Reproductive yield of individuals competing for light in a dense stand of an annual, Xanthium canadense

In a dense stand, individuals compete with each other for resources, especially for light. Light availability decreases with increasing depth in the canopy, thus light competition becoming stronger with time in the vegetative phase. In the reproductive phase, on the other hand, leaves start senescing, and the light environment, particularly of smaller individuals, will be improved. To study the effect of change in light climate on reproduction of individuals, we established an experimental stand of an annual, Xanthium canadense, and assessed temporal changes in whole plant photosynthesis through the reproductive phase with particular reference to light availability of individuals. At flowering, 83% of individuals were still alive, but only 27% survived to set seeds. Most of the individuals that died in the reproductive phase were smaller than those that produced seeds. Individuals that died at the early stage of the reproductive phase had a lower leaf to stem mass ratio, suggesting that the fate of individuals was determined partly by the pattern of biomass allocation in this period. At the early stage of the reproductive phase, leaf area index (LAI) of the stand was high and larger individuals had higher whole plant photosynthesis than smaller individuals. Although light availability at later stages was improved with reduction in LAI, whole plant photosynthesis was very low in all individuals due to a lower light use efficiency, which was caused by a decrease in photosynthetic N use efficiency. We conclude that light competition was still strong at the early stage of the reproductive phase and that later improvement of light availability did not ameliorate the photosynthesis of smaller individuals.     

Soil water status influences plant nitrogen use: a case study

We studied differences in nitrogen use efficiency (NUE) among six species [Calamagrostis epigejos (L.) Roth., Carex duriuscula C.A. Mey., Phragmites communis (L.) Trin., Salix gordejevii Y.L. Chang, Salix cheilophila Schneid., and Typha minima Funk.] growing in two contrasting habitat types, i.e., a riverine wetland with high water supply and a riparian zone with low water supply. The two sites were different in soil water supply, but not in nitrogen supply. Here, NUE was defined as the total net primary production per unit nitrogen absorbed. There was no significant difference in NUE between the species growing in the riverine wetland (Carex duriuscula, P. communis, S. cheilophila, T. minima) and the species growing in the river bank (Carex duriuscula, Calamagrostis epigejos, P. communis, S. gordejevii). We further analyzed NUE as the product of the nitrogen productivity (A, the rate of dry matter production per unit of nitrogen in the plant) and the mean residence time of nitrogen (MRT, the period of time a unit of nitrogen is present in the plant). The species growing in the riverine wetland had larger A but lower MRT than the species growing in the river bank. There was an inverse relationship between A and MRT. Consequently, NUE was similar among species and habitats. These results suggested that environmental factors, such as soil water supply, can influence N use by plants.     

Developing a disturbance index for five East African forests using GIS to analyse historical forest use as an important driver of current land use/cover

A means of deriving a disturbance index reflecting forest use history is demonstrated here to establish a disturbance gradient and enable comparison of different forest areas within and across individual forests. Detailed reference is made to Kakamega Forest in western Kenya for which a long‐term time series has been established, although the study is spread to four further forests in Kenya and Uganda. A wide variety of sources are drawn upon for spatially resolved data that are integrated in a geographic information system. Three indices are derived: for commercial disturbance, local disturbance, and forest cover change. Results show a wide range of disturbance values (from low to heavy) for the research sites within Kakamega Forest, while results for Budongo and Mabira Forest sites show low and moderate levels, respectively. Correlations of low disturbance levels with nature or national reserves appear to be marked, while a correlation of disturbance with differing management authority is also suggested with Kenya Wildlife Service achieving the lowest disturbance levels. Results from the index are reviewed against other means of estimating disturbance with the conclusion that disturbance evaluations should be both spatially resolved and long‐term in nature.     

Xanthophyll-cycle pigments and photosynthetic capacity in tropical forest species: a comparative field study on canopy,gap and understory plants

Xanthophyll-cycle pigments and photosynthetic capacity (PS_max) were analyzed in 25 species from different light environments (canopy, gap, understory) within a Panamanian tropical forest. (1) Sun-exposed leaves of canopy tree species showed the highest photosynthetic capacities and largest xanthophyll-cycle pools (violaxanthin, antheraxanthin, zeaxanthin) of about 87 mmol mol^-1 chlorophyll with only small amounts of -carotene [about 7 mmol mol^-1 chlorophyll = 8% of total (+) carotene pool]. Under high natural photon flux densities (PFDs) canopy leaves rapidly converted up to 96% of the xanthophyll-cycle pool into zeaxanthin. The back reaction to violaxanthin occurred much faster in low light than in complete darkness. At the end of the night, zeaxanthin still accounted for, on average, 14% of the total xanthophyll-cycle pigments. (2) Leaves of gap plants had intermediate values of PS_max and a 43% lower total carotenoid content than canopy leaves. The average size of the xanthophyll-cycle pool was 35 mmol mol^-1 chlorophyll, and -carotene accounted for up to 66% of the total (+) carotene pool. Under high light conditions gap plants converted, on average, 86% of the xanthophyll-cycle pigments into zeaxanthin. The back reaction, following a decrease in ambient PFD, was slower than the forward reaction. At the end of the night, zeaxanthin accounted for, on average, 7% of the xanthophyll-cycle pigments in gap plants. (3) Understory plants showed the lowest values of PS_max and the smallest xanthophyll-cycle pool of about 22 mmol mol^-1 chlorophyll. -Carotene accounted for up to 70% of total carotene. The conversion of xanthophyll-cycle pigments into zeaxanthin was negligible during short sunflecks of 1–2 min duration and PFDs up to about 400 mol m^-2 s^-1. At predawn, leaves of understory plants rarely contained any detectable zeaxanthin. Aechmea magdalenae, an understory CAM plant, showed exceptionally high rates of PS_max per unit leaf area compared to sympatric C₃ understory species.     

Abundance, distribution and life histories of grassland plants: a comparative study of 81 species

1 This study examines the abundance and distribution of grassland plant species in particular relation to features affecting colonization. Seed production (inversely related to seed size) and recruitment success (positively related) affect colonization ability, suggesting that seed size can be used as a key trait.
2 Data on seed size, dispersal mode, life form, geographical range size and abundance were gathered for 81 grassland plant species in a field study area in Sweden. Seed production and plant size were estimated for 69 of these species. Analyses were performed both across species, with species treated as independent data points, and for 43 'phylogenetically independent contrasts'.
3 The cross-species analyses suggested that local abundance was related to life forms but not dispersal or plant size. Perennials were generally most abundant, as were clonal species. If abundance reflects colonization we predicted that species with intermediately sized seeds (or intermediate seed production) would be most abundant, and this was supported by the phylogenetic contrast but not by cross-species analyses. In the former analysis, a high abundance of species was significantly associated with a small seed size deviation (and seed number deviation) from the median values of these traits in the community.
4 Local abundance, seed production and seed size deviation from the community median value were positively related to geographical range size in the cross-species analysis, but no relationships were seen in the phylogenetic contrast analysis.
5 We conclude that colonization processes do have a significant influence on abundance patterns in grasslands. Seed size is a key trait for colonizing ability, and the effects of the trade-off of seed size vs. seed number must be considered. No single mechanism can be identified that influences both abundance and geographical distribution range.     

Hyperspectral leaf signature as an added dimension for species discrimination: case study of four tropical mangroves

Hyperspectral leaf reflectance of a plant provides unique information that is characteristic of that plant. The present investigation is a preliminary attempt to assess whether spectra of leaves of mangrove species recorded under field conditions contain adequate spectral information for discerning mangroves at species rank. The paper highlights the hyperspectral characteristics of leaf surfaces of four prominent tropical mangrove species, viz., Avicennia alba, Avicennia marina, Rhizophora mucronata and Sonneratia caseolaris, found in the tidal forests of India. Hyperspectral observations were recorded using a field spectroradiometer, and pre-processed and averaged reflectance values of samples for three types of arrangements, viz., (1) randomly arranged leaves, (2) dorsal leaf surfaces and (3) ventral leaf surfaces of the species were statistically tested using one-way ANOVA to see whether the values significantly differed at every spectral location. All the four species were statistically different at all the spectral locations with majority of the bands exhibiting 99% confidence level. Finally, discriminant analysis was performed to identify the bands for maximum separability for the three types of arrangement of the leaves of the species taken separately and in different combinations. The optimal Wilks’ Lambda (L) were achieved with: six, three, eleven, six, five, thirteen and eleven wavelengths for discriminating random leaves of the four species, dorsal and ventral surfaces of A. alba, A. marina, R. mucronata, S. caseolaris, upper leaf surfaces of all the species, lower leaf surfaces, respectively. Factor analysis was used as an added tool to identify the wavelengths that were uncorrelated and contained maximum information in the combination of selected wavelengths. The results confirmed the unique spectral signatures of the four species, which could be explained in terms of leaf properties unique to the species. Cellular structure and pigmentation of the isolateral leaves of S. caseolaris are very different from the dorsiventral ones of the other three, which significantly changed the reflectance characteristics of the species.     

Genetic fingerprinting of germplasm accessions as an aid for species conservation: a case study with Borderea chouardii (Dioscoreaceae), one of the most critically endangered Iberian plants

BACKGROUND AND AIMS: Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. METHODS: Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. KEY RESULTS: The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). CONCLUSIONS: The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.     

Poplar in wetland agroforestry: a case study of ecological benefits,site productivity,and economics

Poplars are the major tree component of traditional agroforestry systems throughout the south temperate central area of China that includes all or portions of Jiangsu, Anhui, Zhejiang, Hubei, Henan, Shandong, and Shanxi provinces, an area of ~600,000 km². The lack of experidmental data on the effect of various interplanting systems on crop production represents a serious gap in our knowledge, and consequently, a stable, optimized poplar-crop interplanting pattern is difficult to achieve. In order to develop a poplar-crop interplanting pattern that is economically viable, environmentally sound, technically workable, and socially compatible in floodplain areas, new poplar-crop interplanting patterns were designed using the principle of edge effects. Six patterns were designed and established in 1992 with different narrow – wide spacings, i.e., I: (3 × 3) × 20 m, II: (3 × 3) × 30 m, III: (3 × 3) × 40 m, IV: (4 × 4) . 20 m, V: (4 × 4) × 30 m, and VI: (4 × 4) × 40 m. A randomized block arrangement was used with two replications for each pattern. Based on 7 years of investigation, this paper examines the effects of these patterns on temporal and spatial variations in microclimate at various phenological phases of winter wheat, variations in wheat yield and quality, wood production, biomass productivity and light use efficiency, and economic assessment. The feasibility and viability of these new patterns is also discussed. These preliminary results provide some basic principles for developing optimized poplar-crop interplanting patterns in the wetland plain areas of China.     

Phytosociology as a tool for forest restoration: a study case in the extreme South of Atlantic Forest Biome

The biodiversity loss, due to anthropic activities, has generated the necessity of studies that enable the ecosystem conservation. Nevertheless, the majority of studies restrict themselves to the floristic composition and phytosociological structure from determined pre-established diameter, neglecting attributes of the species, such as its (their) niche (s) of occurrence in the forest, thus, making it difficult to identify potential species for restoration. In this way, the present study aimed to evaluate the structure of a forest fragment in the extreme South of Atlantic Forest Biome, through identification of species in the different layers. There were used 18 parcels of 10 m × 20 m, distributed systematically, where the vegetation was evaluated in four size classes. The characterization of the structure of the arboreal-shrub of the forest was performed by the data comparison of the floristic composition and phytosociological structure. In the fragment of forest studied, there were sampled a total of 2.176 individuals. The floristic composition of the area includes 74 species, belonging to 58 genera and 28 botanical families. We observed differences in relation of richness and diversity of species among the analyzed layers, the intermediate layer presented the lowest richness of species, being the pioneers and initial secondaries the least representatives. Trichilia claussenii, Sorocea bonplandii, Actinostemon concolor, Apuleia leiocarpa and Nectandra megapotamica were the most abundant species and well distributed in the different size classes, and they can be used in the enrichment of areas in process of restoration in the scope of the Deciduous Seasonal Forest in the extreme South of Atlantic Forest Biome. Ocotea puberula, Allophylus edulis, Cedrela fissillis and Machaerium paraguariense formed a group of species with expressive representativeness in the arboreal layer, thus they can be used in the moment of planting as species to the fast covering of the area.     

Rationale of selection for specific nutritional characters in crop improvement withPhaseolus vulgaris L. as a case study

Genetic effects are obtainable for any aspect of transport, accumulation, and efficiency of nutrient use by plants, and for virtually any element. Some of the important characters are: tolerance to acid soils (18% of soils or 2.4 billion ha), tolerance to high pH induced Fe-chlorosis, and tolerance to salinity (about 1,000 m ha). Genotypes which made better use of N and P would be the means of saving fertilizers, especially important to developing countries. A 10% economy of fertilizer use represents a minimum world saving of US$6 billion annually. Phaseolus vulgaris is taken as a model to show that although we know quite a lot about the extent of its nutritional variation, e.g. adaptability to acid soils, and the crop's utilization of N and P, we are handicapped in exploiting this because of lack of genetic information. This in turn depends on knowledge of specific mechanisms, and investigating these must be a priority.IAEA Project BRA/5/009     

The limitations of assessing impacts of land use changes on runoff with a distributed hydrological model: case study of the Hron River

A distributed hydrological model was applied for estimating changes in a runoff regime due to land use changes. The upper Hron river basin, which has an area of 1766 km² and is located in central Slovakia, was selected as the pilot basin. A physically-based rainfall-runoff model with distributed parameters was used for modelling runoff from rainfall and melting snow. The parameters of the model were estimated using climate data from 1981–2000 and from three digital map layers: a land-use map, soil map and digital elevation model. Several scenarios of changes in land use were prepared, and the runoff under the new land use conditions was simulated. Long-term mean annual runoff components and the design maximal mean daily discharges with a return period from 5 to 100 years under the previous and changed land uses were estimated and compared. The simulated runoff changes were confronted with expert judgments and estimates from the literature. Limitations of the use of distributed models for estimating land use changes are discussed.     

Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

Background

State-of-the-art protein-ligand docking methods are generally limited by the traditionally low accuracy of their scoring functions, which are used to predict binding affinity and thus vital for discriminating between active and inactive compounds. Despite intensive research over the years, classical scoring functions have reached a plateau in their predictive performance. These assume a predetermined additive functional form for some sophisticated numerical features, and use standard multivariate linear regression (MLR) on experimental data to derive the coefficients.

Results

In this study we show that such a simple functional form is detrimental for the prediction performance of a scoring function, and replacing linear regression by machine learning techniques like random forest (RF) can improve prediction performance. We investigate the conditions of applying RF under various contexts and find that given sufficient training samples RF manages to comprehensively capture the non-linearity between structural features and measured binding affinities. Incorporating more structural features and training with more samples can both boost RF performance. In addition, we analyze the importance of structural features to binding affinity prediction using the RF variable importance tool. Lastly, we use Cyscore, a top performing empirical scoring function, as a baseline for comparison study.

Conclusions

Machine-learning scoring functions are fundamentally different from classical scoring functions because the former circumvents the fixed functional form relating structural features with binding affinities. RF, but not MLR, can effectively exploit more structural features and more training samples, leading to higher prediction performance. The future availability of more X-ray crystal structures will further widen the performance gap between RF-based and MLR-based scoring functions. This further stresses the importance of substituting RF for MLR in scoring function development.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-291) contains supplementary material, which is available to authorized users.     

Comparison of phenology trends by land cover class: a case study in the Great Basin, USA

Direct impacts of human land use and indirect impacts of anthropogenic climate change may alter land cover and associated ecosystem function, affecting ecological goods and services. Considerable work has been done to identify long‐term global trends in vegetation greenness, which is associated with primary productivity, using remote sensing. Trend analysis of satellite observations is subject to error, and ecosystem change can be confused with interannual variability. However, the relative trends of land cover classes may hold clues about differential ecosystem response to environmental forcing. Our aim was to identify phenological variability and 10‐year trends for the major land cover classes in the Great Basin. This case study involved two steps: a regional, phenology‐based land cover classification and an identification of phenological variability and 10‐year trends stratified by land cover class. The analysis used a 10‐year time series of Advanced Very High Resolution Radiometer satellite data to assess regional scale land cover variability and identify change. The phenology‐based regional classification was more detailed and accurate than national or global products. Phenological variability over the 10‐year period was high, with substantial shifts in timing of start of season of up to 9 weeks. The mean long‐term trends of montane land cover classes were significantly different from valley land cover classes due to a poor response of montane shrubland and pinyon‐juniper woodland to the early 1990s drought. The differential response during the 1990s suggests that valley ecosystems may be more resilient and montane ecosystems more susceptible to prolonged drought. This type of regional‐scale land cover analysis is necessary to characterize current patterns of land cover phenology, distinguish between anthropogenically driven land cover change and interannual variability, and identify ecosystems potentially susceptible to regional and global change.     

Trypanosoma evansi: a comparative study of four diagnostic techniques for trypanosomosis using rabbit as an experimental model

The goal of this study was to compare two parasitological diagnostic techniques, such as by Micro-Haematocrit Centrifugation Technique (MHCT) and Direct Microscopic Examination (DME) with a serological method (iELISA), and a molecular procedure PCR, in rabbits experimentally infected with Trypanosoma evansi, in order to determine their sensitivity throughout the course of disease. The parasitological methods were not able of detecting the presence of the parasite during the phases of low parasitemia, the prepatency period and the chronic phase. In contrast, PCR detected T. evansi in the prepatency and chronic phase, when increase the amount of DNA from 100 to 300 ng. 100% detection was observed with iELISA only in the chronic stage of the disease. In the acute phase, all samples were positively diagnosed using either MHCT or PCR, whereas only few samples were diagnosed by DME. Samples obtained from day 15 post infection were also detected by iELISA. The highest diagnostic register during the course of infection was achieved by the PCR technique (93.8%), followed by iELISA (71.1%), MHCT (59%) and DME (13.6%). Therefore, we recommend the use of PCR in epidemiological studies in order to implement sanitary control plans for the improvement of livestock productivity in the country.