Released 4 years ago, the Wallace EcoMod application (R package wallace) provided an open‐source and interactive platform for modeling species niches and distributions that served as a reproducible ...toolbox and educational resource. wallace harnesses R package tools documented in the literature and makes them available via a graphical user interface that runs analyses and returns code to document and reproduce them. Since its release, feedback from users and partners helped identify key areas for advancement, leading to the development of wallace 2. Following the vision of growth by community expansion, the core development team engaged with collaborators and undertook a major restructuring of the application to enable: simplified addition of custom modules to expand methodological options, analyses for multiple species in the same session, improved metadata features, new database connections, and saving/loading sessions. wallace 2 features nine new modules and added functionalities that facilitate data acquisition from climate‐simulation, botanical and paleontological databases; custom data inputs; model metadata tracking; and citations for R packages used (to promote documentation and give credit to developers). Three of these modules compose a new component for environmental space analyses (e.g., niche overlap). This expansion was paired with outreach to the biogeography and biodiversity communities, including international presentations and workshops that take advantage of the software's extensive guidance text. Additionally, the advances extend accessibility with a cloud‐computing implementation and include a suite of comprehensive unit tests. The features in wallace 2 greatly improve its expandability, breadth of analyses, and reproducibility options, including the use of emerging metadata standards. The new architecture serves as an example for other modular software, especially those developed using the rapidly proliferating R package shiny, by showcasing straightforward module ingestion and unit testing. Importantly, wallace 2 sets the stage for future expansions, including those enabling biodiversity estimation and threat assessments for conservation.
There is an urgent need for large‐scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. ...Understanding these processes is critical for predicting and handling human‐biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.
The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and co‐occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an r package that provides easy access to these data.
The bien r package allows users to access the multiple types of data in the BIEN database. Functions in this package query the BIEN database by turning user inputs into optimised PostgreSQL functions. Function names follow a convention designed to make it easy to understand what each function does. We have also developed a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the bien r package.
The development of the BIEN database represents a significant achievement in biological data integration, cleaning and standardization. Likewise, the bien r package represents an important tool for open science that makes the BIEN database freely and easily accessible to everyone.
In a rapidly changing climate, alpine plants may persist by adapting to new conditions. However, the rate at which the climate is changing might exceed the rate of adaptation through evolutionary ...processes in long-lived plants. Persistence may depend on phenotypic plasticity in morphology and physiology. Here we investigated patterns of leaf trait variation including leaf area, leaf thickness, specific leaf area, leaf dry matter content, leaf nutrients (C, N, P) and isotopes (δ
C and δ
N) across an elevation gradient on Gongga Mountain, Sichuan Province, China. We quantified inter- and intra-specific trait variation and the plasticity in leaf traits of selected species to experimental warming and cooling by using a reciprocal transplantation approach. We found substantial phenotypic plasticity in most functional traits where δ
N, leaf area, and leaf P showed greatest plasticity. These traits did not correspond with traits with the largest amount of intraspecific variation. Plasticity in leaf functional traits tended to enable plant populations to shift their trait values toward the mean values of a transplanted plants' destination community, but only if that population started with very different trait values. These results suggest that leaf trait plasticity is an important mechanism for enabling plants to persist within communities and to better tolerate changing environmental conditions under climate change.
Darwin proposed two seemingly contradictory hypotheses regarding factors influencing the outcome of biological invasions. He initially posited that nonnative species closely related to native species ...would be more likely to successfully establish, because they might share adaptations to the local environment (preadaptation hypothesis). However, based on observations that the majority of naturalized plant species in the United States belonged to nonnative genera, he concluded that the lack of competitive exclusion would facilitate the establishment of alien invaders phylogenetically distinct from the native flora (competition-relatedness hypothesis). To date, no consensus has been reached regarding these opposing hypotheses. Here, following Darwin, we use the flora of the United States to examine patterns of taxonomic and phylogenetic relatedness between native and nonnative taxa across thousands of nested locations ranging in size and extent, from local to regional scales. We find that the probability of observing the signature of environmental filtering over that of competition increases with spatial scale. Further, native and nonnative species tended to be less related in warm, humid environments. Our work provides an empirical assessment of the role of observation scale and climate in biological invasions and demonstrates that Darwin’s two opposing hypotheses need not be mutually exclusive.
Aim
To quantify the impact of the 2019–2020 megafires on Australian plant diversity by assessing burnt area across 26,062 species ranges and the effects of fire history on recovery potential. ...Further, to exemplify a strategic approach to prioritizing plant species affected by fire for recovery actions and conservation planning at a national scale.
Location
Australia.
Methods
We combine data on geographic range, fire extent, response traits and fire history to assess the proportion of species ranges burnt in both the 2019–2020 fires and the past.
Results
Across Australia, suitable habitat for 69% of all plant species was burnt (17,197 species) by the 2019–2020 fires and herbarium specimens confirm the presence of 9,092 of these species across the fire extent since 1950. Burnt ranges include those of 587 plants listed as threatened under national legislation (44% of Australia's threatened plants). A total of 3,998 of the 17,197 fire‐affected species are known to resprout after fire, but at least 2,928 must complete their entire life cycle—from germinant to reproducing adult—prior to subsequent fires, as they are killed by fire. Data on previous fires show that, for 257 species, the historical intervals between fire events across their range are likely too short to allow regeneration. For a further 411 species, future fires during recovery will increase extinction risk as current populations are dominated by immature individuals.
Main conclusion
Many Australian plant species have strategies to persist under certain fire regimes, and will recover given time, suitable conditions and low exposure to threats. However, short fire intervals both before and after the 2019–2020 fire season pose a serious risk to the recovery of at least 595 species. Persistent knowledge gaps about species fire response and post‐fire population persistence threaten the effective long‐term management of Australian vegetation in an increasingly pyric world.
Abstract
Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. ...Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species’ phylogenetic endemism, its macroecological drivers, and how future pressures may affect the conservation status of the identified hotspots. We found that low-to-mid latitudes host most endemism hotspots, with current climate being the strongest driver, and climatic stability across thousands to millions of years back in time as a major co-determinant. These hotspots are mostly located outside of protected areas and face relatively high land-use change and future climate change pressure. Our study highlights the risk from climate change for tree diversity and the necessity to strengthen conservation and restoration actions in global hotspots of phylogenetic endemism for trees to avoid major future losses of tree diversity.
The functional composition of plant communities is commonly thought to be determined by contemporary climate. However, if rates of climate‐driven immigration and/or exclusion of species are slow, ...then contemporary functional composition may be explained by paleoclimate as well as by contemporary climate. We tested this idea by coupling contemporary maps of plant functional trait composition across North and South America to paleoclimate means and temporal variation in temperature and precipitation from the Last Interglacial (120 ka) to the present. Paleoclimate predictors strongly improved prediction of contemporary functional composition compared to contemporary climate predictors, with a stronger influence of temperature in North America (especially during periods of ice melting) and of precipitation in South America (across all times). Thus, climate from tens of thousands of years ago influences contemporary functional composition via slow assemblage dynamics.
Climate may determine functional composition if there is variation in the rates of immigration and exclusion linked to functional traits. We show strong Pleistocene legacies on the contemporary functional composition in the New World plant assemblages consistent with slow community assembly processes.
Species richness of marine mammals and birds is highest in cold, temperate seas-a conspicuous exception to the general latitudinal gradient of decreasing diversity from the tropics to the poles. We ...compiled a comprehensive dataset for 998 species of sharks, fish, reptiles, mammals, and birds to identify and quantify inverse latitudinal gradients in diversity, and derived a theory to explain these patterns. We found that richness, phylogenetic diversity, and abundance of marine predators diverge systematically with thermoregulatory strategy and water temperature, reflecting metabolic differences between endotherms and ectotherms that drive trophic and competitive interactions. Spatial patterns of foraging support theoretical predictions, with total prey consumption by mammals increasing by a factor of 80 from the equator to the poles after controlling for productivity.
The number of tree species on Earth Cazzolla Gatti, Roberto; Reich, Peter B; Gamarra, Javier G P ...
Proceedings of the National Academy of Sciences - PNAS,
02/2022, Volume:
119, Issue:
6
Journal Article, Web Resource
Peer reviewed
Open access
One of the most fundamental questions in ecology is how many species inhabit the Earth. However, due to massive logistical and financial challenges and taxonomic difficulties connected to the species ...concept definition, the global numbers of species, including those of important and well-studied life forms such as trees, still remain largely unknown. Here, based on global ground-sourced data, we estimate the total tree species richness at global, continental, and biome levels. Our results indicate that there are ∼73,000 tree species globally, among which ∼9,000 tree species are yet to be discovered. Roughly 40% of undiscovered tree species are in South America. Moreover, almost one-third of all tree species to be discovered may be rare, with very low populations and limited spatial distribution (likely in remote tropical lowlands and mountains). These findings highlight the vulnerability of global forest biodiversity to anthropogenic changes in land use and climate, which disproportionately threaten rare species and thus, global tree richness.
Abstract
The Arctic is warming twice as fast as the rest of the planet, leading to rapid changes in species composition and plant functional trait variation. Landscape-level maps of vegetation ...composition and trait distributions are required to expand spatially-limited plot studies, overcome sampling biases associated with the most accessible research areas, and create baselines from which to monitor environmental change. Unmanned aerial vehicles (UAVs) have emerged as a low-cost method to generate high-resolution imagery and bridge the gap between fine-scale field studies and lower resolution satellite analyses. Here we used field spectroscopy data (400–2500 nm) and UAV multispectral imagery to test spectral methods of species identification and plant water and chemistry retrieval near Longyearbyen, Svalbard. Using the field spectroscopy data and Random Forest analysis, we were able to distinguish eight common High Arctic plant tundra species with 74% accuracy. Using partial least squares regression (PLSR), we were able to predict corresponding water, nitrogen, phosphorus and C:N values (
r
2
= 0.61–0.88, RMSEmean = 12%–64%). We developed analogous models using UAV imagery (five bands: Blue, Green, Red, Red Edge and Near-Infrared) and scaled up the results across a 450 m long nutrient gradient located underneath a seabird colony. At the UAV level, we were able to map three plant functional groups (mosses, graminoids and dwarf shrubs) at 72% accuracy and generate maps of plant chemistry. Our maps show a clear marine-derived fertility gradient, mediated by geomorphology. We used the UAV results to explore two methods of upscaling plant water content to the wider landscape using Sentinel-2A imagery. Our results are pertinent for high resolution, low-cost mapping of the Arctic.
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