Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity¹. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region². In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.

Summary: The analysis of plant elemental composition and the underlying factors affecting its variation are a current hot topic in ecology. Ecological adaptation to atypical soils may shift plant elemental composition. However, no previous studies have evaluated its relevance against other factors such as phylogeny, climate or individual soil conditions. We evaluated the effect of the phylogeny, environment (climate, soil), and affinity to gypsum soils on the elemental composition of 83 taxa typical of Iberian gypsum ecosystems. We used a new statistical procedure (multiple phylogenetic variance decomposition, MPVD) to decompose total explained variance by different factors across all nodes in the phylogenetic tree of target species (covering 120 million years of Angiosperm evolution). Our results highlight the relevance of phylogeny on the elemental composition of plants both at early (with the development of key preadaptive traits) and recent divergence times (diversification of the Iberian gypsum flora concurrent with Iberian gypsum deposit accumulation). Despite the predominant phylogenetic effect, plant adaptation to gypsum soils had a strong impact on the elemental composition of plants, particularly on sulphur concentrations, while climate and soil effects were smaller. Accordingly, we detected a convergent evolution of gypsum specialists from different lineages on increased sulphur and magnesium foliar concentrations.

Long‐term monitoring of biodiversity is a fundamental part of environmental management, and Citizen Science (CS) approaches are increasing their contribution to such endeavour. CS plant monitoring programmes, however, almost exclusively report on the species presence, which can be used to detect changes in distribution or occupancy areas, but not to assess their local extinction risk. To anticipate the collapse of local populations, we need information on population sizes, trends, temporal fluctuations and threats. This is particularly important in the case of priority species (threatened, endangered and those that need special protection). Here we describe the working protocol of the ‘Adopt a plant’ programme, a collaborative network that is currently monitoring 332 populations of 204 plant taxa (threatened, of community interest, common, rare and habitat indicators) across a heterogeneous landscape in NE Spain. Coordinated by scientists, participants estimate population sizes, record disturbances and follow scientifically rigorous sampling methods to track plant abundances year after year in fixed representative areas within populations. Two simple indices are estimated from that information: the overall trend (mean population abundance change, as percentage; PAch) and temporal fluctuations (standard deviation of annual changes; PAch_sd). The potential of this ongoing high‐quality dataset is demonstrated through the analysis of 242 populations monitored over 3–10 years. Stability is the dominant trend (mean PAch: +0.14%), with priority species having similar PAch and lower PAch_sd than non‐priority ones. Regardless of the priority status, small populations performed worse than large ones. Only 8% of studied populations faced direct human threats. Synthesis and applications. The ‘Adopt a plant’ collaborative monitoring programme was launched in NE of Spain to produce standardized indices of abundance change and other early‐warning signals of concern or risk of population collapse. Such information is crucial to report the conservation status of threatened plants, and plants of Community interest (Habitats Directive). By analysing hundreds of populations, we found that priority plants experienced few threats and did not perform worse than non‐priority ones. This unexpected finding evidences the importance of gathering massive demographic information to refine conservation priorities and to achieve a more comprehensive assessment of flora's vulnerability.

Recent studies have shown the importance of small-scale climate diversification and climate microrefugia for organisms to escape or suffer less from the impact of current climate change. These situations are common in topographically complex terrains like mountains, where many climate-forcing factors vary at a fine spatial resolution. We investigated this effect in a high roughness area of a southern European range (the Pyrenees), with the aid of a network of miniaturized temperature and relative humidity sensors distributed across 2100 m of elevation difference. We modeled the minimum (Tn) and maximum (Tx) temperatures above- and below-ground, and maximum vapor pressure deficit (VPDmax), as a function of several topographic and vegetation variables derived from ALS-LiDAR data and Landsat series. Microclimatic models had a good fit, working better in soil than in air, and for Tn than for Tx. Topographic variables (including elevation) had a larger effect on above-ground Tn, and vegetation variables on Tx. Forest canopy had a significant effect not only on the spatial diversity of microclimatic metrics but also on their refugial capacity, either stabilizing thermal ranges or offsetting free-air extreme temperatures and VPDmax. Our integrative approach provided an overview of microclimatic differences between air and soil, forests and open areas, and highlighted the importance of preserving and managing forests to mitigate the impacts of climate change on biodiversity. Remote-sensing can provide essential tools to detect areas that accumulate different factors extensively promoting refugial capacity, which should be prioritized based on their high resilience.

Androsace cantabrica (Losa & P. Monts.) Kress is a narrow endemic alpine plant restricted to a few high‐elevation localities in the Cantabrian Mountains of northern Spain. Although currently accepted as a distinct species, its close morphological and phylogenetic affinity to related taxa such as Androsace adfinis and Androsace halleri has led to historical uncertainty about its taxonomic status and evolutionary origin. Here, we use the universal Angiosperms353 target capture kit to generate nuclear and plastid data from A. cantabrica and closely related species in section Aretia . We employ phylogenomic analyses to clarify species boundaries and population genomic analyses to inform conservation management, as well as flow cytometry and sequence‐based analysis using allelic frequencies to estimate its ploidy level. Phylogenetic analyses based on nuclear loci support A. cantabrica as a monophyletic clade, distinct from both A. adfinis and the A. halleri and Androsace laggeri clades, although topological incongruence with plastid data suggests historical hybridization. Flow cytometry and allelic frequency‐based analysis indicate that A. cantabrica is tetraploid, differentiating it from A. halleri and A.  laggeri , which are diploid. Population structure analyses reveal a shallow genetic split between eastern and western groups ( F _ST = 0.04485), with higher genetic diversity observed in the east. We estimated the species' distribution, population sizes, and threats, and classified it as Vulnerable under IUCN criteria B1ab(ii,iii) + 2ab(ii,iii). We recommend targeted in situ management, ex situ seed conservation, and the establishment of a micro‐reserve. This study illustrates the utility of Angiosperms353 data for resolving both taxonomic questions and conservation strategies in polyploid, range‐restricted species.

El conocimiento detallado de los endemismos pirenaicos resulta de gran utilidad en la adopción de medidas de conservación y en la investigación de patrones ecológicos de la flora. Describimos la distribución espacial y distintos aspectos florísticos y ecológicos de la lista revisada de endemismos pirenaicos tras la edición digital del “Atlas de flora vascular de los Pirineos”. Las 88 especies endémicas genuinas representan el 2,4% del conjunto de la flora pirenaica, se incluyen en 27 familias taxonómicas y se concentran en la parte central de la cadena. Los endemismos estudiados presentan notables diferencias ecológicas respecto al conjunto de la flora, en términos de una distribución territorial más reducida y localización en altitudes más elevadas, pero no presentan una distribución fragmentada en el conjunto de los Pirineos. Su distribución también indica que la dispersión Este-Oeste es más limitada que la Norte-Sur, a pesar de la barrera altitudinal del eje de la cordillera. Los endemismos son mayoritariamente caméfitos y están más representados en los hábitats rocosos calizos. En conjunto, estos resultados indican que el aislamiento durante las glaciaciones puede haber sido moderado y sirven como punto de partida para futuras investigaciones.