Exploratory analysis of nutrient concentrations in Eucalyptus leaf color patterns

The aim of this study was to evaluate the use of leaf color pattern to analyze leaf nutrient concentrations in Eucalyptus and to establish relationships between color patterns and leaf nutrient concentrations. The study was carried out in Eucalyptus stands at 25 months old using three leaves from the lower of tree crowns classified into five color patterns of Munsell color charts for plant tissues. The principal component analyses and the self-organizing maps were used to aid in the classification of samples in leaf color patterns. Subsequently, the k-means cluster algorithm was performed. In principal component analysis, the 7.5 GY 8/8 leaf color pattern stood out from the others and it was mainly influenced by nitrogen, phosphorous, copper, and potassium concentrations. The samples of 7.5 GY 8/4 leaf color pattern did not present a great nitrogen, phosphorous, sulfur, copper and potassium concentrations as the 7.5 GY 8/8 neither a great manganese, calcium, boron, zinc and iron concentrations as others leaf color patterns. The self-organizing map provides a greater proximity between the 7.5 GY 8/8 and 7.5 GY 8/4 leaf color patterns and the others leaf color patterns were randomly distributed in the U-matrix. Although the k-means algorithm presented two clusters in both analyses, the self-organizing map presented a slight superiority than principal component analysis. Using leaf color patterns was possible to infer about leaf nutrient concentrations in Eucalyptus. Both methods were able to distinguish only the healthy leaves 7.5 GY 8/8 from those whose were in the leaf senescence process

Physical and land-cover variables influence ant functional groups and species diversity along elevational gradients

Of particular importance in shaping species assemblages is the spatial heterogeneity of the environment. The aim of our study was to investigate the influence of spatial heterogeneity and environmental complexity on the distribution of ant functional groups and species diversity along altitudinal gradients in a temperate ecosystem (Pyrenees Mountains). During three summers, we sampled 20 sites distributed across two Pyrenean valleys ranging in altitude from 1,009 to 2,339 m by using pitfall traps and hand collection. The environment around each sampling points was characterized by using both physical and land-cover variables. We then used a self-organizing map algorithm (SOM, neural network) to detect and characterize the relationship between the spatial distribution of ant functional groups, species diversity, and the variables measured. The use of SOM allowed us to reduce the apparent complexity of the environment to five clusters that highlighted two main gradients: an altitudinal gradient and a gradient of environmental closure. The composition of ant functional groups and species diversity changed along both of these gradients and was differently affected by environmental variables. The SOM also allowed us to validate the contours of most ant functional groups by highlighting the response of these groups to the environmental and land-cover variables

Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning

[EN] It is essential to understand the patterning of biota and environmental influencing factors for proper rehabilitation and management at the river basin scale. The Hun-Tai River Basin was extensively sampled four times for macroinvertebrate community and environmental variables during one year. Self-Organizing Maps (SOMs) were used to reveal the aggregation patterns of the 355 samples. Three community types (i.e., clusters) were found (at the family level) based on the community composition, which showed a clearly gradient by combining them with the representative environmental variables: minimally impacted source area, intermediately anthropogenic impacted sites, and highly anthropogenic impacted downstream area, respectively. This gradient was corroborated by the decreasing trends in density and diversity of macroinvertebrates. Distance from source, total phosphorus and water temperature were identified as the most important variables that distinguished the delineated communities. In addition, the sampling season, substrate type, pH and the percentage of grassland were also identified as relevant variables. These results demonstrated that macroinvertebrates communities are structured in a hierarchical manner where geographic and water quality prevail over temporal (season) and habitat (substrate type) features at the basin scale. In addition, it implied that the local-scale environment variables affected macroinvertebrates under the longitudinal gradient of the geographical and anthropogenic pressure. More than one family was identified as the indicator for each type of community. Abundance contributed significantly for distinguishing the indicators, while Baetidae with higher density indicated minimally and intermediately impacted area and lower density indicated highly impacted area. Therefore, we suggested the use of abundance data in community patterning and classification, especially in the identification of the indicator taxa. (C) 2018 Elsevier B.V. All rights reserved.This work was supported by the National Natural Science Foundation of China (51779275, 41501204, 51479219) and the IWHR Research & Development Support Program (WE0145B532017).Zhang, M.; Muñoz Mas, R.; Martinez-Capel, F.; Qu, X.; Zhang, H.; Peng, W.; Liu, X. (2018). Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning. The Science of The Total Environment. 634:749-759. https://doi.org/10.1016/j.scitotenv.2018.04.021S74975963

Biogeographic classification of the Caspian Sea

Like other inland seas, the Caspian Sea (CS) has been influenced by climate change and anthropogenic disturbance during recent decades, yet the scientific understanding of this water body remains poor. In this study, an eco-geographical classification of the CS based on physical information derived from space and in situ data is developed and tested against a set of biological observations. We used a two-step classification procedure, consisting of (i) a data reduction with self-organizing maps (SOMs) and (ii) a synthesis of the most relevant features into a reduced number of marine ecoregions using the hierarchical agglomerative clustering (HAC) method. From an initial set of 12 potential physical variables, 6 independent variables were selected for the classification algorithm, i.e., sea surface temperature (SST), bathymetry, sea ice, seasonal variation of sea surface salinity (DSSS), total suspended matter (TSM) and its seasonal variation (DTSM). The classification results reveal a robust separation between the northern and the middle/southern basins as well as a separation of the shallow nearshore waters from those offshore. The observed patterns in ecoregions can be attributed to differences in climate and geochemical factors such as distance from river, water depth and currents. A comparison of the annual and monthly mean Chl <i>a</i> concentrations between the different ecoregions shows significant differences (one-way ANOVA, <i>P</i> < 0.05). In particular, we found differences in phytoplankton phenology, with differences in the date of bloom initiation, its duration and amplitude between ecoregions. A first qualitative evaluation of differences in community composition based on recorded presence–absence patterns of 25 different species of plankton, fish and benthic invertebrate also confirms the relevance of the ecoregions as proxies for habitats with common biological characteristics

Self-organizing map algorithm for assessing spatial and temporal patterns of pollutants in environmental compartments: A review

The evaluation of the spatial and temporal distribution of pollutants is a crucial issue to assess the anthropogenic burden on the environment. Numerous chemometric approaches are available for data exploration and they have been applied for environmental health assessment purposes. Among the unsupervised methods, Self-Organizing Map (SOM) is an artificial neural network able to handle non-linear problems that can be used for exploratory data analysis, pattern recognition, and variable relationship assessment. Much more interpretation ability is gained when the SOMbased model is merged with clustering algorithms. This review comprises: (i) a description of the algorithm operation principle with a focus on the key parameters used for the SOM initialization; (ii) a description of the SOM output features and how they can be used for data mining; (iii) a list of available software tools for performing calculations; (iv) an overview of the SOM application for obtaining spatial and temporal pollution patterns in the environmental compartments with focus on model training and result visualization; (v) advice on reporting SOM model details in a pape

Rainfall fluctuations and vegetation patterns in alkali grasslands – using self-organizing maps to visualise vegetation dynamics

Knowledge about the drivers of vegetation dynamics in grasslands is fundamental to select appro-priate management for conservation purposes. In this study, we provide a detailed analysis of vegeta-tion dynamics in alkali grasslands, a priority habitat of the Natura 2000 network. We studied vegetation dynamics in five stands of four alkali grassland types in the Hortobágy National Park (eastern Hunga-ry), between 2009 and 2011. We analysed the effect of fluctuations in precipitation on both the overall vegetation composition and on the cover of each species using Self Organizing Map neural networks (SOM). We found that SOM is a promising tool to reveal plant community dynamics. As we analysed species cover and overall vegetation composition separately, we were able to identify the species re-sponsible for particular vegetation changes. Fluctuations in precipitation (a dry season, followed by a wet and an average season) caused quick shifts in plant species composition because of an increasing cover of halophyte forbs, probably because of salinisation. We observed a similar effect of stress from waterlogging in all studied grassland types. The species composition of Puccinellia grasslands was the most stable over the three years with varying precipitation. This was important as this grassland type contained many threatened halophyte species. Self-organising maps revealed small-scale vegetation changes and provided a detailed visualisation of short-term vegetation dynamics, thus we suggest that the application of this method is also promising to reveal community dynamics in more species-rich habitat types or landscapes

Enhanced data clustering and classification using auto-associative neural networks and self organizing maps

This thesis presents a number of investigations leading to introduction of novel applications of intelligent algorithms in the fields of informatics and analytics. This research aims to develop novel methodologies to reduce dimensions and clustering of highly non-linear multidimensional data. Improving the performance of existing methodologies has been based on two fundamental approaches. The first is to look into making novel structural re-arrangements by hybridisation of conventional intelligent algorithms which are Auto-Associative Neural Networks (AANN) and Self Organizing Maps (SOM) for data clustering improvement. The second is to enhance data clustering and classification performance by introducing novel fundamental algorithmic changes known as M3-SOM in the data processing and training procedure of conventional SOM. Both approaches are tested, benchmarked and analysed using three datasets which are Iris Flowers, Italian Olive Oils and Wine through case studies for dimension reduction, clustering and classification of complex and non-linear data. The study on AANN alone shows that this non-linear algorithm is able to efficiently reduce dimensions of the three datasets. This paves the way towards structurally hybridising AANN as dimension reduction method with SOM as clustering method (AANNSOM) for data clustering enhancement. This hybrid AANNSOM is then introduced and applied to cluster Iris Flowers, Italian Olive Oils and Wine datasets. The hybrid methodology proves to be able to improve data clustering accuracy, reduce quantisation errors and decrease computational time when compared to SOM in all case studies. However, the topographic errors showed inconsistency throughout the studies and it is still difficult for both AANNSOM and SOM to provide additional inherent information of the datasets such as the exact position of a data in a cluster. Therefore, M3-SOM, a novel methodology based on SOM training algorithm is proposed, developed and studied on the same datasets. M3-SOM was able to improve data clustering and classification accuracy for all three case studies when compared to conventional SOM. It is also able to obtain inherent information about the position of one data or "sub-cluster" towards other data or sub-cluster within the same class in Iris Flowers and Wine datasets. Nevertheless, it faces difficulties in achieving the same level of performance when clustering Italian Olive Oils data due to high number of data classes. However, it can be concluded that both methodologies have been able to improve data clustering and classification performance as well as to discover inherent information inside multidimensional data

Fire disturbance promotes biodiversity of plants, lichens and birds in the Siberian subarctic tundra

Fire shapes the world's terrestrial ecosystems and has been influencing biodiversity patterns for millennia. Anthropogenic drivers alter fire regimes. Wildfires can amplify changes in the structure, biodiversity and functioning of the fast-warming tundra ecosystem. However, there is little evidence available, how these fires affect species diversity and community composition of tundra ecosystems over the long term. We studied long-term fire effects on community composition and diversity at different trophic levels of the food web in the subarctic tundra of Western Siberia. In a space-for-time approach we compared three large fire scars (>44, 28 and 12 years old) to unburnt controls. We found that diversity (measured as species richness, Shannon index and evenness) of vascular and non-vascular plants and birds was strongly affected by fire, with the greatest species richness of plants and birds for the intermediate-age fire scar (28 years). Species composition of plants and birds still differed from that of the control >44 years after fire. Increased deciduous shrub cover was related to species richness of all plants in a hump-shaped manner. The proportion of southern (taiga) bird species was highest in the oldest fire scar, which had the highest shrub cover. We conclude that tundra fires have long-term legacies with regard to species diversity and community composition. They may also increase landscape-scale species richness and facilitate range expansions of more southerly distributed species to the subarctic tundra ecosystem