METHODS: Pollen dispersal patterns and male fecundity variation of Shorea leprosula and Shorea parvifolia ssp. parvifolia on Peninsular Malaysian were investigated during two general flowering seasons (2001 and 2002), using a neighbourhood model modified by including terms accounting for variation in male fecundity among individual trees to express heterogeneity in flowering.
KEY RESULTS: The pollen dispersal patterns of the two dipterocarp species were affected by differences in conspecific tree flowering density, and reductions in conspecific tree flowering density led to an increased selfing rate. Active pollen dispersal and a larger number of effective paternal parents were observed for both species in the season of greater magnitude of general flowering (2002).
CONCLUSIONS: The magnitude of general flowering, male fecundity variation, and distance between pollen donors and mother trees should be taken into account when attempting to predict the effects of management practices on the self-fertilization and genetic structure of key tree species in tropical forest, and also the sustainability of possible management strategies, especially selective logging regimes.
METHODS: A large dataset was gathered, including four 2-year series of monthly sowings of 28 sorghum varieties in Mali and two 1-year series of monthly sowings of eight rice varieties in the Philippines to compare with previously published monthly sowings in Japan and Malaysia, and data from sorghum breeders in France, Nicaragua and Colombia. An additive linear model of the duration in days to panicle initiation (PI) and flowering time using daylength and daily changes in sunrise and sunset times was implemented.
KEY RESULTS: Simultaneous with the phyllochron, the duration to PI of field crops acclimated to the mean temperature at seedling emergence within the usual range of mean cropping temperatures. A unique additive linear model combining daylength and daily changes in sunrise and sunset hours was accurately fitted for any type of response in the duration to PI to the sowing date without any temperature input. Once calibrated on a complete and an incomplete monthly sowing series at two tropical latitudes, the model accurately predicted the duration to PI of the concerned varieties from the equatorial to the temperate zone.
CONCLUSIONS: Including the daily changes in sunrise and sunset times in the updated photoperiodism model largely improved its accuracy at the latitude of each experiment. More research is needed to ascertain its multi-latitudinal accuracy, especially at latitudes close to the equator.
METHODS: We collected foliar samples (n = 1533) comprising 90 families, 198 genera and 495 plant species from ultramafic soils, further foliar samples (n = 177) comprising 45 families, 80 genera and 120 species from non-ultramafic soils and corresponding soil samples (n = 393 from ultramafic soils and n = 66 from non-ultramafic soils) from Kinabalu Park (Sabah, Malaysia). The data were geographically (Kinabalu Park) and edaphically (ultramafic soils) constrained. The inclusion of a relatively high proportion (approx. 14 %) of samples from hyperaccumulator species [with foliar concentrations of aluminium and nickel (Ni) >1000 μg g-1, cobalt, copper, chromium and zinc >300 μg g-1 or manganese (Mn) >10 mg g-1] allowed for hypothesis testing.
KEY RESULTS: Frequency distribution graphs for most elements [calcium (Ca), magnesium (Mg) and phosphorus (P)] were unimodal, although some were skewed left (Mg and Mn). The Ni frequency distribution was bimodal and the separation point for the two modes was between 250 and 850 μg g-1.
CONCLUSIONS: Accounting for statistical probability, the established empirical threshold value (>1000 μg g-1) remains appropriate. The two discrete modes for Ni indicate ecophysiologically distinct behaviour in plants growing in similar soils. This response is in contrast to Mn, which forms the tail of a continuous (approximately log-normal) distribution, suggestive of an extension of normal physiological processes.
Methods: Observations were performed using light microscopy and scanning electron microscopy. Ancestral states of selected wood and pith characters were reconstructed using an existing molecular phylogeny for Nepenthes and a broader Caryophyllales framework. Pairwise comparisons were assessed for possible relationships between wood anatomy and developmental stages, growth habits, substrates and ecology.
Key Results: Wood anatomy of Nepenthes is diffuse porous, with mainly solitary vessels showing simple, bordered perforation plates and alternate intervessel pits, fibres with distinctly bordered pits (occasionally septate), apotracheal axial parenchyma and co-occurring uni- and multiseriate rays often including silica bodies. Precipitation and growth habit (stem length) are linked with vessel density and multiseriate ray height, while soil type correlates with vessel diameter, vessel element length and maximum ray width. For Caryophyllales as a whole, silica grains, successive cambia and bordered perforation plates are the result of convergent evolution. Peculiar helical sculpturing patterns within various cell types occur uniquely within the insectivorous clade of non-core Caryophyllales.
Conclusions: The wood anatomical variation in Nepenthes displays variation for some characters dependent on soil type, precipitation and stem length, but is largely conservative. The helical-banded fibre-sclereids that mainly occur idioblastically in pith and cortex are synapomorphic for Nepenthes , while other typical Nepenthes characters evolved convergently in different Caryophyllales lineages.
Methods: First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces.
Key Results: The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots.
Conclusion: Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.
Methods: To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred.
Key Results: Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed.
Conclusions: Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric speciation may have occurred. By contrast, Artocarpus diversity east of Borneo (where many of the islands have no historical connections to the landmasses of the Sunda and Sahul shelves) is unique and probably the product of over water long-distance dispersal events and subsequent diversification in allopatry. This work represents the most comprehensive Artocarpus phylogeny and biogeography study to date and supports Borneo as an evolutionary biodiversity hotspot.
METHODS: We examined how isotopic enrichment varied in the diverse genus Nepenthes, among species producing pitchers for invertebrate capture and species exhibiting mutualisms for the collection of mammal excreta. Enrichment factors were calculated from δ15N and δ13C values from eight Nepenthes species and naturally occurring hybrids along with co-occurring reference (non-carnivorous) plants from three mountain massifs in Borneo: Mount Kinabalu, Mount Tambuyukon and Mount Trus Madi.
RESULTS: All Nepenthes examined, except N. edwardsiana, were significantly enriched in 15N compared to co-occurring non-carnivorous plants, and 15N enrichment was more than two-fold higher in species with adaptations for the collection of mammal excreta compared with other Nepenthes.
CONCLUSIONS: The collection of mammal faeces clearly represents a highly effective strategy for heterotrophic nitrogen gain in Nepenthes. Species with adaptations for capturing mammal excreta occur exclusively at high elevation (i.e. are typically summit-occurring) where previous studies suggest invertebrate prey are less abundant and less frequently captured. As such, we propose this strategy may maximize nutritional return by specializing towards ensuring the collection and retention of few but higher-value N sources in environments where invertebrate prey may be scarce.
METHODS: Three-dimensional plant reconstruction, based on stereo cameras, combined with ray tracing was implemented to explore the light environment within the Bambara groundnut-proso millet intercropping system and associated monocrops. Gas exchange data were used to predict the total carbon gain of each component crop.
KEY RESULTS: The shading influence of the tall proso millet on the shorter Bambara groundnut results in a reduction in total canopy light interception and carbon gain. However, the increased leaf area index (LAI) of proso millet, higher photosynthetic potential due to the C4 pathway and sub-optimal photosynthetic acclimation of Bambara groundnut to shade means that increasing the number of rows of millet will lead to greater light interception and carbon gain per unit ground area, despite Bambara groundnut intercepting more light per unit leaf area.
CONCLUSIONS: Three-dimensional reconstruction combined with ray tracing provides a novel, accurate method of exploring the light environment within an intercrop that does not require difficult measurements of light interception and data-intensive manual reconstruction, especially for such systems with inherently high spatial possibilities. It provides new opportunities for calculating potential productivity within multi-species cropping systems, enables the quantification of dynamic physiological differences between crops grown as monoculture and those within intercrops, and enables the prediction of new productive combinations of previously untested crops.
METHODS: Adaxial walls of leaf epidermal cells were characterized using high-pressure-frozen freeze-substituted specimens, which retain their native dimensions during observations using transmission and scanning microscopy, accompanied by energy-dispersive X-ray spectroscopy to identify the role of biogenic silica in wall-based iridescence. Biogenic silica was experimentally removed using aqueous Na2CO3 and optical properties were compared using spectral reflectance.
KEY RESULTS AND CONCLUSIONS: Blue iridescence is produced in the adaxial epidermal cell wall, which contains helicoid lamellae. The blue iridescence from cell surfaces is left-circularly polarized. The position of the silica granules is entrained by the helicoid microfibrillar layers, and granules accumulate at a uniform position within the helicoids, contributing to the structure that produces the blue iridescence, as part of the unit cell responsible for 2 ° Bragg scatter. Removal of silica from the walls eliminated the blue colour. Addition of silica nanoparticles on existing cellulosic lamellae is a novel mechanism for adding structural colour in organisms.
SCOPE: Extensive review of ecological literature and field observations shows Lepidosperma species to be important components of many ecosystems, often dominating understorey and sedge-rich communities. For the first time, a detailed ecological review of a Cyperaceae genus is presented.
CONCLUSIONS: Lepidosperma species are long-lived perennials with significant abundance and persistence in the landscape. Speciation patterns in the genus are of considerable interest due to complex biogeographical patterns and a high degree of habitat specificity. Potential benefits exist for medicinal products identified from several Lepidosperma species. Over 178 organisms, including 26 mammals, 42 birds, six reptiles, five amphibians, eight arachnids, 75 insects, three crustaceans and 13 fungi, are found to be dependent on, or making use of, Lepidosperma species. A significant relationship exists between Lepidosperma species and the moth genus Elachista. Implications for the conservation and ecology of both sedges and associated species are discussed.
METHODS: Fourteen datasets extracted from three published papers were used in a meta-analysis to examine the cyclic behaviour of the Arabidopsis thaliana photosynthesis-related gene CAB2 and the clock oscillator genes TOC1 and LHY in T cycles and N-H cycles.
KEY RESULTS: Changes in the rhythms of CAB2, TOC1 and LHY in plants subjected to non-24-h light:dark cycles matched the hypothesized changes in their behaviour as predicted by the solar clock model, thus validating it. The analysis further showed that TOC1 expression peaked ∼5·5 h after mid-day, CAB2 peaked close to noon, while LHY peaked ∼7·5 h after midnight, regardless of the cycle period, the photoperiod or the light:dark period ratio. The solar clock model correctly predicted the zeitgeber timing of these genes under 11 different lighting regimes comprising combinations of seven light periods, nine dark periods, four cycle periods and four light:dark period ratios. In short cycles that terminated before LHY could be expressed, the solar clock correctly predicted zeitgeber timing of its expression in the following cycle.
CONCLUSIONS: Regulation of gene phases by the solar clock enables the plant to tell the time, by which means a large number of genes are regulated. This facilitates the initiation of gene expression even before the arrival of sunrise, sunset or noon, thus allowing the plant to 'anticipate' dawn, dusk or mid-day respectively, independently of the photoperiod.
METHODS: Phylogenetic analysis was used to identify candidate Dendrobium catenatum R2R3-MYB (DcaMYB) sequences associated with pigment and cell shape development. Gene silencing of candidate DhMYBs in Dendrobium hybrid by direct application of dsRNA to developing flowers was followed by observation of gene expression level and flower phenotypes. Silencing of the structural gene chalcone synthase was used as a comparative control.
KEY RESULTS: Ten candidate flower-associated DcaMYBs were identified. Flowers treated with dsRNA of DhMYB22 and DhMYB60 sequences were less pigmented and had relatively low expression of anthocyanin biosynthetic genes (F3'H and DFR), lower total anthocyanin concentration and markedly lower levels of cyanidin-3-glucoside and cyanidin-3-rutinoside. Petals of DhMYB22-treated flowers and sepals of DhMYB60-treated flowers showed the greatest colour difference relative to the same organs in untreated flowers. DhMYB22-treated flowers had relatively narrow and constricted lips, while DhMYB60-treated flowers had narrow and constricted sepals. No significant difference in shape was observed for DhCHS-treated or untreated flowers.
CONCLUSIONS: Our results demonstrate that DhMYB22 and DhMYB60 regulate pigment intensity and floral organ shape in Dendrobium. This is a first report of MYB regulation of floral organ shape in orchids.
SCOPE: For this review, we analysed recent research publications reporting specifically on plant transcription factor (TF) expression in association with PGPB, to determine if there are any common findings and to identify gaps that offer opportunities for focused future research.
CONCLUSIONS: The inoculation of plants with PGPB elicits a dynamic and temporal response. Initially, there is an upregulation of defence-responsive TFs, followed by their downregulation in an intermediate phase, and finally, another upregulation, providing longer term stress tolerance. PGPB priming activates plant defences in the form of induced systemic resistance (ISR), often via the MAMP/MAPK pathways and involving one or more of the major plant hormone-signalling pathways and their crosstalk. Following PGPB priming, the TF families most commonly reported as expressed across different plants and for different pathogens are ERF and WRKY, while the TFs most commonly expressed across different plants for different abiotic stresses are ERF and DREB. There were inconsistencies between studies regarding the timing of the shift from the initial phase to the intermediate phase, and some of the TFs expressed during this process have not been fully characterized. This calls for more research to investigate the regulatory functions and phases of TF expression, to enhance crop resilience. Most reports on abiotic stresses have focused on salinity and drought, with fewer studies addressing nutrient deficiency, heavy metals, flooding and other stresses, highlighting the need for further research in these areas.