The flavonol branch pathway has remained intact for millions of years, and is almost exclusively involved in the responses of plants to a wide array of stressful agents, despite the fact that evolution of flavonoid metabolism has produced >10 000 structures. Pollastri and Tattini (pp. 1225–1233) discuss the emerging functional roles of flavonols in the responses of present-day plants to different stresses, and consider how they may have performed a wide array of such roles during the colonization of land by plants.

Chromatin remodelling complexes are known to be responsiblefor nucleosome mobility leading to increased accessibility of DNA for binding proteins. Raut et al. (pp. 1235–1246) provide an overview of the subject and investigate histone octamer trans-transfer in partially purified nuclear extracts of wheat, Triticum aestivum. They find ATP-dependent octamer displacement in trans from a histone H1-depleted native donor chromatin of wheat to a labelled synthetic nucleosome positioning sequence, with activity mediated by ATP hydrolysis. The results suggest that wheat nuclei possess a typical chromatin remodelling activity similar to that in other eukaryotes. This is the first report of chromatin remodelling activity in vitro from plants.

Atherosperma moschatum is the most widespread Australian cool temperate rainforest tree yet its response to the cold and dry glacials is largely unknown. Worth et al. (pp. 1247–1256) investigate the species' chloroplast phylogeography and discover low but structured chloroplast DNA variation consistent with glacial survival in both northern and southern parts of the species' range. Lower chloroplast diversity than more cold-tolerant, co-occurring species, Nothofagus cunninghamii and Tasmannia lanceolata, is probably the result of stronger bottlenecks during glacials associated with a narrower climatic niche for A. moschatum.

Pollination-induced floral changes are assumed to enhance the plant's reproductive success. Niu et al. (pp. 1257–1268) examine floral closure in Cyananthus delavayi, a gynodioecious alpine species, and find that it can be induced by a very low pollen load, with pollen type (cross- or self-) being equally effective. The occurrence of floral closure may be determined by the proportion of fertilized ovules, but this response can be too sensitive to ensure sufficient pollen deposition and can, to some extent, lead to a cost in female fitness. The results thus imply that control of floral receptivity does not lead to an optimal fitness gain in this species.

The rhizomatous Trifolium ambiguum from high altitudes in eastern Europe and western Asia, and the stoloniferous T. occidentale from sea level in western Europe are geographically and ecologically divergent. Williams et al. (pp. 1269–1277) hybridize these species and show that, despite separation by the entire breadth of Europe, the speciation process is incomplete, and the species retain most of the genetic compatibilities needed for hybridization. The fertile progeny could lead to new clover breeding strategies.

It is difficult to separate the effects of tree size and light conditions on shoot morphology because short trees usually grow under shade. To avoid this problem, Miyata et al. (pp. 1279–1286) examine allometric characteristics of open-grown current-year leader shoots at the tops of forest tree crowns up to 24 m high. A common response of shoot morphology to tree height was found across the 13 co-occurring hardwood species studied, suggesting that there is a common functional constraint in height development, and it is hypothesized that this reflects an integrated response to height-associated water stress.

Hybridization followed by allopolyploidization is a principal speciation mode for Eleusine (Poaceae) in East Africa and the Americas. Liu et al. (pp. 1287–1298) use low-copy nuclear and plastid markers to determine independent allotetraploid origins for E. kigeziensis and the E. africana–E. coracana clade. Both events may have involved diploid E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The divergence time of the allotetraploid lineage falls into an interval when increasing amplitudes of palaeoclimate variability induced plant speciation in East Africa.

For heterophyllous amphibious plants that experience fluctuating water levels, it is critical to control leaf development precisely in response to environmental cues. Using Rotala hippuris (Lythraceae), an aquatic and semi-aquatic perennial, Momokawa et al. (pp. 1299–1306) manipulate the light environment and find that higher and lower red to far-red (R/FR) ratios cause leaf characters more typical of submerged and aerial leaves, respectively; the effect is seen in both aerial and submerged conditions. High blue light causes a shift towards aerial leaf traits, particularly under R/FR conditions expected near the water surface.

Strongly coherent sandsheaths envelope perennial roots of many monocotyledonous species of arid environments. Shane et al. (pp. 1307–1322) examine the structural development of the subtending roots in the perennial Lyginia barbata and propose that the complex of sandsheath/root hair/epidermis/cortex that forms is a structural unit facilitating water and nutrient uptake while the tissues are alive, recycling scarce phosphorus during senescence, and forming, when dead, a persistent and essential structure for maintenance of a functional stele.

In both animals and plants, prolyl 4-hydroxylases (P4Hs) are regarded as oxygen sensors under hypoxia stress. Zou et al. (pp. 1323–1335) conduct a comprehensive genome-wide analysis of P4H genes in maize, Zea mays (zmP4H), including under waterlogging. They identify nine zmP4H genes, of which five are alternatively spliced into at least 19 transcripts, and find that the ratios zmP4H2/zmP4H2-1 and zmP4H8-4/zmP4H8-5 are regulated by alternative splicing in response to waterlogging in the roots of seedlings, achieving quantitative post-transcriptional regulation.

Specific leaf area (SLA) is the preferred ‘soft’ trait for assessing soil fertility; however, Hodgson et al. (pp. 1337–1345) point out that the components of SLA relate to both fertility (leaf dry matter content, LDMC) and shade (leaf thickness). Using measurements from almost 2000 species, they find that gradients of fertility are frequently also gradients of biomass accumulation with reduced irradiance lower in the canopy. Therefore, SLA often discriminates better than LDMC; but LDMC should be the preferred trait for assessing gradients of soil fertility uncoupled from shade. They conclude that rather than using a single stand-alone predictor, multivariate analyses using several leaf traits is recommended.

Fast-growing willow hybrids (Salix spp.) are currently grown as energy crops on agricultural land mostly in cool-temperate climates, and improved yield under drought is an important breeding goal. Weih et al. (pp. 1347–1353) seek to identify plant traits functionally important for optimization of nitrogen (N) economy under water stress by examining 200 genotypes. They conclude that N-uptake efficiency and leaf N efficiency are important traits to improve growth under drought, and that increased leaf N content (on an area basis) is an acclimation to optimize N economy under such conditions, which makes it an interesting trait for future breeding studies.

Grasses employ silicon-based defences to fight off herbivores, but does this defence come at a cost? Garbuzov et al. (pp. 1355–1363) study the interactive effects of plant-available soil silicon and herbivory on competition between the grasses Poa annua and Lolium perenne. They find that soil silicon mediates interspecific competition among plants via two different mechanisms: directly through its species-specific effects on plant biomass, and indirectly through altering herbivore attack rates. These results suggest that a complex interplay between herbivore abundance, growth–defence trade-offs and the availability of soil silicon in the grasses' local environment may impact on plant community structure.

Plant growth and respiration have unresolved issues, for example in determining how to handle maintenance respiration (MR) in models and whether the ratio of respiration to gross photosynthesis in plant ecosystems is constant or variable. Thornley (pp. 1365–1380) constructs a two-state variable growth model with structure and substrate, applicable on plant to ecosystem scales, that does not represent MR explicitly: rather, it is an ‘emergent’ property. The model suggests that the respiration : photosynthesis ratio is 0·4, and is conservative because it depends on two parameters only, growth efficiency and recycling fraction, whose values are likely to be similar across ecosystems.

Rice (Oryza sativa) plants lose significant amounts of volatile NH₃ from their leaves, but the precise mechanisms involved remain unclear. Kumagai et al. (pp. 1381–1386) study photorespiration and conclude that it is strongly involved in NH₃ emission by rice leaves. They suggest that differences in emissions between the cultivars studied result from differences in glutamine synthetase activities, which will result in different capacities for reassimilation of photorespiratory NH₃. The results also suggest that NH₃ emission in rice leaves is not directly controlled by transpiration and stomatal conductance.