Many indices based on presence‐absence data that compare two communities have been proposed, with the aim to characterize community similarity, species turnover or beta‐diversity, as well as other phenomena like community nestedness. These indices are often mathematically convertible to each other and are thus equivalent in terms of their information content. Based on this information equivalence, we classified all the indices to a few families, showing that only three families reflect ecologically relevant and directly interpretable phenomena, namely species turnover (family of Jaccard index that also includes Sørensen index of similarity), nestedness (the family of indices which compare species overlap with species richness of the species‐poor community), and the uniformity of species richness (comparing species richness of the two communities). Importantly, our analysis shows that any attempt to partition indices, including Baselga's approach to partition turnover and nestedness (i.e. to control an index for an effect of a different phenomenon), leads either to an index belonging to one of the three abovementioned families, or produces indices that do not measure any ecologically relevant phenomenon. We provide guidance on how to apply pairwise indices to make proper inference about ecological phenomena.

ABSTRACT Aim Species richness of local communities may be regulated via negative diversity dependence of colonization or positive diversity dependence of extinction rate. We explore whether and how bird communities are regulated and what determines extinction and colonization rates across communities. Location North America, spanning the United States and Canada. Time Period 1995–2019. Major Taxa Studied Passerines. Methods We used long‐term community time‐series from the North American Breeding Bird Survey (BBS) to analyse spatial patterns in colonization and extinction rates across 646 survey routes. We linked these rates to community species richness, proportion of species pool represented in the local community, richness relative to resource level, mean population size and stability and environmental productivity and its seasonality (approximated by Normalized Difference Vegetation Index, NDVI). We used correlation analyses, generalized linear models, Random Forest and Structural Equation Modelling (SEM). Results Extinction and colonization rates are highly balanced across sites, supporting the idea of diversity regulation. Both rates are lower at sites with higher equilibrium species richness and especially at sites with a higher proportion of the species pool represented in the local community, supporting the diversity‐dependence of colonization rate. In contrast, we did not find any evidence for local diversity‐dependence of extinction rate. However, extinction rates increase with decreasing population sizes of species and are negatively affected by environmental productivity that influences population stability. Main Conclusions Local bird community richness appears regulated, but this regulation stems primarily from a progressive exhaustion of the number of potential colonists from a species pool as local species richness increases, not from a decreasing population size with increasing richness. Local bird diversity is then determined by the interaction of the size of the species pool with local population persistence modulated by environmental productivity. Diversity dynamics is thus essentially equilibrial, but regional and local diversity appear regulated by different mechanisms.

Large-scale patterns of species richness have been attributed to ecological limits, variation in diversification rates, and differences in evolutionary time, yet the relative importance of these drivers remains debated. Here, we present a unifying framework distinguishing four richness-generating scenarios, defined by contrasting roles of evolutionary time and speciation rates, which yields explicit and testable predictions for how evolutionary time, speciation, and environmental factors influence species richness. We applied this framework by analyzing 129 distinct, nonoverlapping clades spanning amphibians, reptiles, birds, and mammals. For each clade, we integrated historical biogeographic reconstructions, multiple estimates of speciation rates, and GIS-based environmental data. Using structural equation modeling, we quantified the direct and indirect effects of evolutionary time, speciation rates, and environmental conditions (productivity, temperature, and precipitation) on species richness. We further tested whether these effects varied systematically with clade-level traits, including age, physiology, diversity, and geographic extent. Productivity emerged as the dominant predictor of species richness, exerting strong and consistent direct effects that were largely invariant to clade traits. In contrast, speciation rates contributed little to species richness, while the influence of evolutionary time was highly context-dependent and most pronounced in younger clades. Temperature showed consistent direct effects not mediated by productivity, evolutionary time, or speciation rates, whereas precipitation influenced richness primarily via productivity. Together, our results support a productivity-driven equilibrium view of species richness, in which diversity reflects a balance between speciation and extinction regulated by energy availability. Deviations from equilibrium dynamics, particularly in younger clades, highlight the role of evolutionary history on biodiversity gradients.

Macroevolutionary studies have shown that the shape of phylogenetic trees differs in space, time, and between taxa. It is commonly assumed that these differences in tree shape reflect variability in the underlying ecological and evolutionary processes that produced them, and mechanistic eco-evolutionary models are increasingly used to explore this link. A concern in this context is whether conclusions drawn from such mechanistic models are robust to idiosyncrasies in how eco-evolutionary processes are formalized in the models. Here, we use eight mechanistic macroevolutionary models to study how 52 metrics of phylogenetic tree shape respond to variation in the strength of five fundamental processes: competition, dispersal, environmental filtering, niche conservatism, and speciation. We find that models agree on how some tree metrics respond to changes in these processes, in particular dispersal and speciation. However, no tree metric uniquely correlated with a single process, suggesting that single tree metrics have limited utility as shortcuts for inferring the underlying eco-evolutionary processes. Moreover, while it was possible to infer the underlying processes if the data-generating model was known, inference was not consistent across the different models. We conclude that the relationship between phylogenetic patterns and eco-evolutionary processes in macroevolutionary analysis is likely sensitive to the structural and mechanistic details of how a given process is implemented within models.

Tropical savannahs experience pronounced seasonality, especially in rainfall and temperature, shaping plant productivity and resource availability. Yet, temporal patterns in insect diversity remain poorly understood. We investigated seasonal variation in species richness and community composition of moths (herbivores) and mantises (predators) across four main landsystems in Kruger National Park, South Africa. Using light traps during early and late wet seasons, we captured 65 593 moths (817 morphospecies) and 3511 mantises (38 morphospecies). Species richness of both groups significantly increased from the early to the late wet season, particularly in the wetter southern landsystems, likely driven by rainfall-enhanced resource availability and habitat complexity. Community composition varied seasonally and among landsystems, with moths primarily influenced by seasonal changes, whereas mantises responded more strongly to landsystem differences. Our results indicate that rainfall-driven seasonal resource variability is a key determinant of insect phenological patterns in tropical savannahs. Predicted shifts in rainfall patterns due to climate change may alter insect emergence timing and trophic interactions, highlighting the importance of incorporating seasonal dynamics into biodiversity conservation and management strategies.

Historical nonequilibrium processes are often considered the main drivers of global biodiversity patterns. We argue that while biodiversity is often out of equilibrium, the concept of equilibrium is still crucial for interpreting macroecological diversity patterns, and current confusion in the literature stems from misunderstandings concerning equilibrium dynamics. We demonstrate how an equilibrium-based framework, such as the 'Equilibrium Theory of Biodiversity Dynamics' (ETBD), illuminates diversity patterns in space and time, including the latitudinal diversity gradient, even in the out-of-equilibrium context. This framework has profound implications for understanding diversity dynamics during historical, current, and future climate changes, suggesting that while temperate diversity is probably below its equilibrium level, tropical biodiversity could be above its equilibrium, elevating extinction risk in tropical biomes.

Ecologists have long proposed that environments providing more energy can support more species, yet empirical evidence frequently contradicts this expectation. We argue that such inconsistencies result from confounding geographical influences that mask the true relationship between species richness and energy-related factors. Here, by comparing species richness across different climate conditions, we disentangle the direct effects of temperature, precipitation, and primary productivity from the confounding impacts of the area and isolation of various climates. Using a global analysis of terrestrial vertebrates, we reveal clear and consistent relationships between energy-related factors and species richness. Our findings clarify existing ecological theory and illustrate how adopting a climate space perspective advances biodiversity research, providing critical insights into biodiversity patterns and their responses to environmental change.

Farmland birds rank among organisms showing the steepest declines of their European populations. To combat these declines, it is essential to understand demographic mechanisms underlying the negative population trends. For this purpose, we employ a novel modelling approach on a long-term multispecies dataset collected by citizen scientists throughout Czechia. Using this approach, we calculated recruitment, adult survival and population growth rates for 13 farmland bird species on annual basis from 2004 to 2021, and related these demographic rates to species population trends estimated over the same period, as well as to their habitat preferences. We observed a negative relationship between recruitment and adult survival within most species. This relationship becomes increasingly more negative in species breeding in more open habitats. These species also showed steeper population declines and less positive correlation between adult survival and population growth rate than species breeding more woody habitats. These results indicate that the open-habitat farmland birds face strong population regulation. Under such regulation, higher adult survival in some years, that may occur due to, for instance, suitable weather conditions, does not leave much capacity for new recruits, and thus is immediately compensated by low recruitment. We suggest that these demographic processes are underpinned by decreasing carrying capacity of the open habitats which may occur due to shrub encroachment or afforestation of agricultural land that are widespread in Europe. At the same time, species preferring woody habitats enjoy increasing habitat availability in farmland which may lead to population increases over the long-term. Our results indicate that conservation actions are needed to improve the carrying capacity of the open habitats, especially during the breeding season. For example, some initiatives aiming for mitigation of climate change impacts by afforestation should be carefully reconsidered to avoid adverse impacts on open habitat species.

Understanding the variability of processes leading to the emergence of new lineages is one of the major tasks of macroevolution as a scientific field. Recent years have seen the rise of rate-variable diversification models and metrics that estimate the rates of species diversification at the tips of phylogenetic trees and are thus potentially useful for predicting future evolutionary success of individual species. These methods use various assumptions about the variability and heritability of diversification rates. However, the general performance of rate-variable diversification methods have never been consistently tested against real world data. Here we explore the capacity of multiple rate-variable diversification methods to predict near-future diversification using temporal slices of empirical fossil and extant phylogenies. We do this using a newly developed approach similar to generalized linear models, allowing us to quantify the relationship between predictor tip rates and subsequent diversification rates derived from a probability distribution of numbers of daughter species. We find that tip rates estimated from current methods have non-zero but limited capacity to predict diversification in both fossil and extant phylogenies. The quality of the predictions depends not only on the methods used but also on the specific phylogeny, suggesting that diversification dynamics in some taxa may be more predictable in principle. Our results suggest that future cladogenesis can be, to a certain extent, predicted using existing tip rate methods, but the quality of such predictions is highly variable and depends on factors that are difficult to evaluate in practical applications. ### Competing Interest Statement The authors have declared no competing interest. Czech Science Foundation, https://ror.org/01pv73b02, GAČR 24-12851O, GAČR 20-29554X

Afrotropical savannas are biodiversity-rich ecosystems increasingly threatened by woody plant encroachment. In southern Africa, the leguminous tree Colophospermum mopane dominates over one-third of the savanna region and is projected to expand substantially under climate change. Yet, the consequences of its local dominance for biodiversity remain poorly understood. We conducted the first landscape-scale, multi-taxon assessment of mopane’s bottom-up effects, analysing species richness and community composition of vascular plants, insects, birds, bats, and non-flying mammals across a gradient of mopane cover in Kruger National Park, South Africa. Our replicated plot-based study found that species richness of birds, mammals, bats, and insects declined significantly with increasing mopane dominance, with the steepest reductions in birds. Plant overall species richness was unaffected, although grasses showed a weak positive trend. We also revealed significant community compositional shifts in birds, bats, and mammals, while insect communities lost species without systematic composition change. Functional-group analyses confirmed species richness declines for herbivores across taxa, and for bird carnivores and omnivores, pointing to mopane’s role as a strong ecological filter that reduces host plant and other resources availability, with consequences to the higher trophic levels. These results highlight mopane dominance as a potential driver of biodiversity simplification in African savannas, with cascading implications for ecosystem functioning. Given projections of mopane expansion and its socioeconomic value to local communities, management and policy must avoid promoting mopane dominance in land-use or restoration schemes. Safeguarding heterogeneous savanna mosaics will be essential for conserving biodiversity and ecosystem resilience under climate change. ### Competing Interest Statement The authors have declared no competing interest. Czech Science Foundation, https://ror.org/01pv73b02, 18-18495S, 21-24186M

AimDespite the evidenced importance of insects in savannah ecosystems, the drivers of their diversity patterns remain poorly understood, particularly in the Afrotropical region. This study addresses part of this gap by investigating the effects of climate, habitat, disturbance and vegetation variables on species richness and community composition of phytophagous and predatory insects in South African savannahs.LocationKruger National Park (KNP), South Africa.TaxonPhytophagous insects (moths) and carnivorous insects (mantises).MethodsMoths and mantises were light-trapped in 60 plots distributed across KNP during two seasons. Direct and indirect effects of environmental variables on insect species richness were analysed using structural equation models, and on community composition through distance-based redundancy analyses (db-RDA).ResultsBased on an extensive dataset of 65,593 moth individuals representing 817 species and 3511 mantis individuals representing 38 species, we identified plant communities as the primary driver of species richness and community structure for both insect groups. The effects of vegetation on insect communities were indirectly shaped by climate, particularly mean temperature (negatively correlated with precipitation), through its effects on plant species richness. Additionally, a complex interplay among bedrock type, water availability and disturbance from large herbivores further shaped insect diversity.Main ConclusionsOur findings highlight the critical role of plant species richness in determining insect diversity patterns in savannah ecosystems. We also confirmed the region's vulnerability to climate change, as decreasing precipitation and increasing temperatures alter vegetation composition and biomass, consequently affecting insect communities. Effective conservation strategies should focus on managing large herbivores to maintain diverse vegetation, which is crucial for supporting insect diversity. Priority should be given to balancing water availability and disturbance intensity, particularly in preserving the health of rivers and their surroundings, to mitigate the adverse effects of climate change on these ecosystems.

Large-scale temporal and spatial biodiversity patterns have traditionally been explained by multitudinous particular factors and a few theories. However, these theories lack sufficient generality and do not address fundamental interrelationships and coupled dynamics among resource availability, community abundance, and species richness. We propose the equilibrium theory of biodiversity dynamics (ETBD) to address these linkages. According to the theory, equilibrium levels of species richness and community abundance emerge at large spatial scales because of the population size dependence of speciation and/or extinction rates, modulated by resource availability and the species abundance distribution. In contrast to other theories, ETBD includes the effect of biodiversity on community abundance and thus addresses phenomena such as niche complementarity, facilitation, and ecosystem engineering. It reveals how alternative stable states in both diversity and community abundance emerge from these nonlinear biodiversity effects. The theory predicts how the strength of these effects alters scaling relationships among species richness, (meta)community abundance, and resource availability along different environmental gradients. Using data on global-scale variation in tree species richness, we show how the general framework is useful for clarifying the role of speciation, extinction, and resource availability in driving macroecological patterns in biodiversity and community abundance, such as the latitudinal diversity gradient.

Aim: To determine how species richness gradients-commonly considered universal-vary across the phylogenetic hierarchy of birds and mammals, and to uncover how clade age and size predetermine the gradients. Location: Global. Time Period: Last 120 million years.Taxa Studied Birds and mammals (similar to 15,000 species). Methods: We used large-scale phylogenies of birds and mammals and captured the species richness gradient for each of their monophyletic clades. Gradient strength was quantified with respect to latitude, environmental productivity and temperature using multiple measures (raw slopes, log transformation, log-log transformation, and correlations). To distinguish statistical from biological effects, we compared the observed gradients to those generated by null models that randomly reassigned species to clades while preserving the phylogeny and species distributions. Results: Species richness gradients show considerable variation. Small and young clades exhibited inconsistent gradients-including reverse or flat gradients-while older and larger clades converged on steep, consistent gradients. Even moderately large clades (similar to 500 species) commonly displayed reverse gradients. Null models replicated this trend but only partially, implying that biological effects also drive gradient variation. These phylogenetic trends were sensitive to the choice of gradient measure: raw slopes frequently inflated the strength of this trend and the apparent differences among clades, while log and log-log transformations revealed only moderate trends. Main Conclusions: Species richness gradients are not universal, nor are they phylogenetic scale-invariant. Instead, they follow systematic trends across the phylogenetic hierarchy. Young, small clades often bear signatures of their region of origin and historical dispersal, whereas older, larger clades converge on similar gradients. Recognising the variation and the phylogenetic trends within it elucidates the formation of biodiversity patterns. We offer guidelines for choosing gradient measures, arguing that multiple metrics, combined with careful use of null models, are necessary for a nuanced understanding of how, and why, global biodiversity patterns diverge from the presumed universal gradients.

AbstractThe savanna ecosystem is dominated by grasses, which are a key food source for many species of grazing animals. This relationship creates a diverse mosaic of habitats and contributes to the high grass species richness of savannas. However, how grazing interacts with environmental conditions in determining grass species richness and abundance in savannas is still insufficiently understood. In the Kruger National Park, South Africa, we recorded grass species and estimated their covers in 60 plots 50 × 50 m in size, accounting for varying proximity to water and different bedrocks. To achieve this, we located plots (i) near perennial rivers, near seasonal rivers, and on crests that are distant from all water sources and (ii) on nutrient‐rich basaltic and nutrient‐poor granitic bedrock. The presence and abundance of large herbivores were recorded by 60 camera traps located in the same plots. Grass cover was higher at crests and seasonal rivers than at perennial rivers and on basalts than on granites. The relationship between grass species richness and herbivore abundance or species richness was positive at crests, while that between grass species richness and herbivore species richness was negative at seasonal rivers. We found no support for controlling the dominance of grasses by herbivores in crests, but herbivore‐induced microsite heterogeneity may account for high grass species richness there. In contrast, the decrease in grass species richness with herbivore species richness at seasonal rivers indicates that the strong grazing pressure over‐rides the resistance of some species to grazing and trampling. We suggest that the relationships between grasses and herbivores may work in both directions, but the relationship is habitat‐dependent, so that in less productive environments, the effect of herbivores on vegetation prevails, while in more productive environments along rivers the effect of vegetation and water supply on herbivores is more important.

Northern glacial refugia are a hotly debated concept. The idea that many temperate organisms survived the Last Glacial Maximum (LGM; ~26.5 to 19 thousand years) in several sites across central and northern Europe stems from phylogeographic analyses, yet direct fossil evidence has thus far been missing. Here, we present the first unequivocal proof that thermophilous trees such as oak ( Quercus ), linden ( Tilia ), and common ash ( Fraxinus excelsior ) survived the LGM in Central Europe. The persistence of the refugium was promoted by a steady influx of hydrothermal waters that locally maintained a humid and warm microclimate. We reconstructed the geological and palaeohydrological factors responsible for the emergence of hot springs during the LGM and argue that refugia of this type, allowing the long-term survival and rapid post-LGM dispersal of temperate elements, were not exceptional in the European periglacial zone.

This preprint of a book chapter presents the newly proposed Equilibrium Theory of Biodiversity Dynamics (ETBD), whose aim is to conceptualize large-scale dynamics of species richness via addressing the population size-dependence of speciation and extinction rates, the resulting diversity-dependence of these rates, and their modulation by the environment. It provides the most general framework for understanding large-scale biodiversity patterns such as the latitudinal diversity gradient (LDG) and temporal patterns of biodiversity changes. The theory has been published elsewhere in its full form that includes all the derivations (Okie & Storch 2004, American Naturalist https://doi.org/10.1086/733103), but here it is presented in a simpler and user-friendly way, focusing on its major implications comprising macroecological scaling relationships between energy (or resource) availability, species richness and community abundance. ### Competing Interest Statement The authors have declared no competing interest.

The Living Planet Index (LPI) measures the average change in population size of vertebrate species over recent decades and has been repeatedly used to assess the changing state of nature. The LPI indicates that vertebrate populations have decreased by almost 70% over the last 50 years. This is in striking contrast with current studies based on the same population time series data that show that increasing and decreasing populations are balanced on average. Here, we examine the methodological pipeline of calculating the LPI to search for the source of this discrepancy. We find that the calculation of the LPI is biased by several mathematical issues which impose an imbalance between detected increasing and decreasing trends and overestimate population declines. Rather than indicating that vertebrate populations do not substantially change, our findings imply that we need better measures for providing a balanced picture of current biodiversity changes. We also show some modifications to improve the reliability of the LPI. The Living Planet Index is a widely used metric to measure the global population trends of vertebrates. This in-depth analysis of the methodology underlying the index reveals fundamental issues and identifies modifications that partly alleviate them.

Abstract Population growth is the sum of survival and recruitment, and knowledge of these two vital rates is crucial for understanding population dynamics. Moreover, animal populations often contain varying number of transient (i.e. nonresident) individuals that do not contribute to these rates but may bias their estimates. The widely used Pradel (1996, Biometrics, 52: 703) survival‐recruitment model for capture–mark–recapture data is only able to handle resident individuals on a fixed study area across a particular study period. Yet, numerous capture–mark–recapture data sets, from a wide range of taxa, feature transient individuals. The most widespread sources of avian demographic data, based on citizen science projects, feature both transient individuals and changes in the study area over time. We present an extension of the Pradel model that accounts for the presence of transient individuals and changes in the study area. In contrast to known extensions of the Cormack–Jolly–Seber models in which transients are modelled as a proportion of newly captured individuals, our novel approach models transient individuals as a proportion of all birds captured. In addition, we present a new simple way to visualize the interlinkage of the vital rates produced by our extended Pradel model. We demonstrate utilization of the model using capture–mark–recapture data collected by a constant‐effort mist‐netting citizen science programme in the Czech Republic, presenting demographic rates of two species with different population dynamics. To demonstrate the newly achieved ability to analyse the phenomenon of transience, we show the differences in transience and its temporal trends between wet and dry habitats. Removing the limitations of the Pradel model opens up new potential for much wider range of applications. Furthermore, our novel parametrization of transients as a proportion of all birds captured facilitates biological interpretation of the transience parameter and the study of transience as a biological phenomenon. Calculating all demographic parameters in a single model also opens up a unique possibility to take into account their correlated error distributions in follow‐up analyses. Our model can be further extended in several ways and can serve as a basic building block in a wide range of demographic analyses.