Genetic architecture and phenotypic plasticity of thermally-regulated traits in an eruptive species, Dendroctonus ponderosae

Evidence for an adult summer diapause in mountain pine beetle (Coleoptera: Curculionidae) that varies geographically and among haplogroups

Identifying dormancy traits is important for predicting insect population success, particularly in a changing climate that could disrupt evolved traits. The mountain pine beetle (Dendroctonus ponderosae Hopkins) is native to North America, is responsible for millions of acres of tree mortality, and is expanding northward in Canada. Research has identified thermal traits important to epidemic-phase ecology that vary among populations. Genomic research identified 3 mountain pine beetle haplogroups representing Pleistocene glacial refugia. Significant variation in generation timing aligning with the haplogroups has been observed. The adult stage was previously identified as the likely cause of differences among populations, although the mechanism(s) remain unclear. We tested for an adult summer diapause that varies among populations from 2 haplogroups, southern Colorado (CO) (central haplogroup) and southern Idaho (ID) (eastern haplogroup) using respirometry and reproduction experiments. Warm temperatures (25 °C) resulted in reduced respiration rates of central haplogroup mountain pine beetle compared to a cool temperature treatment (15 °C), whereas respiration of the eastern haplogroup did not differ between the treatments. Mated pairs of central haplogroup mountain pine beetle reared/held at 15 °C were more likely to be classified with a higher reproductive success rating compared to pairs reared/held at 25 °C. These results support a facultative summer adult diapause in southern CO central haplogroup mountain pine beetle. Manifestation of this diapause was low/absent among adults from the northerly ID location. This diapause likely serves to maintain univoltinism shown to be important for mountain pine beetle epidemic-phase ecology. The variation occurring among haplogroups highlights the long-term, evolved processes driving local adaptations in mountain pine beetle.

Directional epistasis is common in morphological divergence

Epistasis is often portrayed as unimportant in evolution. While random patterns of epistasis may have limited effects on the response to selection, systematic directional epistasis can have substantial effects on evolutionary dynamics. Directional epistasis occurs when allele substitutions that change a trait also modify the effects of allele substitution at other loci in a systematic direction. In this case, trait evolution may induce correlated changes in allelic effects and additive genetic variance (evolvability) that modify further evolution. Although theory thus suggests a potentially important role for directional epistasis in evolution, we still lack empirical evidence about its prevalence and magnitude. Using a new framework to estimate systematic patterns of epistasis from line-crosses experiments, we quantify its effects on 197 size-related traits from diverging natural populations in 24 animal and 17 plant species. We show that directional epistasis is common and tends to become stronger with increasing morphological divergence. In animals, most traits displayed negative directionality toward larger size, suggesting that epistatic constraints reducing evolvability toward larger size. Dominance was also common but did not systematically alter the effects of epistasis.

Rearranging and completing the puzzle: Phylogenomic analysis of bark beetles Dendroctonus reveals new hypotheses about genus diversification

Studies carried out on bark beetles within Dendroctonus have been extensive and revealed diverse information in different areas of their natural history, taxonomy, evolution, and interactions, among others. Despite these efforts, phylogenetic hypotheses have remained obscured mainly due to limited information analyzed (taxonomic, gene sampling, or both) in studies focused on obtaining evolutionary hypotheses for this genus. With the aim of filling these gaps in the evolutionary history for Dendroctonus, we analyzed ∼1800 loci mapped to a reference genome obtained for 20 of the 21 species recognized to date, minimizing the impact of missing information and improving the assumption of orthology in a phylogenomic framework. We obtained congruent phylogenetic topologies from two phylogenomic inference strategies: loci concatenation (ML framework) and a multispecies coalescent model (MSC) through the analysis of site pattern frequencies (SNPs). Dendroctonus is composed of two major clades (A and B), each containing five and four subclades, respectively. According to our divergence dating analysis, the MRCA for Dendroctonus dates back to the early Eocene, while the MRCA for each major clade diverged in the mid-Eocene. Interestingly, most of the speciation events of extant species occurred during the Miocene, which could be correlated with the diversification of pine trees (Pinus). The MRCA for Dendroctonus inhabited large regions of North America, with all ancestors and descendants of clade A having diversified within this region. The Mexican Transition Zone is important in the diversification processes for the majority of clade A species. For clade B, we identified two important colonization events to the Old World from America: the first in the early Oligocene from the Arctic to Asia (via Beringia), and the second during the Miocene from the Arctic-Western-Alleghany region to Europe and Siberia (also via Beringia). Our genomic analyses also supported the existence of hidden structured lineages within the frontalis complex, and also that D. beckeri represent a lineage independent from D. valens, as previously suggested. The information presented here updates the knowledge concerning the diversification of a genus with remarkable ecological and economic importance.

Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens

BACKGROUND

Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area.

RESULTS

Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation.

CONCLUSIONS

Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.

Predicting Emerald Ash Borer Adult Emergence and Peak Flight Activity in Winnipeg, Manitoba, Canada

The invasive emerald ash borer (Agrilus planipennis Fairmaire; Coleoptera: Buprestidae) has killed tens of millions of ash (Fraxinus spp.) trees across North America. A. planipennis was first detected in Winnipeg, Manitoba in 2017 and has the potential to become a serious threat to the city's ash canopy which accounts for ~30% of the public tree inventory. The goal of this study was to predict when adult A. planipennis emergence and peak activity would occur in Winnipeg to help logistical planning for the implementation of a city-wide management program. The management program would focus on detection and limiting the spread of the beetle with the objective of preserving ash trees as long as possible allowing for more proactive management of the EAB infestation. To predict adult emergence and peak activity of A. planipennis, we used local weather station data to calculate the number of degree-days accumulated in each year for the 1970–2019 period using three different degree-day accumulation models. Developmental thresholds for A. planipennis were derived from previous North American studies. The estimated mean emergence dates for the 50-year period were June 14 ± 8.5 days (double sine model), June 14 ± 8.5 days (single sine model), and June 19 ± 9.1 days (standard model) whereas the peak activity dates were July 16 ± 8.8 days (double sine model), July 17 ± 8.7 days (single sine model), and July 21 ± 9.4 days (standard model). Meteorological records indicate that temperatures in the Winnipeg region have increased over the study period. However, our predicted emergence dates do not significantly differ over the 50 years examined in the study, although estimated peak activity dates are significantly earlier, suggesting that EAB movement may benefit from climate change. The results from this study will provide managers with information regarding the temporal behavior of A. plannipennis in Winnipeg allowing for improved timing of control measures and monitoring, thereby extending the projected life span of a significant ash tree population within the Winnipeg urban region. The management model developed for Winnipeg could serve as an example for other locations in the prairie region of North America.

Phytochemicals as mediators for host range expansion of a native invasive forest insect herbivore

Mountain pine beetle (MPB) has recently invaded jack pine forests in western Canada. This invasion signifies a climate change-induced range expansion by a native insect. The mechanism underlying this invasion is unknown, but likely involves phytochemicals that play critical roles in MPB biology. Thus far, studies have investigated the compatibility of jack pine chemistry with beetles and their microbial symbionts. I have identified three phytochemical mechanisms that have likely facilitated the host range expansion of MPB. First, jack pine chemistry is overall similar to that of the historical hosts of MPB. In particular, jack pine chemistry is compatible with beetle pheromone production, aggregation on host trees and larval development. Furthermore, the compatibility of jack pine chemistry maintains beneficial interactions between MPB and its microbial symbionts. Second, compared with historical hosts, the novel host not only has lower concentrations of toxic and repellent defense chemicals, but also contains large concentrations of chemicals promoting host colonization by MPB. These patterns are especially pronounced when comparing novel hosts with well-defended historical hosts. Finally, before MPBs arrived in jack pine forests, they invaded a zone of hybrids of novel and historical hosts that likely improved beetle success on jack pine, as hybrids show chemical characteristics of both hosts. In conclusion, the phytochemistry of jack pine has likely facilitated the biological invasion of this novel host by MPB.

Biological Aspects of Mountain Pine Beetle in Lodgepole Pine Stands of Different Densities in Colorado, USA

Research Highlights: The biology of mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, in Colorado’s lodgepole pine forests exhibits similarities and differences to other parts of its range. Brood emergence was not influenced by stand density nor related to tree diameter. The probability of individual tree attack is influenced by stocking and tree size. Findings have implications for understanding MPB as a disturbance agent and for developing management strategies. Background and Objectives: MPB causes extensive tree mortality of lodgepole pine, Pinus contorta Douglas ex Loudon, across the western US and Canada and is probably the most studied bark beetle in North America. However, most of the current knowledge on the biology and ecology of MPB in lodgepole pine comes from the Intermountain Region of the US and western Canada. Little information is available from Colorado. This is the first study addressing effects of stand stocking levels on the biology of MPB and quantifying phloem consumption. In addition, although data are available on the conditions that foster stand infestation, this is the first study estimating the probability of individual tree attack among stands of known different stocking. Materials and Methods: Studies were conducted in managed lodgepole pine stands in Colorado. Unbaited traps were used to monitor MPB flight across stands of different densities. Cages were used to monitor emergence and bark samples to determine attack densities, and phloem consumption in trees growing under different stocking. Beetle collections were used to determine emergence across the growing season. Tree mortality data from plots of different densities were used to examine the probability of individual tree infestation. Results: More beetles were caught flying through higher density stands. More attacks were observed in lower stocking stands but there were no differences in the number of insects emerging nor phloem consumption. There was no relationship between tree size and beetle emergence. Peak flight occurred in early to mid-August and only one peak of beetle emergence occurred. The probability of tree attack was influenced by stand stocking and tree diameter. Conclusions: In general, aspects of the biology of MPB in Colorado exhibit similarities and differences with other regions. The data suggest the need to more closely examine how MPB functions in stands of different stocking and how the distribution of tree sizes influence the probability of infestation and extent of mortality in stands. Biological characteristics of MPB in Colorado need further examination, particularly as climate change continues to manifest. Baseline information will be critical to refine management approaches, and extend the understanding of how MPB contributes to shape forest composition and structure in Colorado.

Evidence for a Prepupal Diapause in the Mountain Pine Beetle (Dendroctonus ponderosae)

Dormancy strategies, including diapause and quiescence, enable insects to evade adverse conditions and ensure seasonally appropriate life stages. A mechanistic understanding of a species' dormancy is necessary to predict population response in a changing climate. Climate change is influencing distribution patterns and population success of many species, including Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae: Scolytinae), the most important mortality agent of pines in western North America. Diapause is considered absent in D. ponderosae, and quiescence in the final larval stage prior to pupation (i.e., prepupal) is considered the main dormancy strategy. We evaluated if a facultative diapause in the prepupal stage, rather than a pupation threshold ~15°C (i.e., quiescence), could describe pupation patterns in two latitudinally separated D. ponderosae populations in the western United States. We hypothesized that if pupation occurs at lower temperatures than previously described, and if significant prepupal developmental delays occur, diapause is a likely physiological mechanism. Although there was considerable variation within and between populations, pupation occurred below the previously established threshold suggesting a prepupal facultative diapause that is induced when late instars experience cool temperatures. Individuals that pupated at temperatures below 15°C also had developmental delays, relative to development at warmer temperatures, consistent with diapause development. Pupation patterns differed between populations wherein diapause was induced at cooler temperatures and diapause development was shorter in southern compared with northern D. ponderosae. Recognition of a facultative diapause that varies among and between populations is critical for making predictions about future population response and range expansion in a changing climate.

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations. This striking progression of reproductive isolation is coupled with extensive gene specialization, natural selection, and elevated genetic differentiation on both sex chromosomes. Closely related populations isolated by hybrid male sterility also show fixation of alternative neo-Y haplotypes that differ in structure and male-specific gene content. Our results suggest that neo-sex chromosome evolution can drive rapid functional divergence between closely related populations irrespective of ecological drivers of divergence.

The evolution of new sex chromosomes potentially generates reproductive isolation. Here, Bracewell et al. combine crossing experiments with population and functional genomics to characterize neo-sex chromosome evolution and incipient speciation in the mountain pine beetle, Dendroctonus ponderosae.

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

Evaluating Predators and Competitors in Wisconsin Red Pine Forests for Attraction to Mountain Pine Beetle Pheromones for Anticipatory Biological Control

Mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae), is an irruptive tree-killing species native to pine forests of western North America. Two potential pathways of spread to eastern forests have recently been identified. First, warming temperatures have driven range expansion from British Columbia into Albertan jack pine forests that are contiguous with the Great Lakes region. Second, high temperatures and drought have fostered largescale outbreaks within the historical range, creating economic incentives to salvage killed timber by transporting logs to midwestern markets, which risks accidental introduction. We evaluated the extent to which local predators and competitors that exploit bark beetle semiochemicals would respond to D. ponderosae in Wisconsin. We emulated D. ponderosae attack by deploying lures containing synthetic aggregation pheromones with and without host tree compounds and blank control traps in six red pine plantations over 2 yr. Predator populations were high in these stands, as evidenced by catches in positive control traps, baited with pheromones of local bark beetles and were deployed distant from behavioral choice plots. Only one predator, Thanasimus dubius F. (Coleoptera: Cleridae) was attracted to D. ponderosae's aggregation pheromones relative to blank controls, and its attraction was relatively weak. The most common bark beetles attracted to these pheromones were lower stem and root colonizers, which likely would facilitate rather than compete with D. ponderosae. There was some, but weak, attraction of potentially competing Ips species. Other factors that might influence natural enemy impacts on D. ponderosae in midwestern forests, such as phenological synchrony and exploitation of male-produced pheromones, are discussed.

Towards an evolutionary understanding of questing behaviour in the tick Ixodes ricinus

The tick Ixodes ricinus finds its hosts by climbing vegetation and adopting a sit-and-wait tactic. This “questing” behaviour is known to be temperature-dependent, such that questing increases with temperature up to a point where the vapor pressure deficit (drying effect) forces ticks down to rehydrate in the soil or mat layer. Little if any attention has been paid to understanding the questing of ticks from an evolutionary perspective. Here we ask whether populations from colder climatic conditions respond differently in terms of the threshold temperature for questing and the rate of response to a fixed temperature. We find significant variation between populations in the temperature sensitivity of questing, with populations from cooler climates starting questing at lower temperatures than populations from warmer temperatures. Cool climate populations also quest sooner when the temperature is held constant. These patterns are consistent with local adaptation to temperature either through direct selection or acclimation and challenge the use of fixed thresholds for questing in modeling the spread of tick populations. Our results also show how both time and temperature play a role in questing, but we are unable to explain the relationship in terms of degree-time used to model Arthropod development. We find that questing in response to temperature fits well with a quantitative genetic model of the conditional strategy, which reveals how selection on questing may operate and hence may be of value in understanding the evolutionary ecology of questing.

Experimental evaluation of reproductive response to climate warming in an oviparous skink

The impact of climate warming on organisms is increasingly being recognized. The experimental evaluation of phenotypically plastic responses to warming is a critical step in understanding the biological effects and adaptive capacity of organisms to future climate warming. Oviparous Scincella modesta live in deeply-shaded habitats and they require low optimal temperatures during embryonic development, which makes them suitable subjects for testing the effects of warming on reproduction. We raised adult females and incubated their eggs under different thermal conditions that mimicked potential climate warming. Female reproduction, embryonic development and hatchling traits were monitored to evaluate the reproductive response to warming. Experimental warming induced females to lay eggs earlier, but it did not affect the developmental stage of embryos at oviposition or the reproductive output. The high temperatures experienced by gravid females during warming treatments reduced the incubation period and increased embryonic mortality. The locomotor performance of hatchlings was not affected by the maternal thermal environment, but it was affected by the warming treatment during embryonic development. Our results suggest that climate warming might have a profound effect on fitness-relevant traits both at embryonic and post-embryonic stages in oviparous lizards.

Integrating phenotypic plasticity within an Ecological Genomics framework: recent insights from the genomics, evolution, ecology, and fitness of plasticity

E.B. Ford's 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work in order to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. In this review, we argue that the integration of an ecological genomics framework in studies of phenotypic plasticity is a promising approach to elucidate the causal links between genes and the environment, particularly during colonization of novel environments, environmental change, and speciation. This review highlights some of the questions and hypotheses generated from a mechanistic, evolutionary, and ecological perspective, in order to direct the continued and future use of genomic tools in the study of phenotypic plasticity.

Contemporary climate change and terrestrial invertebrates: evolutionary versus plastic changes

To forecast the responses of species to future climate change, an understanding of the ability of species to adapt to long-term shifts in temperature is crucial. We present a review on evolutionary adaptation and phenotypic plasticity of temperature-related traits in terrestrial invertebrates. The evidence for adaptive evolution in melanization is good, but we caution that genetic determination needs to be tested in each individual species, and complex genetic correlations may exist. For phenological traits allochronic data sets provide powerful means to track climate-induced changes; however, rarely are responses deconstructed into evolutionary and plastic responses. Laboratory studies suggest climate change responses in these traits will be driven by both. For stress resistance, the evidence for shifts in traits is poor. Studies leaning heavily on Drosophila have demonstrated potential limits to evolutionary responses in desiccation and heat resistance. Quantifying the capacity for these species to respond plastically and extending this work to other taxa will be an important next step. We also note that, although not strictly speaking a species trait, the response of endosymbionts to heat stress requires further study. Finally, while clearly genetic, and possibly adaptive, the anonymous nature of latitudinal shifts in clines of genetic markers in Drosophila prevents further interpretation.