Jasmine K. Janes

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

BackgroundThe mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests.ResultsWe developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insects biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle.ConclusionsDespite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.

The K=2 conundrum

Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow. structure, the most highly cited of several clustering‐based methods, was developed to provide robust estimates without the need for populations to be determined a priori. structure introduces the problem of selecting the optimal number of clusters, and as a result, the ΔK method was proposed to assist in the identification of the “true” number of clusters. In our review of 1,264 studies using structure to explore population subdivision, studies that used ΔK were more likely to identify K = 2 (54%, 443/822) than studies that did not use ΔK (21%, 82/386). A troubling finding was that very few studies performed the hierarchical analysis recommended by the authors of both ΔK and structure to fully explore population subdivision. Furthermore, extensions of earlier simulations indicate that, with a representative number of markers, ΔK frequently identifies K = 2 as the top level of hierarchical structure, even when more subpopulations are present. This review suggests that many studies may have been over‐ or underestimating population genetic structure; both scenarios have serious consequences, particularly with respect to conservation and management. We recommend publication standards for population structure results so that readers can assess the implications of the results given their own understanding of the species biology.

How the mountain pine beetle (Dendroctonus ponderosae) breached the Canadian Rocky Mountains

The mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins), a major pine forest pest native to western North America, has extended its range north and eastward during an ongoing outbreak. Determining how the MPB has expanded its range to breach putative barriers, whether physical (nonforested prairie and high elevation of the Rocky Mountains) or climatic (extreme continental climate where temperatures can be below −40 °C), may contribute to our general understanding of range changes as well as management of the current epidemic. Here, we use a panel of 1,536 single nucleotide polymorphisms (SNPs) to assess population genetic structure, connectivity, and signals of selection within this MPB range expansion. Biallelic SNPs in MPB from southwestern Canada revealed higher genetic differentiation and lower genetic connectivity than in the northern part of its range. A total of 208 unique SNPs were identified using different outlier detection tests, of which 32 returned annotations for products with putative functions in cholesterol synthesis, actin filament contraction, and membrane transport. We suggest that MPB has been able to spread beyond its previous range by adjusting its cellular and metabolic functions, with genome scale differentiation enabling populations to better withstand cooler climates and facilitate longer dispersal distances. Our study is the first to assess landscape-wide selective adaptation in an insect. We have shown that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this forest pest species.

Influence of warming on soil water potential controls seedling mortality in perennial but not annual species in a temperate grassland

In a water-limited system, the following hypotheses are proposed: warming will increase seedling mortality; elevated atmospheric CO2 will reduce seedling mortality by reducing transpiration, thereby increasing soil water availability; and longevity (i.e. whether a species is annual or perennial) will affect the response of a species to global changes. Here, these three hypotheses are tested by assessing the impact of elevated CO2 (550 micromol mol(-1) and warming (+2 degrees C) on seedling emergence, survivorship and establishment in an Australian temperate grassland from autumn 2004 to autumn 2007. Warming impacts on seedling survivorship were dependent upon species longevity. Warming reduced seedling survivorship of perennials through its effects on soil water potential but the seedling survivorship of annuals was reduced to a greater extent than could be accounted for by treatment effects on soil water potential. Elevated CO2 did not significantly affect seedling survivorship in annuals or perennials. These results show that warming will alter recruitment of perennial species by changing soil water potential but will reduce recruitment of annual species independent of any effects on soil moisture. The results also show that exposure to elevated CO2 does not make seedlings more resistant to dry soils.

Decomposition and nitrogen transformation rates in a temperate grassland vary among co-occurring plant species

Background and aimsDecomposition of organic matter varies depending upon interactions between the composition of the organic matter and the source of the microbial community, with differences in these interactions among vegetation types leading to the Home Field Advantage (HFA) hypothesis whereby decomposition of litters is faster in soils previously conditioned by them. It is possible that HFA operates on smaller scales within plant communities with ecosystem processes responding to subtle changes of plant community dominance.Methods and resultsUsing field measurements and laboratory incubations, we found a strong plant species effect on nitrogen availability and transformations and the relative importance of autotrophic and heterotrophic processes to nitrification. We found that the origin of the soil microbial community had little influence on litter decomposition when litter quality was high but was important with low-quality litter, most of which was root material.ConclusionsOur results demonstrate that plant species identity has a substantial impact on both litter decomposition and N cycling even within a single vegetation type and on an extremely local scale via both litter chemistry and specificity of the associated soil microbial community. Therefore, changes in botanical composition could alter decomposition and nutrient release altering ecosystem productivity and carbon sequestration potential.

Adaptive and neutral markers both show continent‐wide population structure of mountain pine beetle (Dendroctonus ponderosae)

Abstract Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single‐nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range‐wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

A molecular phylogeny of the subtribe Pterostylidinae (Orchidaceae): resolving the taxonomic confusion

In the past decade, two major classification schemes of the subtribe Pterostylidinae have resulted in taxonomic confusion because a single well known genus was split into a large number of new genera and subgenera, many of which are difficult to discriminate accurately. These classifications have not been accepted widely among systematists because of poor phylogenetic support for several genera. Analyses of the internal transcribed spacer (ITS) region of nuclear rDNA in a large number of species and samples facilitate further clarification of the relationships within the Pterostylidinae. The phylogenetic trees were reconstructed using parsimony and Bayesian methods. These phylogenetic trees indicate that subtribe Pterostylidinae is monophyletic, and support the concept of a single genus, Pterostylis R.Br. sensu lato within the Pterostylidinae. Two clades representing subgenera correlate with the morphology of the lateral sepals, whereas several of the previously erected genera consistently have poor support. The proposed subgenera are divided further into 10 sections. Several closely related taxa with identical ITS sequences require further scrutiny by population-level molecular techniques to determine their taxonomic status.

A new classification for subtribe Pterostylidinae (Orchidaceae), reaffirming Pterostylis in the broad sense.

A new classification for subtribe Pterostylidinae (Orchidaceae) is formally described in which there is one genus, Pterostylis R.Br., two subgenera and 10 sections. Five new combinations are made for this classification at the ranks of subgenus and section, viz. Pt. subg. Oligochaetochilus (Szlach.) Janes & Duretto, Pt. sect. Parviflorae (Benth.) Janes & Duretto, Pt. sect. Pharochilum (D.L.Jones & M.A.Clem.) Janes & Duretto, Pt. sect. Stamnorchis (D.L.Jones & M.A.Clem.) Janes & Duretto and Pt. sect. Urochilus (D.L.Jones & M.A.Clem.) Janes & Duretto. Pt. ser. Parviflorae Benth. is lectotypified. To complete the revision, seven new species-level combinations are made for two species from Western Australia, one from New South Wales and four from Queensland, viz. Pt. anaclasta (D.L.Jones) Janes & Duretto, Pt. extranea (D.L.Jones) Janes & Duretto, Pt. pearsonii (D.L.Jones) Janes & Duretto, Pt. pedina (D.L.Jones) Janes & Duretto, Pt. sinuata (D.L.Jones) Janes & Duretto, Pt. timothyi (D.L.Jones) Janes & Duretto and Pt. thulia (D.L.Jones) Janes & Duretto.

What does population structure analysis reveal about the Pterostylis longifolia complex (Orchidaceae)

Morphologically similar groups of species are common and pose significant challenges for taxonomists. Differences in approaches to classifying unique species can result in some species being overlooked, whereas others are wrongly conserved. The genetic diversity and population structure of the Pterostylis longifolia complex (Orchidaceae) in Tasmania was investigated to determine if four species, and potential hybrids, could be distinguished through genomic AFLP and chloroplast restriction-fragment-length polymorphism (RFLP) markers. Analysis of molecular variance (AMOVA) results indicated that little genetic variation was present among taxa, whereas PCoA analyses revealed genetic variation at a regional scale irrespective of taxa. Population genetic structure analyses identified three clusters that correspond to regional genetic and single taxon-specific phenotypic variation. The results from this study suggest that “longifolia” species have persisted throughout the last glacial maximum in Tasmania and that the complex may be best treated as a single taxon with several morphotypes. These results could have serious evolutionary and conservation implications as taxonomic changes could result in the instatement of a single, widespread taxon in which rarer morphotypes are not protected.

Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers.

An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.