Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach.

The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.

An Overview of Factors Affecting the Functional Quality of Common Wheat (Triticum aestivum L.).

Wheat (Triticum aestivum L.) is one of the most important crops worldwide, and, as a resilient cereal, it grows in various climatic zones. Due to changing climatic conditions and naturally occurring environmental fluctuations, the priority problem in the cultivation of wheat is to improve the quality of the crop. Biotic and abiotic stressors are known factors leading to the deterioration of wheat grain quality and to crop yield reduction. The current state of knowledge on wheat genetics shows significant progress in the analysis of gluten, starch, and lipid genes responsible for the synthesis of the main nutrients in the endosperm of common wheat grain. By identifying these genes through transcriptomics, proteomics, and metabolomics studies, we influence the creation of high-quality wheat. In this review, previous works were assessed to investigate the significance of genes, puroindolines, starches, lipids, and the impact of environmental factors, as well as their effects on the wheat grain quality.

Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species.

The rye genome has a large size with a high level of cytosine methylation, which makes it particularly convenient for studying the occurrence of potential cytosine demethylation intermediates. Levels of global 5-hydroxymethylcytosine (5hmC) were analysed by enzyme-linked immunosorbent assay (ELISA) and mass spectrometry in four rye species: Secale cereale, Secale strictum, Secale sylvestre, and Secale vavilovii. The amount of 5hmC showed interspecific variation, and was also variable among organs, i.e. coleoptiles, roots, leaves, stems, and caryopses. 5-Formylcytosine (5fC), 5-carboxycytosine (5caC), and 5-hydroxymethyluracil (5hmU) were also found to be present in the DNA of all species; their global level varied among species and organs. The 5hmC level clearly correlated with the 5-methylcytosine (5mC) quantity. The mass spectrometry analysis carried out on the 5mC enriched fraction supported this relationship. Highly methylated sequences also contained higher amounts of 5fC and most of all 5hmU, but not 5caC. The analysis of the distribution of 5hmC in chromosomes distinctly indicated the co-localization of 5mC with 5hmC in the same chromosomal regions. The regularities in the levels of 5hmC and other rare modifications of bases in the DNA may indicate that they play a role in the regulation of the rye genome.

Epigenetic Changes Occurring in Plant Inbreeding.

Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.

A new pattern of parasitism in water mites (Hydrachnidia)? An insight into their relationships with pupae of caddisflies (Trichoptera).

To date, relatively few data have been available regarding the parasitism of water mite larvae on caddisflies; most available information relates to the adult stadia, fewer to caddisfly larvae, with just single references to pupae. The present paper examines the occurrence (phoresy and parasitism) of Piona stjordalensis larvae (119 individuals) on the larvae and pupae of Mystacides longicornis. It is possible that water mite larvae exhibit a new type of parasitism on caddisflies, with two consecutive parasitic larval stadia: one on the pupa, the other on the imago.

Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept.

The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krapiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as "marshes" (marshland surface), "shrubs" (shrub surface), and "forests" (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequence of the effects of both internal factors and external ones, originating from the entire river's catchment, which is in accord with the basic assumptions of the RCC.

Anthropogenic transformations of river ecosystems are not always bad for the environment: Multi-taxa analyses of changes in aquatic and terrestrial environments after dredging of a small lowland river.

Rivers are one of the most commonly transformed aquatic ecosystems. Most papers present significantly negative effects of activities such as dredging or channel regulation on the ecological status of rivers. The purpose of this work was to compare the response of various groups of invertebrates (Mollusca, Hydrachnidia, Odonata, Heteroptera, Coleoptera and Trichoptera) to an intervention involving dredging in conjunction with the removal of riparian vegetation. Habitat diversity increased after the dredging, and more individuals and species were caught than before the dredging. The increase in habitat diversity after the dredging translated into an increase in the species diversity of most investigated groups. Individual groups of invertebrates showed varied responses to the dredging, depending on the role of the terrestrial phase in their life cycle: the greater the role of the terrestrial phase in the life cycle, the more the group was affected by changes in the terrestrial environment following the intervention. In consequence, the intervention had the greatest negative impact on insects, and among these, on adult Odonata. The following conclusions can be drawn: (1) Dredging can benefit a previously anthropogenically transformed river ecosystem by increasing habitat diversity; (2) Odonata are particularly useful for assessing the impact of this type of intervention on invertebrate communities. They can be considered good indicators of habitat disturbances in both aquatic and terrestrial ecosystems.

Effects of dredging on the vegetation in a small lowland river.

BACKGROUND: Conventional river engineering operations have a substantial influence on the fluvial ecosystem. Regulation and channelization generally reduce the physical heterogeneity of river beds and banks and the heterogeneity of habitats. They determine the character, diversity and species richness of plant communities. The effect of river regulation on vegetation has been repeatedly investigated, but few studies have been conducted within reaches of previously regulated rivers. The aim of this work is to expand and current knowledge about the impact of dredging on the vegetation of a regulated section of a lowland river. MATERIALS & METHODS: The study included pre-dredging (1 year before) and post-dredging surveys (results 1 and 2 years after dredging). The vegetation was analysed in terms of species composition, origin of species, life forms, distribution of Grime's life strategies, and selected ecological factors. The Shannon-Wiener biodiversity index (H) and evenness were also analysed in each year of the study. The impact of dredging on the vascular flora was assessed by 'before-after-control-impact' (BACI) analysis. RESULTS: The number of species and biodiversity as measured by the Shannon-Wiener index (H) increased in the analysed section of the river valley. However, enrichment of the flora was observed only on the floodplain, on the surface of the deposited dredging material, while the number of species in the river channel decreased, as dredging of the river bed and levelling of the banks had markedly reduced habitat diversity. Although species richness in the second year after the dredging approached the values recorded before the intervention, the absence of particularly species or phytocenoses associated with shallow river banks and sandbars was still observed. The change in habitat conditions and the destruction of the vegetation cover during the dredging enabled penetration by numerous previously unrecorded alien species of plants and apophytes. There was a perceptible increase in the role of therophytes in the flora. It is worth noting that the number of alien species and therophytes declined significantly in the second year after the dredging. Analysis of the proportions of species representing various life strategies showed that previously unrecorded species with the type R (ruderal) life strategy had appeared, representing by pioneer species occurring in frequently disturbed habitats. There was also a marked increase in the share of species representing the mixed C-R (competitive-ruderal) strategy, occurring in habitats with low levels of stress, whose competitive abilities are limited by repeated disturbances. By the second year after the dredging, however, these changes were largely no longer observed. CONCLUSIONS: Through appropriate maintenance of the regulated river, it can be rapidly recolonized by vegetation after the procedure, but it may lead to the loss of some species and phytocoenoses.

Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers.

BACKGROUND: Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. METHODS: The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA). RESULTS: The low value of Dice's coefficient (0.369) along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. DISCUSSION: The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.