Temporal variation in spatial genetic structure during population outbreaks: Distinguishing among different potential drivers of spatial synchrony

Recruitment and migration patterns reveal a key role for seed banks in the meta-population dynamics of an aquatic plant

Progressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant's population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity.

Spatiotemporal dynamics of forest geometrid outbreaks

We highlight recent developments and avenues for advancement, which can improve insight into the causes of changes in the spatiotemporal dynamics of forest Geometridea moth species (hereafter 'geometrids'). Some forest geometrids possess fundamental biological traits, which make them particularly liable to outbreak range expansions and host shifts mitigated by climate change. Indeed, recently observed changes in geometrid spatiotemporal dynamics represent both new research opportunities and challenges for empirically testing drivers of intra- and interspecific spatial synchrony, including the role of trophic interactions and biological traits (e.g. dispersal ability). We advocate that the emerging field of near-term ecological forecasting holds promise for studies of the spatiotemporal dynamics of forest geometrids and could be tailored to give both accurate predictions at management-relevant timescales and new insights into the mechanisms that underlie spatiotemporal population dynamics.

Of clockwork and catastrophes: advances in spatiotemporal dynamics of forest Lepidoptera

We applied a systematic global literature survey from the last 2.5 years on spatiotemporal population dynamics - broadly defined - of Lepidopteran forest pests. Articles were summarized according to domain-specific (planetary ecology - remote sensing, evolutionary ecology - genetics and genomics, and theoretical ecology - modeling) contributions to contemporary investigation of the above theme. 'Model systems' dominating our literature survey were native Choristoneura fumiferana and invasive Lymantria dispar. These systems represent opposing ends of a more general equilibrium-disequilibrium gradient, with implications for less-studied taxa. The dynamics of Lepidopteran systems defy simple modeling approaches. Technologies and insights emerging from 'slower' science domains are informing more complex theory, including predictions of spread, impacts, or both posed by more recent invasions and the disrupting effects of climate change.

Advances in understanding the drivers of population spatial synchrony

The causes of spatial synchrony in population dynamics are often elusive. We review how recent advances have enhanced understanding of the causes of the spatial synchrony of insect populations and revealed previously underappreciated complexities in patterns of synchrony. We highlight how regional-scale studies of population genetic structure have helped elucidate the role of dispersal in population synchronization and how novel data-analytic approaches have revealed variation in spatial synchrony across timescales and geographies and the underlying drivers. We also stress the limited current understanding of the impacts of climate change on the spatial synchrony of insect populations and the potential ramifications of these effects for pest management as well as species conservation.

Host association, environment, and geography underlie genomic differentiation in a major forest pest

Diverse geographic, environmental, and ecological factors affect gene flow and adaptive genomic variation within species. With recent advances in landscape ecological modelling and high‐throughput DNA sequencing, it is now possible to effectively quantify and partition their relative contributions. Here, we use landscape genomics to identify determinants of genomic differentiation in the forest tent caterpillar, Malacosoma disstria, a widespread and irruptive pest of numerous deciduous tree species in North America. We collected larvae from multiple populations across Eastern Canada, where the species experiences a diversity of environmental gradients and feeds on a number of different host tree species, including trembling aspen (Populus tremuloides), sugar maple (Acer saccharum), red oak (Quercus rubra), and white birch (Betula papyrifera). Using a combination of reciprocal causal modelling (RCM) and distance‐based redundancy analyses (dbRDA), we show that differentiation of thousands of genome‐wide single nucleotide polymorphisms (SNPs) among individuals is best explained by a combination of isolation by distance, isolation by environment (spatial variation in summer temperatures and length of the growing season), and differences in host association. Configuration of suitable habitat inferred from ecological niche models was not significantly related to genomic differentiation, suggesting that M. disstria dispersal is agnostic with respect to habitat quality. Although population structure was not discretely related to host association, our modelling framework provides the first molecular evidence of host‐associated differentiation in M. disstria, congruent with previous documentation of reduced growth and survival of larvae moved between natal host species. We conclude that ecologically mediated selection is contributing to variation within M. disstria, and that divergent adaptation related to both environmental conditions and host association should be considered in ongoing research and management of this important forest pest.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.

A feasibility trial of genomics-based diagnosis detecting insecticide resistance of the diamondback moth

BACKGROUND

Insecticide resistance management has been key for crop protection for over 70 years and is increasingly important because the development of new active ingredients has decreased in recent years. By monitoring the development of resistance in a timely manner, we can effectively prolong insecticide efficacy. Genomic-based diagnosis can reliably predict resistance development if information on resistant mutations against major pesticides is available. Here, we developed a feasibility trial of genomics-based diagnosis of insecticide resistance in diamondback moth (Plutella xylostella) populations in Nagano Prefecture, Japan. Amplicon sequencing analyses using a next-generation sequencer (Illumina MiSeq) for major insecticides, including diamides, pyrethroids, Bacillus thuringiensis (Bt) toxin (Cry1Ac), organophosphates, and spinosyns, were conducted.

RESULTS

Mutations related to the resistance of pyrethroids, organophosphates, and diamides (flubendiamide and chlorantraniliprole) prevailed, while those of a diamide (cyantraniliprole), Bt (Cry1Ac), and spinosyns were scanty, suggesting that they are still effective. The results of the genomics-based diagnosis were generally concordant with the results of bioassays. Resistance development tendencies were generally uniform across Nagano.

CONCLUSION

An insecticide-resistance management campaign can be conducted in Nagano Prefecture with a quick genomic-based diagnosis in early spring while bioassay is the only option for monitoring resistances whose mutations are unavailable. Our study is the first step in the future management of insecticide resistance in all significant pests. © 2022 Society of Chemical Industry.

Moths passing in the night: Phenological and genomic divergences within a forest pest complex

Temporal separation of reproductive timing can contribute to species diversification both through allochronic speciation and later reinforcement of species boundaries. Such phenological differences are an enigmatic component of evolutionary divergence between two major forest defoliator species of the spruce budworm complex: Choristoneura fumiferana and C. occidentalis. While these species interbreed freely in laboratory settings, natural hybridization rates have not been reliably quantified due to their indistinguishable morphology. To assess whether temporal isolation is contributing to reproductive isolation, we collected adult individuals throughout their expected zone of sympatry in western Canada at 10-day intervals over two successive years, assigning taxonomic identities using thousands of single nucleotide polymorphisms. We found unexpectedly broad sympatry between C. fumiferana and C. occidentalis biennis and substantial overlap of regional flight periods. However, flight period divergence was much more apparent on a location-by-location basis, highlighting the importance of considering spatial scale in these analyses. Phenological comparisons were further complicated by the biennial life cycle of C. o. biennis, the main subspecies of C. occidentalis in the region, and the occasional occurrence of the annually breeding subspecies C. o. occidentalis. Nonetheless, we demonstrate that biennialism is not a likely contributor to reproductive isolation within the species complex. Overall, interspecific F1 hybrids comprised 2.9% of sequenced individuals, confirming the genomic distinctiveness of C. fumiferana and C. occidentalis, while also showing incomplete reproductive isolation of lineages. Finally, we used F ST-based outlier and genotype-environment association analyses to identify several genomic regions under putative divergent selection. These regions were disproportionately located on the Z linkage region of C. fumiferana, and contained genes, particularly antifreeze proteins, that are likely to be associated with overwintering success and diapause. In addition to temporal isolation, we conclude that other mechanisms, including ecologically mediated selection, are contributing to evolutionary divergence within the spruce budworm species complex.

Quantifying and predicting population connectivity of an outbreaking forest insect pest

CONTEXT

Dispersal has a key role in the population dynamics of outbreaking species such as the spruce budworm (Choristoneura fumiferana) as it can synchronize the demography of distant populations and favor the transition from endemic to epidemic states. However, we know very little about how landscape structure influences dispersal in such systems while such knowledge is essential for better forecasting of spatially synchronous population dynamics and to guide management strategies.

OBJECTIVES

We aimed to characterize the spatial environmental determinants of spruce budworm dispersal to determine how these features affect outbreak spread in Quebec (Canada). We then apply our findings to predict expected future landscape connectivity and explore its potential consequences on future outbreaks.

METHODS

We used a machine-learning landscape genetics approach on 447 larvae covering most of the outbreak area and genotyped at 3562 SNP loci to identify the main variables affecting connectivity.

RESULTS

We found that the connectivity between outbreak populations was driven by the combination of precipitation and host cover. Our forecasting suggests that between the current and next outbreaks, connectivity may increase between Ontario and Quebec, and might decrease in the eastern part, which could have the effect of limiting outbreak spread from Ontario and Quebec to the eastern provinces.

CONCLUSIONS

Although we did not identify any discrete barriers, low connectivity areas might constrain dispersal in the current and future outbreaks and should in turn, be intensively monitored. However, continued sampling as the outbreak progresses is needed to confirm the temporal stability of the observed patterns.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10980-021-01382-9.

Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA-based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.

Landscape-scale population connectivity in two parasitoid species associated with the spruce budworm: Testing the birdfeeder effect using genetic data

Periodic and spatially synchronous outbreaks of insect pests have dramatic consequences for boreal and sub-boreal forests. Within these multitrophic systems, parasitoids can be stabilizing agents by dispersing toward patches containing higher host density (the so-called birdfeeder effect). However, we know little about the dispersal abilities of parasitoids in continuous forested landscapes, limiting our understanding of the spatiotemporal dynamics of host-parasitoid systems, and constraining our ability to predict forest resilience in the context of global changes. In this study, we investigate the spatial genetic structure and spatial variation in genetic diversity of two important species of spruce budworm larval parasitoids during outbreaks: Apanteles fumiferanae Viereck (Braconidae) and Glypta fumiferanae (Viereck) (Ichneumonidae). Using parasitoids sampled in 2014 from 26 and 29 locations across a study area of 350,000 km² , we identified 1,012 and 992 neutral SNP loci for A. fumiferanae (N = 279 individuals) and G. fumiferanae (N = 382), respectively. Using DAPC, PCA, AMOVA, and IBD analyses, we found evidence for panmixia and high genetic connectivity for both species, matching the previously described genetic structure of the spruce budworm within the same context, suggesting similar effective dispersal during outbreaks and high parasitoid population densities between outbreaks. We also found a significant negative relationship between genetic diversity and latitude for A. fumiferanae but not for G. fumiferanae, suggesting that northern range limits may vary by species within the spruce budworm parasitoid community. These spatial dynamics should be considered when predicting future insect outbreak severities in boreal landscapes.

The Vision of Managing for Pest-Resistant Landscapes: Realistic or Utopic?

PURPOSE OF REVIEW

Forest managers have long suggested that forests can be made more resilient to insect pests by reducing the abundance of hosts, yet this has rarely been done. The goal of our paper is to review whether recent scientific evidence supports forest manipulation to decrease vulnerability. To achieve this goal, we first ask if outbreaks of forest insect pests have been more severe in recent decades. Next, we assess the relative importance of climate change and forest management-induced changes in forest composition/structure in driving these changes in severity.

RECENT FINDINGS

Forest structure and composition continue to be implicated in pest outbreak severity. Mechanisms, however, remain elusive. Recent research elucidates how forest compositional and structural diversity at neighbourhood, stand, and landscape scales can increase forest resistance to outbreaks. Many recent outbreaks of herbivorous forest insects have been unprecedented in terms of duration and spatial extent. Climate change may be a contributing factor, but forest structure and composition have been clearly identified as contributing to these unprecedented outbreaks.

SUMMARY

Current research supports using silviculture to create pest-resistant forest landscapes. However, the precise mechanisms by which silviculture can increase resistance remains uncertain. Further, humans tend to more often create pest-prone forests due to political, economic, and human resistance to change and a short-sighted risk management perspective that focuses on reactive rather than proactive responses to insect outbreak threats. Future research efforts need to focus on social, political, cultural, and educational mechanisms to motivate implementation of proven ecological solutions if pest-resistant forests are to be favoured by management.

Migration trajectories of the diamondback moth Plutella xylostella in China inferred from population genomic variation

BACKGROUND

The diamondback moth (DBM), Plutella xylostella (Lepidoptera: Plutellidae), is a notorious pest of cruciferous plants. In temperate areas, annual populations of DBM originate from adult migrants. However, the source populations and migration trajectories of immigrants remain unclear. Here, we investigated migration trajectories of DBM in China using genome-wide single nucleotide polymorphisms (SNPs) genotyped using double-digest RAD (ddRAD) sequencing. We first analyzed patterns of spatial and temporal genetic structure among southern source and northern recipient populations, then inferred migration trajectories into northern regions using discriminant analysis of principal components (DAPC), assignment tests, and spatial kinship patterns.

RESULTS

Temporal genetic differentiation among populations was low, indicating that sources of recipient populations and migration trajectories are stable. Spatial genetic structure indicated three genetic clusters in the southern source populations. Assignment tests linked northern populations to the Sichuan cluster, and central-eastern populations to the southern and Yunnan clusters, indicating that Sichuan populations are sources of northern immigrants and southern and Yunnan populations are sources of central-eastern populations. First-order (full-sib) and second-order (half-sib) kin pairs were always found within populations, but ~ 35-40% of third-order (cousin) pairs were found in different populations. Closely related individuals in different populations were found at distances of 900-1500 km in ~ 35-40% of cases, while some were separated by > 2000 km.

CONCLUSION

This study unravels seasonal migration patterns in the DBM. We demonstrate how careful sampling and population genomic analyses can be combined to help understand cryptic migration patterns in insects. © 2020 Society of Chemical Industry.

Having it all: hybridizing conventional and community science monitoring for enhanced data quality and cost savings

Large-scale monitoring is used to track population trends for many ecologically and economically important wildlife species. Often, population monitoring involves professional staff travelling to collect data (i.e., conventional monitoring) or in efforts to reduce monitoring costs, by engaging volunteers (i.e., community science). Although many studies have discussed the advantages and disadvantages of conventional vs. community science monitoring, few have made direct, quantitative comparisons between these two approaches. We compared data quality and financial costs between contemporaneous and overlapping conventional and community science programs for monitoring a major forest pest, the spruce budworm ( Choristoneura fumiferanae Clem.). Although community science trapping sites were clumped around urban areas, abundance estimates from the programs were strongly spatially correlated. However, annual program expenditures were nearly four times lower in the community science versus the conventional program. We modelled a hypothetical hybrid model of the two programs, which provided full spatial coverage and potentially the same data, but at half the cost of the conventional program and with the added opportunity for public engagement. Our study provides a unique quantitative analysis of merits and costs of conventional versus community science monitoring. Our study offers insights on how to assess wildlife monitoring programs where multiple approaches exist.

Large-scale genetic admixture suggests high dispersal in an insect pest, the apple fruit moth

Knowledge about population genetic structure and dispersal capabilities is important for the development of targeted management strategies for agricultural pest species. The apple fruit moth, Argyresthia conjugella (Lepidoptera, Yponomeutidae), is a pre-dispersal seed predator. Larvae feed on rowanberries (Sorbus aucuparia), and when rowanberry seed production is low (i.e., inter-masting), the moth switches from laying eggs in rowanberries to apples (Malus domestica), resulting in devastating losses in apple crops. Using genetic methods, we investigated if this small moth expresses any local genetic structure, or alternatively if gene flow may be high within the Scandinavian Peninsula (~850.000 km², 55^o - 69^o N). Genetic diversity was found to be high (n = 669, mean He = 0.71). For three out of ten tetranucleotide STRs, we detected heterozygote deficiency caused by null alleles, but tests showed little impact on the overall results. Genetic differentiation between the 28 sampling locations was very low (average FST = 0.016, P < 0.000). Surprisingly, we found that all individuals could be assigned to one of two non-geographic genetic clusters, and that a third, geographic cluster was found to be associated with 30% of the sampling locations, with weak but significant signals of isolation-by-distance. Conclusively, our findings suggest wind-aided dispersal and spatial synchrony of both sexes of the apple fruit moth over large areas and across very different climatic zones. We speculate that the species may recently have had two separate genetic origins caused by a genetic bottleneck after inter-masting, followed by rapid dispersal and homogenization of the gene pool across the landscape. We suggest further investigations of spatial genetic similarities and differences of the apple fruit moth at larger geographical scales, through life-stages, across inter-masting, and during attacks by the parasitoid wasp (Microgaster politus).

Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.

Tracking insect outbreaks: a case study of community-assisted moth monitoring using sex pheromone traps

Insect outbreaks can cover vast geographic areas making it onerous to cost-effectively monitor populations to address management or ecological questions. Community science (or citizen science), which entails engaging the public to assist with data collection, provides a possible solution to this challenge for the spruce budworm ( Choristoneura fumiferana Clemens), a major defoliating pest in North America. Here, we lay out the Budworm Tracker Program, a contributory community science program developed to help monitor spruce budworm moths throughout eastern Canada. The program outsources free pheromone trap kits to volunteers who periodically check and collect moths from their traps throughout the budworm flight period, then return them in a prepaid envelope to the organizers. Over three years, the program engaged an average of 216–375 volunteers and yielded a data return rate of 68%–89%, for a total of 16 311–54 525 moths per year. Volunteer retention among years was 71%–89%. Data from this program offer compelling evidence for the range of long-distance moth dispersal. Although our program was designed for spruce budworm, this template could easily be adapted for forestry, urban forestry, and agricultural systems to monitor any of the numerous organisms for which there is an established trapping method.

A Conceptual Framework for the Spruce Budworm Early Intervention Strategy: Can Outbreaks be Stopped?

The spruce budworm, Choristoneura fumiferana, Clem., is the most significant defoliating pest of boreal balsam fir (Abies balsamea (L.) Mill.) and spruce (Picea sp.) in North America. Historically, spruce budworm outbreaks have been managed via a reactive, foliage protection approach focused on keeping trees alive rather than stopping the outbreak. However, recent theoretical and technical advances have renewed interest in proactive population control to reduce outbreak spread and magnitude, i.e., the Early Intervention Strategy (EIS). In essence, EIS is an area-wide management program premised on detecting and controlling rising spruce budworm populations (hotspots) along the leading edge of an outbreak. In this article, we lay out the conceptual framework for EIS, including all of the core components needed for such a program to be viable. We outline the competing hypotheses of spruce budworm population dynamics and discuss their implications for how we manage outbreaks. We also discuss the practical needs for such a program to be successful (e.g., hotspot monitoring, population control, and cost–benefit analyses), as well as the importance of proactive communications with stakeholders.