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Environmental heterogeneity is one of the most fundamental drivers of species diversity. For decades, ecologists have suggested that heterogeneity–diversity relationships are generally positive. But today, a greater variety of heterogeneity–diversity relationships is discussed. In this study, we contrasted two hypotheses for wood‐inhabiting fungi: The classical heterogeneity–diversity hypothesis, which predicts positive relationships due to an increase in niche dimensionality with increasing heterogeneity. And the more recently stated area‐heterogeneity trade‐off hypothesis, that predicts a unimodal pattern due to an inherent trade‐off between the number of occupied niches and the effective area per species. It allows positive and negative relationships only as special cases.We sampled 3715 deadwood objects on 135 plots along a forest structure gradient in the Black Forest, Germany, and recorded 284 wood‐inhabiting fungal species. To assess heterogeneity of deadwood structures, we calculated two multidimensional structural diversity indices: Structural richness was used as a measure of available niche space, and structural divergence as a measure of multivariate variance within that niche space. Those indices were then related to species richness estimates for rare, common and dominant species using the framework of Hill numbers.We found a linear, positive effect of structural richness and a unimodal effect for structural divergence on estimated species diversity. Structural richness, but not structural divergence, was strongly correlated with the number of sampled deadwood objects. No clear differences between the responses of rare, common and dominant species to the two heterogeneity gradients were found. We also estimated the mean abundance as a proxy for mean population size, which decreased significantly with structural richness but was non‐significantly related to structural divergence.Synthesis. In general, the results of this study suggest a unimodal heterogeneity–diversity relationship for deadwood‐inhabiting fungi and are thereby in line with the area‐heterogeneity trade‐off hypothesis. Thus, the negative effect of heterogeneity should lead to lower species richness and a higher risk of stochastic extinctions at high levels of heterogeneity. However, as deadwood amount and deadwood diversity are often strongly correlated, we argue that the positive effect of resource availability on species richness may mask the negative effect of structural heterogeneity in some cases. [ABSTRACT FROM AUTHOR]

Aim: Successional changes in functional diversity provide insights into community assembly by indicating how species are filtered into local communities based on their traits. Here, we assess successional changes in taxonomic and functional richness, evenness and redundancy along gradients of climate, soil pH and forest cover. Location: Neotropics. Time period: Last 0–100 years. Major taxa studied: Trees. Methods: We used 22 forest chronosequence studies and 676 plots across the Neotropics to analyse successional changes in Hill's taxonomic and functional diversity of trees, and how these successional changes vary with continental‐scale gradients in precipitation, soil pH and surrounding forest cover. Results: Taxonomic and functional richness and functional redundancy increased, while taxonomic and functional evenness decreased over time. Functional richness and evenness changed strongly when not accounting for taxonomic richness, but changed more weakly after statistically accounting for taxonomic richness, indicating that changes in functional diversity are largely driven by taxonomic richness. Nevertheless, the successional increases in functional richness when correcting for taxonomic richness may indicate that environmental heterogeneity and limiting similarity increase during succession. The taxonomically‐independent successional decreases in functional evenness may indicate that stronger filtering and competition select for dominant species with similar trait values, while many rare species and traits are added to the community. Such filtering and competition may also lead to increased functional redundancy. The changes in taxonomically‐independent functional diversity varied with resource availability and were stronger in harsh, resource‐poor environments, but weak in benign, productive environments. Hence, in resource‐poor environments, environmental filtering and facilitation are important, whereas in productive environments, weaker abiotic filtering allows for high initial functional diversity and weak successional changes. Main conclusion: We found that taxonomic and functional richness and functional redundancy increased and taxonomic and functional evenness decreased during succession, mainly caused by the increasing number of rare species and traits due to the arrival of new species and due to changing (a)biotic filters. [ABSTRACT FROM AUTHOR]

Depending on the strength of the relationship between biodiversity and aboveground biomass (AGB), diversity loss could lead to varied declines in carbon storage, compromising the role of forests as carbon sink. This study assesses different factors affecting the diversity–AGB relationship, including small trees (diameter < 7.5 cm) and considering different diversity metrics (Hill numbers), plot sizes (80, 400 and 1000 m2) and successional age categories (8–22, 23–30 and > 60 years). The study compares these relationships across three types of tropical dry forests: deciduous, semi-deciduous, and semi-evergreen. Results reveal the highest deviance values in plots with large trees in the 400 m2 size (d2 = 40.4), decreasing when small trees were included (d2 = 25.8). Higher deviance values show the major contribution of large trees to diversity and AGB of 400 m2 plots, while lower deviance values indicate the high contribution of small trees to diversity but limited contribution to AGB. When analyzing only large trees, deviance decreased with the order of Hill numbers. However, incorporating small trees increased deviance for higher Hill numbers. This is because abundance of small and large trees together has a greater influence on AGB. The diversity–AGB relationship was more prevalent and stronger in the semideciduous forest, which had marked orographic and successional age variation. The strongest diversity–AGB effect occurred in early successional ages, weakening in older stages. Our results show that accuracy in estimating the diversity–AGB relationship varies with plant size, diversity parameters, plot size and forest type. [ABSTRACT FROM AUTHOR]

Environmental factors mediating community change over time have been well documented for vascular plants, but not for their non‐vascular relatives, bryophytes. Elevation is one variable that has been explored regarding bryophyte community change wherein as elevation increases, bryophyte communities increase in diversity and abundance, whereas diversity and abundance decline for vascular plant communities. This begs the question, how might other environmental variables such as slope and aspect influence bryophyte communities, and how might these variables drive community changes over time? Our study focused on bryophyte communities in high elevation, spruce‐fir zones in the Great Smoky Mountains National Park (GSMNP), located in the Southeastern United States to answer this question. Plots established in 2007 were revisited and reinventoried in 2020. Comparisons were drawn to determine whether changes in bryophyte coverage corresponded to canopy cover change and environmental factors including elevation, slope, and aspect. Diversity and abundance at the two timepoints were analyzed. Alpha diversity and turnover across orders of q were compared for different elevation zones. Bryophyte alpha diversity at q = 0 significantly declined over time in association with elevation, but at q = 2, changes in alpha diversity varied according to changes in gap fraction, a measure of canopy cover, and slope. Bryophyte coverage remained stable except in the highest elevation zone dominated by fir trees where there was a decline in coverage predicted by aspect. There were high rates of turnover across all elevation zones regardless of Hill number. In contrast with other studies which examine how environmental variables mediate community changes at q = 0, the species richness of a community, our study shows that the environmental drivers of bryophyte community change vary depending on how abundance is weighted. [ABSTRACT FROM AUTHOR]

The hyperdiverse wood‐inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood‐drilling samples in 18 forests from France to Armenia and identified fungi by meta‐barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old‐growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old‐growth forests. [ABSTRACT FROM AUTHOR]

Marine sponges play a vital role in the reef's benthic community; however, understanding how their diversity and abundance vary with depth is a major challenge, especially on marginal reefs in areas deeper than 30 m. To help bridge this gap, we used underwater videos at 24 locations between 2‐ and 62‐meter depths on a marginal reef system in the Southwestern Atlantic to investigate the effect of depth on the sponge metacommunity. Specifically, we quantified the abundance, density, and taxonomic composition of sponge communities, and decomposed their gamma (γ) diversity into alpha (α) and beta (β) components. We also assessed whether beta diversity was driven by species replacement (turnover) or by nesting of local communities (nestedness). We identified 2020 marine sponge individuals, which belong to 36 species and 24 genera. As expected, deep areas (i.e., those greater than 30 m) presented greater sponge abundance and more than eightfold the number of sponges per square meter compared to shallow areas. About 50% of the species that occurred in shallow areas (<30 m) also occurred in deep areas. Contrarily to expectations, alpha diversity of rare (0Dα), typical (1Dα), or dominant (2Dα) species did not vary with depth, but the shallow areas had greater beta diversity than the deep ones, especially for typical (1Dβ) and dominant (2Dβ) species. Between 92.7% and 95.7% of the beta diversity was given by species turnover both inside and between shallow and deep areas. Our results support previous studies that found greater sponge abundance and density in deep areas and reveal that species sorting is stronger at smaller depths, generating more beta diversity across local communities in shallow than deep areas. Because turnover is the major driver at any depth, the entire depth gradient should be considered in management and conservation strategies. [ABSTRACT FROM AUTHOR]

Plant species diversity is key to ecosystem functioning, but in recent decades anthropogenic activities have prompted an alarming decline in this community trait. Thus, developing strategies to understand diversity dynamics based on affordable and efficient remote sensing monitoring is essential, as well as examining the relevance of spatial scale and vegetation structural complexity to these dynamics. Here, we used two mathematical approaches to assess the relationship between tropical woody species diversity and spectral diversity in a human-modified landscape in two vegetation types differing in their degree of complexity. Vegetation complexity was measured through the fraction of species that concentrate different proportions of the cumulative importance value index. Species diversity was assessed using Hill numbers at three spatial scales, and metrics of spectral heterogeneity, vegetation indices, as well as raw data from Landsat 9 and Sentinel-2 sensors were calculated and analysed through general linear models (GLM) and Random Forest. Vegetation complexity emerged as an important variable in modelling species from remote sensing metrics, indicating the need to model species diversity by vegetation type rather than region. Hill numbers showed different relationships with remotely sensed metrics, in consistency with the scale-dependency of ecological processes on species diversity. Contrary to multiple previous reports, in our study, GLMs produced the best fits between Hill numbers of all orders and remotely sensed metrics. If we are to meet the need of conducting efficient and speedy woody species diversity monitoring globally, we propose modelling this diversity from remotely-sensed variables as an attractive strategy, so long as the intrinsic properties of each vegetation type are acknowledged to avoid under- or overestimation biases. [ABSTRACT FROM AUTHOR]

The Western Amazon is a highly biodiverse area. Zooplankton diversity studies in the region have been primarily conducted in Peru and Colombia, with limited research in the Ecuadorian Amazon. To address this gap, our research aimed to enhance taxonomic knowledge and understand zooplankton diversity patterns in the Napo and Pastaza lower basins at different spatial and temporal scales. Two sampling expeditions were conducted in the high waters of 2021 and rising waters of 2022. Dry conditions in 2021 led to lower-than-expected water levels. The study identified 107 zooplankton species, revealing variations in richness and composition between years, lakes, and depth strata. Grande Lake, deeper and wider than Delfincocha, exhibited significant turnover variations across strata in both seasons. Despite a relative longitudinal homogenization between channels and floodplains during high waters, beta diversity across vertical and temporal gradients highlighted complex dynamic zooplankton communities in both lakes. In addition, we include the first records of 44 taxa for the Ecuadorian Amazon and 36 for Ecuador. These findings emphasize the need for targeted research and conservation efforts in the face of escalating environmental threats to the Western Amazon. [ABSTRACT FROM AUTHOR]

Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter". [ABSTRACT FROM AUTHOR]

Abstract Environmental factors mediating community change over time have been well documented for vascular plants, but not for their non‐vascular relatives, bryophytes. Elevation is one variable that has been explored regarding bryophyte community change wherein as elevation increases, bryophyte communities increase in diversity and abundance, whereas diversity and abundance decline for vascular plant communities. This begs the question, how might other environmental variables such as slope and aspect influence bryophyte communities, and how might these variables drive community changes over time? Our study focused on bryophyte communities in high elevation, spruce‐fir zones in the Great Smoky Mountains National Park (GSMNP), located in the Southeastern United States to answer this question. Plots established in 2007 were revisited and reinventoried in 2020. Comparisons were drawn to determine whether changes in bryophyte coverage corresponded to canopy cover change and environmental factors including elevation, slope, and aspect. Diversity and abundance at the two timepoints were analyzed. Alpha diversity and turnover across orders of q were compared for different elevation zones. Bryophyte alpha diversity at q = 0 significantly declined over time in association with elevation, but at q = 2, changes in alpha diversity varied according to changes in gap fraction, a measure of canopy cover, and slope. Bryophyte coverage remained stable except in the highest elevation zone dominated by fir trees where there was a decline in coverage predicted by aspect. There were high rates of turnover across all elevation zones regardless of Hill number. In contrast with other studies which examine how environmental variables mediate community changes at q = 0, the species richness of a community, our study shows that the environmental drivers of bryophyte community change vary depending on how abundance is weighted.

Abstract The hyperdiverse wood‐inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood‐drilling samples in 18 forests from France to Armenia and identified fungi by meta‐barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old‐growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old‐growth forests.

Abstract Marine sponges play a vital role in the reef's benthic community; however, understanding how their diversity and abundance vary with depth is a major challenge, especially on marginal reefs in areas deeper than 30 m. To help bridge this gap, we used underwater videos at 24 locations between 2‐ and 62‐meter depths on a marginal reef system in the Southwestern Atlantic to investigate the effect of depth on the sponge metacommunity. Specifically, we quantified the abundance, density, and taxonomic composition of sponge communities, and decomposed their gamma (γ) diversity into alpha (α) and beta (β) components. We also assessed whether beta diversity was driven by species replacement (turnover) or by nesting of local communities (nestedness). We identified 2020 marine sponge individuals, which belong to 36 species and 24 genera. As expected, deep areas (i.e., those greater than 30 m) presented greater sponge abundance and more than eightfold the number of sponges per square meter compared to shallow areas. About 50% of the species that occurred in shallow areas (

Ants (Hym., Formicidae) have been recognized as vital components of arid ecosystems. Determining the diversity patterns of ants and the ecological factors behind these patterns is expected to improve our understanding of the functioning of arid ecosystems. Here, we explored patterns of ant species diversity and community composition along an elevational gradient (800 to 2800 m) in the arid area of Central Iran. The elevational gradient in ant diversity and the effects of environmental factors on various indices of ant diversity and species composition were investigated using generalized linear mixed models and variance partitioning analysis. We recorded 34 ant species of 12 genera and 8 tribes from 120 surveyed quadrats. Climate variables were the most important predictors of ant community structure. Indices of ant alpha diversity including Hill numbers and taxonomic diversity increased with elevation. Hill numbers were negatively influenced by temperature, while they were positively affected by precipitation. The observed diversity pattern could be explained by the diversity-productivity hypothesis. In our study area, the maximum primary productivity and consequently the maximum species diversity occurred at high elevations, where precipitation is high and temperature is lower than the extremes that could limit plant productivity. Ant assemblages are expected to become increasingly composed of warm-tolerant species in response to warmer and drier conditions driven by climate change. The distribution of species with lower heat tolerance will be limited to high-elevation areas in Central Iran. These areas could act as refuges for ants and should be considered priorities for conservation

Reports increasingly point to substantial declines in wild bee abundance and diversity, yet there is uncertainty about how best to measure these attributes in wild bee populations. Two commonly used methods are passive trapping with bee bowls or active netting of bees on flowers, but each of these has drawbacks. Comparing the outcomes of the two methods is complicated by their uncomparable units of effort. The abundance distribution of bee species is also typically highly skewed, making it difficult to accurately assess diversity when rarer species are unlikely to be caught. The effective number of species, or Hill numbers, provides a way forward by basing the response metric on the number of equally abundant species. Our goal is to compare the effective number of bee species captured between hand netting and bowl trapping in wheatgrass prairie in South Dakota and tallgrass prairie in Minnesota, USA. Species overlap between the two methods ranged from ~40% to ~60%. Emphasis placed on rare species was important, so that 95% confidence limits overlapped between the two methods for species richness but netting exceeded trapping for Shannon's and Simpson's diversities. Netting always captured more bee species with fewer bee individuals than trapping. In most cases, the number of bees captured in bowl traps indicated substantial over‐sampling, with little increase in bee species detected. Correlations between bee and floral abundance, richness, and diversity differed between netted and trapped samples. We conclude that netting and trapping together produce a more complete account of species richness, but shifting sampling emphasis from trapping to netting will result in fewer bees, but more bee species captured. Due to the different relationships between bee and floral diversities that depended on sampling method, it is unwise to compare habitat associations determined by netting with those determined by trapping. [ABSTRACT FROM AUTHOR]

The Younger Dryas-Holocene transition represents a period of significant thermal change, comparable in magnitude to modern warming, yet in a colder context and without the effect of anthropogenic disturbance. This is useful as a reference to tackle how biodiversity is affected by temperature in natural conditions. Here, we addressed the thermal change during this period in a southern Baltic coastal lake (Konarzewo Lake, Poland), as inferred by chironomid remains. We evaluated changes in chironomid communities and used Hill numbers to explore how commonness and rarity underlie biodiversity changes attributable to warming. We found evidence of warming at Konarzewo Lake during the Younger Dryas-Holocene transition, with inferred temperatures in the Younger Dryas period supporting the NW–SE gradient in Younger Dryas summer temperatures across Europe. Chironomid communities drastically changed during the thermal transition. However, Hill numbers showed no response to temperature when rare morphotypes were emphasized (order q = 0) or a weak response when they were balanced with common morphotypes (order q = 1). Hill number of order q = 2, emphasizing the most common morphotypes, consistently increased with temperature across different sample sizes or coverages. This illustrates how common morphotypes, rather than the rare ones, may boost biodiversity facing warming. [ABSTRACT FROM AUTHOR]

Biodiversity–ecosystem functioning (BEF) research has provided strong evidence and mechanistic underpinnings to support positive effects of biodiversity on ecosystem functioning, from single to multiple functions. This research has provided knowledge gained mainly at the local alpha scale (i.e. within ecosystems), but the increasing homogenization of landscapes in the Anthropocene has raised the potential that declining biodiversity at the beta (across ecosystems) and gamma scales is likely to also impact ecosystem functioning. Drawing on biodiversity theory, we propose a new statistical framework based on Hill–Chao numbers. The framework allows decomposition of multifunctionality at gamma scales into alpha and beta components, a critical but hitherto missing tool in BEF research; it also allows weighting of individual ecosystem functions. Through the proposed decomposition, new BEF results for beta and gamma scales are discovered. Our novel approach is applicable across ecosystems and connects local‐ and landscape‐scale BEF assessments from experiments to natural settings. [ABSTRACT FROM AUTHOR]

Ants (Hym., Formicidae) have been recognized as vital components of arid ecosystems. Determining the diversity patterns of ants and the ecological factors behind these patterns is expected to improve our understanding of the functioning of arid ecosystems. Here, we explored patterns of ant species diversity and community composition along an elevational gradient (800 to 2800 m) in the arid area of Central Iran. The elevational gradient in ant diversity and the effects of environmental factors on various indices of ant diversity and species composition were investigated using generalized linear mixed models and variance partitioning analysis. We recorded 34 ant species of 12 genera and 8 tribes from 120 surveyed quadrats. Climate variables were the most important predictors of ant community structure. Indices of ant alpha diversity including Hill numbers and taxonomic diversity increased with elevation. Hill numbers were negatively influenced by temperature, while they were positively affected by precipitation. The observed diversity pattern could be explained by the diversity-productivity hypothesis. In our study area, the maximum primary productivity and consequently the maximum species diversity occurred at high elevations, where precipitation is high and temperature is lower than the extremes that could limit plant productivity. Ant assemblages are expected to become increasingly composed of warm-tolerant species in response to warmer and drier conditions driven by climate change. The distribution of species with lower heat tolerance will be limited to high-elevation areas in Central Iran. These areas could act as refuges for ants and should be considered priorities for conservation. [ABSTRACT FROM AUTHOR]

Biodiversity plays a pivotal role in sustaining ecosystem processes, encompassing diverse biological species, genetic types and the intricacies of ecosystem composition. However, the precise definition of biodiversity at the individual level remains a challenging endeavour. Hill numbers, derived from Rényi's entropy, have emerged as a popular measure of diversity, with a recent unified framework extending their application across various levels, from genetics to ecosystems. In this study, we employ a computational approach to exploring the diversity of mitochondrial heteroplasmy using real‐world data. By adopting Hill numbers with q = 2, we demonstrate the feasibility of quantifying mitochondrial heteroplasmy diversity within and between individuals and populations. Furthermore, we investigate the alpha diversity of mitochondrial heteroplasmy among different species, revealing heterogeneity at multiple levels, including mitogenome components and protein‐coding genes (PCGs). Our analysis explores large‐scale mitochondrial heteroplasmy data in humans, examining the relationship between alpha diversity at the mitogenome components and PCGs level. Notably, we do not find a significant correlation between these two levels. Additionally, we observe significant correlations in alpha diversity between mothers and children in blood samples, exceeding the reported R2 value for allele frequency correlations. Moreover, our investigation of beta diversity and local overlay similarity demonstrates that heteroplasmy variant distributions in different tissues of children more closely resemble those of their mothers. Through systematic quantification and analysis of mitochondrial heteroplasmy diversity, this study enhances our understanding of heterogeneity at multiple levels, from individuals to populations, providing new insights into this fundamental dimension of biodiversity. [ABSTRACT FROM AUTHOR]

Second-growth forests represent the largest area of forest in southern Mexico and can provide relevant information on how their structural attributes in are linked to anthropogenic factors and for their forest management. However, a knowledge gap remains at national level with little scientific literature available. Therefore, this research aimed to investigate the structure and tree richness of second-growth forests in the south of Quintana Roo State, México. With stratified sampling through participatory mapping of local collaborators, secondary tropical forests of 7, 15, 27, 37, and ≥ 48 to 80 years (y) old-growth were identified. We categorized forests into three successional stage classes: 5-20 y (Class I; forests of 7 and 15 y); 25-40 y (Class II; forests of 27 and 37 y), and old-growth forest (Class III; forests 48-80 y). In each forest (7, 15, 27, 37, 48, and 80 y of time since abandonment [tSA]) three plots were randomly chosen and established within the forest. Each age class was composed of two forests and six sample plots. In total there were 18 plots of 500 m2 each. Subsequently, we: i) calculated the land use intensity (LUI) to which the sites were subjected, ii) described the following structural attributes: floristic similarity, true diversity (effective number of species), stem density, and basal area (AB), and iii) evaluated if tSA and LUI influence the aforementioned structural attributes. Tree diversity was characterized with Hill numbers associated with observed species richness (0D), richness of equally abundant species (1D), and dominant species (2D). Forest structure was analyzed by density (number of trees ha−1) and distribution of stems by diameter class ha−1 and basal area (BA, m2 ha−1). The second-growth forest was derived from the milpa agricultural system under moderate land use intensity (LUI index = 0.02 - 0.1). Floristic structure was at least similar between Class I and Class III. Forest age and LUI do not affect tree composition of the forests (p ≥ 0.1667). However, these two factors affected stem density and BA. Only the species richness (0D) of second-growth forest and old-growth forest was influenced by tSA (p = 0.0002). In second-growth forests, Classes I and II, 78 species (0D) were recorded, 8 and 8 exclusive species, 28 and 36 equally abundant species (1D), and 15 to 24 dominant species (2D). In the old-growth forest, Class III, 70 species were recorded, and 38 and 26 equally abundant (1D) and dominant species (2D), as well as 5 exclusive species. The density of stems decreased with increasing forest age and increasing BA. Second-growth forest and old-growth forest all showed a high density of small diameter stems. These results indicate that second-growth forests are important tree species reservoirs (including those for timber purposes), comparable to old-growth or mature forests, and therefore they are relevant not only as biodiversity conservation areas or carbon sinks, but also for planned sustainable forest management.

Ice‐free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0–5 cm) and deeper (7.5–20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha‐diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta‐diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes. [ABSTRACT FROM AUTHOR]

Conditions conducive to fires are becoming increasingly common and widespread under climate change. Recent fire events across the globe have occurred over unprecedented scales, affecting a diverse array of species and habitats. Understanding biodiversity responses to such fires is critical for conservation. Quantifying post‐fire recovery is problematic across taxa, from insects to plants to vertebrates, especially at large geographic scales. Novel datasets can address this challenge. We use presence‐only citizen science data from iNaturalist, collected before and after the 2019–2020 megafires in burnt and unburnt regions of eastern Australia, to quantify the effect of post‐fire diversity responses, up to 18 months post‐fire. The geographic, temporal, and taxonomic sampling of this dataset was large, but sampling effort and species discoverability were unevenly spread. We used rarefaction and prediction (iNEXT) with which we controlled sampling completeness among treatments, to estimate diversity indices (Hill numbers: q = 0–2) among nine broad taxon groupings and seven habitats, including 3885 species. We estimated an increase in species diversity up to 18 months after the 2019–2020 Australian megafires in regions which were burnt, compared to before the fires in burnt and unburnt regions. Diversity estimates in dry sclerophyll forest matched and likely drove this overall increase post‐fire, while no taxon groupings showed clear increases inconsistent with both control treatments post‐fire. Compared to unburnt regions, overall diversity across all taxon groupings and habitats greatly decreased in areas exposed to extreme fire severity. Post‐fire life histories are complex and species detectability is an important consideration in all post‐fire sampling. We demonstrate how fire characteristics, distinct taxa, and habitat influence biodiversity, as seen in local‐scale datasets. Further integration of large‐scale datasets with small‐scale studies will lead to a more robust understanding of fire recovery. [ABSTRACT FROM AUTHOR]

Limited knowledge exists about rock outcrops in Argentina, especially in the Puna ecoregion. This study investigated small and medium-sized mammal diversity using caves and crevices in Desert Puna's rocky areas. Three rock outcrop sites, >1 km apart at Don Carmelo Reserve, were equipped with five camera traps each. Monitoring spanned 34 days (dry season) and 22 days (wet season). Five mammal species utilized caves and crevices, with 99% sampling coverage in both seasons. The wet season had slightly higher species richness, while the dry season showed higher diversity. Co-occurrence analysis revealed multiple rodent species sharing caves, indicating substantial species sharing and potential interactions in this habitat. These findings enhance our understanding of mammalian communities and the ecological complexities of the Puna ecoregion. Rock outcrops are important environments worldwide because of the biodiversity they support. Rock outcrops represent stable refuges for wildlife, providing a space with thermal buffering, water and food in Desert Puna. We suggest it is necessary to include restrictions on human activities likely to affect rock outcrops, for they are sites of high local diversity. [ABSTRACT FROM AUTHOR]

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Based on sampling data, we propose a rigorous standardization method to measure and compare beta diversity across datasets. Here beta diversity, which quantifies the extent of among‐assemblage differentiation, relies on Whittaker's original multiplicative decomposition scheme, but we use Hill numbers for any diversity order q ≥ 0. Richness‐based beta diversity (q = 0) quantifies the extent of species identity shift, whereas abundance‐based (q > 0) beta diversity also quantifies the extent of difference among assemblages in species abundance. We adopt and define the assumptions of a statistical sampling model as the foundation for our approach, treating sampling data as a representative sample taken from an assemblage. The approach makes a clear distinction between the theoretical assemblage level (unknown properties/parameters of the assemblage) and the sampling data level (empirical/observed statistics computed from data). At the assemblage level, beta diversity for N assemblages reflects the interacting effect of the species abundance distribution and spatial/temporal aggregation of individuals in the assemblage. Under independent sampling, observed beta (= gamma/alpha) diversity depends not only on among‐assemblage differentiation but also on sampling effort/completeness, which in turn induces dependence of beta on alpha and gamma diversity. How to remove the dependence of richness‐based beta diversity on its gamma component (species pool) has been intensely debated. Our approach is to standardize gamma and alpha based on sample coverage (an objective measure of sample completeness). For a single assemblage, the iNEXT method was developed, through interpolation (rarefaction) and extrapolation with Hill numbers, to standardize samples by sampling effort/completeness. Here we adapt the iNEXT standardization to alpha and gamma diversity, that is, alpha and gamma diversity are both assessed at the same level of sample coverage, to formulate standardized, coverage‐based beta diversity. This extension of iNEXT to beta diversity required the development of novel concepts and theories, including a formal proof and simulation‐based demonstration that the resulting standardized beta diversity removes the dependence of beta diversity on both gamma and alpha values, and thus reflects the pure among‐assemblage differentiation. The proposed standardization is illustrated with spatial, temporal, and spatiotemporal datasets, while the freeware iNEXT.beta3D facilitates all computations and graphics. [ABSTRACT FROM AUTHOR]

Anthropogenic disturbances and seasonal changes significantly impact diversity and community composition of ants, but their effects are often intertwined. We investigated these drivers on Lang Tengah Island, a location with a pronounced monsoon season and three resorts that close during this period. We surveyed four sites, two disturbed and two undisturbed, before and after the monsoon season, using pitfall traps to sample epigaeic ant communities. Undisturbed habitats had higher species diversity, but both habitats (undisturbed and disturbed sites) have a high proportion of ants with characteristics of being encroached by generalist and invasive/tramp ant species. Post-monsoon sampling yielded an increase in species richness and diversity. Seasonal changes, such as monsoonal rains, can temporarily alter ant interactions and resource distribution, potentially maintaining diversity. Future studies should validate these findings for ant communities under similar pressures, using ant composition and functional roles for conservation and management purposes. [ABSTRACT FROM AUTHOR]

Context: Globally, an estimated 1.3% of the bird species have gone extinct over the past millennia, largely owing to habitat loss. Aims: This study investigated bird–habitat associations and assemblages in the Owabi Ramsar wetland. Methods: The study was conducted over 5 months (May–September 2019) in four habitat types (agricultural land, built-up, forest reserve, and open-water area). Data were collected in 84 plots across four habitats (i.e. built-up area = 25, forest reserve = 25, agricultural land = 25 and open-water area = 9 plots), using a point-count technique. The Gambin model, non-metric multidimensional scaling, Chao-1, and Hill numbers models were used to evaluate differences in bird diversity and composition among the habitat types. Key results: In all, 1260 individual birds, belonging to 81 species, were encountered. Many of the species occurred in the forest habitat (n = 46, 56.8%. Species from the agricultural land (n = 37) and built-up (n = 30) were mainly habitat generalists that used these two habitats as their shared feeding station. Bird–habitat specialisation grouping equally showed the forest specialists to be the highest (n = 23, 38.4%), whereas the open water had the least number of habitat specialisation associations (e.g. white-faced whistling duck, n = 20, 24.7%). Five species were widely distributed in all four habitats (e.g. bronze-mannikins and white-throated bee-eaters), indicating their broad habitat preferences and ability to adapt to varied conditions. The forest reserve tended to be the most diverse, which was likely mediated by factors such as nesting microhabitats, varied food availability, and human-led activities. Conclusions: This study highlighted bird dietary structure and associated habitat type and bird-habitat specialisation in four different land-use types at Owabi Ramsar wetland. Implications: Given the increasing level of disturbance, there is the likelihood that the population of forest-dependent and open water-dependent birds will be lost or will have to change or modify their behaviour to be similar to that of open-tolerant or open-country birds if managers of the Owabi Wildlife Sanctuary fail to implement the recommended management interventions highlighted. Global bird population decline has led to renewed interest in bird–habitat selection studies. This study, which aimed at assessing bird habitat preference, found the farmlands and built-up as the most preferred habitats, whereas the open water was the least preferred. The forest reserve was the most diverse, owing to food availability and less disturbance. The findings highlighted the need to incorporate habitat demographic information into conservation planning and management. Photograph by Rockson Acolatse. [ABSTRACT FROM AUTHOR]

Aim of study: To assess the association of deforestation and forest use with tree diversity and dominance of pine species. Area of study: La Malinche National Park, central Mexico. Material and methods: Three forest stands were selected on each of four slopes in La Malinche National Park, in which the percent forest cover was determined using a concave spherical densitometer. Additionally, we estimated logging, firewood, and ocoteo as indirect measures of forest use. In each forest stand, we set five 0.1-ha circular plots and we recorded tree species, diameter at breast height, and height of all individuals ≥1.5 m. We estimated diversity using Hill numbers (qD). We identified dominant species from rank-abundance curves, and explored the dissimilarity between forest stands for the three q orders. Using generalized linear mixed-effects models, we evaluated the relationships of deforestation and forest use with species diversity and pine dominance, and studied the effect of pine dominance on the abundance of other tree species through generalized linear models. Main results: We recorded a total of 16 tree species; a pine (Pinus montezumae) was the dominant species. The diversity of tree species was not associated with forest use or deforestation, but deforestation increased Pinus dominance, with a strong slope effect. Research highlights: Regulation and control of forest use should be prioritized to avoid further deforestation and the transformation of species-diverse forests into monospecific forests, further increasing the dominance of P. montezumae. We also suggest reforesting with native species and those scarcely represented to increase forest cover and maintain tree diversity.

Abstract Reports increasingly point to substantial declines in wild bee abundance and diversity, yet there is uncertainty about how best to measure these attributes in wild bee populations. Two commonly used methods are passive trapping with bee bowls or active netting of bees on flowers, but each of these has drawbacks. Comparing the outcomes of the two methods is complicated by their uncomparable units of effort. The abundance distribution of bee species is also typically highly skewed, making it difficult to accurately assess diversity when rarer species are unlikely to be caught. The effective number of species, or Hill numbers, provides a way forward by basing the response metric on the number of equally abundant species. Our goal is to compare the effective number of bee species captured between hand netting and bowl trapping in wheatgrass prairie in South Dakota and tallgrass prairie in Minnesota, USA. Species overlap between the two methods ranged from ~40% to ~60%. Emphasis placed on rare species was important, so that 95% confidence limits overlapped between the two methods for species richness but netting exceeded trapping for Shannon's and Simpson's diversities. Netting always captured more bee species with fewer bee individuals than trapping. In most cases, the number of bees captured in bowl traps indicated substantial over‐sampling, with little increase in bee species detected. Correlations between bee and floral abundance, richness, and diversity differed between netted and trapped samples. We conclude that netting and trapping together produce a more complete account of species richness, but shifting sampling emphasis from trapping to netting will result in fewer bees, but more bee species captured. Due to the different relationships between bee and floral diversities that depended on sampling method, it is unwise to compare habitat associations determined by netting with those determined by trapping.

The Western Amazon is a highly biodiverse area. Zooplankton diversity studies in the region have been primarily conducted in Peru and Colombia, with limited research in the Ecuadorian Amazon. To address this gap, our research aimed to enhance taxonomic knowledge and understand zooplankton diversity patterns in the Napo and Pastaza lower basins at different spatial and temporal scales. Two sampling expeditions were conducted in the high waters of 2021 and rising waters of 2022. Dry conditions in 2021 led to lower-than-expected water levels. The study identified 107 zooplankton species, revealing variations in richness and composition between years, lakes, and depth strata. Grande Lake, deeper and wider than Delfincocha, exhibited significant turnover variations across strata in both seasons. Despite a relative longitudinal homogenization between channels and floodplains during high waters, beta diversity across vertical and temporal gradients highlighted complex dynamic zooplankton communities in both lakes. In addition, we include the first records of 44 taxa for the Ecuadorian Amazon and 36 for Ecuador. These findings emphasize the need for targeted research and conservation efforts in the face of escalating environmental threats to the Western Amazon.

The distribution and abundance of fish for the Orinoco River basin drainages are influenced by hydrometric seasonality and the structural complexity of the habitat, so understanding how fish assemblages are structured on a temporal and spatial scale is essential for biological conservation. Therefore, the purpose of this study was to describe the fish assemblage for the Mitimiti stream and test the hypothesis of spatial and temporal variation. To do this, collections were made at four sampling stations on the Mitimiti stream, during three contrasting rainfall seasons, with the help of a 10 m x 1.5 m trawl net and a 2 mm mesh eye. The diversity of fish assemblages was analyzed using Hill numbers, abundance-based dissimilarity, and a Canonical Correspondence Analysis (CCA). In total, 2493 individuals and 115 species were recorded, where the orders with the highest dominance were Characiformes and Blenniiformes. Regarding the diversity of order q = 0, no significant differences were found between the hydrological periods and the sampling stations, however, the low water period and St3 exhibited the highest species richness. The most dissimilar hydrological period was the high water season and the variables that significantly influenced fish assemblage were water temperature (p = 0.02) and dissolved oxygen (p = 0.05).

An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyse network sampling data. The proposed method integrates the following four inference procedures: (i) assessment of sample completeness of networks; (ii) asymptotic analysis via estimating the true network diversity; (iii) non-asymptotic analysis based on standardizing sample completeness via rarefaction and extrapolation with network diversity; and (iv) estimation of the degree of unevenness or specialization in networks based on standardized diversity. Interaction data between European trees and saproxylic beetles are used to illustrate the proposed procedures. The software iNEXT.link has been developed to facilitate all computations and graphics. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'. [ABSTRACT FROM AUTHOR]

Declining temperate forest biodiversity is a global challenge to future sustainability and resilience. Canopy tree diversity has declined in northern hardwood forests (NHFs) of the Great Lakes region since European colonization, with current tree regeneration patterns suggesting this trend may continue. However, regional (106 ha) patterns and drivers are underexplored. We used data from 141 managed NHF stands, Michigan, USA, to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand‐level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6–7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (Fraxinus americana and Fagus grandifolia, insect/pathogen limited; Ostrya virginiana, small maximum size). For the 11 most common species, conspecific canopy density (+, seedlings, significant for 10 species) and stand basal area (−, saplings, 3 species) most consistently associated with density; deer use, site quality, and substrate were less predictive. Patterns of relative density by size class among 18 species present on >10% of sites were consistent with species life history strategy and/or establishment/recruitment barriers. For seven species (including Tsuga canadensis, Betula alleghaniensis), relative density was lowest in the seedling layer, suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (Acer saccharum, Quercus rubra), reduced sapling relative density compared with seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., F. grandifolia, O. virginiana, Pinus strobus) had highest relative density for saplings, suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most dense for Acer rubrum and Prunus spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. americana, consistent with recent pest‐related canopy mortality. Collectively our analyses suggest sustained low diversity and shifting composition are driven by limited local seed availability, limited seedling establishment substrate, deep shading, and abundant deer. Management aimed at overcoming these limitations may be necessary to promote future NHF resilience. [ABSTRACT FROM AUTHOR]

The current paper is part of a series exploring how to link diversity measures (e.g., Gini-Simpson index, Shannon entropy, Hill numbers) to a distribution’s original shape and to compare parts of a distribution, in terms of diversity, with the whole. This linkage is crucial to understanding the exact relationship between the density of an original probability distribution, denoted by p ( x ), and the diversity D in non-uniform distributions, both within parts of a distribution and the whole. Empirically, our results are an important advance since we can compare various parts of a distribution, noting that systems found in contemporary data often have unequal distributions that possess multiple diversity types and have unknown and changing frequencies at different scales (e.g. income, economic complexity ratings, rankings, etc.). To date, we have proven our results for discrete distributions. Our focus here is continuous distributions. In both instances, we do so by linking case-based entropy, a diversity approach we developed, to a probability distribution’s shape for continuous distributions. This allows us to demonstrate that the original probability distribution g _1 , the case-based entropy curve g _2 , and the slope of diversity g _3 ( c _( _a _, _x _) versus the ${c}_{(a,x)}* \mathrm{ln}{A}_{(a,x)}$ curve) are one-to-one (or injective). Put simply, a change in the probability distribution, g _1 , leads to variations in the curves for g _2 and g _3 . Consequently, any alteration in the permutation of the initial probability distribution, which results in a different form, will distinctly define the graphs g _2 and g _3 . By demonstrating the injective property of our method for continuous distributions, we introduce a unique technique to gauge the level of uniformity as indicated by D / c . Furthermore, we present a distinct method to calculate D / c for different forms of the original continuous distribution, enabling comparison of various distributions and their components.

Abstract Declining temperate forest biodiversity is a global challenge to future sustainability and resilience. Canopy tree diversity has declined in northern hardwood forests (NHFs) of the Great Lakes region since European colonization, with current tree regeneration patterns suggesting this trend may continue. However, regional (106 ha) patterns and drivers are underexplored. We used data from 141 managed NHF stands, Michigan, USA, to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand‐level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6–7 species and 10% of sites were consistent with species life history strategy and/or establishment/recruitment barriers. For seven species (including Tsuga canadensis, Betula alleghaniensis), relative density was lowest in the seedling layer, suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (Acer saccharum, Quercus rubra), reduced sapling relative density compared with seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., F. grandifolia, O. virginiana, Pinus strobus) had highest relative density for saplings, suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most dense for Acer rubrum and Prunus spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. americana, consistent with recent pest‐related canopy mortality. Collectively our analyses suggest sustained low diversity and shifting composition are driven by limited local seed availability, limited seedling establishment substrate, deep shading, and abundant deer. Management aimed at overcoming these limitations may be necessary to promote future NHF resilience.

Recent studies have shown the crucial role of plant cover in the spectral signals of remote sensing images. However, how plant species cover affects the spectral-species diversity relationship remains largely unknown. To clarify this, we conducted a study in wetlands and obtained high spatial resolution multispectral images collected by unmanned aerial vehicles (UAVs). Quadrat information was obtained through a field survey. The traditional species diversity indexes and Hill numbers of each quadrat were computed by species density and cover. The mean, standard deviation, and coefficient of variation of the normalized difference vegetation index (NDVI) were computed based on the multispectral images. We employed univariate and multivariate regression models to assess the ability of spectral information to predict species diversity and the explanatory degree of variables to the multivariate regression models were decomposed. The results showed that rather than species density, spectral indexes were more strongly related to species diversity indexes computed by species cover, and the robustness and universality of the methods that predict plant species diversity based on spectral indexes have been improved by considering species cover. Meanwhile, in light of the flexibility of Hill numbers that assign different weights to dominant and rare species in the community, we believe that Hill numbers are the better choice in the spectral-species diversity studies, which can suitable to various communities with different density-cover relationships. In addition, our study also provided an insightful perspective for future spectral-plant species diversity research.

A number of metrics for quantifying the amount of functional redundancy in a community have been proposed over the years.Two of the most popular metrics are based on comparing a taxonomic diversity measure with a generalized form of the same measure that accounts for functional dissimilarities between taxa. These two metrics express redundancy as either an absolute or relative difference between the taxonomic diversity measure and its generalized form. Because they express the amount of redundancy in a community in terms of raw diversity values, both redundancy metrics are susceptible to the same issues that complicate the interpretation of most commonly used diversity indices.It is possible to overcome these issues by restating these two indices using a Hill numbers framework. As a growing number of authors have noted, these modified metrics provide a more intuitive quantitative definition of functional redundancy when used to rank communities. Beyond this intuitive definition, measuring redundancy in terms of Hill numbers allows researchers to control the influence of rare taxa on the output value, enabling ecologists to better predict how a community is expected to respond when exposed to an external perturbation that selectively eliminates rare or common taxa.Here I show that, of the two possible Hill number‐based redundancy metrics, the form based on a popular absolute redundancy metric is extremely sensitive to differences in taxonomic diversity and can provide a misleading picture of how much redundancy is present in a community. For this reason, I argue that Hill number‐based functional redundancy should be quantified using a relative metric that explicitly accounts for differences in effective taxonomic diversity.The proposed Hill number‐based relative redundancy measure is shown to provide a much more complete picture of the distribution of redundant taxa within a community, highlighting subtle patterns that are completely missed by the Hill number‐based absolute redundancy metric. I include open‐source R code for calculating the indices discussed here. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Individual‐level trait diversity has been identified as an essential component of trait diversity (TD), influencing community assembly and structure. Traditionally, one employs trait diversity indices to measure facets of individual‐level trait diversity (divergence, richness and evenness). However, the application of species‐level trait diversity indices to individual‐level traits data and their implications have not been adequately studied. Thus, we examined the possible challenges of using four commonly used multi‐trait TD indices: Rao's quadratic entropy (Rao), functional dispersion (FDis), functional evenness (FEve) and functional richness (FRic); two indices primarily developed to measure individual‐level trait diversity: trait evenness distribution (TED‐for evenness) and trait onion peeling (TOP‐for richnness); and a modified version of TED (TEDM‐for evenness). Additionally, we considered an index that integrates both evenness and richness by generalizing ordinary Hill indices for traits (coined HIT). We measured individual‐level trait diversity with these indices using simulated traits data and experimental data from a growth experiment with cyanobacteria. Comparing the observed trends from the indices with the expected trends, we observed that only the trait divergence indices (FDis and Rao) produced the expected trends in the simulation scenarios and experimental data. TED and TEDM are not robust against the number of individuals used, and FEve is not sensitive to some changes in the location of individuals in the trait space. Also, TOP proved to be a discontinuous function dependent on the number of individuals, and FRic did not produce the anticipated trend when changes in the trait space did not affect the edges of the trait space. HIT did produce the anticipated changes, but it was only reliable when many individuals were sampled. In summary, applying these individual‐level trait diversity indices to quantify anything except trait divergence may lead to misinterpretation of the original situation of trait distribution in the trait space if their specific properties are not adequately considered. [ABSTRACT FROM AUTHOR]

Copyright of Biotropica is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In ecology, multifunctionality metrics measure the simultaneous performance of multiple ecosystem functions. If species diversity describes the variety of species that together build the ecosystem, multifunctionality attempts to describe the variety of functions these species perform. A range of methods have been proposed to quantify multifunctionality, successively attempting to alleviate problems that have been identified with the previous methods. This has led to a proliferation of more‐or‐less closely related metrics which, however, lack an overarching theoretical framework. Here we borrow from the comprehensive framework of species diversity to derive a new metric of multifunctionality. Analogously to the effective number of species used to quantify species diversity, the metric we propose is influenced both by the number of functions as well as, crucially, the evenness of performance levels across functions. In addition, the effective multifunctionality also considers the average level at which the functions are performed. The result is a measure of the cumulative performance of the system were all functions provided equally. The framework allows for the inclusion of the correlation structure among functions, thus allowing it to account for non‐independence between functions. We show that the average metric is a special case of the newly proposed metric when all functions are uncorrelated and performed at equal levels. We hope that by providing a new metric of multifunctionality anchored in the rigorous framework of species diversity based on effective numbers, we will overcome the considerable skepticism that the larger community of ecologists has built against indices of multifunctionality. We thereby hope to help popularize this important concept which, like biological diversity, describes a fundamental property of ecosystems and thus lies at the heart of ecology. [ABSTRACT FROM AUTHOR]

Different species-specific traits of woody plant species, feeding preferences of herbivores together with resulting effects on plant competition are expected to translate into different plant community structures and expressions of biodiversity. We studied the diversity of woody plant species (trees and shrubs) and structural diversity of forest trees, using a 30-year and an 18-year dataset of ungulate exclosure-control plot pairs in a mixed alpine forest community in Austria. We surveyed the tallest individuals per tree species and plot and analyzed the collective of top-height individuals per plot pair. Incidence data for exclosure and control plots were aggregated. Comparing species diversity and diversity of height classes on the plots throughout time, we calculated diversity profiles based on Hill numbers. Diversity of top height individuals and structural diversity, expressed by height classes, were two diversity aspects that differed between exclosures and control plots. Other diversity estimates of woody plant species showed huge variation without significant differences between plots. Height growth was significantly suppressed by ungulate herbivory. Effects of ungulate herbivores in forest ecosystems are highly complex and context-dependent and thus not reducible to simple top-down forces. Long-term surveys provide data that reflect "ultimate" effects of herbivory interacting with other drivers of community dynamics. [ABSTRACT FROM AUTHOR]

Although tropical dry forests are among the most degraded and fragmented biomes in the world, we still have a poor understanding of their basic ecological features and conservation status, particularly in the Neotropics. Here, we assess the diversity, composition, structure and conservation value of tropical dry forests in a highly fragmented landscape in Nicaragua. We established 31 plots and transects in and along river corridors, secondary forests, living fences and pasture-woodlands. We recorded all trees with diameters at breast height ≥ 2.5 cm using Hill numbers (qD, where q = 0, 1 or 2) and estimated the richness and diversity of trees in each forest type. We calculated the Importance Value Index (IVI) to species and family levels and, finally, performed a Non-Metric Multidimensional Scaling (NMDS) ordination and an Analysis of Similarities (ANOSIM) using the Bray–Curtis index of similarity. Diversity (1D, 2D) but not species richness (0D) differed between forest types (P = 0.01 and 0.66, respectively). IVI was highest for the legume family Fabaceae, followed by the Moraceae and Malvaceae (27.8, 11.1 and 10.5, respectively). Vachellia pennatula , Guazuma ulmifolia and Bursera simaruba had IVIs >30%, the former two being the most abundant trees in all forest types. An analysis of community similarity revealed that each forest type had a distinct composition (P < 0.01, R 2 = 0.30), thereby underlining the importance of conserving all these different types of land cover. [ABSTRACT FROM AUTHOR]

Green infrastructure on rooftops in urban areas can enhance important ecosystem services. In addition to mitigating water runoff and regulating building temperatures, green roofs can provide food and nesting resources for wildlife. Rooftop gardens can also be utilized to cultivate food crops, giving them the potential to attenuate instances of food insecurity which are commonplace in many urban areas. Given that many crops depend on bee pollination, it is imperative to characterize the rooftop bee community. Therefore, we sampled three urban food roofs near downtown St. Louis, MO during the 2017 and 2018 growing seasons. We found 38 bee species utilizing the rooftop farms. We then compared the rooftop bee communities to those of two nearby ground-level community gardens. The roofs had lower abundances of Bombus species than the ground-level sites while non-native cavity nesters in the genus Megachile were overrepresented. These results indicate that the rooftop bee communities represent a nested subset of the species found at ground level. This has important implications for the management of green roofs for growing crops, as this shift in bee community structure may play a role in determining which crops can be adequately supported with pollination services.

Dung beetles are important actors in the self‐regulation of ecosystems by driving nutrient cycling, bioturbation, and pest suppression. Urbanization and the sprawl of agricultural areas, however, destroy natural habitats and may threaten dung beetle diversity. In addition, climate change may cause shifts in geographical distribution and community composition. We used a space‐for‐time approach to test the effects of land use and climate on α‐diversity, local community specialization (H2′) on dung resources, and γ‐diversity of dung‐visiting beetles. For this, we used pitfall traps baited with four different dung types at 115 study sites, distributed over a spatial extent of 300 km × 300 km and 1000 m in elevation. Study sites were established in four local land‐use types: forests, grasslands, arable sites, and settlements, embedded in near‐natural, agricultural, or urban landscapes. Our results show that abundance and species density of dung‐visiting beetles were negatively affected by agricultural land use at both spatial scales, whereas γ‐diversity at the local scale was negatively affected by settlements and on a landscape scale equally by agricultural and urban land use. Increasing precipitation diminished dung‐visiting beetle abundance, and higher temperatures reduced community specialization on dung types and γ‐diversity. These results indicate that intensive land use and high temperatures may cause a loss in dung‐visiting beetle diversity and alter community networks. A decrease in dung‐visiting beetle diversity may disturb decomposition processes at both local and landscape scales and alter ecosystem functioning, which may lead to drastic ecological and economic damage. [ABSTRACT FROM AUTHOR]

Copyright of Methods in Ecology & Evolution is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Phlebotomine sand flies are critical vectors of Leishmania parasites, impacting public health significantly. This study focused on assessing the diversity of sand flies in a rural area of El Carmen de Bolívar Municipality, northern Colombia, employing rarefaction curves and Hill numbers to understand potential vector communities and inform environmental management. From January 2018 to April 2019 (five samplings), sand flies were collected using CDC light traps with blue LED in domestic/peridomestic/sylvatic ecotopes, identifying species per Young and Duncan (1994) and Galati (2003). Hill numbers provided diversity estimates across samples, while Principal Component Analysis correlated with environmental factors with phlebotomine species presence and abundance. 8,784 phlebotomine individuals were collected; 56.4 % females and 43.6% males (ratio 3:2). These individuals belonged to eight species: Pintomyia evansi, Psychodopygus panamensis, Lutzomyia gomezi, Micropygomyia cayennensis, Evandromyia dubitans, Psathyromyia aclydifera, Pintomyia serrana , and Pintomyia rangeliana ; with Pi. evansi being the most abundant species (74.39 %; 6,530 exemplars). The ANOVA showed no significant differences between phlebotomine sand flies abundances across ecotopes (p = 0.018). Species of epidemiological relevance as Pi. evansi and Lu. gomezi not show a positive correlation with environmental variables evaluated, only Ps. panamensis was positively correlated with precipitation. However, the study emphasizes the need for a continuous sand fly monitoring and research to enhance leishmaniasis control strategies, highlighting the necessity to expand knowledge on phlebotomine diversity and environmental interactions to understand vector ecology and disease dynamics better. [ABSTRACT FROM AUTHOR]

Abstract Background Understanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks. Results Here we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation. Conclusions Methods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.

Abstract Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. Biodiversity has at least three dimensions: (a) Taxonomic diversity (TD): a measure that is sensitive to the number and abundances of species. (b) Phylogenetic diversity (PD): a measure that incorporates not only species abundances but also species evolutionary histories. (c) Functional diversity (FD): a measure that considers not only species abundances but also species' traits. We integrate the three dimensions of diversity under a unified framework of Hill numbers and their generalizations. Our TD quantifies the effective number of equally abundant species, PD quantifies the effective total branch length, mean‐PD (PD divided by tree depth) quantifies the effective number of equally divergent lineages, and FD quantifies the effective number of equally distinct virtual functional groups (or functional ‘species’). Thus, TD, mean‐PD and FD are all in the same units of species/lineage equivalents and can be meaningfully compared. Like species richness, empirical TD, PD and FD based on sampling data depend on sampling effort and sample completeness. For TD (Hill numbers), the iNEXT (interpolation and extrapolation) standardization was developed for standardizing sample size or sample completeness (as measured by sample coverage, the fraction of individuals that belong to the observed species) to make objective comparisons across studies. This paper extends the iNEXT method to the iNEXT.3D standardization to encompass all three dimensions of diversity via sample size‐ and sample coverage‐based rarefaction and extrapolation under the unified framework. The asymptotic diversity estimates (i.e. sample size tends to infinity and sample coverage tends to unity) are also derived. In addition to individual‐based abundance data, the proposed iNEXT.3D standardization is adapted to deal with incidence‐based occurrence data. We apply the integrative framework and the proposed iNEXT.3D standardization to measure temporal alpha‐diversity changes for estuarine fish assemblage data spanning four decades. The influence of environmental drivers on diversity change are also assessed. Our analysis informs a mechanistic interpretation of biodiversity change in the three dimensions of diversity. The accompanying freeware, iNEXT.3D, developed during this project, facilitates all computation and graphics.