From Extremely Acidic to Alkaline – Diversity of Aquatic Invertebrates in Forest Mining Lakes Under the Pressure of Acidification

Human activities, including mining industry, have considerably degraded the water habitats worldwide. Acidification has severely affected aquatic environments with acidifying pollutants and constitute threat to freshwater biodiversity. The study area is unique for addressing the effects of mining-related acidification on biodiversity in freshwater ecosystems along a pH gradient (2.4-9.6). Using multivariate ordination techniques, we analysed taxa distribution to determine how variations in invertebrate composition correlated with environmental factors. The results revealed differences in pH of water, salinity indicators, hardness, and content of calcium, nitrites, and iron. The highest iron content, relatively high values of conductivity and chlorides was found in the extremely acidic mining lakes. A clear decreasing tendency was observed for the number of taxa with increasing acidity (Oligochaeta, Chironomidae, Glossiphonidae). The density of Hirudinidae, Lestidae, Libellulidae, Caenidae, Sialidae, Dytiscidae, Helodidae, Hydrophilidae and Polycentropodidae increased along with decreasing pH. Specific communities were found with increasing acidity, therefore a progressive increase in acidity will probably have further influence on biological life and water chemistry. The data yielded offer an opportunity to fill knowledge gaps concerning less-studied aquatic environments and links environmental pollution with communities, which is especially important because forest habitats are especially exposed to different climatic factors and threats.

MiBiOmics: an interactive web application for multi-omics data exploration and integration

Background Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system. However, it can become challenging given the often-large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills. Results Here, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements classical ordination techniques and the inference of omics-based (multilayer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states. Conclusions MiBiOmics provides easy-access to exploratory ordination techniques and to a network-based approach for integrative multi-omics analyses through an intuitive and interactive interface. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics.

MiBiOmics: An interactive web application for multi-omics data exploration and integration

BackgroundMulti-omics experimental approaches are becoming common practice in biological and medical sciences underlying the need to design new integrative techniques and applications to enable the holistic characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows us to acquire additional insights and generate novel hypotheses about a given biological system. However, it can often become challenging given the large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills.ResultsHere, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements advanced ordination techniques and the inference of omics-based (multi-layer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states.ConclusionsThrough an intuitive and interactive interface, MiBiOmics provides easy-access to ordination techniques and to a network-based approach for integrative multi-omics analyses. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics.

Systematic Review of the Roost-Site Characteristics of North American Forest Bats: Implications for Conservation

Continued declines in North American bat populations can be largely attributed to habitat loss, disease, and wind turbines. These declines can be partially mitigated through actions that boost reproductive success; therefore, management aimed at promoting availability of high-quality roosting habitat is an important conservation goal. Following the principles of the umbrella species concept, if co-occurring species share similar roost-tree preferences, then management practices targeting one species may confer conservation benefits to another. We conducted a systematic review of roost-site characteristics of thirteen species inhabiting eastern temperate forests to: (1) synthesize existing knowledge across species; (2) assess niche overlap among co-occurring species; and (3) evaluate the potential for currently protected species to serve as conservation umbrellas. We performed multivariate ordination techniques to group species based on the seven most-reported roost-site characteristics, including tree species, diameter at breast height, tree health, roost type, tree height, canopy closure, and roost height. Species sorted into three roosting guilds: (1) southern wetland inhabitants; (2) foliage specialists; and (3) dead tree generalists. Myotis septentrionalis and Perimyotis subflavus had significant roost-niche overlap with five and four other species respectively, and their existing protections make them suitable umbrellas for other bats in the North American eastern temperate forests.

Vegetation Dynamics and Diversity Status in Mughal Garden Wah, Pakistan

Classification and ordination of vegetation of Mughal Garden, Wah, Pakistan was done along with assessment of diversity status. A total of 45 species were recorded in vegetation survey belonging to 24 families with Asteraceae and Poaceae being the largest families. Herbs dominated the flora of Wah Garden by 44.4%, shrubs 15.5%, trees 13.3%, grasses 11.1%, creeping herbs 11.1%, ferns 2.2% and aquatic herbs 2.2%. About 35.5% species were annuals, 28.8% perennials, 13.3% annuals or perennials, 8.8% annuals or biennials, 8.8% deciduous, 2.2% coniferous and evergreen species. In case of life form of species, Therophytes and Megaphanerophytes were the most prevalent among species indirect ordination techniques TWINSPAN and DCA were employed that produced two major groups which were further divided into five communities and three major groups, respectively. Shannon-Wiener diversity index, Simpson Index of diversity and Hill’s N1 and N2 diversity numbers were calculated and verified by data attribute plot through DCA suggesting reduced species diversity as Shannon-Wiener diversity index ranged between 0 and 1.67 due to increased anthropogenic activity. The outcome of this research will be useful in providing information on identification of species that are present, their distribution patterns, and classification which would help in management and conservation of native vegetation in future.

Temporal and Vertical Relations between Various Environmental Factors in the Largest Lake of Łęczna-Włodawa Lake District (Eastern Poland)

Due to global warming and increasing water eutrophication, understanding in-lake relationships is paramount to prevent excessive pollution and further negative changes in lakes. The physico-chemical and biological parameters, as well as nutrient variabilities, both temporal and vertical (in the water column), were studied in the largest Łęczna-Włodawa lake. The study was conducted during two consecutive water years, from November 2015 to September 2017. The non-parametric Kruskal–Wallis ANOVA, test H was used to detect variability between years, and among seasons and lake depths in water temperature, electrical conductivity, pH, ORP, concentration of dissolved oxygen as well as concentration of NO3−, PO43−, TP and chlorophyll a. One-way analysis of variance (ANOVA) was used to detect any differences in Secchi depth (SD) and concentration of NH4+, NO2−, and TN. Ordination techniques: Detrended correspondence analysis (DCA), and Principal Components Analysis (PCA) were used to describe the relationships among 13 environmental variables and distribution of samples. Results showed significant differences (P < 0.05) between two years of the study for most variables except of water temperature, visibility, concentration of PO43−, TN and TP, which corresponded with highly different weather conditions in both years. All of the tested variables, except for nutrients, differed significantly among seasons. Most parameters showed fluctuation in depth, especially in summer and in winter, despite the fact that no hypolimnion or long-lasting thermocline was observed in the study period. However, variability of Chl-a was statistically significant only. The results emphasized complex and multi-directional relations between tested variables, dependent on both external (catchment) and internal (in-lake) processes.

Avian Community Structure as a Function of Season, Habitat Type, and Disturbance, in Mole National Park, Northern Region (Ghana)

The study assessed factors that influenced bird-habitat preference, diversity, and spatial distribution in Mole National Park. Birds were identified using point count sampling method, while ordination techniques were performed to determine the influence of environmental factors on bird-habitat preference. A total of 4951 individuals belonging to 131 species were identified across the four habitat types in the wet (n= 3033) and dry (n= 1648) seasons. Despite the high abundance and richness of birds in the woodland and shrubland habitats, grassland habitat was the most diverse, due to the high spatial evenness distribution of the birds. Bushfire, patchiness, and animal trampling were the key environmental determinants in bird assemblages and habitat preferences and accounted for 62.02% and 81.82% variations in the two seasons. Rarer birds like White-Backed Vulture (NT) and White-Headed Vulture (CR), Bateleur Eagle (NT), and Woolly-Necked Stork (VU), with high conservation concern, suggest intensification of conservation effort, while the dominance of Sahel Bush-sparrow was probably due to their broad range habitat preferences and ability to adapt to environmental conditions across these habitats. These species could be used as indicators of habitat quality, if future scenarios restrict their movement or distribution in narrow range habitats.

Diversity and gradients of vegetation of Sivrihisar Mountains (Eskişehir-Turkey)

This study was carried out to determine the plant communities and understand the main topographical driving factors of floristic differentiation in the Sivrihisar Mountains (Eskişehir Province). Vegetation samplings were carried out according to the Braun-Blanquet approach. The relevés were stored in the TURBOVEG database management program. Hierarchical classification was carried out in PC-ORD program with Ward’s method and Euclidean distance as a resemblance measure. The diagnostic species were identified by a fidelity measure in the JUICE program. The results of the classification were visualized by ordination techniques in the CANOCO package by using principal component analysis. In conclusion, except for the degraded forest community, all the 7 steppe and 1 scrub plant communities studied were identified and described as new associations. Also, a syntaxonomical scheme for the vegetation of Sivrihisar Mountains was suggested.

On the Use of Redundancy Analysis to Study the Property Crime in Poland

Redundancy analysis (RDA) is a canonical form of principal components analysis (PCA) and is one of, so‑called, linear ordination techniques. The goal of ordination is to represent objects and response variables relationships as faithfully as possible in a low‑dimensional space. Redundancy analysis is also a technique of exploratory data analysis. Graphical presentation of the results using the ordination biplots or triplots can facilitate the analysis of the relationship between the variation in the set of the response variables and the variation of the explanatory variables. In the paper, redundancy analysis was applied to assess the relationships between the selected socio‑economic factors and the intensity of the crime against property in Poland.

The identification of Oligo-Miocene mammalian palaeocommunities from the Riversleigh World Heritage Area, Australia and an appraisal of palaeoecological techniques

Fourteen of the best sampled Oligo-Miocene local faunas from the Riversleigh World Heritage Area, north-western Queensland, Australia are analysed using classification and ordination techniques to identify potential mammalian palaeocommunities and palaeocommunitytypes. Abundance data for these faunas are used, for the first time, in conjunction with presence/absence data. An early Miocene Faunal Zone B and two middle Miocene Faunal Zone C palaeocommunities are recognised, as well as one palaeocommunity type. Change in palaeocommunity structure, between the early Miocene and middle Miocene, may be the result of significant climate change during the Miocene Carbon Isotope Excursion. The complexes of local faunas identified will allow researchers to use novel palaeocommunities in future analyses of Riversleigh’s fossil faunas. The utility of some palaeoecological multivariate indices and techniques is examined. The Dice index is found to outperform other binary similarity/distance coefficients, while the UPGMA algorithm is more useful than neighbour joining. Evidence is equivocal for the usefulness of presence/absence data compared to abundance.