Sugar Pine Research Articles

First evidence for the conifer Pinus, as Pinuxylon selmeierianum sp. nov., during the Paleogene on Wootton Peninsula, northern Ellesmere Island, Nunavut, Canada

We describe a new fossil wood species of pine, Pinuxylon selmeierianum sp. nov., for a piece of petrified wood encased within a concretion that was recovered in marine, fine-grained sandstones of the Paleogene Eureka Sound Group on Wootton Peninsula, Ellesmere Island. The fossil wood is allochthonous, having drifted in from a nearby landmass. Within the fossil wood genus Pinuxylon Gothan, 1905, Pinuxylon selmeierianum sp. nov. shares anatomical characteristics with the haploxylon sections Parrya Mayr, 1890 and Strobus Little and Critchfield, 1969. The new species is most closely related to the extant Pinus lambertiana Douglas, 1827, a species belonging to section Strobus. Our study provides the first evidence for a fossil Pinus Linné, 1753 on Wootton Peninsula, supporting the idea that Pinus was an “Arctic conifer”, and providing insights into Paleogene vegetation at high latitudes.

Assessing the durability, stability, and usability of genetic resistance to a non‐native fungal pathogen in two pine species

Societal Impact StatementDamage to white pine forests by white pine blister rust, caused by the non‐native invasive fungal pathogen Cronartium ribicola, is affecting people across western North America. The loss of white pine forests can impact economic opportunities as well as ecosystem and human well‐being. In this paper we quantify the durability, stability, and usability of natural genetic resistance to the disease in two white pine species using long‐term field trials. By combining quantitative genetic resistance breeding programs with data from field validation trials, land managers and policy makers will be able to better ensure healthy forests for the future. Summary Many tree species are susceptible to non‐native pathogens or pests. Their level of susceptibility can be so severe that they are extirpated, and their use for forest restoration or reforestation is curtailed. Programs to find, enhance, and utilize genetic resistance in tree species are underway. Because trees are long‐lived, resistance must be effective for decades to centuries to be useful. Resistance needs to be durable, stable, and present at a useful level. Field plantings provide the best opportunity to assess resistance durability and stability across a range of environments. In this paper we examine the durability and stability of resistance levels, previously identified in seedling screening trials, of two white pine species, Pinus monticola (western white pine) and P. lambertiana (sugar pine) to white pine blister rust, using eight 15 to 20‐year‐old field trials in Oregon and northern California. We found that resistance varies for each host species and in different environments. Major gene resistance (MGR) may have limited utility and the search for resistance should include all types of resistance, as quantitative disease resistance (QDR) appears to be more durable than MGR in the long term at many sites in our study. Our data provide encouragement and support for the use of long‐term field validation studies in combination with quantitative genetic resistance breeding programs. We advocate for an increased use of field trials to ensure that resistance is effective for restoration and recovery against invasive pathogens and pests.

Effect of fire and thinning on fine-scale genetic structure and gene flow in fire-suppressed populations of sugar pine (Pinus lambertiana Dougl.)

Historically, frequent, low-severity fires in dry western North American forests were a major driver of ecological patterns and processes, creating resilient ecosystems dominated by widely-spaced pine species. However, a century of fire-suppression has caused overcrowding, altering forest composition to shade-tolerant species, while increasing competition and leaving trees stressed and susceptible to pathogens, insects, and high-severity fire. Exacerbating the issue, fire incidence is expected to increase with changing climate, while fire season has been observed to begin earlier and last longer than historic trends. Forest thinning and prescribed fire have been identified as important management tools to mitigate these risks. Yet little is known of how thinning, fire, or their interaction affect contemporary evolutionary processes of constituent pine species that influence fitness and play an important role in the opportunity for selection and population persistence. We assessed the impact of widely used fuel reduction treatments on fine-scale gene flow on an ecologically important and historically dominant shade-intolerant pine species of the Sierra Nevada, Pinus lambertiana Dougl. Treatment prescription (no-thin-no-fire, thin-no-fire, and fire-and-thin) was found to differentially affect both fine-scale spatial and genetic structure as well as effective gene flow in this species. Specifically, the thin-no-fire prescription increases genetic structure (spatial autocorrelation of relatives) between adults and seedlings, while seed and pollen dispersal increase and decrease, respectively, as a function of increasing disturbance intensity. While these results may be specific to the stands at our study site, they indicate how assumptions relating to genetic effects based on spatial structure can be misleading (for instance, in many stands the presence or absence of spatial structure was not indicative the presence or absence of genetic structure). It is likely that these disequilibrated systems will continue to evolve on unknown evolutionary trajectories. The long-term impacts of management practices on reduced fitness from inbreeding depression should be continually monitored to ensure resilience to increasingly frequent and severe fire, drought, and pest stresses.

Fuel dynamics after reintroduced fire in an old-growth Sierra Nevada mixed-conifer forest

BackgroundSurface fuel loadings are some of the most important factors contributing to fire intensity and fire spread. In old-growth forests where fire has been long excluded, surface fuel loadings can be high and can include woody debris ≥100 cm in diameter. We assessed surface fuel loadings in a long-unburned old-growth mixed-conifer forest in Yosemite National Park, California, USA, and assessed fuel consumption from a management-ignited fire set to control the progression of the 2013 Rim Fire. Specifically, we characterized the distribution and heterogeneity of pre-fire fuel loadings, both along transects and contained in duff mounds around large trees. We compared surface fuel consumption to that predicted by the standard First Order Fire Effects Model (FOFEM) based on pre-fire fuel loadings and fuel moistures. We also assessed the relationship between tree basal area—calculated for two different spatial neighborhood scales—and pre-fire fuel loadings.ResultsPre-fire total surface fuel loading averaged 192 Mg ha−1 and was reduced by 79% by the fire to 41 Mg ha−1 immediately after fire. Most fuel components were reduced by 87% to 90% by the fire, with the exception of coarse woody debris (CWD), which was reduced by 60%. Litter depth in duff mounds were within 1 SD of plot means, but duff biomass for the largest trees (>150 cm diameter at breast height [DBH]) exceeded plot background levels. Overstory basal area generally had significant positive relationships with pre-fire fuel loadings of litter, duff, 1-hour, and 10-hour fuels, but the strength of the relationships differed between overstory components (live, dead, all [live and dead], species), and negative relationships were observed between live Pinus lambertiana Douglas basal area and CWD. FOFEM over-predicted rotten CWD consumption and under-predicted duff consumption.ConclusionsSurface fuel loadings were characterized by heterogeneity and the presence of large pieces. This heterogeneity likely contributed to differential fire behavior at small scales and heterogeneity in the post-fire environment. The reductions in fuel loadings at our research site were in line with ecological restoration objectives; thus, ecologically restorative burning during fire suppression is possible.

Resolving Form-Structure-Function Relationships in Plants with MRI for Biomimetic Transfer.

In many biomimetic approaches, a deep understanding of the form-structure-function relationships in living and functionally intact organisms, which act as biological role models, is essential. This knowledge is a prerequisite for the identification of parameters that are relevant for the desired technical transfer of working principles. Hence, non-invasive and non-destructive techniques for static (3D) and dynamic (4D) high-resolution plant imaging and analysis on multiple hierarchical levels become increasingly important. In this study we demonstrate that magnetic resonance imaging (MRI) can be used to resolve the plants inner tissue structuring and functioning on the example of four plant concept generators with sizes larger than 5 mm used in current biomimetic research projects: Dragon tree (Dracaena reflexa var. angustifolia), Venus flytrap (Dionaea muscipula), Sugar pine (Pinus lambertiana) and Chinese witch hazel (Hamamelis mollis). Two different MRI sequences were applied for high-resolution 3D imaging of the differing material composition (amount, distribution, and density of various tissues) and condition (hydrated, desiccated, and mechanically stressed) of the four model organisms. Main aim is to better understand their biomechanics, development, and kinematics. The results are used as inspiration for developing novel design and fabrication concepts for bio-inspired technical fiber-reinforced branchings and smart biomimetic actuators.

Forest structure and climate mediate drought-induced tree mortality in forests of the Sierra Nevada, USA.

Extreme drought stress and associated bark beetle population growth contributed to an extensive tree mortality event in California, USA, resulting in more than 129million trees dying between 2012 and 2016. Although drought is an important driver of this mortality event, past and ongoing fire suppression and the consequent densification of forests may have contributed. In some areas, land management agencies have worked to reduce stand density through mechanical treatments and prescribed fire to restore forests to less dense, more open conditions that are presumably more resilient to disturbance and changing climate. Here, we evaluate if stand structural conditions associated with treated (e.g., thinned and prescribed burned) forests in the Sierra Nevada of California conferred more resistance to the bark beetle epidemic and drought event of 2012-2016. We found that, compared to untreated units, treated units had lower stand densities, larger average tree diameters, and greater dominance of pines (Pinus), the historically dominant trees. For all tree species studied, mortality was substantially greater in climatically drier areas (i.e., lower elevations and latitudes). Both pine species studied (ponderosa pine [Pinus ponderosa] and sugar pine [Pinus lambertiana]) had greater mortality in areas where their diameters were larger, suggesting a size preference for their insect mortality agents. For ponderosa pine, the tree species experiencing greatest mortality, individual-tree mortality probability (for a given tree diameter) was significantly lower in treated stands. Ponderosa pine mortality was also positively related to density of medium- to large-sized conspecific trees, especially in areas with lower precipitation, suggesting that abundance of nearby host trees for insect mortality agents was an important determinant of pine mortality. Mortality of incense cedar (Calocedrus decurrens) and white fir (Abies concolor) was positively associated with basal area, suggesting sensitivity to competition during drought, but overall mortality was lower, likely because the most prevalent and effective mortality agents (the bark beetles Dendroctonus brevicomis and D.ponderosae) are associated specifically with pine species within our study region. Our findings suggest that forest thinning treatments are effective in reducing drought-related tree mortality in forests, and they underscore the important interaction between water and forest density in mediating bark beetle-caused mortality.

Which trees die during drought? The key role of insect host‐tree selection

Abstract During drought, the tree subpopulations (such as size or vigour classes) that suffer disproportionate mortality can be conceptually arrayed along a continuum defined by the actions of biotic agents, particularly insects. At one extreme, stress dominates: insects are absent or simply kill the most physiologically stressed trees. At the opposite extreme, host selection dominates: outbreaking insects kill trees independently of their stress, instead selecting trees based on size or other traits. Intermediate responses are also possible. Yet for mixed‐species forests, we lack a broad understanding of the relative importance of insects in determining exactly which subpopulations of trees suffer disproportionate mortality during drought, and whether these subpopulations differ among co‐occurring tree species. During an extreme drought, we documented the roles of native bark beetles in the mortality of five tree species in California’s Sierra Nevada. We analysed the patterns and agents of tree mortality in 12 permanent plots and the patterns of mortality in 89 temporary plots. Most tree mortality was associated with bark beetles. However, the growth rates (an indicator of chronic stress) and sizes of trees that suffered greatest bark beetle‐related mortality differed sharply among tree taxa, variously conforming with domination by stress (Abies concolor), domination by host selection (Pinus lambertiana and P. ponderosa) or a mix of the two (Calocedrus decurrens). Quercus kelloggii mortality remained relatively low. Thus, even during extreme drought substantial proportions of stressed trees survived because they were of sizes that mostly avoided fatal insect attack. Conversely, substantial proportions of comparatively unstressed trees died because they were of sizes that were selectively killed by outbreaking insects. Synthesis. Native bark beetles were primarily responsible for determining which subpopulations of trees suffered greatest mortality during drought. However, idiosyncratic host‐tree selection by the different bark beetle taxa meant that the tree subpopulations suffering greatest mortality differed strikingly among tree taxa—for example, high mortality of small trees of one species, but of large trees of another. If idiosyncratic host‐tree selection by biotic mortality agents proves to be a generally common phenomenon, it could help explain weak broadscale correlations between tree traits and tree mortality during drought.

Drought Impacts and Compounding Mortality on Forest Trees in the Southern Sierra Nevada

The increase in compounding disturbances, such as “hotter droughts” coupled with insect outbreaks, has significant impacts on the integrity of forested ecosystems and their subsequent management for important ecosystem services and multiple-use objectives. In the Southern Sierra Nevada, years of severe drought have resulted in unprecedented tree mortality across this mountainous landscape. Additionally, past land management practices, including fire suppression, have led to overly stocked, homogenous forest stand structures, dominated by small diameter, shade-tolerant and fire-intolerant tree species. Thus, the current condition of the landscape has further increased the susceptibility of forest trees to multiple stressors. We sought to determine the effects of extreme drought and insect outbreaks on tree mortality and their influence on forest stand structure and composition. To characterize mortality patterns, we monitored the condition of mature forest trees (>25.4 cm diameter at breast height) across 255 monitoring plots with four repeated measurements from 2015 through 2017. Tree mortality varied by species and through time. Reductions in pine species (Pinus lambertiana Douglas and P. ponderosa Lawson & C. Lawson) occurred earlier in the study period than Abies concolor (Gord. & Glend.) Lindl. Ex Hildebr. or Calocedrus decurrens (Torr.) Florin. Across species, larger tree size, most often associated with tree height, was consistently related to increased survival in mature, overstory trees. As expected, sites with greater pine stocking and subsequently more bark beetle (Curculionidae: Scolytinae) host availability had increased pine mortality, especially for P. ponderosa. For Abies concolor, lower overstory basal area increased tree survival for this species. This study highlights the importance of effective forest monitoring, especially during a period of unprecedented ecological change as the compounding disturbance had a disproportional effect on pine species in smaller diameter classes. Proactive forest management may be necessary to maintain and promote these ecologically important species in heterogeneous mixtures across the landscape.

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

BackgroundDe novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.ResultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.ConclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.

Persistence of fire-killed conifer snags in California, USA

BackgroundCoarse woody debris has numerous functions in forest ecosystems, including wildlife habitat, fuel loading, and nutrient cycling. Standing dead trees, or snags, are particularly important resources for wildlife, and guidelines for snag recruitment and retention are integral parts of forest management. However, snag persistence is not well understood and existing models are poorly validated. We monitored fire-killed conifer snag persistence after four California wildfires and one prescribed fire. Species sampled included white fir (Abies concolor [Gord. & Glend.] Lindl. ex Hildebr.), incense-cedar (Calocedrus decurrens [Torr.] Florin), Jeffrey pine (Pinus jeffreyi [Balf.]), sugar pine (Pinus lambertiana Douglas), and ponderosa pine (Pinus ponderosa Lawson & C. Lawson var. ponderosa C. Lawson).ResultsFire-injured trees that survived at least one year post fire were monitored for 10 years after they died. We developed two sets of species-specific snag persistence rates: a simplified model based only on time since death, and a full model that included tree characteristics. The primary factors affecting persistence rates in all models were snag age (years since death) and species. Secondary factors included diameter at breast height, time between fire and tree death, and crown injury. Snag persistence rates decreased with snag age. Yellow pine snags (a combined group of ponderosa pine and Jeffrey pine) fell significantly faster than any other species. Larger-diameter snags persisted longer than smaller-diameter snags for all species. Incense-cedar trees that survived longer post fire persisted longer as snags.ConclusionsThis study provides land managers with guidance on snag longevity, which can aid in planning for long-term wildlife habitat, fuel loading estimates, and forest structural diversity.

Multi-scale assessment of post-fire tree mortality models

Post-fire tree mortality models are vital tools used by forest land managers to predict fire effects, estimate delayed mortality and develop management prescriptions. We evaluated the performance of mortality models within the First Order Fire Effects Model (FOFEM) software, and compared their performance to locally-parameterised models based on five different forms. We evaluated all models at the individual tree and stand levels with a dataset comprising 34174 trees from a mixed-conifer forest in the Sierra Nevada, California that burned in the 2013 Rim Fire. We compared stand-level accuracy across a range of spatial scales, and we used point pattern analysis to test the accuracy with which mortality models predict post-fire tree spatial pattern. FOFEM under-predicted mortality for the three conifers, possibly because of the timing of the Rim Fire during a severe multi-year drought. Locally-parameterised models based on crown scorch were most accurate in predicting individual tree mortality, but tree diameter-based models were more accurate at the stand level for Abies concolor and large-diameter Pinus lambertiana, the most abundant trees in this forest. Stand-level accuracy was reduced by spatially correlated error at small spatial scales, but stabilised at scales ≥1ha. The predictive error of FOFEM generated inaccurate predictions of post-fire spatial pattern at small scales, and this error could be reduced by improving FOFEM model accuracy for small trees.

Tree mortality following drought in the central and southern Sierra Nevada, California, U.S.

Much of California, U.S. experienced a severe drought in 2012–2015 inciting a large tree mortality event in the central and southern Sierra Nevada. We assessed causal agents and rates of tree mortality, and short-term impacts to forest structure and composition based on a network of 11.3-m fixed-radius plots installed within three elevation bands on the Eldorado, Stanislaus, Sierra and Sequoia National Forests (914–1219, 1219–1524 and 1524–1829 m on the Eldorado, Stanislaus, Sierra; 1219–1524, 1524–1829, and 1829–2134 m on the Sequoia), where tree mortality was most severe. About 48.9% of trees died between 2014 and 2017. Tree mortality ranged from 46.1 ± 3.3% on the Eldorado National Forest to 58.7 ± 3.7% on the Sierra National Forest. Significantly higher levels of tree mortality occurred in the low elevation band (60.4 ± 3.0%) compared to the high elevation band (46.1 ± 2.9%). Ponderosa pine, Pinus ponderosa Dougl. ex Laws., exhibited the highest levels of tree mortality (89.6%), with 39.4% of plots losing all P. ponderosa. Mortality of P. ponderosa was highest at the lowest elevations, concentrated in larger-diameter trees, and attributed primarily to colonization by western pine beetle, Dendroctonus brevicomis LeConte. About 89% of P. ponderosa in the three largest diameter classes were killed, representing loss of an important structural component of these forests with implications to wildlife species of conservation concern. Sugar pine, P. lambertiana Dougl., exhibited the second highest levels of tree mortality (48.1%). Mortality of P. lambertiana was concentrated in the mid-diameter classes and attributed primarily to colonization by mountain pine beetle, D. ponderosae Hopkins. White fir, Abies concolor (Gord. & Glend.) Lindl. ex Hildebr., and incense cedar, Calocedrus decurrens (Torr.) Florin, exhibited 26.3% and 23.2% mortality, respectively. Only one Quercus died. Tree mortality (numbers of trees killed) was positively correlated with tree density and slope. A time lag was observed between the occurrence of drought and the majority of tree mortality. Tree regeneration (seedlings and saplings) was dominated by C. decurrens and Quercus spp., representing a potential long-term shift in composition from forests that were dominated by P. ponderosa. About 22.2% of plots contained plant species considered invasive, including cheatgrass, Bromus tectorum L., ripgut brome, Bromus diandrus Roth, bull thistle, Cirsium vulgare (Savi) Ten., and yellow star-thistle, Centaura solstitalis L. The implications of these and other results to recovery and management of drought-impacted forests in the central and southern Sierra Nevada are discussed.

Characterizing Forest Floor Fuels Surrounding Large Sugar Pine (Pinus lambertiana) in the Klamath Mountains, California

Fire exclusion has contributed to substantial basal accumulations of forest floor fuels in many historically fire-prone forests in western North America. These accumulations can contribute to undesired impacts (e.g., elevated tree mortality, more smoke production). Thus, managers interested in limiting some of these impacts require a better understanding of the spatial factors contributing to forest floor fuel variation in long-unburned forests. To address this need, we measured the forest floor mound size and depth of each layer at four distances from the tree (base, half, edge, and beyond) in each cardinal direction from the tree, and a subset of density measures for each layer and position around 25 large sugar pine (Pinus lambertiana) in the Klamath Mountains of California. Based on our study we found: 1) duff depths were greater than litter depths and both decreased with distance from tree; 2) duff densities were typically greater than litter but were highly variable with distance to tree; 3) litter and duff depths were positively correlated with loading; 4) use of a previously developed depth-to-loading equation performed well, but tended to underestimate litter loading and overestimate duff loading; and 5) tree size was the most strongly related to basal accumulations of forest floor fuels. Our results indicate there are consistent tree characteristics that can help predict the accumulation of forest floor fuels. This research can help provide managers with site-specific equations to inform fuel and fire treatments in areas with substantial basal accumulation in forests with large sugar pine.

What mediates tree mortality during drought in the southern Sierra Nevada?

Severe drought has the potential to cause selective mortality within a forest, thereby inducing shifts in forest species composition. The southern Sierra Nevada foothills and mountains of California have experienced extensive forest dieback due to drought stress and insect outbreak. We used high-fidelity imaging spectroscopy (HiFIS) and light detection and ranging (LiDAR) from the Carnegie Airborne Observatory (CAO) to estimate the effect of forest dieback on species composition in response to drought stress in Sequoia National Park. Our aims were (1) to quantify site-specific conditions that mediate tree mortality along an elevation gradient in the southern Sierra Nevada Mountains, (2) to assess where mortality events have a greater probability of occurring, and (3) to estimate which tree species have a greater likelihood of mortality along the elevation gradient. A series of statistical models were generated to classify species composition and identify tree mortality, and the influences of different environmental factors were spatially quantified and analyzed to assess where mortality events have a greater likelihood of occurring. A higher probability of mortality was observed in the lower portion of the elevation gradient, on southwest- and west-facing slopes, in areas with shallow soils, on shallower slopes, and at greater distances from water. All of these factors are related to site water balance throughout the landscape. Our results also suggest that mortality is species-specific along the elevation gradient, mainly affecting Pinus ponderosa and Pinus lambertiana at lower elevations. Selective mortality within the forest may drive long-term shifts in community composition along the elevation gradient.

Finding loci associated to partial resistance to white pine blister rust in sugar pine (Pinus lambertiana Dougl.).

White pine blister rust (WPBR) is an exotic disease threatening five-needle pines in North America. In spite of its relatively recent introduction, some five-needle pines such as sugar pine (Pinus lambertiana) have developed both complete (major) gene resistance and partial (quantitative) resistance to WPBR. While significant effort has been dedicated to clone and locate the position of the major gene of WPBR resistance in sugar pine, the genetic basis of quantitative resistance remains largely unknown in all Strobus pines. In this work, we took a preliminary approach to identify potential genotype × phenotype associations using the results of long-term survival and symptoms of infection in both experimental and applied breeding populations. Our study found significant associations between several genes and WPBR disease symptoms such as normal active cankers and blights, important symptoms in the development of partial resistance. No significant associations were found with percentage of survival, probably due to the complex inheritance of the disease and long time to infection. With this study, we hope to lay the ground for further genome-wide association studies using large phenotypic data sets in sugar pine and other Strobus pines.

Predicting Post-Fire Tree Mortality for 12 Western US Conifers Using the First Order Fire Effects Model (FOFEM)

Accurate prediction of fire-caused tree mortality is critical for making sound land management decisions such as developing burning prescriptions and post-fire management guidelines. To improve efforts to predict post-fire tree mortality, we developed 3-year post-fire mortality models for 12 Western conifer species—white fir (Abies concolor [Gord. & Glend.] Lindl. ex Hildebr.), red fir (Abies magnifica A. Murray bis), subalpine fir (Abies lasiocarpa [Hook.] Nutt.), incense cedar (Calocedrus decurrens [Torr.] Florin), western larch (Larix occidentalis Nutt.), lodgepole pine (Pinus contorta Douglas ex Loudon var. latifolia Engelm. ex S. Watson), whitebark pine (Pinus albicaulis Engelm.), ponderosa pines (Pinus ponderosa Lawson & C. Lawson var. scopulorum Engelm and var. ponderosa C. Lawson), Jeffrey pine (Pinus jeffreyi Balf.), sugar pine (Pinus lambertiana Douglas), Engelmann spruce (Picea engelmannii Parry ex Engelm.), and Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco var. glauca [Beissn.] Franco)—by pooling data collected from multiple fire-injury studies. Two sets of models were created: one for use in pre-fire planning in which only crown injury and tree diameter (DBH) were potential variables, and a second, optimal model for use in post-fire planning that used all significant variables. Predictive accuracy of all models was compared to the accuracy of the general, non-species specific mortality model used in the First Order Fire Effects Model (FOFEM) prior to version 5.7. The new species-specific models improved prediction of fire-caused tree mortality by 0 % to 48 %. Model accuracy increased the most for red fir, incense cedar, western larch, and whitebark pine, and increased the least for Engelmann spruce. The models in the post-fire option provided higher accuracy compared to the pre-fire models, but also required additional inputs. These new models were added to FOFEM beginning with version 5.7, and the options in the FOFEM Mortality Module were expanded. We describe the new options in FOFEM and how to use the software to predict tree mortality for pre-fire and post-fire planning, as well as modeling limitations and assumptions. The additions to FOFEM offer improved accuracy in predicting post-fire tree mortality for 12 Western conifer species and allow direct inputs of fire injury to increase software applicability to prescribed fire and post-fire forest management.

Contrasting Impacts of Climate and Competition on Large Sugar Pine Growth and Defense in a Fire-Excluded Forest of the Central Sierra Nevada

Many forest ecosystems with a large pine component in the western United States have experienced environmental stress associated with climate change and increased competition with forest densification in the absence of fire. Information on how changes in climate and competition affect carbon allocation to tree growth and defense is needed to anticipate changes to tree vigor and, ultimately, stand structure. This study retrospectively examined the influence of annual climate and competition measures on the growth and defense of 113 large sugar pines (Pinus lambertiana) in a mixed-conifer forest of the central Sierra Nevada of California. We found that growth in large sugar pine was positively associated with higher January temperatures and lower intraspecific competition. Resin duct size was negatively associated with climatic water deficit and total competition, while resin duct area contrastingly showed a positive relationship with total competition. From 1979 to 2012, the rates of growth increased, while resin duct size decreased. Our results suggest that tree vigor measures can respond differently to climate and competition factors that may lead to separate growth and defense trends over time. Stress associated with warmer temperatures and higher competition may distinctly influence individual tree and stand-level vigor with potential implications for future forest dynamics.

From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly’s NG50 is 1.94 million bp, an eightfold increase.

Effects of climate on competitive dynamics in mixed conifer forests of the Sierra Nevada

Trees in more competitive environments appear to respond to climate differently than trees in less competitive environments. In turn, climate patterns may affect inter- or intra-specific competition, favoring certain individuals over others. Using dendrochronological methods, we sampled cores from dominant pine trees and their nearby competitors in 40 stands in the northern Sierra Nevada. Our dendroclimatological analyses showed complex responses to climate for the dominant pine and their competitors. Pinus lambertiana Dougl. and Pinus ponderosa Dougl. Ex P. & C. Laws benefited from cooler temperatures in the past May; all species benefited from warmer winter temperatures; Calocedrus decurrens (Torr.) Florin benefited from cooler temperatures in the past summer, while Abies concolor (Gord. & Glend.) Lindl.) and the two pine species benefited from cooler temperatures in the present summer. All species showed consistently positive effects from increased precipitation and increased moisture availability. A competition ratio calculated as the ratio between the dominant tree’s radial increments to the competitor’s indicated that climate could influence competition through one of two mechanisms. One, negative responses to climate conditions that were negative for one species but neutral for another tended to drive the competition ratios. Two, conditions that were negative for both competing trees tended to hurt competitors more than dominant trees, while conditions that were generally positive tended to help competitors more than dominant trees. These results suggest that the dominant pine trees may be more resilient to climate stress than competitors. Reducing competition via management such as thinning may increase climatic resilience for all species and possibly have positive competitive results for competitors. Increasing temperatures will tend to harm Sierra Nevada conifers in the summer and spring, but may show some benefit over the winter as long as precipitation is not reduced.

Long-Term Performance of Preservative-Treated Shingles of Western Wood Species

Abstract The performance of western hemlock, sugar pine, and western larch as alternatives to western redcedar (WRC) for roof shingles was investigated on outdoor roof racks with and without an initial brush or dip treatment with either pentachlorophenol (penta) or chromated copper arsenate (CCA). Untreated shingles of all species experienced degradation over a 32-year exposure in western Oregon, but WRC provided the best performance. Penta treatments improved performance to some extent, but the best protection was provided by a dip treatment in CCA prior to installation. The results illustrate the benefits of even shallow surface protection in aboveground exposures.