Beta-diversity of Central European forests decreases along an elevational gradient due to the variation in local community assembly processes

Beta-diversity has been repeatedly shown to decline with increasing elevation, but the causes of this pattern remain unclear, partly because they are confounded by coincident variation in alpha- and gamma-diversity. We used 8,795 forest vegetation-plot records from the Czech National Phytosociological Database to compare the observed patterns of beta diversity to null-model expectations (beta-deviation) controlling for the effects of alpha- and gamma-diversity. We tested whether \b{eta}-diversity patterns along a 1,200 m elevation gradient exclusively depend on the effect of varying species pool size, or also on the variation of the magnitude of community assembly mechanisms determining the distribution of species across communities (e.g., environmental filtering, dispersal limitation). The null model we used is a novel extension of an existing null-model designed for presence/absence data and was specifically designed to disrupt the effect of community assembly mechanisms, while retaining some key features of observed communities such as average species richness and species abundance distribution. Analyses were replicated in ten subregions with comparable elevation ranges. Beta-diversity declined along the elevation gradient due to a decrease in gamma-diversity, which was steeper than the decrease in alpha-diversity. This pattern persisted after controlling for alpha- and gamma-diversity variation, and the results were robust when different resampling schemes and diversity metrics were used. We conclude that in temperate forests the pattern of decreasing beta-diversity with elevation does not exclusively depend on variation in species pool size, as has been hypothesized, but also on variation in community assembly mechanisms. The results were consistent across resampling schemes and diversity measures, thus supporting the use of vegetation plot databases for understanding...Comment: Accepted version 25 pages, 5 figures, 1 tabl

Grasp force estimation from the transient EMG using high-density surface recordings.

Objective: Understanding the neurophysiological signals underlying voluntary motor control and decoding them for prosthesis control are among the major challenges in applied neuroscience and bioengineering. Usually, information from the electrical activity of residual forearm muscles (i.e. the electromyogram, EMG) is used to control different functions of a prosthesis. Noteworthy, forearm EMG patterns at the onset of a contraction (transient phase) have shown to contain predictive information about upcoming grasps. However, decoding this information for the estimation of grasp force was so far overlooked. Approach: High Density-EMG signals (192 channels) were recorded from twelve participants performing a pick-and-lift task. The final grasp force was estimated offline using linear regressors, with four subsets of channels and ten features obtained using three channels-features selection methods. Two different evaluation metrics (absolute error and R2), complemented with statistical analysis, were used to select the optimal configuration of the parameters. Different windows of data starting at the grasp force (GF) onset were compared to determine the time at which the grasp force can be ascertained from the EMG signals. Main results: The prediction accuracy improved by increasing the window length from the moment of the onset and kept improving until the steady state at which a plateau of performances was reached. With our methodology, estimations of the grasp force through 16 EMG channels reached an absolute error of 2.52% the maximum voluntary force using only transient information and 1.99% with the first 500ms of data following the onset. Significance: The final GF estimation from transient EMG was comparable to the one obtained using steady state data, confirming our hypothesis that the transient phase contains information about the final grasp force. This result paves the way to fast online myoelectric controllers capable of decoding grasp strength from the very early portion of the EMG signal

Changing patterns of conflict between humans, carnivores and crop-raiding prey as large carnivores recolonize human-dominated landscapes

Large carnivores are making remarkable comebacks in Europe, but how this affects human-wildlife conflict remains unclear. Rebounding carnivore populations lead to increasing livestock depredation, which in turn leads to greater economic losses for farmers. However, returning carnivores could also influence the behavior of wild ungulates, which are themselves responsible for major crop damage and associated economic losses. Here, we exploit the natural experiment of a rebounding wolf population in the Italian Apennines to study how this affected both types of human-wildlife conflic. We used large datasets of wolf occurrences (n = 351), livestock depredation events (n = 165), and crop damage events by wild boar (n = 3442) to independently model the determinants of livestock depredation and crop damage distribution in relation to wolf habitat suitability over a ten-year period of increasing wolf numbers. These analyses yielded two major insights. First, livestock depredations were mainly related to insufficient prevention measures (e.g. lacking fencing) rather than landscape context, providing a clear pathway to conflict mitigation. Second, crop damage decreased in areas of higher wolf habitat suitability and became more likely in areas of lower wolf habitat suitability, closer to settlements. This suggests increasing predation pressure forces wild boars to avoid the most suitable wolf habitat, leading to a redistribution of crop damage in the landscape. More generally, our study highlights complex human-wildlife interactions as large carnivores recover in human-dominated landscapes, suggesting that multiple, co-occurring conflicts need to be assessed jointly and adaptively in order to foster coexistence between humans and wildlife

sPlotOpen : an environmentally balanced, open-access, global dataset of vegetation plots

Motivation: Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co-occurring within delimited local areas. This allows species absences to be inferred, information seldom provided by existing global plant datasets. Although many vegetation plots have been recorded, most are not available to the global research community. A recent initiative, called ‘sPlot’, compiled the first global vegetation plot database, and continues to grow and curate it. The sPlot database, however, is extremely unbalanced spatially and environmentally, and is not open-access. Here, we address both these issues by (a) resampling the vegetation plots using several environmental variables as sampling strata and (b) securing permission from data holders of 105 local-to-regional datasets to openly release data. We thus present sPlotOpen, the largest open-access dataset of vegetation plots ever released. sPlotOpen can be used to explore global diversity at the plant community level, as ground truth data in remote sensing applications, or as a baseline for biodiversity monitoring. Main types of variable contained: Vegetation plots (n = 95,104) recording cover or abundance of naturally co-occurring vascular plant species within delimited areas. sPlotOpen contains three partially overlapping resampled datasets (c. 50,000 plots each), to be used as replicates in global analyses. Besides geographical location, date, plot size, biome, elevation, slope, aspect, vegetation type, naturalness, coverage of various vegetation layers, and source dataset, plot-level data also include community-weighted means and variances of 18 plant functional traits from the TRY Plant Trait Database. Spatial location and grain: Global, 0.01–40,000 m². Time period and grain: 1888–2015, recording dates. Major taxa and level of measurement: 42,677 vascular plant taxa, plot-level records. Software format: Three main matrices (.csv), relationally linked

Global patterns of vascular plant alpha diversity

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional ‘scaling anomalies’ (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity

Distribution of spawning and nursery grounds for deep–water red shrimps in the central western Mediterranean Sea

The presence of spawning and nursery grounds of Aristeids in the central western Mediterranean Sea were investigated using fishery-independent data (trawl surveys, 1994–2012). Spatial distributions were generated for mature animals and recruits, for both spring/summer and autumn data, using an inverse distance-weighted deterministic interpolation. The persistence index was used to identify stable spawning and nursery grounds in the Sardinian slope region for Aristaeomorpha foliacea and Aristeus antennatus. Areas of aggregation for recruits and mature females appear to be connected with important physical habitat features. The analysis also suggests a seasonal bathymetric distribution for nursery areas. The recruits of A. foliacea are located in the upper part of the continental slope (377-450 m) in spring/summer and reach greater depths (468-628 m) in autumn. For A. antennatus, for which nursery areas only emerge in autumn, there is presumably an opposite ontogenic migration, from deep sea to upper slope, during the summer (575-681 m). The results also indicate a partial overlap between the nursery and spawning grounds of both species. In this particular area, local environmental conditions such as upwelling events or the presence of canyons and seamounts seem to play an important role in their distribution. This study also generated relevant information on the spatial and temporal distribution of seasonal or persistent aggregations of spawners and recruits, providing scientific elements to suggest the protection of these important resources

Cerebellar Atrophy in Congenital Fibrosis of the Extraocular Muscles Type 1

We described a family with a molecularly confirmed form of CFEOM1 and a late-onset cerebellar syndrome. Brain MRI showed vermis atrophy in two older family members, who also manifested gait impairment, whereas both neurological examination and neuroimaging findings were normal in a younger relative who harbored the same mutation

sPlot – the global vegetation-plot database

Vegetation-plot databases contain biodiversity data on presence and relative abundance of plants co- occurring in the same community. Compared to databases based on occurrence records of individual species aggregated at the level of grid cells, vegetation-plot databases have the advantage of providing information on species relative cover, co-occurrences, and to provide more reliable information on true absences. Although large collections of plant community data are now available at national to regional level, they are rarely accessible at continental or global extents, as their compilation is technically and conceptually challenging, due to different data formats and taxonomical nomenclatures used. Here we present the sPlot database, which merges and standardizes data contributed by more than 100 regional, national and continental databases, and contains records from 1,121,244 vegetation plots, for a total of 23,586,216 plant species entries with relative cover or abundance. All plots are georeferenced, although with varying precision, their size varies from less than 1 m 2 to 25 ha, and span from year 1885 to 2015. The vegetation-plot data are stored in a SQLite database, managed with TURBOVEG v3 software, and further processed in R for data integration and analysis. In order to make sPlot suitable for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level we performed three steps. 1) We standardized the species lists of the different databases in sPlot through the construction of a taxonomic backbone using existing databases on accepted plant species names. 2) We calculated functional attributes of each plot (community-weighted means and variances of traits) using gap-filled data from the global plant trait database TRY. 3) We generated a phylogeny for 50,167 out of the 54,519 vascular plant species occurring in sPlot. Finally, in addition to the information provided by the data owners, we retrieved for each plot information on environmental conditions (i.e. climate, soil) and the biogeographic context (i.e. biomes) from external sources. sPlot provides a unique, integrated global repository of data that would otherwise be fragmented in unconnected and structurally inconsistent databases at national or regional level. We believe that sPlot can be the basis for a new generation of studies, not only to address fundamental ecological questions related to plant diversity patterns or community assembly rules, but also to foster further development and testing of macroecological theories and as an information baseline for refining interdisciplinary conservation studies in a human-dominated, changing world. Further information: https://www.idiv.de/en/sdiv/working_groups/wg_pool/splot.htm

Plant taxonomic and phylogenetic turnover increases toward climatic extremes and depends on historical factors in European beech forests

Aims: The effect of biogeographical processes on the spatial turnover component of beta-diversity over large spatial extents remains scarcely understood. Here, we aim at disentangling the roles of environmental and historical factors on plant taxonomic and phylogenetic turnover, while controlling for the effects of species richness and rarity. Location: European beech (Fagus sylvatica) forests in Europe. Methods: We aggregated plant species occurrences from vegetation plots in spatial grid cells of 0.25º × 0.25º to calculate the spatial turnover component of taxonomic (TBD) and phylogenetic (PBD) beta-diversity for each cell. We also calculated the deviation of PBD given TBD (PBD), which measures the importance of phylogenetic turnover after factoring out taxonomic turnover. Beta-diversity was calculated for each grid cell as the mean pairwise dissimilarity between the focal cell and all other cells. We used structural equation modeling (SEM) to examine the relationships between environmental (climate, soil pH, and distance from the geographical distribution limit of beech) and historical (distance from beech glacial refugia) predictors and beta-diversity metrics. Results: We found a geographically consistent variation in taxonomic and phylogenetic turnover. Overall, TBD and PBD increased significantly toward more extreme climatic conditions, on more acidic soils, and toward the margins of beech distribution. The effects of environmental variables and the distance from glacial refugia on beta-diversity metrics were mediated by species richness and rarity. Phylogenetic turnover was low in relation to taxonomic turnover (i.e., high PBD) in areas closer to glacial refugia. Conclusions: Continental-scale patterns of beta-diversity in European beech forests are the result of complementary ecological and evolutionary processes. In general, beech forests are taxonomically and phylogenetically more distinct in climatically marginal areas of their European range. However, the spatial variation of beta-diversity in European beech forest flora is still strongly characterized by the distribution of groups of closely related species that evolved or survived in glacial refugia.The study was supported by the Czech Science Foundation (project no.19-28491X). I.B. and J.A.C. were funded by the Basque Government (IT936-16)

A checklist for using Beals’ index with incomplete floristic monitoring data : reply to Christensen et al. (2021): Problems in using Beals’ index to detect species trends in incomplete floristic monitoring data

Christensen et al. criticized the application of Beals’ index of sociological favourability to adjust for incomplete species lists when comparing repeated surveys. Their main argument was that using Beals’ conditional occurrence probabilities would systematically underestimate biodiversity change compared to using observed frequencies. Although this might be the case for rare species, as we explicitly stated in our original publication, we here use a worked-out example to show that this criticism is unjustified for species that are sufficiently represented in the reference data set. In our opinion, the misconception derives from ignoring one of the key requirements for applying Beal's index, which is the use of a sufficiently large reference data set to derive a reliable co occurrence matrix. We here show how the predicted probability for the occurrence of a species depends on the size of the reference data set and give recommendations on the premises for applying Beals’ approach for monitoring purposes