Species richness at continental scales is dominated by ecological limits

Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous

Palaeontologists have long sought to explain the diversification of individual clades to whole biotas at global scales. Advances in our understanding of the spatial distribution of the fossil record through geological time, however, has demonstrated that global trends in biodiversity were a mosaic of regionally heterogeneous diversification processes. Drivers of diversification must presumably have also displayed regional variation to produce the spatial disparities observed in past taxonomic richness. Here, we analyse the fossil record of ammonoids, pelagic shelled cephalopods, through the Late Cretaceous, characterised by some palaeontologists as an interval of biotic decline prior to their total extinction at the Cretaceous-Paleogene boundary. We regionally subdivide this record to eliminate the impacts of spatial sampling biases and infer regional origination and extinction rates corrected for temporal sampling biases using Bayesian methods. We then model these rates using biotic and abiotic drivers commonly inferred to influence diversification. Ammonoid diversification dynamics and responses to this common set of diversity drivers were regionally heterogeneous, do not support ecological decline, and demonstrate that their global diversification signal is influenced by spatial disparities in sampling effort. These results call into question the feasibility of seeking drivers of diversity at global scales in the fossil record.

Detecting the ecological footprint of selection

The structure of communities is influenced by many ecological and evolutionary processes, but the way these manifest in classic biodiversity patterns often remains unclear. Here we aim to distinguish the ecological footprint of selection-through competition or environmental filtering-from that of neutral processes that are invariant to species identity. We build on existing Massive Eco-evolutionary Synthesis Simulations (MESS), which uses information from three biodiversity axes-species abundances, genetic diversity, and trait variation-to distinguish between mechanistic processes. To correctly detect and characterise competition, we add a new and more realistic form of competition that explicitly compares the traits of each pair of individuals. Our results are qualitatively different to those of previous work in which competition is based on the distance of each individual's trait to the community mean. We find that our new form of competition is easier to identify in empirical data compared to the alternatives. This is especially true when trait data are available and used in the inference procedure. Our findings hint that signatures in empirical data previously attributed to neutrality may in fact be the result of pairwise-acting selective forces. We conclude that gathering more different types of data, together with more advanced mechanistic models and inference as done here, could be the key to unravelling the mechanisms of community assembly and question the relative roles of neutral and selective processes.

A multitaxonomic assessment of Natura 2000 effectiveness across European biogeographic regions

The Natura 2000 (N2K) protected area (PA) network is a crucial tool to limit biodiversity loss in Europe. Despite covering 18% of the European Union's (EU) land area, its effectiveness at conserving biodiversity across taxa and biogeographic regions remains uncertain. Testing this effectiveness is, however, difficult because it requires considering the nonrandom location of PAs, and many possible confounding factors. We used propensity score matching and accounted for the confounding effects of biogeographic regions, terrain ruggedness, and land cover to assess the effectiveness of N2K PAs on the distribution of 1769 species of conservation priority in the EU's Birds and Habitats Directives, including mammals, birds, amphibians, reptiles, arthropods, fishes, mollusks, and vascular and nonvascular plants. We compared alpha, beta, and gamma diversity between matched selections of protected and unprotected areas across EU's biogeographic regions with generalized linear models, generalized mixed models, and nonparametric tests for paired samples, respectively, for each taxonomic group and for the entire set of species. PAs in N2K hosted significantly more priority species than unprotected land, but this difference was not consistent across biogeographic regions or taxa. Total alpha diversity and alpha diversity of amphibians, arthropods, birds, mammals, and vascular plants were significantly higher inside PAs than outside, except in the Boreal biogeographical region. Beta diversity was in general significantly higher inside N2K PAs than outside. Similarly, gamma diversity had the highest values inside PAs, with some exceptions in Boreal and Atlantic regions. The planned expansion of the N2K network, as dictated by the European Biodiversity Strategy for 2030, should therefore target areas in the southern part of the Boreal region where species diversity of amphibians, arthropods, birds, mammals, and vascular plants is high and species are currently underrepresented in N2K.

Unveiling the underlying drivers of Phanerozoic marine diversification

In investigating global patterns of biodiversity through deep time, many large-scale drivers of diversification have been proposed, both biotic and abiotic. However, few robust conclusions about these hypothesized effectors or their roles have been drawn. Here, we use a linear stochastic differential equation (SDE) framework to test for the presence of underlying drivers of diversification patterns before examining specific hypothesized drivers. Using a global dataset of observations of skeletonized marine fossils, we infer origination, extinction and sampling rates (collectively called fossil time series) throughout the Phanerozoic using a capture-mark-recapture approach. Using linear SDEs, we then compare models including and excluding hidden (i.e. unmeasured) drivers of these fossil time series. We find evidence of large-scale underlying drivers of marine Phanerozoic diversification rates and present quantitative characterizations of these. We then test whether changing global temperature, sea-level, marine sediment area or continental fragmentation could act as drivers of the fossil time series. We show that it is unlikely any of these four abiotic factors are the hidden drivers we identified, though there is evidence for correlative links between sediment area and origination/extinction rates. Our characterization of the hidden drivers of Phanerozoic diversification and sampling will aid in the search for their ultimate identities.

Eco-evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae)

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.

DeepDive: estimating global biodiversity patterns through time using deep learning

Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.

Phages in different habitats and their ability to carry antibiotic resistance genes

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification

Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.

Saccharomycotina yeasts defy long-standing macroecological patterns

The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.

An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates

AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.

Limited ecological opportunity influences the tempo of morphological evolution in birds

According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.

Ecological structure of diversity-dependent diversification in Phanerozoic marine bivalves

Rigorous analysis of diversity-dependence-the hypothesis that the rate of proliferation of new species is inversely related to standing diversity-requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment-water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.

Diversity across organisational scale emerges through dispersal ability and speciation dynamics in tropical fish

BACKGROUND

Biodiversity exists at different levels of organisation: e.g. genetic, individual, population, species, and community. These levels of organisation all exist within the same system, with diversity patterns emerging across organisational scales through several key processes. Despite this inherent interconnectivity, observational studies reveal that diversity patterns across levels are not consistent and the underlying mechanisms for variable continuity in diversity across levels remain elusive. To investigate these mechanisms, we apply a spatially explicit simulation model to simulate the global diversification of tropical reef fishes at both the population and species levels through emergent population-level processes.

RESULTS

We find significant relationships between the population and species levels of diversity which vary depending on both the measure of diversity and the spatial partitioning considered. In turn, these population-species relationships are driven by modelled biological trait parameters, especially the divergence threshold at which populations speciate.

CONCLUSIONS

To explain variation in multi-level diversity patterns, we propose a simple, yet novel, population-to-species diversity partitioning mechanism through speciation which disrupts continuous diversity patterns across organisational levels. We expect that in real-world systems this mechanism is driven by the molecular dynamics that determine genetic incompatibility, and therefore reproductive isolation between individuals. We put forward a framework in which the mechanisms underlying patterns of diversity across organisational levels are universal, and through this show how variable patterns of diversity can emerge through organisational scale.

Phylogenetic structure of body shape in a diverse inland ichthyofauna

Body shape is a fundamental metric of animal diversity affecting critical behavioral and ecological dynamics and conservation status, yet previously available methods capture only a fraction of total body-shape variance. Here we use structure-from-motion (SFM) 3D photogrammetry to generate digital 3D models of adult fishes from the Lower Mississippi Basin, one of the most diverse temperate-zone freshwater faunas on Earth, and 3D geometric morphometrics to capture morphologically distinct shape variables, interpreting principal components as growth fields. The mean body shape in this fauna resembles plesiomorphic teleost fishes, and the major dimensions of body-shape disparity are similar to those of other fish faunas worldwide. Major patterns of body-shape disparity are structured by phylogeny, with nested clades occupying distinct portions of the morphospace, most of the morphospace occupied by multiple distinct clades, and one clade (Acanthomorpha) accounting for over half of the total body shape variance. In contrast to previous studies, variance in body depth (59.4%) structures overall body-shape disparity more than does length (31.1%), while width accounts for a non-trivial (9.5%) amount of the total body-shape disparity.

Sunken trees in the deep sea link terrestrial and marine biodiversity

Wood in the deep sea serves as a substantial food source in an otherwise barren environment, forming specialized, endemic, and diverse community assemblages. This biodiversity reliance on a terrestrial source creates a linkage by which anthropogenic impacts on land can alter the deep oceans. Knowledge of the alpha- or beta-diversity of entire wood-fall communities, and wooden drivers of each would elucidate the terrestrial and deep-sea linkage. We report on a multifactorial experiment in the deep ocean in which alpha- and beta-diversity of 43 wood falls and 11 tree species are quantified over time, wood density, and wood size. We tested multiple hypotheses seeking to link how biodiversity on land may impact the biodiversity in the deep oceans. A tremendous biodiversity occurred among these wood falls in the deep Gulf of Mexico; 114 invertebrate species from 10 phyla. Time, wood hardness, and wood size all impacted various components of community structure. In many cases, these effects were additive. Species occurring on softwoods versus hardwoods and small versus large wood falls were compositionally different. Although various processes can control community structure, this experiment suggests a strong influence of environmental filtering and host specificity of wood-fall invertebrates suggesting an intimate coupling to tree biodiversity and biomass on land.

Saccharomycotina yeasts defy longstanding macroecological patterns

The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth1; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild2. Here, we trained machine learning models on 12,221 occurrence records and 96 environmental variables to infer global distribution maps for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversification. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many longstanding macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and latitude-dependent range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.

Conceptual and empirical bridges between micro- and macroevolution

Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.

Clade density and the evolution of diversity-dependent diversification

The assumption of an ecological limit to the number of species in a given region is frequently invoked in evolutionary studies, yet its empirical basis is remarkably meager. We explore this assumption by integrating data on geographical distributions and phylogenetic relationships of nearly six thousand terrestrial vertebrate species. In particular, we test whether sympatry with closely-related species leads to decreasing speciation rates. We introduce the concept of clade density, which is the sum of the areas of overlap between a given species and other members of its higher taxon, weighted by their phylogenetic distance. Our results showed that, regardless of the chosen taxon and uncertainty in the phylogenetic relationships between the studied species, there is no significant relationship between clade density and speciation rate. We argue that the mechanistic foundation of diversity-dependent diversification is fragile, and that a better understanding of the mechanisms driving regional species pools is sorely needed.

Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea

This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.

Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation

Adaptive radiation is proposed to play a key role in generating differences in species richness among lineages and geographical regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analysing (i) the temporal patterns of diversification of Caribbean Eleutherodactylus frogs, and (ii) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of Eleutherodactylus differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation which gradually decreases towards the present. Eleutherodactylus diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, Eleutherodactylus shows higher carrying capacity. Our results indicate that ecological opportunity per se is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.

Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan

Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.

Evolutionary time and species diversity in aquatic ecosystems worldwide

The latitudinal diversity gradient (LDG) is frequently described as the most dramatic biodiversity pattern on Earth, yet ecologists and biogeographers have failed to reach consensus on its primary cause. A key problem in explaining the LDG involves collinearity between multiple factors that are predicted to affect species richness in the same direction. In terrestrial systems, energy input, geographic area, and evolutionary time for species accumulation tend to covary positively with species richness at the largest spatial scales, such that their individual contributions to the LDG are confounded in global analyses. I review three diversity patterns from marine and freshwater systems that break this collinearity and which may thus provide stronger tests of the influence of time on global richness gradients. Specifically, I contrast biodiversity patterns along oceanic depth gradients, in geologically young versus ancient lakes, and in the north versus south polar marine biomes. I focus primarily on fishes due to greater data availability but synthesize patterns for invertebrates where possible. I find that regional-to-global species richness generally declines with depth in the oceans, despite the great age and stability of the deep-sea biome. Geologically ancient lakes generally do not contain more species than young lakes, and the Antarctic marine biome is not appreciably more species rich than the much younger Arctic marine biome. However, endemism is consistently higher in older systems. Patterns for invertebrate groups are less clear than for fishes and reflect a critical need for primary biodiversity data. In summary, the available data suggest that species richness is either decoupled from or only weakly related to the amount of time for diversification. These results suggest that energy, productivity, or geographic area are the primary drivers of large-scale diversity gradients. To the extent that marine and terrestrial diversity gradients result from similar processes, these examples provide evidence against a primary role for evolutionary time as the cause of the LDG.

Evolutionary opportunity and the limits of community similarity in replicate radiations of island lizards

Ecological community structure ultimately depends on the production of community members by speciation. To understand how macroevolution shapes communities, we surveyed Anolis lizard assemblages across elevations on Jamaica and Hispaniola, neighbouring Caribbean islands similar in environment, but contrasting in the richness of their endemic evolutionary radiations. The impact of diversification on local communities depends on available spatial opportunities for speciation within or between ecologically distinct sub-regions. In the spatially expansive lowlands of both islands, communities converge in species richness and average morphology. But communities diverge in the highlands. On Jamaica, where limited highland area restricted diversification, communities remain depauperate and consist largely of elevational generalists. In contrast, a unique fauna of high-elevation specialists evolved in the vast Hispaniolan highlands, augmenting highland richness and driving islandwide turnover in community composition. Accounting for disparate evolutionary opportunities may illuminate when regional diversity will enhance local diversity and help predict when communities should converge in structure.

Mapping species diversification metrics in macroecology: Prospects and challenges

The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.

Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time

What controls species diversity and diversification is one of the major questions in evolutionary biology and paleontology. Previous studies have addressed this issue based on various plant and animal groups, geographic regions, and time intervals. However, as most previous research focused on terrestrial or marine ecosystems, our understanding of the controls on diversification of biota (and particularly invertebrates) in freshwater environments in deep time is still limited. Here, we infer diversification rates of North American freshwater gastropods from the Late Triassic to the Pleistocene and explore potential links between shifts in speciation and extinction and major changes in paleogeography, climate, and biotic interactions. We found that variation in the speciation rate is best explained by changes in continental fragmentation, with rate shifts coinciding with major paleogeographic reorganizations in the Mesozoic, in particular the retreat of the Sundance Sea and subsequent development of the Bighorn wetland and the advance of the Western Interior Seaway. Climatic events in the Cenozoic (Middle Eocene Climate Optimum, Miocene Climate Optimum) variably coincide with shifts in speciation and extinction as well, but no significant long-term association could be detected. Similarly, no influence of diversity dependence was found across the entire time frame of ~ 214 Myr. Our results indicate that short-term climatic events and paleogeographic changes are relevant to the diversification of continental freshwater biota, while long-term trends have limited effect.

Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification

Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

Global variation in diversification rate and species richness are unlinked in plants

Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.

Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

Terrestrial forcing of marine biodiversification

The diversification of the three major marine faunas during the Phanerozoic was intimately coupled to the evolution of the biogeochemical cycles of carbon and nutrients via nutrient runoff from land and the diversification of phosphorus-rich phytoplankton. Nutrient input to the oceans has previously been demonstrated to have occurred in response to orogeny and fueling marine diversification. Although volcanism has typically been associated with extinction, the eruption of continental Large Igneous Provinces (LIPs) is also a very significant, but previously overlooked, source of phosphorus involved in the diversification of the marine biosphere. We demonstrate that phosphorus input to the oceans peaked repeatedly following the eruption and weathering of LIPs, stimulating the diversification of nutrient-rich calcareous and siliceous phytoplankton at the base of marine food webs that in turn helped fuel diversification at higher levels. These developments were likely furthered by the evolution of terrestrial floras. Results for the Meso-Cenozoic hold implications for the Paleozoic Era. Early-to-middle Paleozoic diversity was, in contrast to the Meso-Cenozoic, limited by nutrient-poor phytoplankton resulting from less frequent tectonism and poorly-developed terrestrial floras. Nutrient runoff and primary productivity during the Permo-Carboniferous likely increased, based on widespread orogeny, the spread of deeper-rooting forests, the fossil record of phytoplankton, and biogeochemical indices. Our results suggest that marine biodiversity on geologic time scales is unbounded (unlimited), provided sufficient habitat, nutrients, and nutrient-rich phytoplankton are also available in optimal amounts and on optimal timescales.

Latitudinal Diversity Gradient in the Changing World: Retrospectives and Perspectives

The latitudinal diversity gradient (LDG) is one of the most extensive and important biodiversity patterns on the Earth. Various studies have established that species diversity increases with higher taxa numbers from the polar to the tropics. Studies of multicellular biotas have supported the LDG patterns from land (e.g., plants, animals, forests, wetlands, grasslands, fungi, and so forth) to oceans (e.g., marine organisms from freshwater invertebrates, continental shelve, open ocean, even to the deep sea invertebrates). So far, there are several hypotheses proposed to explore the diversity patterns and mechanisms of LDG, however, there has been no consensus on the underlying causes of LDG over the past few decades. Thus, we reviewed the progress of LDG studies in recent years. Although several explanations for the LDG have been proposed, these hypotheses are only based on species richness, evolution and the ecosystems. In this review, we summarize the effects of evolution and ecology on the LDG patterns to synthesize the formation mechanisms of the general biodiversity distribution patterns. These intertwined factors from ecology and evolution in the LDG are generally due to the wider distribution of tropical areas, which hinders efforts to distinguish their relative contributions. However, the mechanisms of LDG always engaged controversies, especially in such a context that the human activity and climate change has affected the biodiversity. With the development of molecular biology, more genetic/genomic data are available to facilitate the estimation of global biodiversity patterns with regard to climate, latitude, and other factors. Given that human activity and climate change have inevitably impacted on biodiversity loss, biodiversity conservation should focus on the change in LDG pattern. Using large-scale genetic/genomic data to disentangle the diversity mechanisms and patterns of LDG, will provide insights into biodiversity conservation and management measures. Future perspectives of LDG with integrative genetic/genomic, species, evolution, and ecosystem diversity patterns, as well as the mechanisms that apply to biodiversity conservation, are discussed. It is imperative to explore integrated approaches for recognizing the causes of LDG in the context of rapid loss of diversity in a changing world.

Geographical range overlap networks and the macroecology of species co-occurrence

Direct interactions among species are only possible if there is some overlap in their geographical distributions. However, despite intense focus of macroecological research on species geographical ranges, relatively little theoretical and empirical work has been done on the evolution of range overlap. In this study we explore a simple model of range overlap based on a log-normal distribution of species range sizes along a one-dimensional domain, with or without absorbing boundary conditions. In particular, we focus on the mean and variance of range overlap distributions, as well as the topology of the resulting overlap networks with respect to their degree distribution, evenness, and betweenness scores. According to the model, there is an approximately linear relationship between many aspects of the distribution of range overlaps and their underlying species distributions, such as their mean and variance. However, the expected mean number of non-zero range overlaps for a given species varied from linear to convex depending on the variance of the underlying geographical range distribution. The expected topology of range overlap networks varied substantially depending on the mean and variance in the corresponding geographical distributions, particularly in the case of the degree and closeness distributions. Finally, we test the expectations of our model against five datasets of altitudinal distributions of Neotropical birds. We found strong departures from the expectations based on our model, which could potentially result from phylogenetic niche conservatism related to altitudinal gradients in environmental conditions, or from the asymmetric colonization of mountains by species from lowlands. Potential applications of range overlap networks to a variety of ecological and evolutionary phenomena are discussed.

Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.

Drivers of diversification in freshwater gastropods vary over deep time

Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. However, whether the impact of biotic and abiotic controls on diversification changes over time is poorly understood. Here, we use a large fossil dataset, a multivariate birth-death model and a comprehensive set of biotic and abiotic predictors, including a new index to quantify tectonic complexity, to estimate the drivers of diversification for European freshwater gastropods over the past 100 Myr. The effects of these factors on origination and extinction are estimated across the entire time frame as well as within sequential time windows of 20 Myr each. Our results find support for temporal heterogeneity in the factors associated with changes in diversification rates. While the factors impacting speciation and extinction rates vary considerably over time, diversity-dependence and topography are consistently important. Our study highlights that a high level of heterogeneity in diversification rates is best captured by incorporating time-varying effects of biotic and abiotic factors.

Landscape Evolution as a Diversification Driver in Freshwater Fishes

The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (<0.5%) or total aquatic habitat volume (<0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.

Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’.

Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species.

Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates

Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.

Biotic and Abiotic Controls on the Phanerozoic History of Marine Animal Biodiversity

During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change.

A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities

Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.

Biodiversity across space and time in the fossil record

The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.

Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling

Microbial communities are hugely diverse, but we do not yet understand how species invasions and extinctions drive and limit their diversity. On the one hand, the ecological limits hypothesis posits that diversity is primarily limited by environmental resources. On the other hand, the diversity‐begets‐diversity hypothesis posits that such limits can be easily lifted when new ecological niches are created by biotic interactions. To find out which hypothesis better explains the assembly of microbial communities, we used metabolic modelling. We represent each microbial species by a metabolic network that harbours thousands of biochemical reactions. Together, these reactions determine which carbon and energy sources a species can use, and which metabolic by‐products—potential nutrients for other species—it can excrete in a given environment. We assemble communities by modelling thousands of species invasions in a chemostat‐like environment. We find that early during the assembly process, diversity begets diversity. By‐product excretion transforms a simple environment into one that can sustain dozens of species. During later assembly stages, the creation of new niches slows down, existing niches become filled, successful invasions become rare, and species diversity plateaus. Thus, ecological limitations dominate the late assembly process. We conclude that each hypothesis captures a different stage of the assembly process. Species interactions can raise a community's diversity ceiling dramatically, but only within limits imposed by the environment.

A positive relationship between functional redundancy and temperature in Cenozoic marine ecosystems

The long-term effects of climate change on biodiversity and biogeographic patterns are uncertain. There are known relationships between geographic area and both the number of species and the number of ecological functional groups-termed the species-area relationship and the functional diversity-area relationship, respectively. We show that there is a positive relationship between the number of species in an area, the number of ecological functional groups, and oceanic temperature in the shallow-marine fossil record of New Zealand over a time span of ~40 million years. One implication of this relationship is that functional redundancy increases with temperature. This reveals a long-lived and persistent association between the spatial structuring of biodiversity, the temperature-dependence of functional redundancy, and shallow-marine biodiversity in mid-latitudes.

Tempo and mode of morphological evolution are decoupled from latitude in birds

The latitudinal diversity gradient is one of the most striking patterns in nature, yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions-namely, competition-can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait dependent. Our results indicate that species interactions do not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur’s classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lotka-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.

Understanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities, in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable states, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.

Productivity, niche availability, species richness, and extinction risk: Untangling relationships using individual-based simulations

It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology.

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs

Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.