Jan Špaček

Species Distribution Modelling (SDM) involves utilizing observations of a given species and its surrounding environment to produce a sound approximation of the species' potential distribution. The intricate relationships between organisms and their surroundings, coupled with the profusion of data, have captured the attention of ecologists and statisticians alike. Consequently, they have directed their efforts towards exploring the potential of machine learning techniques. Our study employs an ensemble machine learning approach to simulate the global ecological niche modelling of Ganoderma lucidum fungus. This involves the utilization of various environmental predictors and the averaging of multiple algorithms to achieve a comprehensive analysis. 563 spatially thinned presence points of G. lucidum were projected with three bio-climatic time frames, namely current, 2050, and 2070, and four Representative Concentration Pathways (RCPs), namely 2.6, 4.5, 6.0, and 8.5, as well as non-climatic variables (surface soil features, land use, rooting depth and water storage capacity at rooting zone). We observed excellent model qualities as the Area Under the receiver operating Curve (AUC) approached 0.90. Random Forest was identified as the best individual algorithm, while the Maxent entropy was identified as the least effective for Ecological Niche Modelling (ENM) of G. lucidum. Globally, under the current bio-climatic and non-bioclimatic projection, optimum habitat for this fungus covers 12510876.3 km2 area while, maximum area (13248546.9 Sq. km.) under this habitat class with future projections was recorded with RCP of 8.5 in 2070. The primary determinants of its current global distribution were ecosystem rooting depth, water storage capacity, and precipitation seasonality. While, with two future bioclimatic time frames and RCPs, Isothermality was identified as the most influential predictor. Based on our assessment, it has been determined that this particular fungus is exhibiting a persistent pattern of proliferation across the regions of Europe, America, and certain areas of India. The present investigation sought to underscore the importance of discerning the native habitats of this species, taking into account both current and anticipated climatic shifts. This knowledge is essential for effectively coordinating the artificial cultivation and natural harvesting of G. lucidum, which is necessary to meet the ever-increasing industrial demands.

AbstractAimSpreading infectious diseases associated with introduced pathogens can have devastating effects on native biota and human livelihoods. We analyse the global distribution of 100 major alien fungal and oomycete pathogens with substantial socio‐economic and environmental impacts and examine their taxonomy, ecological characteristics, temporal accumulation trajectories, regional hot‐ and coldspots of taxon richness and taxon flows between continents.LocationGlobal.TaxonAlien/cryptogenic fungi and fungus‐like oomycetes, pathogenic to plants or animals.MethodsTo identify over/underrepresented classes and phyla, we performed Chi2 tests of independence. To describe spatial patterns, we calculated the region‐wise richness and identified hot‐ and coldspots, defined as residuals after correcting taxon richness for region area and sampling effort via a quasi‐Poisson regression. We examined the relationship with environmental and socio‐economic drivers with a multiple linear regression and evaluated a potential island effect. Regional first records were pooled over 20‐year periods, and for global flows the links between the native range to the alien regions were mapped.ResultsPeronosporomycetes (Oomycota) were overrepresented among taxa and regional taxon richness was positively correlated with area and sampling effort. While no island effect was found, likely due to host limitations, hotspots were correlated with human modification of terrestrial land, per capita gross domestic product, temperate and tropical forest biomes, and orobiomes. Regional first records have increased steeply in recent decades. While Europe and Northern America were major recipients, about half of the taxa originate from Asia.Main ConclusionsWe highlight the putative importance of anthropogenic drivers, such as land use providing a conducive environment, contact opportunities and susceptible hosts, as well as economic wealth likely increasing colonisation pressure. While most taxa were associated with socio‐economic impacts, possibly partly due to a bias in research focus, about a third show substantial impacts to both socio‐economy and the environment, underscoring the importance of maintaining a wholescale perspective across natural and managed systems.

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

To clarify biogeographic patterns of two mushroom species (Phallus merulinus and Geastrum courtecuissei) previously reported from Myanmar, sequence data of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were retrieved from GenBank. The BLAST search and phylogenetic analyses of Phallus indicated that P. merulinus and P. atrovolvatus from wide areas, including Australia, Myanmar, Thailand, Brazil, and French Guiana, cannot be distinguished molecularly. The species was, therefore, considered widespread across tropical to subtropical regions. In contrast, G. courtecuissei from Myanmar was tightly clustered exclusively with G. courtecuissei from Central and South America, supporting the idea of its disjunct distribution between Southeast Asia (Myanmar) and Central-South Americas.

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long-distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns’ spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Aim: Due to the sessile nature of flowering plants, movements to new geographical areas occur mainly during seed dispersal. Frugivores tend to be efficient dispersers because animals move within the boundaries of their preferable niches, so seeds are more likely to be transported to environments tha…

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

Climate change has the potential to change the distribution of pests globally and their resistance to pesticides, thereby threatening global food security in the 21st century. However, predicting where these changes occur and how they will influence current pest control efforts is a challenge. Using…

Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase in occurrence data sets has generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of m…

Aims: Species distribution models (SDMs) are often used to forecast potential distributions of important invasive or rare species. However, situations where models could be the most valuable ecologically or economically, such as for predicting invasion risk, often pose the greatest challenges to SDM…