on 68 individuals from six populations reared from infected host leaves of Robinia pseudoacacia L. collected in China. Fourteen loci were found to be polymorphic, with the number of alleles ranging from 3 to 10. The observed heterozygosity varied evenly from 0.2667 to 0.6540. For populations, the observed heterozygosity ranged from 0.1429 to 1.000. The allele frequency of the predominant allele varied from 0.250 to 0.500. All loci with negative FST values indicated heterozygote excess in each locus with six populations. Of 14 loci, four were observed to have FST values up to 0.05, which indicated negligible genetic differentiation within the population. Significant deviations (P < 0.05) from the expected Hardy-Weinberg equilibrium, as evaluated using the Markov chain algorithm for each locus and for all six populations, were observed, and genotypic linkage disequilibrium was clearly detected. These markers represent a useful tool to design strategies for integrated pest management and in the study of population evolution in this important introduced pest.

Hybridization and the spread of the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), in the northwestern United States

Hybridization may be an important process interjecting variation into insect populations enabling host plant shifts and the origin of new economic pests. Here, we examine whether hybridization between the native snowberry-infesting fruit fly Rhagoletis zephyria (Snow) and the introduced quarantine pest R. pomonella (Walsh) is occurring and may aid the spread of the latter into more arid commercial apple-growing regions of central Washington state, USA. Results for 19 microsatellites implied hybridization occurring at a rate of 1.44% per generation between the species. However, there was no evidence for increased hybridization in central Washington. Allele frequencies for seven microsatellites in R. pomonella were more 'R. zephyria-like' in central Washington, suggesting that genes conferring resistance to desiccation may be adaptively introgressing from R. zephyria. However, in only one case was the putatively introgressing allele from R. zephyria not found in R. pomonella in the eastern USA. Thus, many of the alleles changing in frequency may have been prestanding in the introduced R. pomonella population. The dynamics of hybridization are therefore complex and nuanced for R. pomonella, with various causes and factors, including introgression for a portion, but not all of the genome, potentially contributing to the pest insect's spread.

Exceptionally High Levels of Genetic Diversity in Wheat Curl Mite (Acari: Eriophyidae) Populations from Turkey

Recent research on the wheat curl mite species complex has revealed extensive genetic diversity that has distinguished several genetic lineages infesting bread wheat (Triticum aestivum L.) and other cereals worldwide. Turkey is the historical region of wheat and barley (Hordeum vulgare L.) domestication and diversification. The close relationship between these grasses and the wheat curl mite provoked the question of the genetic diversity of the wheat curl mite in this region. The scope of the study was to investigate genetic differentiation within the wheat curl mite species complex on grasses in Turkey. Twenty-one wheat curl mite populations from 16 grass species from nine genera (Agropyron sp., Aegilops sp., Bromus sp., Elymus sp., Eremopyrum sp., Hordeum sp., Poa sp., Secale sp., and Triticum sp.) were sampled in eastern and southeastern Turkey for genetic analyses. Two molecular markers were amplified: the cytochrome oxidase subunit I coding region of mtDNA (COI) and the D2 region of 28S rDNA. Phylogenetic analyses revealed high genetic variation of the wheat curl mite in Turkey, primarily on Bromus and Hordeum spp., and exceptionally high diversity of populations associated with bread wheat. Three wheat-infesting wheat curl mite lineages known to occur on other continents of the world, including North and South America, Australia and Europe, were found in Turkey, and at least two new genetic lineages were discovered. These regions of Turkey exhibit rich wheat curl mite diversity on native grass species. The possible implications for further studies on the wheat curl mite are discussed.

Detecting adaptive evolution based on association with ecological gradients: orientation matters!

Population genetic signatures of local adaptation are frequently investigated by identifying loci with allele frequencies that exhibit high correlation with ecological variables. One difficulty with this approach is that ecological associations might be confounded by geographic variation at selectively neutral loci. Here, we consider populations that underwent spatial expansion from their original range, and for which geographical variation of adaptive allele frequency coincides with habitat gradients. Using range expansion simulations, we asked whether our ability to detect genomic regions involved in adaptation could be impacted by the orientation of the ecological gradients. For three ecological association methods tested, we found, counter-intuitively, fewer false-positive associations when ecological gradients aligned along the main axis of expansion than when they aligned along any other direction. This result has important consequences for the analysis of genomic data under non-equilibrium population genetic models. Alignment of gradients with expansion axes is likely to be common in scenarios in which expanding species track their ecological niche during climate change while adapting to changing environments at their rear edge.