Recent publications

Growth decline and divergent tree ring isotopic composition (δ13C and δ18O) contradict predictions of CO2 stimulation in high altitudinal forests.

Fri, 10 May 2013 12:57:11 MST

Human-induced changes in atmospheric composition are expected to affect primary productivity across terrestrial biomes. Recent changes in productivity have been observed in many forest ecosystems, but low-latitude upper tree line forests remain to be investigated. Here, we use dendrochronological methods and isotopic analysis to examine changes in productivity, and their physiological basis, in Abies religiosa (Ar) and Pinus hartwegii (Ph) trees growing in high-elevation forests of central Mexico. Six sites were selected across a longitudinal transect (Transverse Volcanic Axis), from the Pacific Ocean toward the Gulf of Mexico, where mature dominant trees were sampled at altitudes ranging from 3200 to 4000 m asl. A total of 60 Ar and 84 Ph trees were analyzed to describe changes in growth (annual-resolution) and isotopic composition (decadal-resolution) since the early 1900s. Our results show an initial widespread increase in basal area increment (BAI) during the first half of the past century. However, BAI has decreased significantly since the 1950s with accentuated decline after the 1980s in both species and across sites. We found a consistent reduction in atmosphere to wood ¹³C discrimination, resulting from increasing water use efficiency (20–60%), coinciding with rising atmospheric CO₂. Changes in ¹³C discrimination were not followed, however, by shifts in tree ring δ¹⁸O, indicating site- and species-specific differences in water source or uptake strategy. Our results indicate that CO₂ stimulation has not been enough to counteract warming-induced drought stress, but other stressors, such as progressive nutrient limitation, could also have contributed to growth decline. Future studies should explore the distinct role of resource limitation (water vs. nutrients) in modulating the response of high-elevation ecosystems to atmospheric change.

Competition theory – science and application in mixed forest stands: review of experimental and modelling methods and suggestions for future research

Fri, 10 May 2013 11:56:21 MST

Competition in forest stands has long been of interest to researchers. However, much of the knowledge originates from empirical studies that examined the effects of competition. For instance, many studies were focused on the effects of the presence of herbaceous species on the development of tree seedlings or the decrease in individual tree growth with increases in stand density. Several models that incorporate competitive effects have been developed to predict tree and stand growth, but with simplified representations of competitive interactions. While these studies provided guidance useful for forest management, they contributed only partially to furthering our understanding of competitive mechanisms. Also, most competition studies were conducted in single-species stands. As competitive interactions occurring in mixed stands are characterized by a higher degree of complexity than those in single-species stands, a better understanding of these mechanisms can contribute to developing optimal management scenarios. The dynamics of forest stands with at least two species may be affected not only by competition, but also by facilitation or complementarity mechanisms. Thus, knowledge of the mechanisms may provide insight into the relative importance of intra- versus inter-specific competition and whether competition is symmetric or asymmetric. Special attention to the implementation of field experimental designs is warranted for mixed stands. While traditional spacing trials are appropriate for single-species stands, the examination of competitive interactions in mixed stands requires more complex experimental designs to examine the relative importance of species combinations. Forest productivity models allow resource managers to test different management scenarios, but again most of these models were developed for single-species stands. As competitive interactions are more complex in mixed stands, models developed to predict their dynamics will need to include more mechanistic representations of competition.

A new genus and species of fairyfly, Tinkerbella nana (Hymenoptera, Mymaridae), with comments on its sister genus Kikiki, and discussion on small size limits in arthropods.

Thu, 09 May 2013 09:02:21 MST

A new genus and species of fairyfly, Tinkerbella nana (Hymenoptera: Mymaridae) gen. n. and sp. n., is described from Costa Rica. It is compared with the related genus Kikiki Huber and Beardsley from the Hawaiian Islands, Costa Rica and Trinidad. A specimen of Kikiki huna Huber measured 158 μm long, thus holding the record for the smallest winged insect. The smallest size possible, as measured by body length, for flying insects and wingless arthropods is discussed.

Synopsis of adventive species of Coleoptera (Insecta) recorded from Canada. Part 2: Staphylinidae.

Tue, 30 Apr 2013 12:16:04 MST

A synopsis of adventive species of Staphylinidae (Coleoptera) in Canada is provided. Of the over 1654 rove beetle species recorded from Canada, 156 species in 76 genera and 13 subfamilies are reported as adventive, constituting about 9.4% of the fauna. The majority of adventive species belong to two subfamilies, Staphylininae (51 species) and Aleocharinae (49), and the genera with the most species are Philonthus (16), Atheta (8), Aleochara (7) and Quedius (7). All 156 adventive species are reviewed, including diagnostic features (supported by 156 colour habitus photos and 230 black and white images of diagnostic characters), native range, detailed distribution in Canada (with 151 distribution maps), general distribution in the USA, early Canadian and North American records and habitat information. New jurisdictional records are Atheta longicornis (Gravenhorst) from Alberta, Philonthus sanguinolentus (Gravenhorst) from eastern Canada (Ontario) and Xantholinus longiventris Heer from Canada (British Columbia).

Impact of salvage logging on stand structure and beetle diversity in boreal balsam fir forest, 20 years after a spruce budworm outbreak.

Tue, 30 Apr 2013 09:48:24 MST

Spruce budworm outbreaks represent the most important natural disturbance in the boreal balsam fir (Abies balsamea (L.) Mill.) forest of Canada, killing trees over wide areas and thus generating large amounts of dead wood. This disturbance is part of the dynamic processes occurring within balsam fir forests, and its effects on biodiversity need to be understood in order to move closer towards sustainable forest management. We described stand structure and used beetles as biodiversity indicators to compare the ecological value of salvaged stands, managed afterwards with three different silvicultural treatments, with unsalvaged stands, 20 years after the last spruce budworm outbreak. Our experimental design involved five replicated stands of each of the four disturbance types for a total of 20 stands. A total of 3124 Coleoptera belonging to 47 families and 269 taxa were captured over 3 months of sampling. Results showed that habitat attributes still differed 20 years after a spruce budworm outbreak between unsalvaged and treated salvaged stands, such as more abundant and diverse dead wood in unsalvaged stands. Salvage logging and silvicultural treatments led to different beetle communities than in unsalvaged stands, even though abundance and richness did not change significantly. Most indicator species identified were saproxylic and associated with unsalvaged stands, suggesting salvage logging generated the largest changes to the original ecosystem while additional effects of the silvicultural treatments were less pronounced. This may result from the 67% reduction in downed dead wood volumes (e.g., 138 m³/ha in unsalvaged stands vs 46 m³/ha in managed stands). Even if this volume of dead wood is still relatively high, it is less diverse than in unsalvaged stands and includes almost no recent dead wood. Salvage logging affected saproxylic beetle communities, suggesting that the retention of naturally disturbed stands may help in implementing ecosystem management in boreal balsam fir forest and move closer towards sustainable management.

Canadian national taper models.

Tue, 30 Apr 2013 09:29:37 MST

Work was done to gather stem taper data for most forest tree species across Canada. They were used for producing taper models to be applied for the purposes of the national forest inventory and for regional purposes when regional taper models are not available. The models are based on squared DBH and on measured or predicted tree height. A taper equation based on the dimensional analysis approach was adopted to fit Canadian national taper models using the collected data. The model parameters were estimated using a mixed model for taking into account variance heterogeneity and within-tree autocorrelation. In spite of the different protocols for data collection, the accuracy of the proposed stem taper models is similar to that found in previous studies. Consequently, the models seem suitable for pre-harvest estimation of sawlog volume nationally or regionally.

Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications.

Mon, 29 Apr 2013 14:47:17 MST

RNA transcripts such as mRNA or microRNA are frequently used as biomarkers to determine disease state or response to therapy. Reverse transcription (RT) in combination with quantitative PCR (qPCR) has become the method of choice to quantify small amounts of such RNA molecules. In parallel with the democratization of RT-qPCR and its increasing use in biomedical research or biomarker discovery, we witnessed a growth in the number of gene expression data analysis methods. Most of these methods are based on the principle that the position of the amplification curve with respect to the cycle-axis is a measure for the initial target quantity: the later the curve, the lower the target quantity. However, most methods differ in the mathematical algorithms used to determine this position, as well as in the way the efficiency of the PCR reaction (the fold increase of product per cycle) is determined and applied in the calculations. Moreover, there is dispute about whether the PCR efficiency is constant or continuously decreasing. Together this has lead to the development of different methods to analyze amplification curves. In published comparisons of these methods, available algorithms were typically applied in a restricted or outdated way, which does not do them justice. Therefore, we aimed at development of a framework for robust and unbiased assessment of curve analysis performance whereby various publicly available curve analysis methods were thoroughly compared using a previously published large clinical data set (Vermeulen et al., 2009). The original developers of these methods applied their algorithms and are co-author on this study. We assessed the curve analysis methods' impact on transcriptional biomarker identification in terms of expression level, statistical significance, and patient-classification accuracy. The concentration series per gene, together with data sets from unpublished technical performance experiments, were analyzed in order to assess the algorithms’ precision, bias, and resolution. While large differences exist between methods when considering the technical performance experiments, most methods perform relatively well on the biomarker data. The data and the analysis results per method are made available to serve as benchmark for further development and evaluation of qPCR curve analysis methods (http://qPCRDataMethods.hfrc.nl).

Powers, S.E.; Ascough II, J.C.; Nelson, R.G.; Larocque, G.R. 2011. Modeling water and soil quality environmental impacts associated with bioenergy crop production and biomass removal in the Midwest USA. Ecol. Model. 222:2430-2447.

Mon, 29 Apr 2013 12:34:09 MST

The removal of corn stover or production of herbaceous crops such as switchgrass (Panicum virgatum) or big bluestem (Andropogon gerardii) as feedstocks for bioenergy purposes has been shown to have significant benefits from an energy and climate change perspective. There is potential, however, to adversely impact water and soil quality, especially in the United States Corn Belt where stover removal predominantly occurs and possibly in other areas with herbaceous energy crops depending upon a number of geo-climatic and economic factors. The overall goal of this research was to provide a thorough and mechanistic understanding of the relationship between stover and herbaceous crop production management practices and resulting range of impacts on soil and water quality, with a focus on eastern Iowa, USA. Comparisons of the production of herbaceous bioenergy crops to continuous corn (Zea mays L.) and cornsoybean (Glycine max L.) rotations on five different soils representative of the region were performed. Indices for total nutrient (nitrogen and phosphorus) loss to surface water and groundwater, total soil loss due to water and wind erosion, and cumulative soil carbon loss were derived to assess long-term sustainability. The Agricultural Policy/Environmental eXtender (APEX) agroecosystem model was used to quantify the sustainability indices and to generate sufficient data to provide a greater understanding of variables that affect water and soil quality than previously possible. The results clearly show the superiority of herbaceous crop production from a soil and water quality perspective. They also show, however, that compared to traditional cropping systems (e.g., corn-soybean rotations with conventional tillage), soil and water quality degradation can be reduced under certain conditions at the same time stover is removed.

Linking adaptation, delimitation of evolutionarily significant units (ESUs), and gene function: a case study using hemlock looper ecotypes.

Mon, 29 Apr 2013 11:51:31 MST

Developing genetic markers for the identification of recently diverged groups, such as ecotypes or species complexes, remains difficult due to challenges with incomplete lineage sorting, hybridization and introgression. Genome-wide scans of single nucleotide polymorphisms (SNPs) have proven useful for inferring patterns of genetic differentiation at the population level. In combination with a new analytical technique, the discriminant analysis of principal components (DAPC), and within the framework of iterative taxonomy, it may also be possible to extract a combination of SNPs as markers for the delimitation of closely related groups. In addition, since DAPC identifies the loci contributing the most to group clustering, it may be possible to link putative biological function to differences that define group boundaries. We tested this technique on two ecotypes of the hemlock looper (Lambdina fiscellaria), which differ in terms of number of larval stadia, developmental rate and fecundity. It was possible to separately cluster the two ecotypes with 95% correct assignment using 27 SNPs. We also determined that a storage hexamerin carried eight of these SNPs, including the two highest contributing loci, of which the top contributor was nonsynonymous. Other studies have found this protein to be highly expressed just before metamorphosis, pointing to a possible connection between its role in clustering ecotypes and its biological function. These SNP markers can now be further developed for high throughput delimitation of individuals of unknown ecotype identity.

Identification of odor-processing genes in the emerald ash borer, Agrilus planipennis.

Mon, 29 Apr 2013 09:53:23 MST

Background: Insects rely on olfaction to locate food, mates, and suitable oviposition sites for successful completion of their life cycle. Agrilus planipennis Fairmaire (emerald ash borer) is a serious invasive insect pest that has killed tens of millions of North American ash (Fraxinus spp) trees and threatens the very existence of the genus Fraxinus. Adult A. planipennis are attracted to host volatiles and conspecifics; however, to date no molecular knowledge exists on olfaction in A. planipennis. Hence, we undertook an antennae-specific transcriptomic study to identify the repertoire of odor processing genes involved in A. planipennis olfaction.

Methodology and Principal Findings: We acquired 139,085 Roche/454 GS FLX transcriptomic reads that were assembled into 30,615 high quality expressed sequence tags (ESTs), including 3,249 isotigs and 27,366 non-isotigs (contigs and singletons). Intriguingly, the majority of the A. planipennis antennal transcripts (59.72%) did not show similarity with sequences deposited in the non-redundant database of GenBank, potentially representing novel genes. Functional annotation and KEGG analysis revealed pathways associated with signaling and detoxification. Several odor processing genes (9 odorant binding proteins, 2 odorant receptors, 1 sensory neuron membrane protein and 134 odorant/xenobiotic degradation enzymes, including cytochrome P450s, glutathione-S-transferases; esterases, etc.) putatively involved in olfaction processes were identified. Quantitative PCR of candidate genes in male and female A. planipennis in different developmental stages revealed developmental- and sex-biased expression patterns.

Conclusions and Significance: The antennal ESTs derived from A. planipennis constitute a rich molecular resource for the identification of genes potentially involved in the olfaction process of A. planipennis. These findings should help in understanding the processing of antennally-active compounds (e.g. 7-epi-sesquithujene) previously identified in this serious invasive pest.