The use of CO2 flux measurements in models of the global terrestrial carbon budget

CO₂ flux measurements give access to two critical terms of the carbon budget of terrestrial ecosystems, the gross primary productivity (GPP) and the net ecosystem productivity (NEP). CO₂ fluxes measured by micrometeorological methods have spatial and temporal characteristics that make them potentially useful in modelling the global terrestrial carbon budget. The first use is in parameterizing ecosystem physiological processes. We present an example, based on parameterizing the mean light response of GPP. This parameterization can be used in diagnostic, satellite-based GPP models. A global application leads to realistic estimates of global GPP. The second use is in testing the seasonality of fluxes predicted by global models. Our example of this use tests two global GPP models. One is a diagnostic, satellite-based model, and one is a prognostic, process-based model. Despite the limitations of the models, both agree reasonably well with the measurements. The agreements and disagreements are useful in addressing the problems of available input datasets and representation of processes, in global models. Long-term CO₂ flux measurements give access to key variables of terrestrial vegetation models and therefore offer exciting perspectives.     

Recovery of ponderosa pine ecosystem carbon and water fluxes from thinning and stand‐replacing fire

Carbon uptake by forests is a major sink in the global carbon cycle, helping buffer the rising concentration of CO₂ in the atmosphere, yet the potential for future carbon uptake by forests is uncertain. Climate warming and drought can reduce forest carbon uptake by reducing photosynthesis, increasing respiration, and by increasing the frequency and intensity of wildfires, leading to large releases of stored carbon. Five years of eddy covariance measurements in a ponderosa pine (Pinus ponderosa)‐dominated ecosystem in northern Arizona showed that an intense wildfire that converted forest into sparse grassland shifted site carbon balance from sink to source for at least 15 years after burning. In contrast, recovery of carbon sink strength after thinning, a management practice used to reduce the likelihood of intense wildfires, was rapid. Comparisons between an undisturbed‐control site and an experimentally thinned site showed that thinning reduced carbon sink strength only for the first two posttreatment years. In the third and fourth posttreatment years, annual carbon sink strength of the thinned site was higher than the undisturbed site because thinning reduced aridity and drought limitation to carbon uptake. As a result, annual maximum gross primary production occurred when temperature was 3 °C higher at the thinned site compared with the undisturbed site. The severe fire consistently reduced annual evapotranspiration (range of 12–30%), whereas effects of thinning were smaller and transient, and could not be detected in the fourth year after thinning. Our results show large and persistent effects of intense fire and minor and short‐lived effects of thinning on southwestern ponderosa pine ecosystem carbon and water exchanges.     

Quantifying the impact of daily and seasonal variation in sap pH on xylem dissolved inorganic carbon estimates in plum trees

In studies on internal CO₂ transport, average xylem sap pH (pH_x) is one of the factors used for calculation of the concentration of dissolved inorganic carbon in the xylem sap ([]). Lack of detailed pH_x measurements at high temporal resolution could be a potential source of error when evaluating [] dynamics. In this experiment, we performed continuous measurements of CO₂ concentration ([CO₂]) and stem temperature (T_stem), complemented with pH_x measurements at 30‐min intervals during the day at various stages of the growing season (Day of the Year (DOY): 86 (late winter), 128 (mid‐spring) and 155 (early summer)) on a plum tree (Prunus domestica L. cv. Reine Claude d'Oullins). We used the recorded pH_x to calculate [] based on T_stem and the corresponding measured [CO₂]. No statistically significant difference was found between mean [] calculated with instantaneous pH_x and daily average pH_x. However, using an average pH_x value from a different part of the growing season than the measurements of [CO₂] and T_stem to estimate [] led to a statistically significant error. The error varied between 3.25 ± 0.01% under‐estimation and 3.97 ± 0.01% over‐estimation, relative to the true [] data. Measured pH_x did not show a significant daily variation, unlike [CO₂], which increased during the day and declined at night. As the growing season progressed, daily average [CO₂] (3.4%, 5.3%, 7.4%) increased and average pH_x (5.43, 5.29, 5.20) decreased. Increase in [CO₂] will increase its solubility in xylem sap according to Henry's law, and the dissociation of [] will negatively affect pH_x. Our results are the first quantifying the error in [] due to the interaction between [CO₂] and pH_x on a seasonal time scale. We found significant changes in pH_x across the growing season, but overall the effect on the calculation of [] remained within an error range of 4%. However, it is possible that the error could be more substantial for other tree species, particularly if pH_x is in the more sensitive range (pH_x > 6.5).     

Modelling ozone effects on adult beech trees through simulation of defence, damage, and repair costs: Implementation of the CASIROZ ozone model in the ANAFORE forest model

Ozone affects adult trees significantly, but effects on stem growth are hard to prove and difficult to correlate with the primary sites of ozone damage at the leaf level. To simulate ozone effects in a mechanistic way, at a level relevant to forest stand growth, we developed a simple ozone damage and repair model (CASIROZ model) that can be implemented into mechanistic photosynthesis and growth models. The model needs to be parameterized with cuvette measurements on net photosynthesis and dark respiration. As the CASIROZ ozone sub-model calculates effects of the ozone flux, a reliable representation of stomatal conductance and therefore ozone uptake is necessary to allow implementation of the ozone sub-model. In this case study the ozone sub-model was used in the ANAFORE forest model to simulate gas exchange, growth, and allocation. A preliminary run for adult beech (FAGUS SYLVATICA) under different ozone regimes at the Kranzberg forest site (Germany) was performed. The results indicate that the model is able to represent the measured effects of ozone adequately, and to distinguish between immediate and cumulative ozone effects. The results further help to understand ozone effects by distinguishing defence from damage and repair. Finally, the model can be used to extrapolate from the short-term results of the field study to long-term effects on tree growth. The preliminary simulations for the Kranzberg beech site show that, although ozone effects on yearly growth are variable and therefore insignificant when measured in the field, they could become significant at longer timescales (above 5 years, 5 % reduction in growth). The model offers a possible explanation for the discrepancy between the significant effects on photosynthesis (10 to 30 % reductions simulated), and the minor effects on growth. This appears to be the result of the strong competition and slow growth of the Kranzberg forest, and the importance of stored carbon for the adult beech (by buffering effects on carbon gain). We finally conclude that inclusion of ozone effects into current forest growth and yield models can be an important improvement into their overall performance, especially when simulating younger and less dense forests.     

Genetic diversity of hop stunt viroid from symptomatic and asymptomatic citrus trees in Iran

Hop stunt viroid as the causal agent of cachexia disease has detected from citrus trees in different areas in Iran. Although cachexia has not been reported as a decline disease for citrus trees, it can impair crop quality and reduce plant yields. This study was undertaken to molecularly detect HSVd among different commercial citrus cultivars and determine genetic diversity of this viroid in Mazandaran province of Iran. Sampling was performed from symptomatic and symptomless citrus cultivars in Mazandaran province. HSVd specific primers were used for molecular detection. SSCP and sequencing were applied to assay HSVd genetic diversity. Results showed the detection of HSVd in all symptomatic Satsuma (25 out of 25), Clementine (25 out of 25), sweet lime (20 out of 20) and sweet orange cv. Valencia (7 out of 7), as well as, 31% (14 out of 22), 100% (12 out of 12) and 33% (5 out of 15) of page mandarin, lemon and grapefruit trees, respectively. 10 different HSVd genomes were identified by sequencing the SSCP profiles among which HSVd‐IR1 had the most frequency.     

Respiratory carbon use and carbon storage in mid‐rotation loblolly pine (Pinus taeda L.) plantations: the effect of site resources on the stand carbon balance

We used estimates of autotrophic respiration (R_A), net primary productivity (NPP) and soil CO₂ evolution (S_ff), to develop component carbon budgets for 12‐year‐old loblolly pine plantations during the fifth year of a fertilization and irrigation experiment. Annual carbon use in R_A was 7.5, 9.0, 15.0, and 15.1 Mg C ha^?1 in control (C), irrigated (I), fertilized (F) and irrigated and fertilized (IF) treatments, respectively. Foliage, fine root and perennial woody tissue (stem, branch, coarse and taproot) respiration accounted for, respectively, 37%, 24%, and 39% of R_A in C and I treatments and 38%, 12% and 50% of R_A in F and IF treatments. Annual gross primary production (GPP=NPP+R_A) ranged from 13.1 to 26.6 Mg C ha^?1. The I, F, and IF treatments resulted in a 21, 94, and 103% increase in GPP, respectively, compared to the C treatment. Despite large treatment differences in NPP, R_A, and carbon allocation, carbon use efficiency (CUE=NPP/GPP) averaged 0.42 and was unaffected by manipulating site resources. Ecosystem respiration (R_E), the sum of S_ff, and above ground R_A, ranged from 12.8 to 20.2 Mg C ha^?1 yr^?1. S_ff contributed the largest proportion of R_E, but the relative importance of S_ff decreased from 0.63 in C treatments to 0.47 in IF treatments because of increased aboveground R_A. Aboveground woody tissue R_A was 15% of R_E in C and I treatments compared to 25% of R_E in F and IF treatments. Net ecosystem productivity (NEP=GPP‐R_E) was roughly 0 in the C and I treatments and 6.4 Mg C ha^?1 yr^?1 in F and IF treatments, indicating that non‐fertilized treatments were neither a source nor a sink for atmospheric carbon while fertilized treatments were carbon sinks. In these young stands, NEP is tightly linked to NPP; increased ecosystem carbon storage results mainly from an increase in foliage and perennial woody biomass.     

Future wood productivity of Pinus radiata in New Zealand under expected climatic changes

The physiologically based growth model CenW was used to simulate wood‐productivity responses of Pinus radiata forests to climate change in New Zealand. The model was tested under current climatic conditions against a comprehensive set of observations from growth plots located throughout the country. Climate change simulations were based on monthly climate change fields of 12 GCMs forced by the SRES B1, A1B and A2 emission scenarios for 2040 and 2090. Simulations used either constant or increasing CO₂ concentrations corresponding to the different emission scenarios. With constant CO₂, there were only slight growth responses to climate change across the country as a whole. More specifically, there were slight growth reductions in the warmer north but gains in the cooler south, especially at higher altitudes. For sites where P. radiata is currently grown, and across the full suite of GCMs and emission scenarios, changes in wood productivity averaged +3% for both 2040 and 2090. When increasing CO₂ concentration was also included, responses of wood productivity were generally positive, with average increases of 19% by 2040 and 37% by 2090. These responses varied regionally, ranging from relatively minor changes in the north of the country to very significant increases in the south, where the beneficial effect of increasing CO₂ combined with the beneficial effect of increasing temperatures. These relatively large responses to CO₂ depend on maintenance of the current adequate fertility levels in most commercial plantations. Productivity enhancements came at the expense of some soil‐carbon losses. Average losses for the country were simulated to average 3.5% under constant CO₂ and 1.5% with increasing CO₂ concentration. Again, there were regional differences, with larger losses for regions with lesser growth enhancements, and lesser reductions in regions where greater productivity enhancements could partly balance the effect of faster decomposition activity.     

Ozone effects in a drier climate: implications for stomatal fluxes of reduced stomatal sensitivity to soil drying in a typical grassland species

The widely distributed temperate grassland species Dactylis glomerata was grown in competition with Ranunculus acris at two different watering regimes and exposed for 20 weeks to eight ozone treatments with mean concentrations ranging from 16.2 to 89.5 ppb, representing pre‐industrial to predicted post‐2100 ozone climates. Measurements of stomatal conductance were used to parameterize ozone flux models for D. glomerata. For the first time, a modification was made to the standard flux model to account for the observed decrease in sensitivity of stomatal conductance to reduced water availability with increasing ozone. Comparison of calculated cumulative ozone flux between the two versions of the model demonstrated that exclusion of the ozone effect on stomatal conductance in the standard flux model led to a large underestimation of ozone fluxes at mid‐ to high‐ozone concentrations. For example, at a mean ozone concentration of 55 ppb (as predicted for many temperate areas in the next few decades), the standard flux model underestimated ozone fluxes in D. glomerata by 30–40% under reduced water availability. Although the modified flux model does not markedly change the flux‐based critical level for D. glomerata, this study indicates that use of the standard flux model to quantify the risk of ozone damage to a widely distributed grassland species such as D. glomerata in areas where high ozone concentrations and reduced soil moisture coincide could lead to an underestimation of effects. Thus, this study has shown that under predicted future climate change and ozone scenarios, ozone effects on vegetation may be even greater than previously predicted in the drier areas of the world.     

Uptake of SO2 in shoots of Scots pine: field measurements of net flux of sulphur in relation to stomatal conductance

Abstract. Net fluxes of gaseous sulphur compounds, water vapour and carbon dioxide to current- and one-year-old shoots of Scots pine were simultaneously measured in the field. The shoots were fumigated in temperature-controlled assimilation chambers with sulphur dioxide at concentrations ranging from 40 to 250 μg m⁻³ (15–95 ppb). The hypothesis that stomatal opening regulates the uptake of sulphur dioxide was tested. The following conclusions were reached concerning the dry deposition of sulphur dioxide to a dry coniferous shoot.
There was a marked diurnal variation in the uptake rate of sulphur dioxide. The net deposition velocity of sulphur was about three times higher during the day than during the night during July-October. Stomatal opening was not the primary factor controlling the dry deposition rate of sulphur dioxide. The net dry deposition rate was significantly smaller than the calculated rate based on stomatal conductances for water vapour.
Part of this deviation could be explained by re-emission of reduced sulphur compound(s) from the needles. The re-emission of sulphur was a light-dependent process and might be of great significance for the sulphur balance calculations.
A variable deposition velocity should be used in atmospheric transport models to account for the diurnal and seasonal variation in the surface resistance of a dry canopy.     

Modelled net carbon gain responses to climate change in boreal trees: Impacts of photosynthetic parameter selection and acclimation

Boreal forests are crucial in regulating global vegetation‐atmosphere feedbacks, but the impact of climate change on boreal tree carbon fluxes is still unclear. Given the sensitivity of global vegetation models to photosynthetic and respiration parameters, we determined how predictions of net carbon gain (C‐gain) respond to variation in these parameters using a stand‐level model (MAESTRA). We also modelled how thermal acclimation of photosynthetic and respiratory temperature sensitivity alters predicted net C‐gain responses to climate change. We modelled net C‐gain of seven common boreal tree species under eight climate scenarios across a latitudinal gradient to capture a range of seasonal temperature conditions. Physiological parameter values were taken from the literature together with different approaches for thermally acclimating photosynthesis and respiration. At high latitudes, net C‐gain was stimulated up to 400% by elevated temperatures and CO₂ in the autumn but suppressed at the lowest latitudes during midsummer under climate scenarios that included warming. Modelled net C‐gain was more sensitive to photosynthetic capacity parameters (V_cmax, J_max, Arrhenius temperature response parameters, and the ratio of J_max to V_cmax) than stomatal conductance or respiration parameters. The effect of photosynthetic thermal acclimation depended on the temperatures where it was applied: acclimation reduced net C‐gain by 10%–15% within the temperature range where the equations were derived but decreased net C‐gain by 175% at temperatures outside this range. Thermal acclimation of respiration had small, but positive, impacts on net C‐gain. We show that model simulations are highly sensitive to variation in photosynthetic parameters and highlight the need to better understand the mechanisms and drivers underlying this variability (e.g., whether variability is environmentally and/or biologically driven) for further model improvement.     

Disparate effects of global‐change drivers on mountain conifer forests: warming‐induced growth enhancement in young trees vs. CO2 fertilization in old trees from wet sites

Theory predicts that the postindustrial rise in the concentration of CO₂ in the atmosphere (c_a) should enhance tree growth either through a direct fertilization effect or indirectly by improving water use efficiency in dry areas. However, this hypothesis has received little support in cold‐limited and subalpine forests where positive growth responses to either rising c_a or warmer temperatures are still under debate. In this study, we address this issue by analyzing an extensive dendrochronological network of high‐elevation Pinus uncinata forests in Spain (28 sites, 544 trees) encompassing the whole biogeographical extent of the species. We determine if the basal area increment (BAI) trends are linked to climate warming and increased c_a by focusing on region‐ and age‐dependent responses. The largest improvement in BAI over the past six centuries occurred during the last 150 years affecting young trees and being driven by recent warming. Indeed, most studied regions and age classes presented BAI patterns mainly controlled by temperature trends, while growing‐season precipitation was only relevant in the driest sites. Growth enhancement was linked to rising c_a in mature (151–300 year‐old trees) and old‐mature trees (301–450 year‐old trees) from the wettest sites only. This finding implies that any potential fertilization effect of elevated c_a on forest growth is contingent on tree features that vary with ontogeny and it depends on site conditions (for instance water availability). Furthermore, we found widespread growth decline in drought‐prone sites probably indicating that the rise in c_a did not compensate for the reduction in water availability. Thus, warming‐triggered drought stress may become a more important direct driver of growth than rising c_a in similar subalpine forests. We argue that broad approaches in biogeographical and temporal terms are required to adequately evaluate any effect of rising c_a on forest growth.     

Carbon cost of plant nitrogen acquisition: global carbon cycle impact from an improved plant nitrogen cycle in the Community Land Model

Plants typically expend a significant portion of their available carbon (C) on nutrient acquisition – C that could otherwise support growth. However, given that most global terrestrial biosphere models (TBMs) do not include the C cost of nutrient acquisition, these models fail to represent current and future constraints to the land C sink. Here, we integrated a plant productivity‐optimized nutrient acquisition model – the Fixation and Uptake of Nitrogen Model – into one of the most widely used TBMs, the Community Land Model. Global plant nitrogen (N) uptake is dynamically simulated in the coupled model based on the C costs of N acquisition from mycorrhizal roots, nonmycorrhizal roots, N‐fixing microbes, and retranslocation (from senescing leaves). We find that at the global scale, plants spend 2.4 Pg C yr^?1 to acquire 1.0 Pg N yr^?1, and that the C cost of N acquisition leads to a downregulation of global net primary production (NPP) by 13%. Mycorrhizal uptake represented the dominant pathway by which N is acquired, accounting for ~66% of the N uptake by plants. Notably, roots associating with arbuscular mycorrhizal (AM) fungi – generally considered for their role in phosphorus (P) acquisition – are estimated to be the primary source of global plant N uptake owing to the dominance of AM‐associated plants in mid‐ and low‐latitude biomes. Overall, our coupled model improves the representations of NPP downregulation globally and generates spatially explicit patterns of belowground C allocation, soil N uptake, and N retranslocation at the global scale. Such model improvements are critical for predicting how plant responses to altered N availability (owing to N deposition, rising atmospheric CO₂, and warming temperatures) may impact the land C sink.     

Evolution of a secondary metabolic pathway from primary metabolism: shikimate and quinate biosynthesis in plants

The shikimate pathway synthesizes aromatic amino acids essential for protein biosynthesis. Shikimate dehydrogenase (SDH) is a central enzyme of this primary metabolic pathway, producing shikimate. The structurally similar quinate is a secondary metabolite synthesized by quinate dehydrogenase (QDH). SDH and QDH belong to the same gene family, which diverged into two phylogenetic clades after a defining gene duplication just prior to the angiosperm/gymnosperm split. Non‐seed plants that diverged before this duplication harbour only a single gene of this family. Extant representatives from the chlorophytes (Chlamydomonas reinhardtii), bryophytes (Physcomitrella patens) and lycophytes (Selaginella moellendorfii) encoded almost exclusively SDH activity in vitro. A reconstructed ancestral sequence representing the node just prior to the gene duplication also encoded SDH activity. Quinate dehydrogenase activity was gained only in seed plants following gene duplication. Quinate dehydrogenases of gymnosperms, represented here by Pinus taeda, may be reminiscent of an evolutionary intermediate since they encode equal SDH and QDH activities. The second copy in P. taeda maintained specificity for shikimate similar to the activity found in the angiosperm SDH sister clade. The codon for a tyrosine residue within the active site displayed a signature of positive selection at the node defining the QDH clade, where it changed to a glycine. Replacing the tyrosine with a glycine in a highly shikimate‐specific angiosperm SDH was sufficient to gain some QDH function. Thus, very few mutations were necessary to facilitate the evolution of QDH genes.     

Nitrogen and carbon contents and δ15N and δ13C signatures in six bryophyte species: assessment of long‐term deposition changes (1980–2010) in Spanish beech forests

In this study we used recent (2010) and herbarium material (1980) of six bryophyte species to assess long‐term atmospheric deposition in natural forested areas in northern Spain. For this purpose, tissue nitrogen and carbon content, as well as δ¹³C and δ¹⁵N signatures of samples of Hypnum cupressiforme, Polytrichastrum formosum, Leucobryum juniperoideum, Rhytidiadelphus loreus, Homalothecium lutescens and Diplophyllum albicans were analysed and comparisons made between years and species. In addition, the usefulness of each of the six species was evaluated. The range of values observed was similar to that in other studies carried out in rural areas. Significantly lower values were found in 2010 for N (H. cupressiforme), δ¹⁵N (R. loreus and D. albicans), C (R. loreus) and δ¹³C (all except L. juniperoideum). Our natural areas are thus now less influenced by atmospheric pollutants than they were, most probably due to changes in some traditional local activities. Differences were observed between species for all the four parameters studied, so different species must not be analysed together. Finally, R. loreus and H. lutescens seem to be good bioindicators, sensitive even with a few samples, although further studies are needed to corroborate their usefulness.     

Elevated CO2 affects photosynthetic responses in canopy pine and subcanopy deciduous trees over 10 years: a synthesis from Duke FACE

Leaf responses to elevated atmospheric CO₂ concentration (C_a) are central to models of forest CO₂ exchange with the atmosphere and constrain the magnitude of the future carbon sink. Estimating the magnitude of primary productivity enhancement of forests in elevated C_a requires an understanding of how photosynthesis is regulated by diffusional and biochemical components and up‐scaled to entire canopies. To test the sensitivity of leaf photosynthesis and stomatal conductance to elevated C_a in time and space, we compiled a comprehensive dataset measured over 10 years for a temperate pine forest of Pinus taeda, but also including deciduous species, primarily Liquidambar styraciflua. We combined over one thousand controlled‐response curves of photosynthesis as a function of environmental drivers (light, air C_a and temperature) measured at canopy heights up to 20 m over 11 years (1996–2006) to generate parameterizations for leaf‐scale models for the Duke free‐air CO₂ enrichment (FACE) experiment. The enhancement of leaf net photosynthesis (A_net) in P. taeda by elevated C_a of +200 μmol mol^?1 was 67% for current‐year needles in the upper crown in summer conditions over 10 years. Photosynthetic enhancement of P. taeda at the leaf‐scale increased by two‐fold from the driest to wettest growing seasons. Current‐year pine foliage A_net was sensitive to temporal variation, whereas previous‐year foliage A_net was less responsive and overall showed less enhancement (+30%). Photosynthetic downregulation in overwintering upper canopy pine needles was small at average leaf N (N_area), but statistically significant. In contrast, co‐dominant and subcanopy L. styraciflua trees showed A_net enhancement of 62% and no A_net–N_area adjustments. Various understory deciduous tree species showed an average A_net enhancement of 42%. Differences in photosynthetic responses between overwintering pine needles and subcanopy deciduous leaves suggest that increased C_a has the potential to enhance the mixed‐species composition of planted pine stands and, by extension, naturally regenerating pine‐dominated stands.     

Seasonal soil‐surface carbon fluxes from the root systems of young Pinus radiata trees growing at ambient and elevated CO2 concentration

Elevated atmospheric CO₂ concentration may result in increased below‐ground carbon allocation by trees, thereby altering soil carbon cycling. Seasonal estimates of soil surface carbon flux were made to determine whether carbon losses from Pinus radiata trees growing at elevated CO₂ concentration were higher than those at ambient CO₂ concentration, and whether this was related to increased fine root growth. Monthly soil surface carbon flux density (f) measurements were made on plots with trees growing at ambient (350) and elevated (650 μmol mol^?1) CO₂ concentration in large open‐top chambers. Prior to planting the soil carbon concentration (0.1%) and f (0.28 μmol m^?2 s^?1 at 15 °C) were low. A function describing the radial pattern of f with distance from tree stems was used to estimate the annual carbon flux from tree plots. Seasonal estimates of fine root production were made from minirhizotrons and the radial distribution of roots compared with radial measurements of f. A one‐dimensional gas diffusion model was used to estimate f from soil CO₂ concentrations at four depths. For the second year of growth, the annual carbon flux from the plots was 1671 g y^?1 and 1895 g y^?1 at ambient and elevated CO₂ concentrations, respectively, although this was not a significant difference. Higher f at elevated CO₂ concentration was largely explained by increased fine root biomass. Fine root biomass and stem production were both positively related to f. Both root length density and f declined exponentially with distance from the stem, and had similar length scales. Diurnal changes in f were largely explained by changes in soil temperature at a depth of 0.05 m. Ignoring the change of f with increasing distance from tree stems when scaling to a unit ground area basis from measurements with individual trees could result in under‐ or overestimates of soil‐surface carbon fluxes, especially in young stands when fine roots are unevenly distributed.     

Historical Stem‐Mapped Permanent Plots Increase Precision of Reconstructed Reference Data in Ponderosa Pine Forests of Northern Arizona

Forest structural reference conditions are widely used to understand how ecosystems have been altered and guide restoration and management objectives. We used six stem‐mapped permanent plots established in the early twentieth century to provide precise structural reference conditions for ponderosa pine forests of northern Arizona prior to Euro‐American settlement. Reference conditions for these plots in 1873–1874 included the following historical attributes: tree densities of 45–127 trees/ha, mean tree diameter at breast height (dbh) of 43.8 cm with a corresponding quadratic mean diameter range of 41.5–51.3 cm, and a stand basal area of 9.2–18.0 m²/ha. The reconstructed diameter distributions (for live ponderosa pine trees with dbh ≥9.14 cm) prior to fire exclusion varied in shape but generally displayed an irregular unimodal distribution. We suggest that management objectives for the structural restoration of ponderosa pine forests of northern Arizona emphasize: (1) conservation and retention of all pre‐settlement (>130 years) trees; (2) reduction of tree densities with a restoration objective ranging between 50 and 150 trees/ha having a large‐tree component between 25 and 50% of the total trees per hectare, respectively; (3) manipulation of the diameter distribution to achieve a unimodal or irregular, uneven‐aged shape (possibly targeting a balanced, uneven‐aged shape on cinder soil types) through the use of harvest and thinning practices that mimic gap disturbances (i.e., individual tree selection system); and (4) retention of 3–11 snags and logs per hectare resulting from natural mortality.     

Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein‐coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species‐specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein‐coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four‐fold higher d_N/d_S ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well‐preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.