Machine learning highlights the importance of primary and secondary production in determining habitat for marine fish and macroinvertebrates

1. Species distribution models for marine organisms are increasingly used for a range of applications, including spatial planning, conservation, and fisheries management. These models have been constructed using a variety of mathematical forms and drawing on both physical and biological independent variables; however, what might be called first-generation models have mainly followed the form of linear models, or smoothing splines, informed by data collected in the context of fish surveys.
2. The performance of different classes of variables were tested in a series of species occurrence models built with machine learning methods, specifically evaluating the potential contribution of lower trophic level data. Random forest models were fitted based on the classification of the absence/presence for fish and macroinvertebrates surveyed on the US Northeast Continental Shelf.
3. The potential variables included physical, primary production, secondary production, and terrain variables. For accepted model fits, six variable importance measures were computed, which collectively showed that physical and secondary production variables make the greatest contribution across all models. In contrast, terrain variables made the least contribution to these models.
4. Multivariable analyses that account for all performance measures reinforce the role of water depth and temperature in defining species presence and absence; however, chlorophyll concentration and some specific zooplankton taxa, such as Metridia lucens and Paracalanus parvus, also make important contributions with strong seasonal variations.
5. Our results suggest that lower trophic level variables, if available, are valuable in the creation of species distribution models for marine organisms.

     

Studies on Low Crossabilities Encountered with the Hordeum bulbosum Method for Haploid Production of Barley, Hordeum vulgare L.

Crosses were made between four spring barley (Hordeum vulgare L.) cultivars and five F₁, hybrids with one genotype of Hordeum bulbosum L. in two locations to investigate further previous low crossabilities which had been found in the barley cultivar ‘Apex’ with H. bulbosum. Data at all the main steps of the H. bulbosum technique were recorded and statistically analyzed. Significant differences between barley genotypes were demonstrated for all characters. It was confirmed that ‘Apex’ has poor crossability with H. bulbosum. Out of the three F₁ hybrids having ‘Apex’ as one parent, two exhibited low crossability similarly to ‘Apex’ but one showed significantly higher seed setting than ‘Apex’. The effect of the location was only significant on seed setting, while genotype X location interactions were significant on seed setting, seed quality and rate of haploid plants in relation 10 florets pollinated. Another problem which has influenced the success rate of the H. bulbosum method was found in the cultivar ‘Havilla’. Although seed setting and seed quality were high for this cultivar, embryo differentiation was low. However, this latter problem was found to influence less the overall success rate than poor crossability. Mahalanobis's distances were calculated and the dendrite of the shortest distances between barley genotypes was plotted.     

Effects of thermal-time artificial scarification on the germination dynamics of black locust (<Emphasis Type="Italic">Robinia pseudoacacia</Emphasis> L.) seeds

The aim of this study was to determine the efficiency of methods for the artificial scarification of black locust seeds based on the influence of the air and liquid nitrogen temperatures. Three populations were selected for the analyses: a managed tree stand, a selected seed stand and a seed orchard. Samples of 200 seeds (4 × 50) were randomly selected. Before scarification, the seeds were stored at ?70 °C for 24 h. Nine different scarification treatments were evaluated. To calculate the germination capacity and the dynamics of germination, observations were made on days 3, 5, 7, 10 and 14 after treatment. For statistical analyses, we used repeated measures analysis of variance. The obtained results indicated that the highest scarification efficiency for black locust seeds occurred in the treatment in liquid nitrogen and in an air temperature range of 85–90 °C. The provenance of seeds had a significant effect on the dynamics of germination. Thermal methods and the use of liquid nitrogen can be alternatives to the labour intensive methods of cutting the seeds or using measures that require specialised equipment.     

Photosynthesis and Assimilate Partitioning in Mungbean in Response to Source-Sink Alteration

The effect of alteration in source-sink ratio by deflowering and defoliation technique on photosynthesis rate was examined in mungbean ( Vigna radiata [L.] Wilczek) var. PS 16. Deflowered plants where sink demand was decreased, maintained a higher rate of photosynthesis in spite of their higher starch content in the leaves. This treatment also increased the partitioning of assimilates to leaves, stem, roots and nodules indicating the existence of alternative sink capacity. The higher rate of photosynthesis of deflowered plants was associated initially with lower stomatal diffusive resistance and subsequently with higher leaf nitrogen content. Increase in sink demand for a particular leaf by excising other source leaves also increased the rate of photosynthesis. These results are discussed in relation to possible regulation through hormones.     

Relationship between phenotypic and genetic diversity of parental genotypes and the frequency of transgression effects in barley (Hordeum vulgare L.)

The aim of the study was to evaluate the relationship between genetic and phenotypic distances of parents and the genetic potential of crosses as measured by the frequency of transgressive segregants in homozygous populations. Material for the study involved 17 barley cross‐combinations. In each cross, the parental genotypes, F₂ hybrids and doubled haploid (DH) lines were analysed. Yield and yield‐related traits were observed in the experiments. Phenotypic (univariate and multivariate) and genetic distances (GD) were investigated between pairs of parental genotypes. Genetic distance was evaluated by using random amplified polymorphic DNA markers. In F₂ generations, the genetic coefficient of variability (GCV) was evaluated. Within all the cross‐combinations studied, each DH line was compared with both parents to distinguish the positive and negative transgressive lines. In addition, the coefficient of gene distribution (r) along parental genomes was evaluated. Relationships between frequency of transgression and both phenotypic and GDs, GCV and r, were assessed by regression analysis. It was found that for all the traits studied the frequency of transgressive lines depended mainly on gene distribution (r). Genetic distance between parents appeared to be significant for the occurrence of transgression effects in plant height, ear length, grain weight per ear and grain yield per plot. Regression analysis has shown that phenotypic differences between parental genotypes were also important for the frequency of transgressive lines. A weak relationship was found between the variation of F₂ hybrids and the occurrence of transgressive lines. The results indicate that occurrence of transgressive segregants in a homozygous population should be considered as a phenomenon dependent simultaneously on several factors characterizing parental genotypes. Among them, the most important are: gene distribution, phenotypic diversity and GD.     

Evaluation of susceptibility of auto- and alloplasmic barley DH lines to Fusarium seedling blight

Auto- and alloplasmic doubled haploid (DH) lines of barley were examined for susceptibility to Fusarium culmorum (W.G.Sm.) Sacc. (isolate KF350) seedling blight. Inoculated kernels were incubated at 20 °C in a chamber saturated to 100% RH a with 12/12 h dark/light cycle. Germination capacity, disease score on a 5-degree scale and root length were evaluated. The data were analysed statistically using three-factor analysis of variance. It was observed that the infection score of roots of DH lines with H. bulbosum cytoplasm was higher than that of their autoplasmic analogues. Length of infected seedling roots expressed as per cent of the control root length ranged from 81 to 56% in autoplasmic DH lines and from 60 to 48% in alloplasmic lines. These differences were statistically significant (at P = 0.01). It was evident, that H. bulbosum cytoplasm increase susceptibility of barley genotypes to Fusarium seedling blight.     

Phenotypic distribution of barley SSD lines and doubled haploids derived from F1 and F2 hybrids

Summary The doubled haploid (DH) system and the single seed descent (SSD) technique are frequently applied in breeding of self-pollinated crops to rapidly obtain homozygous lines from heterozygous hybrids. This study presents a comparison of populations of barley DH and SSD lines in terms of traits of stem structure. The SSD and DH lines derived from F₁ and F₂ hybrids Roland x Apex were examined in a field experiment. On the basis of a comparison of means, variances and correlations between traits in the F1DH, F2DH and SSD populations the occurrence/absence of linkage between genes responsible for the analysed traits was inferred. Independent inheritance was found for 1000-grain weight and the length of particular internodes, spike length and stem wall thickness. Moreover, no linkage was found for stem wall thickness and spike length, length of internodes I, II and thickness of stem walls, stem diameter and thickness of stem walls. The results obtained for the other pairs of traits indicate the presence of linkage.     

Evaluation of hybrid and population cultivars on standard and high-input technology in winter oilseed rape

The problem raised here is the intensification of technology in field crops of winter oilseed rape. Is there a justification for this by explaining what relationship between the yield and individual yielding traits are formed in hybrid and population cultivars. During years 2012–2015 field studies to evaluate five hybrid and five population cultivars response on the standard and high-input technology in winter oilseed rape production have been executed in Poland. High-input technology included: double foliar application (in autumn, and in spring) of micro-nutrients, additional top fertilisation of 40?kg N per ha in spring, double application of the amino-acid bio-stimulators, and additional growth regulator. According to the principle component analysis made for both technologies it was found that hybrids and population cultivars displayed varied response which is explained here on the basis of morphological, growth, and yield elements. The high-input technology improved the yield responded elements e.g. number of siliques and number of seeds per silique as well as winter hardiness. This impact was more evident for population cultivars than for hybrids. We state that high-input technology, as the proposal in this paper, that provided 9.6% increase in seed yield, is biologically justified for winter oilseed rape crop and can be recommended in North and central European countries.