Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation

Agricultural insect pests as models for studying stress-induced evolutionary processes

Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.

Historical museum samples reveal signals of selection and drift in response to changing insecticide use in an agricultural pest moth

In response to environmental and human-imposed selective pressures, agroecosystem pests frequently undergo rapid evolution, with some species having a remarkable capacity to rapidly develop pesticide resistance. Temporal sampling of genomic data can comprehensively capture such adaptive changes over time, for example, by elucidating allele frequency shifts in pesticide resistance loci in response to different pesticides. Here, we leveraged museum specimens spanning over a century of collections to generate temporal contrasts between pre- and post-insecticide populations of an agricultural pest moth, Helicoverpa armigera. We used targeted exon sequencing of 254 samples collected across Australia from the pre-1950s (prior to insecticide introduction) to the 1990s, encompassing decades of changing insecticide use. Our sequencing approach focused on genes that are known to be involved in insecticide resistance, environmental sensation, and stress tolerance. We found an overall lack of spatial and temporal population structure change across Australia. In some decades (e.g., 1960s and 1970s), we found a moderate reduction of genetic diversity, implying stochasticity in evolutionary trajectories due to genetic drift. Temporal genome scans showed extensive evidence of selection following insecticide use, although the majority of selected variants were low impact. Finally, alternating trajectories of allele frequency change were suggestive of potential antagonistic pleiotropy. Our results provide new insights into recent evolutionary responses in an agricultural pest and show how temporal contrasts using museum specimens can improve mechanistic understanding of rapid evolution.

Immigration allows population persistence and maintains genetic diversity despite an attempted experimental extinction

Widespread fragmentation and degradation of habitats make organisms increasingly vulnerable to declines in population size. Immigration is a key process potentially affecting the rescue and persistence of populations in the face of such pressures. Field research addressing severe demographic declines in the context of immigration among interconnected local populations is limited owing to difficulties in detecting such demographic events and the need for long-term monitoring of populations. In a 17-subpopulation metapopulation of the butterfly, Parnassius smintheus, all adults observed in two adjacent patches were removed over eight consecutive generations. Despite this severe and long-term reduction in survival and reproduction, the targeted populations did not go extinct. Here, we use genetic data to assess the role of immigration versus in situ reproduction in allowing the persistence of these populations. We genotyped 471 samples collected from the targeted populations throughout the removal experiment at 152 single nucleotide polymorphisms. We found no reduction in the genetic diversity of the targeted populations over time, but a decrease in the number of loci in Hardy-Weinberg equilibrium, consistent with a high level of immigration from multiple surrounding populations. Our results highlight the role of connectivity and movement in making metapopulations resilient to even severe and protracted localized population reductions.

Temporal collections to study invasion biology

Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution

The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to drift in a small population) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each century-scale time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.

Leveraging RNA Interference to Impact Insecticide Resistance in the Colorado Potato Beetle, Leptinotarsa decemlineata

The Colorado potato beetle, Leptinotarsa decemlineata Say, is a potato pest that can cause important economic losses to the potato industry worldwide. Diverse strategies have been deployed to target this insect such as biological control, crop rotation, and a variety of insecticides. Regarding the latter, this pest has demonstrated impressive abilities to develop resistance against the compounds used to regulate its spread. Substantial work has been conducted to better characterize the molecular signatures underlying this resistance, with the overarching objective of leveraging this information for the development of novel approaches, including RNAi-based techniques, to limit the damage associated with this insect. This review first describes the various strategies utilized to control L. decemlineata and highlights different examples of reported cases of resistances against insecticides for this insect. The molecular leads identified as potential players modulating insecticide resistance as well as the growing interest towards the use of RNAi aimed at these leads as part of novel means to control the impact of L. decemlineata are described subsequently. Finally, select advantages and limitations of RNAi are addressed to better assess the potential of this technology in the broader context of insecticide resistance for pest management.