Dr. Michael Nobis

The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package 'sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.

Urgent conservation action is needed to safeguard biodiversity. One promising approach is the use of surrogate species in species-based conservation strategies, which can indirectly benefit other species that share similar habitat requirements. However, the lack of spatial quantification methods to accurately select representative species at large-scale regions has limited the application of surrogate species in conservation. To address this, our study presents two methods to quantify and select surrogate species for species-based conservation in the Plateau-Mountains-Basin transition region of China (∼486,000 km²). These two methods follow the same selection process, moving from priority conservation species to refined candidate species, and finally to surrogate species. Specifically, we compiled a species list of priority conservation plant species and used multiple datasets to predict the area of habitat maps for these species. We found 140 priority conservation plants distributed around the Sichuan Basin. Building on their distributions, we selected 17 surrogate species using indicator value analysis, considering 18 different subregion combinations and 4 habitat overlap scenarios. Alternatively, we applied a second method, selecting 19 surrogate species based on factor analysis, while considering the correlation analysis of pairwise species combinations. The richness map of these surrogate species shows a distribution pattern similar to that of the 140 priority conservation plants. Based on the distribution patterns of surrogate species, we identified conservation hotspots in the mountains around the Sichuan Basin. By utilizing the fine-scale area of habitat maps, our study offers valuable strategies for selecting surrogate species in species-based conservation efforts aimed at safeguarding biodiversity in ecologically critical regions.

The negative effects of habitat loss on biodiversity are undisputed, while the effect of habitat configuration, i.e., the spatial arrangement of habitat area, has been debated for decades. To develop a more comprehensive understanding, it is important to know when and how configuration matters. In this study, we tested whether forest configuration influences the richness of species in groups characterized by varying shade tolerance in different ways and how such effects are related to habitat amount (i.e., the percentage of forest cover) at the landscape scale. Based on 104 survey plots (each measuring 1 ​km²) of vascular plants on the Swiss Plateau, and using two statistical approaches (i.e., multiple regression and path analysis), we modeled the effects of habitat amount and configuration (measured as number of forest patches, total edge length, and proximity index) across all the plots and separately for three habitat amount classes: <10%, 10%–30%, and >30% forest cover. When we modeled all plots together, we found that, after controlling for habitat amount, the forest configuration significantly affected species richness. When we considered the different habitat amount classes separately, most of the significant effects of habitat configuration on species richness occurred only for habitat amounts of <10% forest cover. Additionally, the response to forest configuration differed among species with different shade tolerances. When forest area was <10%, the effects of the number of patches and the total edge length on the species richness of light-demanding forest species were greater than the effect of habitat amount, whereas neither configuration metric affected the richness of shade-tolerant species. In conclusion, our findings highlight the importance of configuration in landscapes with a small amount of habitat. At the same time, they demonstrate that considering the confounding factors (e.g. species traits) is important for understanding the effects of forest configuration on biodiversity and that generalizations remain a challenge for landscape ecology.

Extinction risk is not randomly distributed among species but depends on species traits, their relationship to climate and land use, and corresponding threats by global change. While knowledge of which factors influence extinction risk is increasingly available for some taxonomic groups, this is still largely lacking for bryophytes. Here, we used random forest models to study which biological and ecological traits and bioclimatic variables are important predictors for extinction risk in European bryophytes. We hypothesized that species with a high extinction risk have a short life span, low dispersal capacities, and are more likely specialists than generalists in terms of ecological traits and bioclimate. Overall, we found bioclimatic variables to be the most important predictors for extinction risk, most notably precipitation seasonality, and related ecological traits such as continentality and elevational range. Important biological traits were plant size, life strategy and sporophyte production. In general, species living at climatic extremes and/or those with a narrow environmental range are more likely to be threatened. In addition, small-sized species and/or species with low reproductive effort and/or larger spore size are more likely to be threatened. Our findings imply that climate change may become an important driver of bryophytes extinction risk and that biological and ecological traits will be most relevant for species in coping with future threats.

Aims: To develop a consistent ecological indicator value system for Europe for five of the main plant niche dimensions: soil moisture (M), soil nitrogen (N), soil reaction (R), light (L) and temperature (T). Study area: Europe (and closely adjacent regions). Methods: We identified 31 indicator value systems for vascular plants in Europe that contained assessments on at least one of the five aforementioned niche dimensions. We rescaled the indicator values of each dimension to a continuous scale, in which 0 represents the minimum and 10 the maximum value present in Europe. Taxon names were harmonised to the Euro+Med Plantbase. For each of the five dimensions, we calculated European values for niche position and niche width by combining the values from the individual EIV systems. Using T values as an example, we externally validated our European indicator values against the median of bioclimatic conditions for global occurrence data of the taxa. Results: In total, we derived European indicator values of niche position and niche width for 14,835 taxa (14,714 for M, 13,748 for N, 14,254 for R, 14,054 for L, 14,496 for T). Relating the obtained values for temperature niche position to the bioclimatic data of species yielded a higher correlation than any of the original EIV systems (r = 0.859). The database: The newly developed Ecological Indicator Values for Europe (EIVE) 1.0, together with all source systems, is available in a flexible, harmonised open access database. Conclusions: EIVE is the most comprehensive ecological indicator value system for European vascular plants to date. The uniform interval scales for niche position and niche width provide new possibilities for ecological and macroecological analyses of vegetation patterns. The developed workflow and documentation will facilitate the future release of updated and expanded versions of EIVE, which may for example include the addition of further taxonomic groups, additional niche dimensions, external validation or regionalisation.

High-resolution, downscaled climate model data are used in a wide variety of applications across environmental sciences. Here we introduce a new, high-resolution dataset, CHELSA-TraCE21k. It is obtained by downscaling TraCE-21k data, using the "Climatologies at high resolution for the earth's land surface areas" (CHELSA) V1.2 algorithm with the objective to create global monthly climatologies for temperature and precipitation at 30 arcsec spatial resolution in 100-year time steps for the last 21 000 years. Paleo-orography at high spatial resolution and for each time step is created by combining high-resolution information on glacial cover from current and Last Glacial Maximum (LGM) glacier databases and interpolations using data from a global model of glacial isostasy (ICE-6G_C) and a coupling to mean annual temperatures from TraCE21k (Transient Climate Evolution of the last 21 000 years) based on the Community Climate System Model version 3 (CCSM3). Based on the reconstructed paleo-orography, mean annual temperature and precipitation were downscaled using the CHELSA V1.2 algorithm. The data were validated by comparisons with the glacial extent of the Laurentide ice sheet based on expert delineations, proxy data from Greenland ice cores, historical climate data from meteorological stations, and a dynamic simulation of species distributions throughout the Holocene. Validations show that the CHELSA-TraCE21k V1.0 dataset reasonably represents the distribution of temperature and precipitation through time at an unprecedented 1 km spatial resolution, and simulations based on the data are capable of detecting known LGM refugia of species.

Aims: Ellenberg-type indicator values are expert-based rankings of plant species according to their ecological optima on main environmental gradients. Here we extend the indicator-value system proposed by Heinz Ellenberg and co-authors for Central Europe by incorporating other systems of Ellenberg-type indicator values (i.e., those using scales compatible with Ellenberg values) developed for other European regions. Our aim is to create a harmonized data set of Ellenberg-type indicator values applicable at the European scale.
Methods: We collected European data sets of indicator values for vascular plants and selected 13 data sets that used the nine-, ten-or twelve-degree scales defined by Ellenberg for light, temperature, moisture, reaction, nutrients and salinity. We compared these values with the original Ellenberg values and used those that showed consistent trends in regression slope and coefficient of determination. We calculated the average value for each combination of species and indicator values from these data sets. Based on species' co-occurrences in European vegetation plots, we also calculated new values for species that were not assigned an indicator value.
Results: We provide a new data set of Ellenberg-type indicator values for 8908 European vascular plant species (8168 for light, 7400 for temperature, 8030 for moisture, 7282 for reaction, 7193 for nutrients, and 7507 for salinity), of which 398 species have been newly assigned to at least one indicator value.
Conclusions: The newly introduced indicator values are compatible with the original Ellenberg values. They can be used for large-scale studies of the European flora and vegetation or for gap-filling in regional data sets. The European indicator values and the original and taxonomically harmonized regional data sets of Ellenberg-type indicator values are available in the Supporting Information and the Zenodo repository.

Invasive Neophyten sind neu auftretende, gebietsfremde Problempflanzen, deren Vorkommen mit ökonomischen, ökologischen oder gesundheitlichen Risiken verbunden sind. Diese Arten breiten sich zum Teil besonders entlang von Verkehrsachsen aus, doch ist ihre Verbreitung wegen der eingeschränkten Zugänglichkeit und der Grösse der Verkehrs-infrastruktur oft kaum bekannt. In der vorliegenden Arbeit werden mit Kamerafahrten und automatisierter Arterkennung durch künstliche Intelligenz (KI) die drei invasive Neophyten Götterbaum (Ailanthus altissima), Schmalblättriges Greiskraut (Senecio inaequidens) und Beifussblättrige Ambrosie (Ambrosia artemisiifolia) auf dem gesamten Nationalstrassennetz kartiert. [...]

Bryophytes are a diverse group of organisms with unique properties, yet they are severely underrepresented in plant trait databases. Building on the recently published European Red List of bryophytes and previous trait compilations, we present the Bryophytes of Europe Traits (BET) dataset, including biological traits such as those related to life history, growth habit, sexual and vegetative reproduction, ecological traits such as indicator values, substrate and habitat, and bioclimatic variables based on the species’ European range. The dataset includes values for 65 traits and 25 bioclimatic variables, containing more than 135 000 trait values with a completeness of 82.7% on average. The dataset will enable future studies in bryophyte biology, ecology and conservation and may help to answer fundamental questions in bryology.

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 available regarding their structural adaptations across evolutionary lineages and environmental conditions. To fill this knowledge gap, we investigated the variation of petiole morphology and anatomy of mainly European woody species to better understand the drivers of internal and external constraints in an evolutionary context.
Methods We studied how petiole anatomical features differed according to whole-plant size, leaf traits, thermal and hydrological conditions, and taxonomic origin in 95 shrubs and trees using phylogenetic distance-based generalized least squares models.
Key Results Two major axes of variation were related to leaf area and plant size. Larger and softer leaves are found in taller trees of more productive habitats. Their petioles are longer, with a circular outline and are anatomically characterized by the predominance of sclerenchyma, larger vessels, interfascicular areas with fibres and indistinct phloem rays. In contrast, smaller and tougher leaves are found in shorter trees and shrubs of colder or drier habitats. Their petioles have a terete outline, phloem composed of small cells and radially arranged vessels, fibreless xylem and lamellar collenchyma. Individual anatomical traits were linked to different internal and external drivers. Petiole length and vessel diameter increase with increasing leaf blade area. Collenchyma becomes absent with increasing temperature, and petiole outline becomes polygonal with increasing precipitation.
Conclusions We conclude that species' temperature and precipitation optima, plant height, and leaf area and thickness exerted a significant control on petiole anatomical and morphological structures not confounded by phylogenetic inertia. Species with different evolutionary histories but similar thermal and hydrological requirements have converged to similar petiole anatomical structures.

Background: We aimed to characterise the geographical distribution of Sørensen-based multi-site dissimilarity (β_sor) and its underlying true turnover (β_sim) and nestedness (β_sne) components for Chinese Lauraceae and to analyse their relationships to current climate and past climate change.
Methods: We used ensembles of small models (ESMs) to map the current distributions of 353 Lauraceae species in China and calculated β_sor and its β_sim and β_sne components. We tested the relationship between β_sor, β_sne and β_sim with current climate and past climate change related predictors using a series of simultaneous autoregressive (SAR_err) models.
Results: Spatial distribution of β_sor of Lauraceae is positively correlated with latitude, showing an inverse relationship to the latitudinal α-diversity (species richness) gradient. High β_sor occurs at the boundaries of the warm temperate and subtropical zones and at the Qinghai-Tibet Plateau due to high β_sne. The optimized SAR_err model explains β_sor and β_sne well, but not β_sim. Current mean annual temperature determines β_sor and β_sne of Lauraceae more than anomalies and velocities of temperature or precipitation since the Last Glacial Maximum.
Conclusions: Current low temperatures and high climatic heterogeneity are the main factors explaining the high multi-site β-diversity of Lauraceae. In contrast to analyses of the β-diversity of entire species assemblages, studies of single plant families can provide complementary insights into the drivers of β-diversity of evolutionarily more narrowly defined entities.

Soil spatial heterogeneity involves nutrients being patchily distributed at a range of scales and is prevalent in natural habitats. However, little is known about the effect of soil spatial configurations at the small scale on plant foraging behavior and plant growth under different resource amounts. Here, we experimentally investigated how a stoloniferous species, Trifolium repens, responded to varied resource amounts and spatial configuration combinations. Plant foraging behavior (i.e., the orientation of the primary stolon, mean length of the primary stolon, foraging precision, and foraging scale) and plant growth (i.e., total biomass, root biomass, shoot biomass, and root/shoot) were compared among differently designed configurations of soil resources in different amounts. The relationships of foraging behavior and plant biomass were analyzed. The results showed that the effect of the spatial configuration of soil resources on Trifolium repens depended on the resource amount. Specifically, when the total resource amount was low, fragmented soil patches promoted root foraging and increased Trifolium repens plant biomass; however, when the total resource amount was high, the soil spatial configuration did not affect foraging behavior or plant growth. Our results also showed that plant growth was facilitated by root foraging scale to adapt to low resource amounts. We conclude that the spatial configuration of soil resources at small scales affects whole plant growth, which is mediated by a distinct foraging strategy. These findings contribute to a better understanding of how the growth strategy of clonal plants responds to heterogeneous environments caused by different resource amounts and its spatial configurations.

Context The effects of landscape structure on biodiversity may change with the spatial and temporal scale at which landscape structure is measured. Identifying the spatial extent and temporal scale at which the biodiversity-landscape relationship is strongest (i.e., the scale of effect) is important to better understand the effect of landscape structure.
Objectives The spatial and temporal scale of effect is analyzed to identify whether it differs in ecologically distinct species groups. How species richness-landscape relationship changes with spatial and temporal scales is tested.
Methods Based on 98 survey plots (1 km²) of vascular plants on the Swiss Plateau, we analyzed the relationships between species richness of different species groups and landscape predictors at different spatial extents (1 km², 4 km², 16 km², 36 km²) and time periods (past landscapes - 1985, 1997, 2009 and the current landscape 2018).
Results The spatial scale of effect was 1 km for most species groups, while the temporal scale of effect differed among species groups. The strength of the species richness-landscape relationship generally decreased with increased spatial extents, while it changed little across temporal scales.
Conclusions Although our study only considered changes in landscape structure over the last c. 30 years, ecologically distinct species groups revealed differences in the temporal scale of effect including a rapid response of neophytes linked to ongoing biological invasions. However, the variation in the species richness-landscape relationship was greater when changing spatial extent than time. We highlight that studying the relationship between landscape structure and biodiversity should consider not only space but also time, and different responses of ecologically distinct species groups.

During the 20^th century human activities drastically altered the natural environment at global and local scales by habitat destruction, urbanisation, intensive agriculture, and climate warming. This anthropogenic pressure has modified species distributions and abundances, and led to the increased spread of neophytes. However, the determination of the magnitude, direction, and drivers of changes remains challenging as comparable historic data is often lacking. Here, we analysed the floristic shifts during the 20^th century based on a historic (1900–1930) and current (2000–2017) floristic survey of the canton of Zurich (Switzerland; 1729 km²) in combination with Landolt ecological indicator values (EIVs) for vascular plants. We used two complementary approaches to quantify the floristic shifts using EIVs for temperature, moisture, continentality, nutrients, soil pH and available light. 1) Regarding 244 map tiles with each a 3 × 3 km² area, we compared the average EIVs for neophytes (i.e., novel species arriving of expanding in the study area) and native species (i.e., species present in Switzerland for centuries). 2) Based on standardized species abundances in the historic and the current flora, we analysed the directed changes by comparing the species’ EIVs of different frequency classes for both the historic and current floristic surveys. Our results showed, that neophyte species arriving or spreading in the study area indicate both a thermophilisation and an eutrophisation. The observed shift in average EIVs for temperature corresponded to about 2 °C, which is in line with the calculated difference in niche centroids for neophytes and native species based on their global distribution (1.78 °C). The indicated thermophilisation and eutrophisation relate to the decrease in abundances of cold-adapted species and species of nutrient poor environments as well as the increase of warm-adapted and nitrophilous/ruderal species. Directed changes in the flora of the study area are likely to be driven by both climatic changes and land-use changes. Increases in trade activity, anthropogenic habitat disturbances and rising temperatures facilitate the establishment and spread of neophytes from warmer and drier regions. In parallel, wetland area and wetland species strongly decreased as well as species thriving on nutrient-poor sites due to intensified agriculture and nitrogen deposition.

Species distribution models (SDMs) are often used to predict the impact of climate change on the future distribution of species. However, the application of species-level SDMs often ignores intraspecific variation and can be problematic. The aim of the study was to incorporate intraspecific information into SDMs and compare predictions of subspecies- and species-level SDMs in a widespread African tree species, Sclerocarya birrea (marula). We used bioclimatic variables and terrain roughness index to calibrate nine algorithms in 'biomod2' platform. Ensemble models were built to predict the current and future suitable habitat of marula and separately its three subspecies, birrea, caffra and multifoliolata. Projections were made to 2041 - 2060 and 2081 - 2100 under three general circulation models and two shared socio-economic pathways. Results showed an expansion of the suitable habitat of marula as well as subspp. birrea and caffra in the two future time periods. The suitable habitat of subsp. multifoliolata, in contrast, contracted in future. Our results show that species-level SDMs may fail to detect climate change risks for intraspecific taxa, and consequently leading to under- or overestimation of the impacts of climate change. Incorporation of intraspecific variation into SDMs improves predictions of the impact of climate change and helps to identify appropriate conservation and management options.

•Key message An ensemble modelling approach was performed to predict the distributions of seven sympatric sclerophyllous oak species in the Hengduan Mountains of Southwest China. Spatial eigenvector filters revealed missing factors in addition to commonly used environmental variables, thus effectively improved predictive accuracy for the montane oak species. This study identified a richness center of sclerophyllous oaks, which provides a reference for proper conservation and utilization of oak resources.
•Context As key species and important trees for construction- and fuel-wood, montane sclerophyllous oaks (Quercus sect. Heterobalanus) in the Hengduan Mountains of Southwest China are threatened by climate change, habitat fragmentation, and human activities.
•Aims This study aims to simulate the potential distributions of seven sympatric sclerophyllous oak species with an emphasis on exploring the relative importance of climatic, non-climatic, and additional spatial factors.
•Methods We performed an ensemble modelling approach of six ecological niche models in combination with spatial eigenvector filters to predict the potential distributions of seven oak species.
•Results The results elucidated that temperature seasonality, followed by land use/cover and the human influence index were the most critical variables controlling oak species distributions. Regardless of the selected algorithm, the best performing models for most oaks combined climatic and non-climatic factors as well as additional spatial filters.
•Conclusion It is necessary to strengthen the conservation of oak species at the junction of Sichuan and Yunnan Province where we found the richness center of the studied oaks. Our research provides essential insights for the rational conservation and management of sclerophyllous oak species, suggesting that spatial constraints might reflect limited ability of migration under future climate change.

Von 2012 bis 2019 arbeiteten 250 Personen ehrenamtlich für die neue Flora des Kantons Zürich. Das umfangreiche Projekt konnte dank Beiträgen verschiedener Sponsoren professionell koordiniert und mit einem Buch und einer Webseite erfolgreich abgeschlossen werden. Die Flora besteht aus Steckbriefen für 1757 im Kanton wildwachsende Pflanzenarten, die sowohl historische als auch aktuelle Angaben zum Vorkommen enthalten. Ausführliche Beschreibungen des Naturraums, eine Bilanzierung des Florenwandels und Exkursionsvorschläge sind wesentliche Elemente des Buchs.

Seit 1839 wurden im Kanton Zürich 1757 wildwachsende Gefässpflanzenarten gezählt. Davon sind 108 Arten (6 %) ausgestorben oder verschollen und 131 Arten (7 %) seit 1930 neu hinzugekommen. Bei einem Viertel der Arten hat die Häufigkeit abgenommen, bei 10 % hat sie zugenommen. Die grössten Artverluste sind bei Arten zu verzeichnen, die auf Ruderalflächen, in Feuchtgebieten oder in Trockenwiesen und -weiden leben. Flächenverluste und die Veränderung der Lebensräume sind die wichtigsten Gründe für diesen Wandel der Flora.

In the 21st century, stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is still the most devastating disease of wheat globally. Despite the critical roles of the alternate host plants, the Berberis species, in the sexual reproduction and spread of Pst, the climate change impacts on the redistribution of Berberis plants, and their potential risk of incurring wheat stripe rust are scarcely discussed in the literature. This study evaluated the potential risk of Pst in wheat cultivation in Sichuan Province, China, for the first time, by analyzing the dynamics of Berberis plants and the change in Pst oversummering range under climate change scenarios. Ensembles of small models (ESMs) in combination with four algorithms were used to project the future (i.e., 2041–2060, 2061–2080, and 2081–2100) distributions of 54 Berberis species in Sichuan Province based on two shared socioeconomic pathways (SSP) scenarios. The species richness of Berberis was predicted to increase in northwestern Sichuan but decreased in southern and eastern Sichuan under both SSP245 and SSP585 scenarios. The mean temperature of the driest quarter was found to be the determinant of the distributional shifts for the majority of Berberis plants. Our overlapping assessments indicated that the risk of wheat stripe rust would be reduced in southwestern Sichuan. In contrast, it would be aggravated in the northwest due to the predicted shifts of Berberis plants northwards and stronger shrinkage of Pst oversummering range occurring in the south than in the north. In the “hotspots” of the stripe rust pathogen, risk assessment in advance could provide a scientific basis for decision-makers and local communities in effectively controlling wheat stripe rust, thus further sustaining food security through adapting to future climate change.