Science Enabled by Specimen Data

Anon. 2023. Ecological Niche Modelling of an Industrially Important Mushroom - Ganoderma lucidum (Leys.) Karsten: A Machine Learning Global Appraisal. Journal of Scientific & Industrial Research 82. https://doi.org/10.56042/jsir.v82i12.1973

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.

Silva-Valderrama, I., J.-R. Úrbez-Torres, and T. J. Davies. 2024. From host to host: The taxonomic and geographic expansion of Botryosphaeriaceae. Fungal Biology Reviews 48: 100352. https://doi.org/10.1016/j.fbr.2023.100352

Fungal pathogens are responsible for 30% of emerging infectious diseases (EIDs) in plants. The risk of a pathogen emerging on a new host is strongly tied to its host breadth; however, the determinants of host range are still poorly understood. Here, we explore the factors that shape host breadth of plant pathogens within Botryosphaeriaceae, a fungal family associated with several devastating diseases in economically important crops. While most host plants are associated with just one or a few fungal species, some hosts appear to be susceptible to infection by multiple fungi. However, the variation in the number of fungal taxa recorded across hosts is not easily explained by heritable plant traits. Nevertheless, we reveal strong evolutionary conservatism in host breadth, with most fungi infecting closely related host plants, but with some notable exceptions that seem to have escaped phylogenetic constraints on host range. Recent anthropogenic movement of plants, including widespread planting of crops, has provided new opportunities for pathogen spillover. We suggest that constraints to pathogen distributions will likely be further disrupted by climate change, and we may see future emergence events in regions where hosts are present but current climate is unfavorable.

Schertler, A., B. Lenzner, S. Dullinger, D. Moser, J. L. Bufford, L. Ghelardini, A. Santini, et al. 2023. Biogeography and global flows of 100 major alien fungal and fungus‐like oomycete pathogens. Journal of Biogeography. https://doi.org/10.1111/jbi.14755

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.

Islomiddinov, Z. Sh., I. M. Mustafaev, J. P. Shirqulova, B. S. Khabibullaev, Y. W. Lim, et al. 2023. The first record of Pisolithus arhizus (Sclerodermataceae, Basidiomycota) in Central Asia. Ukrainian Botanical Journal 80: 337–342. https://doi.org/10.15407/ukrbotj80.04.337

Pisolithus is a genus of gasteroid mycorrhizal symbionts associated with trees of several families of angiosperms and gymnosperms and distributed almost worldwide. Here we report a new record of Pisolithus arhizus from Tashkent, Uzbekistan, the first record of this species in Central Asia. The fruit bodies of P. arhizus were collected in several locations within the city and identified based on morphological characters. The ectomycorrhizal fungus formed symbiotic relationships with Juniperus sp. and Quercus sp. We provide its morphological description and photographs and also discuss our findings in the context of previously known records of this species.

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224

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.

Ramírez, F., V. Sbragaglia, K. Soacha, M. Coll, and J. Piera. 2022. Challenges for Marine Ecological Assessments: Completeness of Findable, Accessible, Interoperable, and Reusable Biodiversity Data in European Seas. Frontiers in Marine Science 8. https://doi.org/10.3389/fmars.2021.802235

The ongoing contemporary biodiversity crisis may result in much of ocean’s biodiversity to be lost or deeply modified without even being known. As the climate and anthropogenic-related impacts on marine systems accelerate, biodiversity knowledge integration is urgently required to evaluate and monit…

Filartiga, A. L., A. Klimeš, J. Altman, M. P. Nobis, A. Crivellaro, F. Schweingruber, and J. Doležal. 2022. Comparative anatomy of leaf petioles in temperate trees and shrubs: the role of plant size, environment and phylogeny. Annals of Botany 129: 567–582. https://doi.org/10.1093/aob/mcac014

Background and Aims Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting ability of the leaf as well as transport of water, nutrients and biochemical signals. Despite the high diversity in petiole size, shape and anatomy, little information is availabl…

Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 2021. Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation 32: e01885. https://doi.org/10.1016/j.gecco.2021.e01885

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…

TREVIÑO-ZEVALLOS, I., I. GARCÍA-CUNCHILLOS, and C. LADO. 2021. New records of Myxomycetes (Amoebozoa) from the tropical Andes. Phytotaxa 522: 231–239. https://doi.org/10.11646/phytotaxa.522.3.6

The Myxomycetes comprise a remarkably diverse group of organisms within Amoebozoa, with over 1000 species currently recognized. These organisms, at the end of their life cycles produce fruiting bodies which are the basis for their systematics. Despite being a biodiversity hotspot, the tropical Andes…