Abstract. Consideration of the scale at which communities are defined both taxonomically and spatially can reconcile apparently contradictory results on the extent to which plants show phylogenetic niche conservatism. In plant communities in north central Florida, we collected species abundances in 55 0.1-ha plots in several state parks. When communities were defined narrowly to include a single phylogenetic lineage, such as Quercus, Pinus, or Ilex, neighbors tended to be less related than expected (phylogenetic overdispersion) or there was no pattern. If the same communities were defined more broadly, such as when all seed plants were included, neighbors tended to be more related than expected (phylogenetic clustering). These results provide evidence that species interactions among close relatives influence community structure, but they also show that niche conservatism is increasingly evident as communities are defined to include greater phylogenetic diversity. We also found that, as the spatial scale is increased to encompass greater environmental heterogeneity, niche conservatism emerges as the dominant pattern. We then examined patterns of trait evolution in relation to trait similarity within communities for 11 functional traits for a single phylogenetic lineage (Quercus) and for all woody plants. Among the oaks, convergent evolution of traits important for environmental filtering contributes to the observed pattern of phylogenetic overdispersion. At the broader taxonomic scale, traits tend to be conserved, giving rise to phylogenetic clustering. The shift from overdispersion to clustering can be explained by the increasing conservatism of traits at broader phylogenetic scales.

Summary The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood‐based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. We phenotyped 396 clonally replicated genotypes of an interspecific pseudo‐backcross pedigree of Populus for wood composition and biomass traits in above‐ and below‐ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. Sixty‐three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen‐dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co‐localization identified the genomic position of potential pleiotropic regulators. Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach.

Summary• Freezing sensitivity of leaves and xylem was examined in four co-occurring Mediterranean oaks ( Quercus spp.) grown in a common garden to determine whether freezing responses of leaves and xylem were coordinated and could be predicted by leaf lifespan.• Freezing-induced embolism and loss of photosynthetic function were measured after overnight exposure to a range of subzero temperatures in both summer and winter.• Both measures were found to be dependent on minimum freezing temperature and were correlated with leaf lifespan and vessel diameter. The dependence of xylem embolism on minimum freezing temperature may result from the decline in water potential with ice temperature that influences the redistribution of water during freezing and leads to an increase in xylem tension. Winter acclimatization had a relatively small effect on the vulnerability to freezing-induced embolism, although leaf photosynthetic function showed a strong acclimatization response, particularly in the two evergreen species.• Quercus ilex , the species with the longest leaf lifespan and narrowest vessel diameters, showed the highest freezing tolerance. This helps explain its ability to inhabit a broad range throughout the Mediterranean region. By contrast, the inability of the deciduous oaks to maintain photosynthetic and vascular function throughout the winter indicates a competitive disadvantage that may prevent them from expanding their ranges.

Eddy covariance nighttime fluxes are uncertain due to potential measurement biases. Many studies report eddy covariance nighttime flux lower than flux from extrapolated chamber measurements, despite corrections for low turbulence. We compared eddy covariance and chamber estimates of ecosystem respiration at the GLEES Ameriflux site over seven growing seasons under high turbulence [summer night mean friction velocity (u*) = 0.7 m s(-1)], during which bark beetles killed or infested 85% of the aboveground respiring biomass. Chamber-based estimates of ecosystem respiration during the growth season, developed from foliage, wood, and soil CO2 efflux measurements, declined 35% after 85% of the forest basal area had been killed or impaired by bark beetles (from 7.1 ± 0.22 μmol m(-2) s(-1) in 2005 to 4.6 ± 0.16 μmol m(-2) s(-1) in 2011). Soil efflux remained at ~3.3 μmol m(-2) s(-1) throughout the mortality, while the loss of live wood and foliage and their respiration drove the decline of the chamber estimate. Eddy covariance estimates of fluxes at night remained constant over the same period, ~3.0 μmol m(-2) s(-1) for both 2005 (intact forest) and 2011 (85% basal area killed or impaired). Eddy covariance fluxes were lower than chamber estimates of ecosystem respiration (60% lower in 2005, and 32% in 2011), but the mean night estimates from the two techniques were correlated within a year (r(2) from 0.18 to 0.60). The difference between the two techniques was not the result of inadequate turbulence, because the results were robust to a u* filter of >0.7 m s(-1). The decline in the average seasonal difference between the two techniques was strongly correlated with overstory leaf area (r(2) = 0.92). The discrepancy between methods of respiration estimation should be resolved to have confidence in ecosystem carbon flux estimates.

A fundamental goal of systems biology is to identify genetic elements that contribute to complex phenotypes and to understand how they interact in networks predictive of system response to genetic variation. Few studies in plants have developed such networks, and none have examined their conservation among functionally specialized organs. Here we used genetical genomics in an interspecific hybrid population of the model hardwood plant Populus to uncover transcriptional networks in xylem, leaves, and roots. Pleiotropic eQTL hotspots were detected and used to construct coexpression networks a posteriori, for which regulators were predicted based on cis-acting expression regulation. Networks were shown to be enriched for groups of genes that function in biologically coherent processes and for cis-acting promoter motifs with known roles in regulating common groups of genes. When contrasted among xylem, leaves, and roots, transcriptional networks were frequently conserved in composition, but almost invariably regulated by different loci. Similarly, the genetic architecture of gene expression regulation is highly diversified among plant organs, with less than one-third of genes with eQTL detected in two organs being regulated by the same locus. However, colocalization in eQTL position increases to 50% when they are detected in all three organs, suggesting conservation in the genetic regulation is a function of ubiquitous expression. Genes conserved in their genetic regulation among all organs are primarily cis regulated (∼92%), whereas genes with eQTL in only one organ are largely trans regulated. Trans-acting regulation may therefore be the primary driver of differentiation in function between plant organs. eQTL | gene network | gene regulation | systems biology | Populus