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Ramírez-Barahona, S. 2024. Incorporating fossils into the joint inference of phylogeny and biogeography of the tree fern order Cyatheales R. Warnock, and M. Zelditch [eds.],. Evolution. https://doi.org/10.1093/evolut/qpae034

Present-day geographic and phylogenetic patterns often reflect the geological and climatic history of the planet. Neontological distribution data are often sufficient to unravel a lineage’s biogeographic history, yet ancestral range inferences can be at odds with fossil evidence. Here, I use the fossilized birth–death process and the dispersal–extinction cladogenesis model to jointly infer the dated phylogeny and range evolution of the tree fern order Cyatheales. I use data for 101 fossil and 442 extant tree ferns to reconstruct the biogeographic history of the group over the last 220 million years. Fossil-aware reconstructions evince a prolonged occupancy of Laurasia over the Triassic–Cretaceous by Cyathealean tree ferns, which is evident in the fossil record but hidden from analyses relying on neontological data alone. Nonetheless, fossil-aware reconstructions are affected by uncertainty in fossils’ phylogenetic placement, taphonomic biases, and specimen sampling and are sensitive to interpretation of paleodistributions and how these are scored. The present results highlight the need and challenges of incorporating fossils into joint inferences of phylogeny and biogeography to improve the reliability of ancestral geographic range estimation.

Vanderhoorn, J. M. M., J. M. Wilmshurst, S. J. Richardson, T. R. Etherington, and G. L. W. Perry. 2024. Revealing the palaeoecology of silent taxa: selecting proxy species from associations in modern vegetation data. Journal of Biogeography. https://doi.org/10.1111/jbi.14826

Aim Species severely under‐represented in fossil pollen records leave gaps in interpretations and reconstructions of past vegetation. These ‘silent taxa’ leave little or no trace due to low pollen production, dispersal, preservation and taxonomic resolution. An approach for including them is through associating them with other species with reliable pollen representation. Here, we demonstrate a method for selecting such a proxy species for the Holocene using modern vegetation data.LocationNew Zealand.TaxonBeilschmiedia tawa (A.Cunn.) Benth. & Hook. F. ex Kirk (Lauraceae).MethodsWe used vegetation plot data to perform a pairwise co‐occurrence analysis of the New Zealand indigenous forest metacommunity to identify species with a strong positive association with Beilschmiedia tawa (tawa), a common tree severely under‐recorded in the pollen record. For those species, we then modelled their realised climatic niches to identify species with high niche overlap. We discuss how well those species could be interpreted from the Holocene fossil pollen record based on the representation of their pollen taxa.ResultsKnightia excelsa (rewarewa; Proteaceae) is a potential proxy for B. tawa in Holocene fossil pollen records, and other, range‐limited species may provide community‐specific proxies. We show combining resampling with sub‐sampling is a robust method for reducing the high false positive rate associated with large co‐occurrence analyses (1000+ sites) by limiting the sample size to 100 sites.Main ConclusionsWe show that the palaeoecology of silent taxa can be studied via proxy species, allowing their past distributions to be better understood. We highlight the importance of modelling many aspects of the realised niche to understand the usefulness and limitations of the silent–proxy association. Future research should focus on testing the underlying assumptions of the silent–proxy relationship so that models built on modern data can confidently be applied to palaeoecological data.

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.

Cohen, S. D. 2023. Estimating the Climate Niche of Sclerotinia sclerotiorum Using Maximum Entropy Modeling. Journal of Fungi 9: 892. https://doi.org/10.3390/jof9090892

Sclerotinia sclerotiorum, a fungal pathogen, causes world-wide crop losses and additional disease management strategies are needed. Modeling the climate niche of this fungus may offer a tool for the selection of biological control organisms and cultural methods of control. Maxent, a modeling technique, was used to characterize the climate niche for the fungus. The technique requires disease occurrence data, bioclimatic data layers, and geospatial analysis. A cross-correlation was performed with ArcGIS 10.8.1, to reduce nineteen bioclimatic variables (WorldClim) to nine variables. The model results were evaluated by AUC (area under the curve). A final model was created with the random seed procedure of Maxent and gave an average AUC of 0.935 with an AUC difference of −0.008. The most critical variables included annual precipitation (importance: 14.1%) with a range of 450 mm to 2500 mm and the mean temperature of the coldest quarter0 (importance: 55.6%) with a range of −16 °C to 24 °C, which contributed the most to the final model. A habitat suitability map was generated in ArcGIS 10.8.1 from the final Maxent model. The final model was validated by comparing results with another occurrence dataset. A Z-Score statistical test confirmed no significant differences between the two datasets for all suitability areas.

Lima, V. P., R. A. Ferreira de Lima, F. Joner, L. D’Orangeville, N. Raes, I. Siddique, and H. ter Steege. 2023. Integrating climate change into agroforestry conservation: A case study on native plant species in the Brazilian Atlantic Forest. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14464

Designing multispecies systems with suitable climatic affinity and identifying species' vulnerability under human‐driven climate change are current challenges to achieve successful adaptation of natural systems. To address this problem, we need to (1) identify groups of species with climatic similarity under climate scenarios and (2) identify areas with high conservation value under predicted climate change.To recognize species with similar climatic niche requirements that can be grouped for mixed cropping in Brazil, we employed ecological niche models (ENMs) and Spearman's ρ for overlap. We also used prioritization algorithms to map areas of high conservation value using two Shared Socioeconomic Pathways (SSP2‐4.5 and SSP5‐8.5) to assess mid‐term (2041–2060) and long‐term (2061–2080) climate change impacts.We identified 15 species groups with finer climatic affinities at different times depicted on hierarchical clustering dendrograms, which can be combined into agroecological agroforestry systems. Furthermore, we highlight the climatically suitable areas for these groups of species, thus providing an outlook of where different species will need to be planted over time to be conserved. In addition, we observed that climate change is predicted to modify the spatial association of these groups under different future climate scenarios, causing a mean negative change in species climatic similarity of 9.5% to 13.7% under SSP2‐4.5 scenario and 9.5% to 10.5% under SSP5‐8.5, for 2041–2060 and 2061–2080, respectively.Synthesis and applications. Our findings provide a framework for agroforestry conservation. The groups of species with finer climatic affinities identified and the climatically suitable areas can be combined into agroecological productive systems, and provide an outlook of where different species may be planted over time. In addition, the conservation priority zones displaying high climate stability for each species individually and all at once can be incorporated into Brazil's conservation plans by policymakers to prioritize specific sites. Lastly, we urge policymakers, conservation organizations and donors to promote interventions involving farmers and local communities, since the species' evaluated have proven to maintain landscapes with productive forest fragments and can be conserved in different Brazilian ecosystems.

Robin-Champigneul, F., J. Gravendyck, H. Huang, A. Woutersen, D. Pocknall, N. Meijer, G. Dupont-Nivet, et al. 2023. Northward expansion of the southern-temperate podocarp forest during the Early Eocene Climatic Optimum: Palynological evidence from the NE Tibetan Plateau (China). Review of Palaeobotany and Palynology: 104914. https://doi.org/10.1016/j.revpalbo.2023.104914

The debated vegetation response to climate change can be investigated through palynological fossil records from past extreme climate conditions. In this context, the early Eocene (53.3 to 41.2 million years ago (Ma)) is often referred to as a model for a greenhouse Earth. In the Xining Basin, situated on the North-eastern Tibetan Plateau (NETP), this time interval is represented by an extensive and well-dated sedimentary sequence of evaporites and red mudstones. Here we focus on the palynological record of the Early Eocene Climatic Optimum (EECO; 53.3 to 49.1 Ma) and study the fossil gymnosperm pollen composition in these sediments. In addition, we also investigate the nearest living relatives (NLR) or botanical affinity of these genera and the paleobiogeographic implications of their occurrence in the Eocene of the NETP. To reach our objective, we complemented transmitted light microscopy with laser scanning- and electron microscopy techniques, to produce high-resolution images, and illustrate the morphological variation within fossil and extant gymnosperm pollen. Furthermore, a morphometric analysis was carried out to investigate the infra- and intrageneric variation of these and related taxa. To place the data in context we produced paleobiogeographic maps for Phyllocladidites and for other Podocarpaceae, based on data from a global fossil pollen data base, and compare these with modern records from GBIF. We also assessed the climatic envelope of the NLR. Our analyses confirm the presence of Phyllocladidites (NLR Phyllocladus, Podocarpaceae) and Podocarpidites (NLR Podocarpus, Podocarpaceae) in the EECO deposits in the Xining Basin. In addition, a comparative study based on literature suggests that Parcisporites is likely a younger synonym of Phyllocladidites. Our findings further suggest that the Phyllocladidites specimens are derived from a lineage that was much more diverse than previously thought, and which had a much larger biogeographical distribution during the EECO than at present. Based on the climatic envelope of the NLR, we suggest that the paleoclimatic conditions in the Xining Basin were warmer and more humid during the EECO. We conclude that phylloclade-type conifers typical of the southern-temperate podocarp forests, had a northward geographical expansion during the EECO, followed by extirpation.

Reichgelt, T., A. Baumgartner, R. Feng, and D. A. Willard. 2023. Poleward amplification, seasonal rainfall and forest heterogeneity in the Miocene of the eastern USA. Global and Planetary Change 222: 104073. https://doi.org/10.1016/j.gloplacha.2023.104073

Paleoclimate reconstructions can provide a window into the environmental conditions in Earth history when atmospheric carbon dioxide concentrations were higher than today. In the eastern USA, paleoclimate reconstructions are sparse, because terrestrial sedimentary deposits are rare. Despite this, the eastern USA has the largest population and population density in North America, and understanding the effects of current and future climate change is of vital importance. Here, we provide terrestrial paleoclimate reconstructions of the eastern USA from Miocene fossil floras. Additionally, we compare proxy paleoclimate reconstructions from the warmest period in the Miocene, the Miocene Climatic Optimum (MCO), to those of an MCO Earth System Model. Reconstructed Miocene temperatures and precipitation north of 35°N are higher than modern. In contrast, south of 35°N, temperatures and precipitation are similar to today, suggesting a poleward amplification effect in eastern North America. Reconstructed Miocene rainfall seasonality was predominantly higher than modern, regardless of latitude, indicating greater variability in intra-annual moisture transport. Reconstructed climates are almost uniformly in the temperate seasonal forest biome, but heterogeneity of specific forest types is evident. Reconstructed Miocene terrestrial temperatures from the eastern USA are lower than modeled temperatures and coeval Atlantic sea surface temperatures. However, reconstructed rainfall is consistent with modeled rainfall. Our results show that during the Miocene, climate was most different from modern in the northeastern states, and may suggest a drastic reduction in the meridional temperature gradient along the North American east coast compared to today.

Alkhalifah, D. H. M., E. Damra, M. B. Melhem, and W. N. Hozzein. 2023. Fungus under a Changing Climate: Modeling the Current and Future Global Distribution of Fusarium oxysporum Using Geographical Information System Data. Microorganisms 11: 468. https://doi.org/10.3390/microorganisms11020468

The impact of climate change on biodiversity has been the subject of numerous research in recent years. The multiple elements of climate change are expected to affect all levels of biodiversity, including microorganisms. The common worldwide fungus Fusarium oxysporum colonizes plant roots as well as soil and several other substrates. It causes predominant vascular wilt disease in different strategic crops such as banana, tomato, palm, and even cotton, thereby leading to severe losses. So, a robust maximum entropy algorithm was implemented in the well-known modeling program Maxent to forecast the current and future global distribution of F. oxysporum under two representative concentration pathways (RCPs 2.6 and 8.5) for 2050 and 2070. The Maxent model was calibrated using 1885 occurrence points. The resulting models were fit with AUC and TSS values equal to 0.9 (±0.001) and 0.7, respectively. Increasing temperatures due to global warming caused differences in habitat suitability between the current and future distributions of F. oxysporum, especially in Europe. The most effective parameter of this fungus distribution was the annual mean temperature (Bio 1); the two-dimensional niche analysis indicated that the fungus has a wide precipitation range because it can live in both dry and rainy habitats as well as a range of temperatures in which it can live to certain limits. The predicted shifts should act as an alarm sign for decision makers, particularly in countries that depend on such staple crops harmed by the fungus.

Baltensperger, A., J. Hagelin, P. Schuette, A. Droghini, and K. Ott. 2022. High dietary and habitat diversity indicate generalist behaviors of northern bog lemmings Synaptomys borealis in Alaska, USA. Endangered Species Research 49: 145–158. https://doi.org/10.3354/esr01211

The northern bog lemming Synaptomys borealis (NBL) is a rare small mammal that is undergoing a federal Species Status Assessment (SSA) under the US Endangered Species Act. Despite a wide North American distribution, very little is known about NBL dietary or habitat needs, both of which are germane to the resiliency of this species to climate change. To quantify diet composition of NBL in Alaska, we used DNA metabarcoding from 59 archived specimens to describe the taxonomic richness and relative abundance of foods in recent diets. DNA analyses revealed a broad diet composed of at least 110 families and 92 genera of bryophytes (mosses and liverworts), graminoids, fungi, forbs, and woody shrubs. Nine bryophyte genera and Carex sedges composed the largest portions of NBL diets. To quantify habitat preference, we intersected 467 georeferenced occurrence records of NBL in Alaska with remotely sensed land cover classes and used a compositional analysis framework that accounts for the relative abundance of land cover types. We did not detect significant habitat preferences for specific land cover types, although NBL frequently occurred in evergreen forest, woody wetlands, and adjacent to water. Our research highlights the importance of bryophytes, among a high diversity of dietary components, and describes NBL as boreal habitat generalists. Results will inform the current federal SSA by quantifying the extent to which ecological constraints are likely to affect NBL in a rapidly changing boreal environment.