Chromosome-level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)

Genome sequencing methods and assembly tools have improved dramatically since the 2013 publication of draft genome assemblies for the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). We conducted proximity ligation library sequencing and scaffolding to improve contiguity, and then used linkage mapping and recent bioinformatic tools for correction and further improvement. The new assemblies have dramatically improved contiguity and gaps compared to the originals: N50 values increased 26- to 36-fold, and the number of gaps were reduced by half. Ninety percent of the content of the assemblies is now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Based on linkage mapping information, the 12 largest scaffolds in both assemblies represent all 11 autosomal chromosomes and the neo-X chromosome. These assemblies now have nearly chromosome-sized scaffolds and will be instrumental for studying genomic architecture, chromosome evolution, population genomics, functional genomics, and adaptation in this and other pest insects. We also identified regions in two chromosomes, including the ancestral-X portion of the neo-X chromosome, with elevated differentiation between northern and southern Canadian populations.

Chromosome-level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)

Genome sequencing methods and assembly tools have improved dramatically since the 2013 publication of draft genome assemblies for the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). We conducted proximity ligation library sequencing and scaffolding to improve contiguity, and then used linkage mapping and recent bioinformatic tools for correction and further improvement. The new assemblies have dramatically improved contiguity and gaps compared to the originals: N50 values increased 26- to 36-fold, and the number of gaps were reduced by half. Ninety percent of the content of the assemblies is now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Based on linkage mapping information, the 12 largest scaffolds in both assemblies represent all 11 autosomal chromosomes and the neo-X chromosome. These assemblies now have nearly chromosome-sized scaffolds and will be instrumental for studying genomic architecture, chromosome evolution, population genomics, functional genomics, and adaptation in this and other pest insects. We also identified regions in two chromosomes, including the ancestral-X portion of the neo-X chromosome, with elevated differentiation between northern and southern Canadian populations.

Growth, Chemistry, and Genetic Profiles of Whitebark Pine Forests Affected by Climate-Driven Mountain Pine Beetle Outbreaks

Climate change-driven Dendroctonus ponderosae outbreaks in semi-naïve Pinus albicaulis may result in rapid natural selection for trees with genotypes and phenotypes associated with survival. In this study, we investigated whether survivors were genetically and chemically different from a living cohort of trees that escaped predation due to smaller size and estimated genetic diversity. We also examined how growth rate and climate sensitivity varied between beetle-killed and surviving trees. Dendroctonus ponderosae predominantly kills large diameter trees; therefore, we predicted that large surviving trees would have distinctive genetic profiles and, due to bottlenecking and drift, survivors would have lower genetic diversity than the abundant smaller mature trees that escaped predation. We found survivors were indeed genetically divergent from the smaller trees but, contrary to expectations, the smaller trees had lower diversity. This suggests that while beetles may select for trees with particular genotypes, other factors are also driving population genetic sub-structuring. Individual tree terpene profiles were diverse and varied by population but showed no clear relationship to survivorship. Two groups of trees with divergent sensitivities to climate were observed in each population, but neither was a clear indicator of survivorship or susceptibility to beetle attack. Growth rate was the best predictor of survivorship with survivors growing significantly slower than beetle-killed trees over their lifetimes although growth rates converged in years just prior to increased beetle activity. Overall, our results suggest that P. albicaulis forests show considerable divergence among populations and within-population genetic sub-structuring, and that they may contain complex mosaics of adaptive potentials to a variety of stressors including D. ponderosae. To protect the ability of this tree to adapt to increasing pressure from beetles, blister rust, and climate change, a top priority should be the maintenance of standing genetic diversity and adaptive shifts in allele frequencies.

Ethanol-Enriched Substrate Facilitates Ambrosia Beetle Fungi, but Inhibits Their Pathogens and Fungal Symbionts of Bark Beetles

Bark beetles (sensu lato) colonize woody tissues like phloem or xylem and are associated with a broad range of micro-organisms. Specific fungi in the ascomycete orders Hypocreales, Microascales and Ophistomatales as well as the basidiomycete Russulales have been found to be of high importance for successful tree colonization and reproduction in many species. While fungal mutualisms are facultative for most phloem-colonizing bark beetles (sensu stricto), xylem-colonizing ambrosia beetles are long known to obligatorily depend on mutualistic fungi for nutrition of adults and larvae. Recently, a defensive role of fungal mutualists for their ambrosia beetle hosts was revealed: Few tested mutualists outcompeted other beetle-antagonistic fungi by their ability to produce, detoxify and metabolize ethanol, which is naturally occurring in stressed and/or dying trees that many ambrosia beetle species preferentially colonize. Here, we aim to test (i) how widespread beneficial effects of ethanol are among the independently evolved lineages of ambrosia beetle fungal mutualists and (ii) whether it is also present in common fungal symbionts of two bark beetle species (Ips typographus, Dendroctonus ponderosae) and some general fungal antagonists of bark and ambrosia beetle species. The majority of mutualistic ambrosia beetle fungi tested benefited (or at least were not harmed) by the presence of ethanol in terms of growth parameters (e.g., biomass), whereas fungal antagonists were inhibited. This confirms the competitive advantage of nutritional mutualists in the beetle’s preferred, ethanol-containing host material. Even though most bark beetle fungi are found in the same phylogenetic lineages and ancestral to the ambrosia beetle (sensu stricto) fungi, most of them were highly negatively affected by ethanol and only a nutritional mutualist of Dendroctonus ponderosae benefited, however. This suggests that ethanol tolerance is a derived trait in nutritional fungal mutualists, particularly in ambrosia beetles that show cooperative farming of their fungi.

Patterns of Diversity in the Symbiotic Mite Assemblage of the Mountain Pine Beetle, Dendroctonus Ponderosae Hopkins

The mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Scolytinae), is an economically important bark beetle species with a wide geographic range spanning from the southwestern United States into northern Canada. This beetle causes extensive tree mortality to 13 pine species. Mites (Acari) are common and abundant symbionts of mountain beetles that may influence their fitness through positive and negative interactions. We present a unique assessment of the mite associates of mountain pine beetles using measures of alpha and beta diversity. We sampled phoretic mites from five beetle populations: Arizona, Colorado, South Dakota, Utah (USA), and Alberta (Canada) that varied in host tree species, local climate, and beetle population level. We collected 4848 mites from 8 genera and 12 species. Fifty to seventy percent of beetles carried mites in flight with the highest mite loads occurring in middle and southern populations; decreasing in northern populations. Mite assemblages (i.e., both richness and composition) varied along a south to north latitudinal gradient and were driven by species turnover (i.e., species replacement). Differences in mite composition increased with distance between populations. We discuss climatic variation, environmental filtering, and host tree differences as factors that could affect differences in mite composition between beetle populations and discuss implications for functional shifts. Our results could represent a model for estimating diversity patterns of mite symbionts associated with other major insect pests in coniferous forest systems.