Modeling Analysis of Primary Controls on Net Ecosystem Productivity of Seven Boreal and Temperate Coniferous Forests Across a Continental Transect

Process-based models are effective tools to synthesize and/or extrapolate measured carbon (C) exchanges from individual sites to large scales. In this study, we used a C- and nitrogen (N)-cycle coupled ecosystem model named CN-CLASS (Carbon Nitrogen-Canadian Land Surface Scheme) to study the role of primary climatic controls and site-specific C stocks on the net ecosystem productivity (NEP) of seven intermediate-aged to mature coniferous forest sites across an east–west continental transect in Canada. The model was parameterized using a common set of parameters, except for two used in empirical canopy conductance–assimilation, and leaf area–sapwood relationships, and then validated using observed eddy covariance flux data. Leaf Rubisco-N dynamics that are associated with soil–plant N cycling, and depend on canopy temperature, enabled the model to simulate site-specific gross ecosystem productivity (GEP) reasonably well for all seven sites. Overall GEP simulations had relatively smaller differences compared with observations vs. ecosystem respiration (RE), which was the sum of many plant and soil components with larger variability and/or uncertainty associated with them. Both observed and simulated data showed that, on an annual basis, boreal forest sites were either carbon-neutral or a weak C sink, ranging from 30 to 180 g C m−2 yr−1; while temperate forests were either a medium or strong C sink, ranging from 150 to 500 g C m−2 yr−1, depending on forest age and climatic regime. Model sensitivity tests illustrated that air temperature, among climate variables, and aboveground biomass, among major C stocks, were dominant factors impacting annual NEP. Vegetation biomass effects on annual GEP, RE and NEP showed similar patterns of variability at four boreal and three temperate forests. Air temperature showed different impacts on GEP and RE, and the response varied considerably from site to site. Higher solar radiation enhanced GEP, while precipitation differences had a minor effect. Magnitude of forest litter content and soil organic matter (SOM) affected RE. SOM also affected GEP, but only at low levels of SOM, because of low N mineralization that limited soil nutrient (N) availability. The results of this study will help to evaluate the impact of future climatic changes and/or forest C stock variations on C uptake and loss in forest ecosystems growing in diverse environments.Earth and Planetary Science

Evapotranspiration and its partitioning during and following a mountain pine beetle infestation of a lodgepole pine stand in the interior of British Columbia, Canada

IntroductionMassive tree mortality events in western Canada due to widespread infestation by mountain pine beetle (MPB) are expected to impact local-to-regional evapotranspiration (ET) dynamics during and after a disturbance. How ecosystem-level ET and its components may vary with canopy-tree mortality (treefall) and subsequent understory recovery remains unclear.MethodsWe used 10 years of continuous eddy-covariance and remote-sensing data (2007–2016) and machine-learning models based on random forest and xgboost to determine forest- and climate-driven effects at temporal scales appropriate for a lodgepole pine-dominated stand following a major, five-year MPB disturbance initiated in the summer of 2006.ResultsTotal annual ET over the 10 years ranged from 207.2 to 384.6 mm, with annual plant transpiration (T) contributing to 57 ± 5.4% (mean ± standard deviation) of annual ET. Annual ET initially declined (2007–2011) and then increased (2011–2016), with ET and T/ET increasing at statistically non-significant rates of approximately 3.2 and 1.2% per year from 2007 to 2016. Air temperature (Ta) and vapor pressure deficit (VPD) were the most important predictors of seasonal variation in ET and T/ET during the 10-year period, with high Ta, VPD, and photosynthetically active radiation (PAR) causing ET and T/ET to increase. Annual ET increased with both increasing spring Ta and decreasing VPD. Annual T/ET was shown to increase with increasing VPD and decrease with increasing volumetric soil water content at a 5-cm depth (VWC5). Enhanced vegetation index (EVI, an indicator of canopy greenness) lagged T and overstory tree mortality, whereas previous- and current-year values of EVI were shown to be poor predictors of annual ET and T/ET.Discussion and conclusionsThese findings suggest that the promotion of climate factors on forest ecosystem-level water vapor fluxes may offset reductions promoted by MPB outbreaks. Climate processes affected water vapor fluxes more than biotic factors, like stand greenness, highlighting the need to include climate-regulatory mechanisms in predictive models of ET dynamics during and subsequent to stand disturbance. Climate and forest-greenness effects on water vapor fluxes need to be explored at even longer time scales, e.g., at decadal scales, to capture long-drawn-out trends associated with stand disturbance and its subsequent recovery

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Potential Species Distribution of Balsam Fir Based on the Integration of Biophysical Variables Derived with Remote Sensing and Process-Based Methods

In this paper we present a framework for modelling potential species distribution (PSD) of balsam fir [bF; Abies balsamea (L.) Mill.] as a function of landscape-level descriptions of: (i) growing degree days (GDD: a temperature related index), (ii) land-surface wetness, (iii) incident photosynthetically active radiation (PAR), and (iv) tree habitat suitability. GDD and land-surface wetness are derived primarily from remote sensing data acquired with the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor on the Terra satellite. PAR is calculated with an existing spatial model of solar radiation. Raster-based calculations of habitat suitability and PSD are obtained by multiplying normalized values of species environmental-response functions (one for each environmental variable) parameterized for balsam fir. As a demonstration of the procedure, we apply the calculations to a high bF-content area in northwest New Brunswick, Canada, at 250-m resolution. Location of medium-to-high habitat suitability values (i.e., >0.50) and actual forests, with >50% bF, matched on average 92% of the time

Physiological and Morphological Variation in Balsam Fir Provenances Growing in New Brunswick, Canada

There is a need to understand the physio-morphological responses of northern tree species to climate change. The hypothesis of the current study was that provenance and light intensity were both influential in the control of intrinsic water-use efficiency (iWUE). Diameter at breast height (DBH)-increment was hypothesized as being more affected by provenance. Intrinsic water-use efficiency (iWUE), the ratio of photosynthesis (A) to stomatal conductance (gs), was assessed in foliage under two levels of photosynthetically active radiation (PAR; i.e., 300 and 1200 μmol m−2 s−1) in 63-year-old balsam fir [Abies balsamea (L.) Mill.] provenances derived from seed sources from across the species’ natural range (namely, within 44–51° N latitudes and 53–102° W longitudes) and cultivated in a common garden in eastern Canada. Diameter at breast height (DBH) of provenances from the common garden were measured when they were 42 and 58 years old (DBH1998, DBH2014). The results confirmed the hypotheses regarding the roles of provenance on iWUE and DBH (p −1 and 11.82–12.78 and 16.38–18.44 cm, respectively. Stomatal conductance of balsam fir had a strong relationship with iWUE at both light settings, whereas A had a weaker relationship with iWUE. There were no significant relationships between iWUE at the two light settings and climatic variables at the provenance source (p > 0.05). Diameter at breast height in 2014 was significantly greater than DBH1998 (p p < 0.05). There was a significant positive relationship between iWUE and DBH measured in 2014. Survivorship of provenances was shown to vary with DBH-increment. The results show that for present-day and future forest management, (i) selection in balsam fir, in relation to iWUE should ideally be based on a criterion of intraspecific stomatal conductance; (ii) shade tolerance of balsam fir, population differentiation, and consistent pace of DBH-growth under variable climatic conditions are important factors in the species’ sustained growth under changes in forest dynamics projected to accompany changes in regional climate; (iii) temperature variables are strong indicators of DBH-increment in balsam fir; (iv) the effect of tree size on its survival is maintained under variable climatic conditions; and (v) there is a clear association between iWUE and the species’ radial growth

Physiological and Morphological Variation in Balsam Fir Provenances Growing in New Brunswick, Canada

There is a need to understand the physio-morphological responses of northern tree species to climate change. The hypothesis of the current study was that provenance and light intensity were both influential in the control of intrinsic water-use efficiency (iWUE). Diameter at breast height (DBH)-increment was hypothesized as being more affected by provenance. Intrinsic water-use efficiency (iWUE), the ratio of photosynthesis (A) to stomatal conductance (gs), was assessed in foliage under two levels of photosynthetically active radiation (PAR; i.e., 300 and 1200 μmol m−2 s−1) in 63-year-old balsam fir [Abies balsamea (L.) Mill.] provenances derived from seed sources from across the species’ natural range (namely, within 44–51° N latitudes and 53–102° W longitudes) and cultivated in a common garden in eastern Canada. Diameter at breast height (DBH) of provenances from the common garden were measured when they were 42 and 58 years old (DBH1998, DBH2014). The results confirmed the hypotheses regarding the roles of provenance on iWUE and DBH (p &lt; 0.05), but showed a diminished role of PAR on iWUE. The lowest and highest mean iWUE and DBH among the provenances ranged between 0.028 and 0.031 and 0.079–0.083 μmol mmol−1 and 11.82–12.78 and 16.38–18.44 cm, respectively. Stomatal conductance of balsam fir had a strong relationship with iWUE at both light settings, whereas A had a weaker relationship with iWUE. There were no significant relationships between iWUE at the two light settings and climatic variables at the provenance source (p &gt; 0.05). Diameter at breast height in 2014 was significantly greater than DBH1998 (p &lt; 0.05). The relationships between DBH2014 and climatic variables at the provenance source were statistically significant (p &lt; 0.05). There was a significant positive relationship between iWUE and DBH measured in 2014. Survivorship of provenances was shown to vary with DBH-increment. The results show that for present-day and future forest management, (i) selection in balsam fir, in relation to iWUE should ideally be based on a criterion of intraspecific stomatal conductance; (ii) shade tolerance of balsam fir, population differentiation, and consistent pace of DBH-growth under variable climatic conditions are important factors in the species’ sustained growth under changes in forest dynamics projected to accompany changes in regional climate; (iii) temperature variables are strong indicators of DBH-increment in balsam fir; (iv) the effect of tree size on its survival is maintained under variable climatic conditions; and (v) there is a clear association between iWUE and the species’ radial growth