Lodgepole Pine Research Articles

Mapping the presence and distribution of tree species in Canada's forested ecosystems

Knowledge of tree species is required to inform management, planning, and monitoring of forests as well as to characterize habitat and ecosystem function. Remotely sensed data and spatial modeling enable mapping of tree species presence and distribution. Following an assessment of tree species identified in the sample-based National Forest Inventory (NFI), we mapped 37 tree species over the 650-Mha, forest-dominated ecosystems of Canada representing 2019 conditions. Landsat imagery and related spectral indices, geographic and climate data, elevation derivatives, and remote sensing-derived phenology are used as predictor variables trained with calibration samples from Canada's NFI using the Random Forests machine learning algorithm. Based upon prior knowledge of tree species distributions, classification models were implemented on a regional basis, meaning only the tree species that are expected in a given mapping region were modeled using local calibration samples. Modeling resulted in class membership probabilities values for each regionally eligible tree species for all treed pixels as well as an indicator of attribution confidence derived from the distance in feature space between the two leading classes. Accuracy assessment was conducted using independent validation data also drawn from the NFI following the same selection rules and indicated an overall accuracy of 93.1% ± 0.1% (95%-confidence interval). Predictor variables informing on geographic, climatic and topographic conditions had the largest importance on the classification models. Nationally, the most common leading tree species were black spruce (Picea mariana; 203 Mha or 57.3% of the treed area), trembling aspen (Populus tremuloides; 34.7 Mha, 9.8%), and lodgepole pine (Pinus contorta; 21.1 Mha, 5.9%). Regionally, there was ecozone-level dominance of other tree species, including subalpine fir (Abies lasiocarpa; Montane Cordillera), western hemlock (Tsuga heterophylla; Pacific Maritime), and balsam fir (Abies balsamea; Atlantic Maritime). Based upon the per-pixel class membership probabilities, species assemblages akin to those in forest inventories can also be produced. Further, given the calibrated reflectance of Landsat imagery, the methods presented herein can be implemented over a time series of images. The approach uses open data as predictor variables, making the method portable to other areas given availability of tree species training data.

Pinus contorta Douglas ex Loudon and climate change: A literature review of opportunities, challenges, and risks in European forests

Lodgepole pine (Pinus contorta Douglas ex Loudon) was distributed from its natural range in western North America to different destinations, primarily to Europe (Scandinavia, British Islands), South America (Chile, Argentina), and New Zealand. It is used for its superior timber production and resistance to environmental conditions. This literature review paper consists of 150 references and presents a summary of research results dealing with the lodgepole pine potential in general with a specific focus on Europe from 1910 to 2022. It summarizes the importance, taxonomy, biological and ecological characteristics, site requirements, production and silviculture, risks and pests, as well as the potential of this tree species for forestry and the wood industry in relation to global climate change. Pinus contorta also has a considerable potential in Central Europe, especially at extreme sites with strong anthropogenic impact and in polluted regions. This tree species is very resistant to climatic factors and extreme events compared to other coniferous tree species. Moreover, its annual increment reached from 3 m<sup>3</sup>·ha<sup>−1</sup>·yr<sup>−1 </sup>on reclamation sites to 18 m<sup>3</sup>·ha<sup>−1</sup>·yr<sup>−1 </sup>in favourable environmental conditions. On the other hand, caution must be taken for possible invasive behaviour outside its natural range. Its importance can increase with ongoing climate change and the decline of native tree species.

Traceability of provenance-collected lodgepole pine in a reforestation chain of custody case study

Traceability of provenance-collected lodgepole pine in a reforestation chain of custody case study

Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations.

While droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e. height growth, drought avoidance based on water-use efficiency inferred from δ13C and pest resistance based on defence traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defences and their evolutionary potential along populations or test sites. Response to selection was weak in defences across test sites, but high for height growth particularly at warm test sites. Response to the selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with a limited evolutionary influence from pest (biotic) pressures.

Essential Oil Compositions of Pinus Species (P. contorta Subsp. contorta, P. ponderosa var. ponderosa, and P. flexilis); Enantiomeric Distribution of Terpenoids in Pinus Species.

Pinus species are important in traditional medicine throughout their ranges, and pine essential oils are of interest in aromatherapy and as topical treatments. In this work, the leaf (needle) essential oils of Pinus ponderosa var. ponderosa and Pinus contorta subsp. contorta from Oregon and Pinus flexilis growing in Idaho, have been obtained by hydrodistillation and analyzed by gas chromatographic techniques. The leaf essential oil of P. ponderosa was dominated by β-pinene (21.5–55.3%), methyl chavicol (8.5–41.5%), α-pinene (3.6–9.6%), δ-3-carene (3.6–6.2%), and α-terpineol (1.4–5.3%). The major components of P. contorta essential oil were β-phellandrene (23.8%), terpinen-4-ol (11.0%). The essential oil of P. flexilis was dominated by α-pinene (37.1%), β-pinene (21.9%), bornyl acetate (12.8%), and camphene (8.5%). Chiral gas chromatography revealed the enantiomeric ratios of α-pinene and limonene to be variable, but (−)-β-pinene predominated in Pinus essential oils.

Development of PCR-based markers for the identification and detection of Lophodermella needle cast pathogens on Pinus contorta var. latifolia and P. flexilis

Morphological similarities and fastidious development of increasingly emerging fungal needle pathogens impede accurate disease diagnosis and early detection. This study analyzed the specificity and sensitivity of polymerase chain reaction (PCR)-based markers developed for emerging needle cast pathogens Lophodermella concolor and L. montivaga co-occurring on Pinus contorta var. latifolia, and Bifusella linearis and L. arcuata on P. flexilis. To design primers, we utilized sequences of the internal transcribed spacer (ITS) region and single-copy gene (RH_2175) of the TCP-1/cpn60 chaperonin family searched through genomes of related species. In addition to the DNA of target and non-target fungal species that were used for primer assays, environmental samples with next generation sequencing data were used to evaluate primer sensitivity. Direct amplification using ITS primer pairs generated 248–260 bp amplicons and successfully differentiated the needle pathogens used in this study. Nested amplification of single-copy gene RH_2175 primer pairs which produced 409–527 bp amplicons detected Rhytismataceae species and discriminated both Lophodermella pathogens on P. contorta var. latifolia, respectively. While ITS-based primers had higher sensitivity than the 2175-based primers, both primer sets for L. concolor and L. montivaga detected their respective pathogens in asymptomatic and symptomatic needles. These molecular tools can help monitor and assess needle diseases for forest management and phytosanitary regimes.

Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine

BackgroundGenomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias.ResultsMT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP.ConclusionsThe power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.

Stand openness predicts hair lichen (Bryoria) abundance in the lower canopy, with implications for the conservation of Canada’s critically imperiled Deep-Snow Mountain Caribou (Rangifer tarandus caribou)

Tree-dwelling hair lichens in the genus Bryoria provide crucial late-winter forage for Deep-Snow Mountain Caribou (DSC), an imperiled ungulate endemic to south-central British Columbia, Canada. Because DSC survival requires continuous access to heavy hair lichen loadings, conservation efforts can benefit from an improved understanding of the factors that contribute to such loadings. Here we quantify the relation of Bryoria abundance to stand spacing by testing an “Angle-To-Canopy-Skyline” (ATCS) protocol as a measure of stand openness and a proxy for ventilation. Fieldwork conducted in 60-year-old conifer forests on a 250-m conical volcano within the range of DSC yielded three principal findings: (1) Bryoria abundance strongly increases with increasing stand openness; (2) Pinus contorta supports much heavier Bryoria loadings than other local host trees; and (3) ATCS is a powerful predictor of arboreal hair lichen abundance in general across a wide range of environmental settings, but does not predict the abundance of foliose lichens. We suggest that canopy openness, at least within the range of DSC, complements stand age as a key factor in the development of heavy Bryoria loadings, consistent with the hypothesis that Bryoria benefits from rapid drying after rain. The possibility that anomalously high Bryoria abundance on Pinus may hold promise for accelerated DSC habitat restoration following clearcut logging is explored but rejected.

Soil transfers from intact to disturbed boreal forests neither alter ectomycorrhizal fungal communities nor improve pine seedling performance

Abstract Forest disturbances can alter mycorrhizal fungal communities with consequences for subsequent plant establishment and growth. One possible mitigation strategy to promote forest recovery following disturbances is inoculation with soil from late‐successional forests. However, whether these soil transfers change the composition of resident fungal communities and how seedling growth responds to such transfers is unknown. To test whether soil transfers can mitigate disturbance‐mediated impacts on ectomycorrhizal fungal (EMF) communities, we transferred soils containing fungal inoculum collected from conspecific late‐successional forests into stands disturbed by wildfire, mountain pine beetle outbreak, clear‐cut logging or salvage logging. Afterward, lodgepole pine seeds were sown to measure germination, establishment and growth of seedlings, and to characterize root‐associated and soil EMF communities by sequencing the ITS1 rDNA region. Despite evidence that soil inocula contained viable EMF communities, transfers did not impact the root‐associated or soil EMF community composition, or seed germination, seedling establishment and growth. Resident EMF community composition remained unchanged upon transfers of fungi from late‐stage successional forests, and disturbance type singularly explained the EMF community composition associated with roots and soils. Ectomycorrhizal fungal taxa typically associated with mature pine forests were particularly abundant on roots of seedlings growing in plots impacted by beetle outbreak, while ‘early‐stage’ EMF taxa were associated with seedlings growing in wildfire and logging disturbances. Synthesis and applications. Following disturbances, soil and root‐associated EMF exhibit high functional redundancy, as seedling performance did not vary with differences in EMF community composition across disturbance types. Our findings suggest that soil transfers are unlikely to be an effective strategy in these stands and may be better targeted to highly degraded forests. The presence and abundance of EMF in disturbed forests should be assessed before committing to soil transfers as part of restoration.

Comparison of ammonium, nitrate, and proton fluxes in mycorrhizal and nonmycorrhizal roots of lodgepole pine in contrasting nitrogen treatments

Relatively few comparative studies exist of nitrogen (N) uptake by ectomycorrhizal (EM) and nonmycorrhizal roots under controlled conditions. Instantaneous and long-term N uptake by EM and nonmycorrhizal roots of lodgepole pine seedlings ( Pinus contorta (Douglas) var. latifolia (Engelm.)) were compared after 9–12 months of preconditioning under high or low N supply, with NH4+ and NO3− in proportions of 90:10 and 10:90. EM roots were inoculated with Amphinema byssoides or Laccaria bicolor. Instantaneous net NH4+, NO3−, and H+ fluxes were measured simultaneously on seedling roots with a microelectrode ion flux measurement system, and seedling organ biomass and N content were measured to infer long-term N uptake. Net NH4+ uptake was observed in EM roots of lodgepole pine but NH4+ efflux was observed in nonmycorrhizal roots. Greater instantaneous N uptake in EM roots was supported by higher root and shoot N contents in seedlings associated with L. bicolor than in noninoculated seedlings. Absence of NH4+ efflux in EM roots suggests that root colonization by EM fungi has the potential to reduce futile cycling of NH4+. EM lodgepole pine appeared to prefer NH4+ over NO3− as an N source and instantaneous NH4+ uptake rates were higher in NH4-starved roots. H+ efflux was observed in most roots. Future work should focus on a greater variety of EM species to explore differences among species in N uptake.

Properties and durability of wood impregnated with high melting point polyethylene wax for outdoor use

In order to develop a new wood product suitable for outdoor applications, a high melting point polyethylene wax was used for high-pressure impregnation treatment of wood. Properties of impregnated wood were studied. Wax in molten state was stable with low viscosity, good fluidity, and easily penetrate into the wood under high pressure. Full-cell process included vacuum (-0.06 MPa for 30 min), high-pressure impregnation (0.75 MPa for 3 h) and pressure release (30 min). Wax contents of treated lodgepole pine (Pinus contorta Douglas ex Loudon.) and eucalyptus (Eucalyptus saligna) were 0.205 g/cm3 and 0.321 g/cm3, respectively. Cell gaps and cell cavities of wood were filled with polyethylene wax. Nanoindentation tests showed that longitudinal mechanical properties of wood cell walls were weakened after impregnation. After a 3 h high-pressure impregnation, hardness of lodgepole pine wood cell walls was reduced by 35.1%, and the modulus of elasticity was reduced by 4.9%. Treated wood had a much lower water absorption and swelling rate than untreated wood, its weathering resistance as well as insect resistance were better.

Using a trait-based approach to asses fire resistance in forest landscapes of the Inland Northwest, USA

ContextSeveral plant traits are associated with resistance to fire, thus fire-resistant species may give rise to more fire-resistant landscapes. However, up-scaling from plant traits to landscape- and regional-scale fire effects remains a challenge.ObjectivesWe test two hypotheses: (1) forests composed of fire-resistant species experience lower fire severity than forests composed of less fire-resistant species; and (2) wildfires affecting forests with greater fire resistance experience smaller patches of high-severity fire.MethodsWe used a predictive map of existing forest types (major tree species dominating forest composition) and a trait-based map of fire resistance. We examined large-scale spatial patterns of fire severity derived from Landsat imagery in 611 wildfires across the range of western larch in the Inland Northwest USA (1985–2014). We then applied structural equation modeling to study complex relationships between fire resistance and high-severity fire in each wildfire.ResultsForest types dominated by fire-resister species (e.g., ponderosa pine) experienced lower fire severity than forest types dominated by non-resister species such as lodgepole pine (fire-embracer) and subalpine fir (fire-avoider). We found a strong negative correlation between the fire resistance index and average values of the relative differenced normalized burn ratio, as well as an indirect relationship between fire resistance and high-severity patch size.ConclusionsThe large-scale differences in fire severity among forest types generally reflect the degree of fire resistance that fire-related traits confer to individual trees species, providing evidence that incorporating plant traits has the potential to assist in assessing fire resistance at large spatial scales.

Drivers of forest change in the Greater Yellowstone Ecosystem

AbstractQuestionsGlobal climate change is predicted to cause widespread shifts in the distribution and composition of forests, particularly in mountain environments where climate exerts strong controls on tree community arrangement. The upslope movement of vegetation has been observed in association with warming temperatures and is especially evident in ecotones—the transition zones between vegetation types. We explored the role of drought and tree mortality on recent changes in high‐elevation forests.LocationGreater Yellowstone Ecosystem, USA.MethodsWe established 19 forest demography plots along an elevational gradient spanning dominant high‐elevation vegetation types.ResultsTree establishment dates indicated the upslope movement of Pinus albicaulis (whitebark pine) treeline and ecotone shift from meadow to forest starting in the 1950s. An expansion of the growing season likely contributed to the upward expansion of the treeline. Comparisons between overstory and understory tree composition suggested ongoing succession in the absence of fire at lower elevations, namely the replacement of Pinus contorta (lodgepole pine) by Abies lasiocarpa (subalpine fir). P. contorta seedlings were distributed at higher elevations than overstory trees of the same species, suggesting some potential for upslope movement with warming conditions; P. albicaulis seedlings, conversely, were distributed throughout all elevations of the transect. Significant tree mortality occurred in Pinus spp. and disproportionately affected P. albicaulis, as a result of a regional Dendroctonus ponderosae (mountain pine beetle) outbreak (2008–2012). Mortality events were strongly associated with drier than average conditions 2–3 years prior to tree death.ConclusionRising sensitivity to arid conditions in the mid‐20th century amid already dense, aging forests appears to have increased susceptibility to beetle‐induced mortality during the most recent drought. Tree species in the study area responded individually to global change stressors, which acted on these forests in complex ways and led to both ecotone shifts and stability. This work highlights the interplay between succession, forest disturbances and climate‐related growth responses in driving forest compositional change in subalpine and treeline environments.

Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria

Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.

Evidence of Coevolution Between Cronartium harknessii Lineages and Their Corresponding Hosts, Lodgepole Pine and Jack Pine.

Variation in rate of infection and susceptibility of Pinus spp. to the fungus Cronartium harknessii (syn. Endocronartium harknessii), the causative agent of western gall rust, has been well documented. To test the hypothesis that there is a coevolutionary relationship between C. harknessii and its hosts, we examined genetic structure and virulence of C. harknessii associated with lodgepole pine (P. contorta var. latifolia), jack pine (P. banksiana), and their hybrids. A secondary objective was to improve assessment and diagnosis of infection in hosts. Using 18 microsatellites, we assessed genetic structure of C. harknessii from 90 sites within the ranges of lodgepole pine and jack pine. We identified two lineages (East and West, FST = 0.677) associated with host genetic structure (r = 0.81, P = 0.001), with East comprising three sublineages. In parallel, we conducted a factorial experiment in which lodgepole pine, jack pine, and hybrid seedlings were inoculated with spores from the two primary genetic lineages. With this experiment, we refined the phenotypic categories associated with infection and demonstrated that stem width can be used as a quantitative measure of host response to infection. Overall, each host responded differentially to the fungal lineages, with jack pine exhibiting more resiliency to infection than lodgepole pine and hybrids exhibiting intermediate resiliency. Taken together, the shared genetic structure between fungus and host species, and the differential interaction of the fungal species with the hosts, supports a coevolutionary relationship between host and pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effects of Planting, Vegetation Management, and Pre-Commercial Thinning on the Growth and Yield of Lodgepole Pine Regenerated after Harvesting in Alberta, Canada

A large long-term field trial was established in the Upper and Lower Foothills sub-regions of the Canadian boreal forest to monitor the effects of planting, vegetation management, and pre-commercial thinning on the development of lodgepole pine stands following harvesting. Data collected at the end of the trial’s regeneration phase, 17 to 20 years after its establishment, were tested for treatment effects and projected to rotation age. Planting generally improved stocking and increased projected growth and yield of lodgepole pine. On modal sites, planted trees were often greatly outnumbered by natural regeneration; however, on others, typically with either poorer or richer soils, satisfactory restocking was not achieved without planting. Control of competing vegetation by herbicide application facilitated regeneration of pine where it was otherwise difficult or impossible on sites with excessive herbaceous or hardwood competition. Pre-commercial thinning accelerated the growth of individual trees and was projected to shorten rotations in dense stands. Responses to the treatments varied depending on environmental factors. Particular treatments may be effective to meet management objectives under some site conditions but unnecessary or counterproductive elsewhere.

Using landscape genomics to delineate seed and breeding zones for lodgepole pine.

Summary Seed and breeding zones traditionally are delineated based on local adaptation of phenotypic traits associated with climate variables, an approach requiring long‐term field experiments. In this study, we applied a landscape genomics approach to delineate seed and breeding zones for lodgepole pine.We used a gradient forest (GF) model to select environment‐associated single nucleotide polymorphisms (SNPs) using three SNP datasets (full, neutral and candidate) and 20 climate variables for 1906 lodgepole pine (Pinus contorta) individuals in British Columbia and Alberta, Canada. The two GF models built with the full (28 954) and candidate (982) SNPs were compared.The GF models identified winter‐related climate as major climatic factors driving genomic patterns of lodgepole pine’s local adaptation. Based on the genomic gradients predicted by the full and candidate GF models, lodgepole pine distribution range in British Columbia and Alberta was delineated into six seed and breeding zones.Our approach is a novel and effective alternative to traditional common garden approaches for delineating seed and breeding zone, and could be applied to tree species lacking data from provenance trials or common garden experiments.

Tree Growth, Foliar Nutrition, and Soil Properties in Mixtures of Lodgepole Pine and Sitka Alder in the Central Interior of British Columbia, Canada: 25-Year Results

Densities of naturally regenerated mixtures of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) and Sitka alder [Alnus viridis subsp. sinuata (Regel) Á. Löve & D. Löve] were manipulated in 1995 at a site logged in 1987 in the central interior of British Columbia, Canada. Four levels of alder retention (0, 500, 1,000, and 2,000 clumps/ha) were combined with a uniform lodgepole pine density of 1,000 stems/ha across all treatments. After 25 years, effects of alder retention on lodgepole pine growth consisted of modest reductions in height and diameter increment, and treatment effects on soil nitrogen were confined to the forest floor organic horizons. Nutritional benefits of alder retention for lodgepole pine were not detected after year 6. The operational silvicultural implication of these findings is that only limited intervention to control Sitka alder in similar stands can be justified.

Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.

The use of next‐generation sequencing (NGS) data sets has increased dramatically over the last decade, but there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single lodgepole pine (Pinus contorta) parent and the maternally derived haploid tissue from 106 full‐sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the single nucleotide polymorphism (SNP) genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded more SNPs and higher error rates by one to two orders of magnitude, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non‐model study systems.

Cumulative Impact of Biotic and Abiotic Damage Agents on Lodgepole Pine Tree Form and Stand Structure in Southern British Columbia

Not all pests kill trees or compromise final tree form; however, the cumulative effect of one or more damage agents over time can significantly limit final expectations at harvest, severely reducing or compromising wood quality and timber supply expectations going forward. This study highlights the effects of damage agents on young lodgepole pine insouthern British Columbia during the formative years of stand development. Over 4,300ntrees were monitored for up to three decades with over 40 damage agents recorded, causing significant repercussions on stocking, health, and form of potential crop trees. By the final assessment, density of potential crop trees had declined dramatically, with 84% affectedby one or more pests, and 63% of natural ingress dead. Most natural ingress was severely suppressed; thus, it is unlikely to fill in stand gaps caused by mortality and damage agents affecting larger potential crop trees. Lodgepole pine terminal weevil and western gall rust were the predominant damage agents influencing form and quality of potential crop trees. Lodgepole pine terminal weevil attacked up to 73% of pine and over 24% suffered multiple attacks. Results from this study emphasize the need for more short- and long-term monitoring of young stands to inform the development of forest policy and promote healthy, resilient new forests. KEYWORDS: lodgepole pine, damage agents, lodgepole pine terminal weevil, western gall rust, Southern British Columbia