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The idea that the number of species within an area is limited by a specific capacity of that area to host species is old yet controversial. Here, we show that the concept of carrying capacity for species richness can be as useful as the analogous concept in population biology. Many lines of empirical evidence indicate the existence of limits of species richness, at least at large spatial and phylogenetic scales. However, available evidence does not support the idea of diversity limits based on limited niche space; instead, carrying capacity should be understood as a stable equilibrium of biodiversity dynamics driven by diversity-dependent processes of extinction, speciation and/or colonization. We argue that such stable equilibria exist even if not all resources are used and if increasing species richness increases the ability of a community to use resources. Evaluating the various theoretical approaches to modelling diversity dynamics, we conclude that a fruitful approach for macroecology and biodiversity science is to develop theory that assumes that the key mechanism leading to stable diversity equilibria is the negative diversity dependence of per-species extinction rates, driven by the fact that population sizes of species must decrease with an increasing number of species owing to limited energy availability. The recently proposed equilibrium theory of biodiversity dynamics is an example of such a theory, which predicts that equilibrium species richness (i.e., carrying capacity) is determined by the interplay of the total amount of available resources, the ability of communities to use those resources, environmental stability that affects extinction rates, and the factors that affect speciation and colonization rates. We argue that the diversity equilibria resulting from these biodiversity dynamics are first-order drivers of large-scale biodiversity patterns, such as the latitudinal diversity gradient.

Earth’s largest biotic crisis occurred during the Permo–Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa’s Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using samplestandardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The “disaster taxon” Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

We are living in a time of rapid environmental changes caused by anthropogenic pressures. Besides direct human exploitation of plant and animal populations and habitat transformation, biodiversity changes in the Anthropocene are affected by less trivial processes including rapid spreading of non‐native species, emergence of novel communities and modifications of ecosystem functioning due to changing nutrient cycles and climate changes. These processes are so complex that confident predictions and effective biodiversity conservation cannot be obtained without a suitable theory of biodiversity dynamics. We argue that such dynamics have particular attractors, i.e. stable equilibria, that are determined by environmental conditions. These stable equilibria set biodiversity limits, i.e. carrying capacities for biodiversity, from local to global scales. We point out the evidence of such limits at various spatiotemporal scales and show, using the new equilibrium theory of biodiversity dynamics (ETBD), how dynamics of diversity depend on non‐linear relationships between number of species, community abundance and population size‐dependent processes of species extinction and origination (speciation or colonization). We show that non‐linear effects of biodiversity on ecosystem functioning can lead to multiple biodiversity equilibria and tipping points. Various human activities, including species introductions, human appropriation of primary production and trophic downgrading, can change local, regional and global diversity equilibria by affecting processes that set equilibrium diversity levels. The existence of equilibrium and out‐of‐equilibrium states has important implications for conservation, restoration and reconciliation ecology. It highlights the need to more effectively and intentionally balance the historical focus on the preservation of natural habitats with management specifically directed towards the processes responsible for long‐term maintenance of biodiversity equilibria. The Anthropocene represents a unique situation in which people make decisions concerning the dynamics of the natural world, and we argue that ecological restoration requires wisely deciding which of the alternative equilibria are worth maintaining.

Aim: Cenozoic dynamics of large-scale species diversity patterns remain poorly understood, especially for the Western Pacific, in part, because of the paucity of well-dated fossil records from the tropics. This article aims to reveal the spatiotemporal dynamics of species diversity in the Western Pacific through the Cenozoic, focusing on the tropical Indo-Australian Archipelago (IAA) biodiversity hotspot. Location: Tropical and north-western Pacific Ocean. Methods: We analysed well-preserved fossil ostracodes from the tropical Western Pacific and combined their diversity data with other published data from the region to reconstruct Cenozoic dynamics of species diversity in the tropical and north-western Pacific Ocean. We fitted generalized additive models to test for differences in richness over time and across geographical regions while accounting for sample-size variation among samples. Results: Low-, mid- and high-latitude regions all show a similar diversity trajectory: diversity is low in the Eocene and Oligocène, increases from the Early Miocene to the Plio-Pleistocene but then declines to the present day. Present-day high biodiversity in these regions was established during the Pliocene with a remarkable diversity increase at that time. Latitudinal diversity patterns are relatively flat and never show a simple decline from the tropics to higher latitudes. Main conclusions: Western Pacific Cenozoic ostracodes exhibit a spatiotemporal pattern of species diversity that is inconsistent with the commonly reported and persistent pattern of declining diversity from the tropics to the extratropics. While this inconsistency could be interpreted as evidence that ostracodes are a contrarian clade, Atlantic ostracodes display a standard latitudinal species diversity gradient. Contrasting patterns between oceans suggest an important role for regional factors (e.g. plate tectonics and temporal geomorphological dynamics) in shaping the biodiversity of the Western Pacific.

The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain this asymmetry: 1) Higher dispersal rate of North American mammals toward the south, 2) higher origination of North American immigrants in South America, 3) higher extinction of mammals with South American origin, and 4) similar dispersal rate but a larger pool of native taxa in North versus South America. We test among these mechanisms by analyzing ∼20,000 fossil occurrences with Bayesian methods to infer dispersal and diversification rates and taxonomic selectivity of immigrants. We find no differences in the dispersal and origination rates of immigrants. In contrast, native South American mammals show higher extinction. We also find that two clades with North American origin (Carnivora and Artiodactyla) had significantly more immigrants in South America than other clades. Altogether, the asymmetry of the interchange was not due to higher origination of immigrants in South America as previously suggested, but resulted from higher extinction of native taxa in southern South America. These results from one of the greatest biological invasions highlight how biogeographic processes and biotic interactions can shape continental diversity.

The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods, and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity account for 21% and 9% of Neotropical diversity, respectively. Five biogeographic areas are identified as distinctive units of long-term Neotropical evolution, including Pan-Amazonia, the Dry Diagonal, and Bahama-Antilles. Diversification dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined towards the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with past climate changes.

Recent studies investigating the relationship between crop genetic diversity and human cultural diversity patterns showed that seed exchanges are embedded in farmers’ social organization. However, our understanding of the social processes involved remains limited. We investigated how farmers’ membership in three major social groups interacts in shaping sorghum seed exchange networks in a cultural contact zone on Mount Kenya. Farmers are members of residence groups at the local scale and of dialect groups clustered within larger ethnolinguistic units at a wider scale. The Chuka and Tharaka, who are allied in the same ethnolinguistic unit, coexist with the Mbeere dialect group in the study area. We assessed farmers’ homophily, propensity to exchange seeds with members of the same group, using exponential random graph models. We showed that homophily is significant within both residence and ethnolinguistic groups. At these two levels, homophily is driven by the kinship system, particularly by the combination of patrilocal residence and ethnolinguistic endogamy, because most seeds are exchanged among relatives. Indeed, residential homophily in seed exchanges results from local interactions between women and their in-law family, whereas at a higher level, ethnolinguistic homophily is driven by marriage endogamy. Seed exchanges and marriage ties are interrelated, and both are limited between the Mbeere and the other groups, although frequent between the Chuka and Tharaka. The impact of these social homophily processes on crop diversity is discussed.

Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates, we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Comparing observed correlations between diversity and diversification rate to those expected from this diversity-independent model, we find evidence for negative diversity-dependence, accounting for up to 12% of the variance in diversification rate, with maximal correlation at a temporal lag of approximately 1 Myr. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian. By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian.

Biodiversity has important implications for the sustainable development of cities. Given the paucity of ground-based experiments, the responses of biodiversity to urbanization and its associated controls on a global scale remain largely unexplored. We present a novel conceptual framework for quantifying the direct and indirect impacts of urbanization on biodiversity in 1523 cities worldwide using the global 100 m grid biodiversity intactness index data (2017–2020) as a proxy for biodiversity. The results show a pervasive positive impact of urbanization on biodiversity in global cities, with a global mean direct and indirect impact of 24.85 ± 9.97% and 16.18 ± 10.92%, respectively. The indirect impact is relatively large in highly urbanized cities in the eastern United States, Western Europe, and the Middle East. The indirect impact is predominantly influenced by urbanization intensity, population density, and background climate. The correlation between urbanization intensity and indirect impact is most pronounced across all climate zones, while the other driving variables influencing the indirect effect exhibited considerable variations. Furthermore, our findings indicate that the biodiversity responses to urbanization are influenced by the biodiversity and development conditions of cities. Our findings have important implications for understanding the impact of urbanization on biodiversity and for future sustainable urban biodiversity.