Biomass equations for European trees : addendum

Abstract

What matters for predicting spatial distributions of trees: techniques, data, or species' characteristics?

Data characteristics and species traits are expected to influence the accuracy with which species' distributions can be modeled and predicted. We compare 10 modeling techniques in terms of predictive power and sensitivity to location error, change in map resolution, and sample size, and assess whether some species traits can explain variation in model performance. We focused on 30 native tree species in Switzerland and used presence-only data to model current distribution, which we evaluated against independent presence-absence data. While there are important differences between the predictive performance of modeling methods, the variance in model performance is greater among species than among techniques. Within the range of data perturbations in this study, some extrinsic parameters of data affect model performance more than others: location error and sample size reduced performance of many techniques, whereas grain had little effect on most techniques. No technique can rescue species that are difficult to predict. The predictive power of species-distribution models can partly be predicted from a series of species characteristics and traits based on growth rate, elevational distribution range, and maximum elevation. Slow-growing species or species with narrow and specialized niches tend to be better modeled. The Swiss presence-only tree data produce models that are reliable enough to be useful in planning and management applications.

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

'Tommy Atkins' mango trees subjected to high density planting in subhumid tropical climate in northeastern Brazil

The objective of this work was to evaluate the effects of high density planting on 'Tommy Atkins' mango trees cultivated in subhumid warm tropical climate in northeastern Brazil. Treatments consisted of five spacial arrangements of plants (8x5 m, 7x4 m, 6x3 m, 5x2 m and 4x2 m), which resulted in the following plant densities: 250 (control), 357, 555, 1,000 and 1,250 plants per hectare. Plant vegetative and reproductive variables, besides fruit quality parameters, were evaluated at seven and eight years after transplantation to the field. In general, high density planting caused reduction in vegetative and reproductive variables of individual mango trees, but had little influence on fruit quality. Above 555 plants per hectare, a significant decrease was observed in mango tree growth. Furthermore, there were decreases in the percentage of flowering, fruit yield per plant and per area. However, planting density up to 357 plants per hectare, in spite of decreasing plant growth and fruit yield per tree, increases fruit yield per area in 30% in comparison to the control.

Mating system parameters in a high density population of andirobas in the Amazon forest

The objective of this work was to estimate the mating system parameters of a andiroba (Carapa guianensis) population using microsatellite markers and the mixed and correlated mating models. Twelve open‑pollinated progeny arrays of 15 individuals were sampled in an area with C. guianensis estimated density of 25.7 trees per hectare. Overall, the species has a mixed reproductive system, with a predominance of outcrossing. The multilocus outcrossing rate (t m = 0.862) was significantly lower than the unity, indicating that self‑pollination occurred. The rate of biparental inbreeding was substantial (t m ‑ t s = 0.134) and significantly different from zero. The correlation of selfing within progenies was high (r s = 0.635), indicating variation in the individual outcrossing rate. Consistent with this result, the estimate of the individual outcrossing rate ranged from 0.598 to 0.978. The multilocus correlation of paternity was low (r p(m) = 0.081), but significantly different from zero, suggesting that the progenies contain full‑sibs. The coancestry within progenies (Θ = 0.185) was higher and the variance effective size (Ne(v) = 2.7) was lower than expected for true half‑sib progenies (Θ = 0.125; Ne(v) = 4). These results suggest that, in order to maintain a minimum effective size of 150 individuals for breeding, genetic conservation, and environmental reforestation programs, seeds from at least 56 trees must be collected.

Evaluation of reed canary grass for different end-uses and in breeding

Selostus: Ruokohelven soveltuvuus non-food-, rehun- ja siementuotantoon

Bud dormancy in apple trees after thermal fluctuations

The objective of this work was to evaluate the effect of heat waves on the evolution of bud dormancy, in apple trees with contrasting chilling requirements. Twigs of 'Castel Gala' and 'Royal Gala' were collected in orchards in Papanduva, state of Santa Catarina, Brazil, and were exposed to constant (3°C) or alternating (3 and 15°C for 12/12 hours) temperature, combined with zero, one or two days a week at 25°C. Two additional treatments were evaluated: constant temperature (3°C), with a heat wave of seven days at 25°C, in the beginning or in the middle of the experimental period. Periodically, part of the twigs was transferred to 25°C for daily budburst evaluation of apical and lateral buds. Endodormancy (dormancy induced by cold) was overcome with less than 330 chilling hours (CH) of constant cold in 'Castel Gala' and less than 618 CH in 'Royal Gala'. A daily 15°C-temperature cycle did not affect the endodormancy process. Heat waves during endodormancy resulted in an increased CH to achieve bud requirements. The negative effect of high temperature depended on the lasting of this condition. Chilling was partly cancelled during dormancy when the heat wave lasted 36 continuous hours or more. Therefore, budburst prediction models need adjustments, mainly for regions with mild and irregular winters, such as those of Southern Brazil.

Microclimate and development of 'Conilon' coffee intercropped with rubber trees

The objective of this work was to evaluate the influence of intercropping 'Conilon' coffee (Coffea canephora) with rubber trees on coffee tree microclimate, nutrition, growth, and yield. Rubber trees were planted in two double rows 33 m apart, with 4x2.3 m spacing between plants. Treatments consisted of the distances from the coffee plants to the rubber trees: 3, 6, 9, 12, and 15 m. Measurements of atmospheric variables (temperature, irradiance, and relative humidity), leaf nutrient concentration, internode length of plagiotropic and orthotropic branches, individual leaf area, chlorophyll content, and yield were performed. Intercropping promotes changes in the microclimatic conditions of coffee plants close to rubber trees, with reduction of temperature and irradiance level and increase in air relative humidity. The proximity of the coffee tree to the rubber trees promotes the elongation of the plagiotropic and orthotropic branches and increases the individual leaf area; however, it does not affect leaf concentrations of N, K, Mg, Fe, Zn, and B in 'Conilon' coffee and does not have a negative impact on yield.

Tolerance to preharvest sprouting and yield of wheat genotypes from different breeding programs

Abstract:The objective of this work was to characterize the performance of elite wheat genotypes from different Brazilian breeding programs for traits associated with grain yield and preharvest sprouting. The study was conducted in 2010 and 2011 in the municipality of Capão do Leão, in the state of Rio Grande do Sul, Brazil, in a randomized complete block design with three replicates. Thirty-three wheat genotypes were evaluated for traits related to preharvest sprouting and grain yield. The estimate of genetic distance was used to predict potential combinations for selection of plants with high grain yield and tolerance to preharvest sprouting. The combined analysis of sprouted grains and falling number shows that the TBIO Alvorada, TBIO Mestre, Frontana, Fundacep Raízes, Fundacep Cristalino, and BRS Guamirim genotypes are tolerant to preharvest sprouting. Combinations of TBIO Alvorada and TBIO Mestre with Fundacep Cristalino show high potential for recovering superior genotypes for high grain yield and tolerance to preharvest sprouting.

Breeding objectives for a Nellore cattle rearing system

Abstract:The objective of this work was to define the traits that should be included as breeding objectives for Nellore cattle, according to simulations with a bio-economic model for rearing systems. The economic values (EVs) of the traits were calculated as the differences between the profits due to an increased performance of 1% in each trait, with the others traits remaining constant. To determine the impact of each selection on the revenue system, two scenarios were simulated based on the traits being selected. In the first scenario, the adopted selection criteria were: weaning weight (WW), weaning rate (WR), yearling weight (YW), and mature cow weight (MCW). In the second scenario, the cumulative productivity (CP) of dams was used as an indirect evaluation of the performance of calves, with all the other traits included, except WW. In the first scenario, an EV of R$ 1.44 kg-1 was obtained for WW. In the second scenario, an EV of R$ 2.91 kg-1 was obtained for CP. The trait with the highest EV in both scenarios was WR, which enhanced the profits by R$ 3.21 for each 1% increased performance. The meat price paid to the producer is the factor with the greatest impact on the EVs of all examined traits.

Stratification of the severity of critically ill patients with classification trees

Background: Development of three classification trees (CT) based on the CART (Classification and Regression Trees), CHAID (Chi-Square Automatic Interaction Detection) and C4.5 methodologies for the calculation of probability of hospital mortality; the comparison of the results with the APACHE II, SAPS II and MPM II-24 scores, and with a model based on multiple logistic regression (LR). Methods: Retrospective study of 2864 patients. Random partition (70:30) into a Development Set (DS) n = 1808 and Validation Set (VS) n = 808. Their properties of discrimination are compared with the ROC curve (AUC CI 95%), Percent of correct classification (PCC CI 95%); and the calibration with the Calibration Curve and the Standardized Mortality Ratio (SMR CI 95%). Results: CTs are produced with a different selection of variables and decision rules: CART (5 variables and 8 decision rules), CHAID (7 variables and 15 rules) and C4.5 (6 variables and 10 rules). The common variables were: inotropic therapy, Glasgow, age, (A-a)O2 gradient and antecedent of chronic illness. In VS: all the models achieved acceptable discrimination with AUC above 0.7. CT: CART (0.75(0.71-0.81)), CHAID (0.76(0.72-0.79)) and C4.5 (0.76(0.73-0.80)). PCC: CART (72(69- 75)), CHAID (72(69-75)) and C4.5 (76(73-79)). Calibration (SMR) better in the CT: CART (1.04(0.95-1.31)), CHAID (1.06(0.97-1.15) and C4.5 (1.08(0.98-1.16)). Conclusion: With different methodologies of CTs, trees are generated with different selection of variables and decision rules. The CTs are easy to interpret, and they stratify the risk of hospital mortality. The CTs should be taken into account for the classification of the prognosis of critically ill patients.

Innovative LIDAR 3D dynamic measurement system to estimate fruit-tree leaf area

In this work, a LIDAR-based 3D Dynamic Measurement System is presented and evaluated for the geometric characterization of tree crops. Using this measurement system, trees were scanned from two opposing sides to obtain two three-dimensional point clouds. After registration of the point clouds, a simple and easily obtainable parameter is the number of impacts received by the scanned vegetation. The work in this study is based on the hypothesis of the existence of a linear relationship between the number of impacts of the LIDAR sensor laser beam on the vegetation and the tree leaf area. Tests performed under laboratory conditions using an ornamental tree and, subsequently, in a pear tree orchard demonstrate the correct operation of the measurement system presented in this paper. The results from both the laboratory and field tests confirm the initial hypothesis and the 3D Dynamic Measurement System is validated in field operation. This opens the door to new lines of research centred on the geometric characterization of tree crops in the field of agriculture and, more specifically, in precision fruit growing.

Metabolic responses of guava trees irrigated withdifferent N and K levels in São Francisco Valley

The guava (Psidium guajava L.) cv. Paluma has been cultivated in São Francisco Valley, Northeastern of Brazil, for in natura consumption and processing purposes. In spite of its importance, there are few scientific knowledge regarding guava physiology, nutrition, irrigation and fertigation. The objective of this work was to evaluate the effect of weather conditions and different concentrations of N and K applied by fertigation in foliar contents of reducing sugars, total soluble sugars, starch, sucrose, amino acids, and proteins. The field experiment was carried out at Bebedouro Experimental Field and the biochemical evaluations at the Laboratory of Seed and Plant Physiology, both located at Embrapa Semi-Árido, Petrolina-PE. The doses of 200 g N and 100 g K2O; 400 g N and 200 g K2O; 600 g N and 300 g K2O; and 800 g N and 400 g K2O per plant were applied in an experiment field. The experimental design was totally randomized blocks, with four treatments and five blocks. The weather conditions influenced the plant photosynthesis, which affects the plants metabolism. Guava presented specific responses to N and K fertigation for each parameter evaluated. The weather conditions during the evaluation period influenced guava responses to N and K fertigation.

Effects of levels of nitrogen and potassium on yield and fruit maturation of irrigated guava trees in the São Francisco Valley

Yield and physical and chemical characteristics of 'Paluma' guava fruit were evaluated as a function of the harvest at different maturity stages, under influence of nitrogen and potassium fertilization, in Petrolina, State of Pernambuco, Brazil. Fertilizer rates were 67 kg N + 33 kg K2O, 133 kg N + 67 kg K2O, 200 kg N + 100 kg K2O and 267 kg N + 133 kg K2O per hectare. Fruits were evaluated at maturity stages 2, 3, 4 and 5, established according to peel color. Higher doses of N and K induced higher yields. Nevertheless, fertilization with 200 kg of N + 100 kg of K per hectare improved fruit quality, delaying ascorbic acid breakdown and conserving pulp firmness. Main changes took place at maturity stages 4 and 5, when the fruit should present ideal conditions for consumption, namely the increase on soluble solids and soluble sugars content.

Irrigation performance and gross water productivity in furrow-irrigated ornamental tree production

In the ornamental plant production region of Girona (Spain), which is one of the largest of its kind in southern Europe, most of the surface is irrigated using wide blocked-end furrows. The objectives of this paper were: (1) to evaluate the irrigation scheduling methods used by ornamental plant producers; (2) to analyse different scenarios in order to assess how they affect irrigation performance; (3) to evaluate the risk of deep percolation; and (4) to calculate gross water productivity. A two-year study in a representative commercial field, planted with Prunus cerasifera ‘Nigra’, was carried out. The irrigation dose applied by the farmers was slightly smaller than the required water dose estimated by the use of two different methods: the first based on soil water content, and the second based on evapotranspiration. Distribution uniformity and application eff iciency were high, with mean values above 87%. Soil water content measurements revealed that even at the end of the furrow, where the infiltrated water depth was greatest, more than 90% of the infiltrated water was retained in the shallowest 40 cm of the soil; accordingly, the risk of water loss due to deep percolation was minimal. Gross water productivity for ornamental tree production was € 11.70 m–3, approximately 20 times higher than that obtained with maize in the same region.