Genome-wide evolutionary response of European oaks during the Anthropocene.

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.

Which oak provenances for the 22nd century in Western Europe? Dendroclimatology in common gardens.

The current distribution area of the two sympatric oaks Quercus petraea and Q. robur covers most of temperate Western Europe. Depending on their geographic location, populations of these trees are exposed to different climate constraints, to which they are adapted. Comparing the performances of trees from contrasting populations provides the insight into their expected resilience to future climate change required for forest management. In this study, the descendants of 24 Q. petraea and two Q. robur provenances selected from sites throughout Europe were grown for 20 years in three common gardens with contrasting climates. The 2420 sampled trees allowed the assessments of the relationship between radial growth and climate. An analysis of 15-year chronologies of ring widths, with different combinations of climate variables, revealed different response patterns between provenances and between common gardens. As expected, provenances originating from sites with wet summers displayed the strongest responses to summer drought, particularly in the driest common garden. All provenances displayed positive significant relationships between the temperature of the previous winter and radial growth when grown in the common garden experiencing the mildest winter temperatures. Only eastern provenances from continental cold climates also clearly expressed this limitation of growth by cold winter temperatures in the other two common gardens. However, ecological distance, calculated on the basis of differences in climate between the site of origin and the common garden, was not clearly related to the radial growth responses of the provenances. This suggests that the gradient of genetic variability among the selected provenances was not strictly structured according to climate gradients. Based on these results, we provide guidelines for forest managers for the assisted migration of Quercus petraea and Q. robur provenances.

The pulse of the tree is under genetic control: eucalyptus as a case study.

The pulse of the tree (diurnal cycle of stem radius fluctuations) has been widely studied as a way of analyzing tree responses to the environment, including the phenotypic plasticity of tree-water relationships in particular. However, the genetic basis of this daily phenotype and its interplay with the environment remain largely unexplored. We characterized the genetic and environmental determinants of this response, by monitoring daily stem radius fluctuation (dSRF) on 210 trees from a Eucalyptus urophylla × E. grandis full-sib family over 2 years. The dSRF signal was broken down into hydraulic capacitance, assessed as the daily amplitude of shrinkage (DA), and net growth, estimated as the change in maximum radius between two consecutive days (ΔR). The environmental determinants of these two traits were clearly different: DA was positively correlated with atmospheric variables relating to water demand, while ΔR was associated with soil water content. The heritability for these two traits ranged from low to moderate over time, revealing a time-dependent or environment-dependent complex genetic determinism. We identified 686 and 384 daily quantitative trait loci (QTL) representing 32 and 31 QTL regions for DA and ΔR, respectively. The identification of gene networks underlying the 27 major genomics regions for both traits generated additional hypotheses concerning the biological mechanisms involved in response to water demand and supply. This study highlights that environmentally induced changes in daily stem radius fluctuation are genetically controlled in trees and suggests that these daily responses integrated over time shape the genetic architecture of mature traits.

Powdery Mildew Decreases the Radial Growth of Oak Trees with Cumulative and Delayed Effects over Years.

Quercus robur and Q. petraea are major European forest tree species. They have been affected by powdery mildew caused by Erysiphe alphitoides for more than a century. This fungus is a biotrophic foliar pathogen that diverts photosynthetate from the plant for its own nutrition. We used a dendrochronological approach to investigate the effects of different levels of infection severity on the radial growth of young oak trees. Oak infection was monitored at individual tree level, at two sites in southwestern France, over a five-year period (2001-2005). Mean infection severity was almost 75% (infected leaf area) at the end of the 2001 growing season, at both sites, but only about 40% in 2002, and 8%, 5% and 2% in 2003, 2004 and 2005, respectively. Infection levels varied considerably between trees and were positively related between 2001 and 2002. Increment cores were taken from each tree to assess annual ring widths and increases in basal area. Annual radial growth was standardised to take the effect of tree size into account. Annual standardised radial growth was significantly and negatively correlated with infection severity in the same year, for both 2001 and 2002, and at both sites. The decrease in growth reached 70-90% for highly infected trees. The earlywood width was poorly correlated with infection severity, but the proportion of latewood in tree rings was lower in highly infected trees (60%) than in less heavily infected trees (85%). Infection in 2001 and 2002 was found to have a cumulative effect on radial growth in these years, together with a delayed effect detectable in 2003. Thus, even non-lethal pathogens like powdery mildew can have a significant impact on tree functioning. This impact should be taken into account in growth and yield models, to improve predictions of forest net primary production.

A dynamic leaf gas-exchange strategy is conserved in woody plants under changing ambient CO2 : evidence from carbon isotope discrimination in paleo and CO2 enrichment studies.

Rising atmospheric [CO2 ], ca , is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water, and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas-exchange that include maintaining a constant leaf internal [CO2 ], ci , a constant drawdown in CO2 (ca  - ci ), and a constant ci /ca . These strategies can result in drastically different consequences for leaf gas-exchange. The accuracy of Earth systems models depends in part on assumptions about generalizable patterns in leaf gas-exchange responses to varying ca . The concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these strategies, provides a unifying framework for understanding leaf gas-exchange responses to ca . To assess leaf gas-exchange regulation strategies, we analyzed patterns in ci inferred from studies reporting C stable isotope ratios (δ(13) C) or photosynthetic discrimination (∆) in woody angiosperms and gymnosperms that grew across a range of ca spanning at least 100 ppm. Our results suggest that much of the ca -induced changes in ci /ca occurred across ca spanning 200 to 400 ppm. These patterns imply that ca  - ci will eventually approach a constant level at high ca because assimilation rates will reach a maximum and stomatal conductance of each species should be constrained to some minimum level. These analyses are not consistent with canalization toward any single strategy, particularly maintaining a constant ci . Rather, the results are consistent with the existence of a broadly conserved pattern of stomatal optimization in woody angiosperms and gymnosperms. This results in trees being profligate water users at low ca , when additional water loss is small for each unit of C gain, and increasingly water-conservative at high ca , when photosystems are saturated and water loss is large for each unit C gain.

Drivers of temporal changes in temperate forest plant diversity vary across spatial scales.

Global biodiversity is affected by numerous environmental drivers. Yet, the extent to which global environmental changes contribute to changes in local diversity is poorly understood. We investigated biodiversity changes in a meta-analysis of 39 resurvey studies in European temperate forests (3988 vegetation records in total, 17-75 years between the two surveys) by assessing the importance of (i) coarse-resolution (i.e., among sites) vs. fine-resolution (i.e., within sites) environmental differences and (ii) changing environmental conditions between surveys. Our results clarify the mechanisms underlying the direction and magnitude of local-scale biodiversity changes. While not detecting any net local diversity loss, we observed considerable among-site variation, partly explained by temporal changes in light availability (a local driver) and density of large herbivores (a regional driver). Furthermore, strong evidence was found that presurvey levels of nitrogen deposition determined subsequent diversity changes. We conclude that models forecasting future biodiversity changes should consider coarse-resolution environmental changes, account for differences in baseline environmental conditions and for local changes in fine-resolution environmental conditions.

Genetic architecture of carbon isotope composition and growth in Eucalyptus across multiple environments.

In the context of climate change, the water-use efficiency (WUE) of highly productive tree varieties, such as eucalypts, has become a major issue for breeding programmes. This study set out to dissect the genetic architecture of carbon isotope composition (δ(13) C), a proxy of WUE, across several environments. A family of Eucalyptus urophylla × E. grandis was planted in three trials and phenotyped for δ(13) C and growth traits. High-resolution genetic maps enabled us to target genomic regions underlying δ(13) C quantitative trait loci (QTLs) on the E. grandis genome. Of the 15 QTLs identified for δ(13) C, nine were stable across the environments and three displayed significant QTL-by-environment interaction, suggesting medium to high genetic determinism for this trait. Only one colocalization was found between growth and δ(13) C. Gene ontology (GO) term enrichment analysis suggested candidate genes related to foliar δ(13) C, including two involved in the regulation of stomatal movements. This study provides the first report of the genetic architecture of δ(13) C and its relation to growth in Eucalyptus. The low correlations found between the two traits at phenotypic and genetic levels suggest the possibility of improving the WUE of Eucalyptus varieties without having an impact on breeding for growth.

Soil water stress affects both cuticular wax content and cuticle-related gene expression in young saplings of maritime pine (Pinus pinaster Ait).

BACKGROUND: The cuticle is a hydrophobic barrier located at the aerial surface of all terrestrial plants. Recent studies performed on model plants, such as Arabidopsis thaliana, have suggested that the cuticle may be involved in drought stress adaptation, preventing non-stomatal water loss. Although forest trees will face more intense drought stresses (in duration and intensity) with global warming, very few studies on the role of the cuticle in drought stress adaptation in these long-lived organisms have been so far reported. RESULTS: This aspect was investigated in a conifer, maritime pine (Pinus pinaster Ait.), in a factorial design with two genetic units (two half-sib families with different growth rates) and two treatments (irrigated vs non-irrigated), in field conditions. Saplings were grown in an open-sided greenhouse and half were irrigated three times per week for two growing seasons. Needles were sampled three times per year for cuticular wax (composition and content) and transcriptome (of 11 genes involved in cuticle biosynthesis) analysis. Non-irrigated saplings (i) had a higher cuticular wax content than irrigated saplings and (ii) overexpressed most of the genes studied. Both these trends were more marked in the faster growing family. CONCLUSIONS: The higher cuticular wax content observed in the non-irrigated treatment associated with strong modifications in products from the decarbonylation pathway suggest that cuticular wax may be involved in drought stress adaptation in maritime pine. This study provides also a set of promising candidate genes for future forward genetic studies in conifers.

Carbon stable isotope ratio of phloem sugars in mature pine trees throughout the growing season: comparison of two extraction methods.

The study presents a comparison of two phloem sugar extraction methods. The amount of phloem sugar extracted and the carbon isotope composition (delta(13)C) of the total extracts and of the main phloem compounds separated by high-performance liquid chromatography (sucrose, glucose, fructose and pinitol) are compared. These two phloem sap extraction methods are exudation in distilled water and a new method using centrifugation, which avoids the addition of any solvent. We applied both extraction methods on phloem discs sampled from 38-year-old Pinus pinaster trees in south-western France throughout the period from June 2007 to December 2008 on different time-scales: hourly, daily and monthly. We found that the centrifugation method systematically extracted ca. 50% less compounds from the phloem discs than the exudation method. In addition, the two extraction methods provided similar delta(13)C values of the total extracts, but the values obtained by the exudation method were 0.6 per thousand more negative than those calculated from the mass balance using the individual constituents. Over the growing season, both extraction methods exhibited lower total sugar content and more (13)C-enriched phloem sap in summer compared with winter values. These findings suggest that both extraction methods can be applied to study the carbon isotope composition of phloem sap, and the centrifugation method has the advantage that no solvent has to be added. The exudation method, however, is more appropriate for the quantification of the amounts of phloem sugars.

Root architecture and wind-firmness of mature Pinus pinaster.

This study aims to link three-dimensional coarse root architecture to tree stability in mature timber trees with an average of 1-m rooting depth. Undamaged and uprooted trees were sampled in a stand damaged by a storm. Root architecture was measured by three-dimensional (3-D) digitizing. The distribution of root volume by root type and in wind-oriented sectors was analysed. Mature Pinus pinaster root systems were organized in a rigid 'cage' composed of a taproot, the zone of rapid taper of horizontal surface roots and numerous sinkers and deep roots, imprisoning a large mass of soil and guyed by long horizontal surface roots. Key compartments for stability exhibited strong selective leeward or windward reinforcement. Uprooted trees showed a lower cage volume, a larger proportion of oblique and intermediate depth horizontal roots and less wind-oriented root reinforcement. Pinus pinaster stability on moderately deep soils is optimized through a typical rooting pattern and a considerable structural adaptation to the prevailing wind and soil profile.