Motif: an open-source R tool for pattern-based spatial analysis

Context

Pattern-based spatial analysis provides methods to describe and quantitatively compare spatial patterns for categorical raster datasets. It allows for spatial search, change detection, and clustering of areas with similar patterns.

Objectives

We developed an R package motif as a set of open-source tools for pattern-based spatial analysis.

Methods

This package provides most of the functionality of existing software (except spatial segmentation), but also extends the existing ideas through support for multi-layer raster datasets. It accepts larger-than-RAM datasets and works across all of the major operating systems.

Results

In this study, we describe the software design of the tool, its capabilities, and present four case studies. They include calculation of spatial signatures based on land cover data for regular and irregular areas, search for regions with similar patterns of geomorphons, detection of changes in land cover patterns, and clustering of areas with similar spatial patterns of land cover and landforms.

Conclusions

The methods implemented in motif should be useful in a wide range of applications, including land management, sustainable development, environmental protection, forest cover change and urban growth monitoring, and agriculture expansion studies. The motif package homepage is https://nowosad.github.io/motif.

     

Artificial Feeding and Laboratory Rearing of Endangered Saproxylic Beetles as a Tool for Insect Conservation

Conservation of threatened animals is frequently limited by lack of knowledge about their ecological preferences, and often artificial feeding is one of the few chances to save endangered species. We investigated the possibility to artificially feed two endangered flat bark beetles dependent on dead wood for their diet—namely, Cucujus cinnaberinus (Scopoli, 1763) and Cucujus haematodes Erichson, 1845—by examining their dietary preferences, life cycle duration, and survival in laboratory conditions. Individuals of the two species were caught in the wild and larvae and adults were fed in laboratory conditions by live or dead prey. Three species of saproxylic beetles: two cerambycids (Acanthocinus griseus Fabricius, 1793 and Rhagium inquisitor Linnaeus, 1758), one scolytid (Ips sexdentatus Börner, 1776) one tenebrionid (Tenebrio molitor (Linnaeus, 1758)) one dipteran (Lucilia sericata (Meigen, 1826)) and one ant (Lasius sp. Fabricius, 1804) were used as prey, with minced meat as a control. Our results indicated high survival and no difference in prey choice between the two flat beetle species. Larvae and adults preferred dead prey, but no significant preference was detected among dead prey taxa, supporting the hypothesis that the two species are opportunistic scavengers. Comparing data with previous results, both species and their developmental stages should be classified as obligate saproxylic organisms with preference to the dead and decaying organic material. Successful artificial feeding and rearing of these endangered species, followed by the release in the wild through rescue or reintroduction programs, therefore appear relevant for their protection and future conservation.     

Aluminosilicates at different levels in rye litter and feed affect the growth and meat quality of broiler chickens

Veterinary Research Communications - Litter sanitation treatments and feed supplements that stimulate bird growth. The aim of this study was to analyse the effects of zeolite (z) and halloysite (h)...     

Effect of snow cover on the distribution of non-migratory sika deer on the top of Mt. Tanzawa,Japan

On the basis of 268 direct sika deer observations and 212 ratio locations of three individuals, the influence of snow on deer distribution was studied. During the period of snow absence or its shallow cover, the deer did not show any preferences towards slope aspect. However, when the snow coverage became deeper, the deer used westerly exposures (having shallower snow cover) more intensively. Later on, when the snow started to melt on the easterly slope aspects deer mostly used those exposures due to relatively abundant food resources.     

High-speed steel tool wear during wood cutting in the presence of high-temperature corrosion and mineral contamination

Dulling of high-speed steel (HSS) cutting tools after milling five wood species has been analyzed. The wood investigated varied in mineral contamination, high-temperature corrosivity (HTC) and density (D). Experiments performed proved that up to date methods for evaluation of mineral contamination in wood should be improved. A new pipe-like form of mineral contamination particles was evidenced. The correlation between the presence of 3D aggregates of silica in wood and high content of K and Ca in the ash was established. Employing multivariable theoretical simulation method, the combined effect of mineral contamination, HTC and wood density on the tool dullness appeared to be a reasonable explanation of the results obtained.     

Soil variability through spatial scales in a permanently disturbed natural spruce-fir-beech forest

Soil variability was assessed in a 74.2-ha area within the Žofínsky prales natural forest. Parameters evaluated for 1765 soil profiles inside 353 graticule plots were as follows: (1) thickness of organic horizons, (2) thickness and form of mineral horizons, (3) humus form (HF), (4) soil taxonomic unit (STU) and (5) anomalies. In addition, soil reaction (pH_KCl) and oxidizable carbon content (C_ox) were measured in the laboratory for 734 samples from the upper mineral (A) and lower mineral (B) horizons. The most frequently occurring humus form was mor followed by moder, hydromor and peaty T-horizon. Entic Podzols, Dystric Cambisols, Haplic Cambisols, Albic Podzols, Histic (or Haplic) Gleysols, Endogleyic Stagnosols, Fibric or Hemic or Sapric Histosols and Stagnic Gleysols were all present at the site despite its homogeneous geological bedrock. Overall coefficient of variance (CV) was lower in terrestrial soils compared with (semi-)hydromorphic soils. Overall variance decreased in both soil groups with increasing depth, as did CV differences between the fine (up to 10 m) and the locality scales. The lowest CV values occurred for C_ox and pH_KCl. The CV values differed between STUs as well. Compared to lower horizons, variograms of upper horizons showed greater autocorrelation at the intermediate spatial scale (10–320 m)—ranging from 50 to 150 m. Semivariance values, however, reached 70–80% of sill already at a distance of 10 m. The most significant factor of variability at all studied spatial scales is presumably the soil disturbance regime, followed by terrain micro-topography and the effect of tree species.     

Macroinvertebrate Community and Chemistry of the Most Atmospherically Acidified Streams in the Czech Republic

We performed a comparative study of strongly acidified mountain streams covering 10 sites in the Czech Republic in the season 1999/2000. The aim of the study was to determine how acidification influenced macroinvertebrate community structure within a relatively narrow pH range. We focused on strongly acidified, non-humic running waters with low ionic content (pH < 4.6, total organic carbon < 10 mg l^?1, specific conductivity < 100 μS cm^?1) and minimum human influence in the catchment. The actual pH values ranged from 3.98 to 4.65, and concentrations of reactive aluminium ranged from 0.2 to 2.0 mg l^?1. Characteristic macroinvertebrates were the stoneflies Leuctra nigra, Nemurella pictetii, and Protonemura spp.; the chironomids Corynoneura spp.; and the caddisfly Plectrocnemia conspersa – the former two stoneflies formed together 46% of total organisms. The sites were divided into three groups with use of divisive classification. Individual groups reflected similarity in water chemistry, catchment characteristics, and geographical proximity. The largest biotic difference detected by PCA was in the abundance of stoneflies, mainly Diura bicaudata and Leuctra major. The strongest correlation with this gradient was shown by pH (and associated heavy metals), followed by the distance from source. The results show that even in such narrow pH range, the number of taxa is determined by the low pH value and related high concentrations of aluminium and heavy metals.     

HPLC analysis of rosmarinic acid in feed enriched with aerial parts of Prunella vulgaris and its metabolites in pig plasma using dual-channel coulometric detection

This paper describes a sensitive isocratic HPLC/ECD method developed for the determination of rosmarinic acid (RA) in plant material, animal feed, and pig plasma. The plasma sample preparation only includes protein precipitation and adjustment of the pH. The applicability of the method was tested on plasma samples of pigs that were exposed to a 91-day oral intake of RA via feed enriched by aerial parts of Prunella vulgaris. The plasma was directly analyzed using the method described as well as after enzymatic hydrolysis. When no hydrolysis step was included, RA and caffeic acid (CA) were quantified in the plasma. In hydrolyzed plasma samples, several other metabolites were determined, including dihydrocaffeic, ferulic, and dihydroferulic acid. The dual-channel coulometric detection employed, as an alternative to mass spectrometry, offers good selectivity and sensitivity owing to the electrochemical properties of the phenolic constituents.     

Needle blight caused by Dothistroma pini in Slovakia: distribution,host range and mating types

Dothistroma needle blight (DNB) has been observed in Slovakia during the last two decades. Up until 2017, Dothistroma septosporum has only been detected and molecularly confirmed to cause DNB in Slovakia. Here, we report the detection of Dothistroma pini at six localities around Slovakia, representing different plantation types. Four pine species (Pinus sylvestris, P. nigra, P. mugo and P. jeffreyi) were confirmed as hosts of D. pini in Slovakia, of which only P. mugo has been previously reported as host in Slovakia. Three gene regions (ITS, EF1 –α, and ß-tubulin) of each of the 13 isolates were sequenced and assigned as D. pini. Based on ITS sequences, the studied isolates represent the haplotypes Dp_HAP.1, Dp_HAP.2. Both mating types were detected but at different localities. Our results suggest that in addition to D. septosporum, D. pini may contribute to DNB also in Slovakia.     

The hosts and geographic range of Dothistroma needle blight in Slovakia

The occurrence and distribution of Dothistroma needle blight (DNB) were studied in 2014–2017 around Slovakia. A total of 84 localities, both native and planted, were investigated, and the presence of DNB was confirmed in 73 of them. In all positive locations, symptoms typical of DNB were observed and the Dothistroma species was confirmed using species‐specific primers either from fungal cultures or directly from needles. Both Dothistroma species—D. septosporum and D. pini—were identified. Both species occurred together in 29 locations, only D. septosporum in 42 and only D. pini in two locations. The host range of D. septosporum included 10 pine species and two spruce species. The host range of D. pini comprised the same number of pine hosts but only one spruce species. Five pine hosts, P. aristata, P. coulteri, P. densiflora, P. jeffreyi, P. × schwerinii, and one spruce host P. abies are new hosts species of D. pini. P. densiflora and Picea pungens have earlier been reported to be susceptible for DNB. In this study, D. septosporum was found from both tree species.