Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

The macro-eco-evolutionary interplay between dispersal, competition and landscape structure in generating biodiversity

Theory links dispersal and diversity, predicting the highest diversity at intermediate dispersal levels. However, the modulation of this relationship by macro-eco-evolutionary mechanisms and competition within a landscape is still elusive. We examine the interplay between dispersal, competition and landscape structure in shaping biodiversity over 5 million years in a dynamic archipelago landscape. We model allopatric speciation, temperature niche, dispersal, competition, trait evolution and trade-offs between competitive and dispersal traits. Depending on dispersal abilities and their interaction with landscape structure, our archipelago exhibits two 'connectivity regimes', that foster speciation events among the same group of islands. Peaks of diversity (i.e. alpha, gamma and phylogenetic), occurred at intermediate dispersal; while competition shifted diversity peaks towards higher dispersal values for each connectivity regime. This shift demonstrates how competition can boost allopatric speciation events through the evolution of thermal specialists, ultimately limiting geographical ranges. Even in a simple landscape, multiple intermediate dispersal diversity relationships emerged, all shaped similarly and according to dispersal and competition strength. Our findings remain valid as dispersal- and competitive-related traits evolve and trade-off; potentially leaving identifiable biodiversity signatures, particularly when trade-offs are imposed. Overall, we scrutinize the convoluted relationships between dispersal, species interactions and landscape structure on macro-eco-evolutionary processes, with lasting imprints on biodiversity.This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks

Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.

Evidence of thermophilization in Afromontane forests

Thermophilization is the directional change in species community composition towards greater relative abundances of species associated with warmer environments. This process is well-documented in temperate and Neotropical plant communities, but it is uncertain whether this phenomenon occurs elsewhere in the tropics. Here we extend the search for thermophilization to equatorial Africa, where lower tree diversity compared to other tropical forest regions and different biogeographic history could affect community responses to climate change. Using re-census data from 17 forest plots in three mountain regions of Africa, we find a consistent pattern of thermophilization in tree communities. Mean rates of thermophilization were +0.0086 °C·y-1 in the Kigezi Highlands (Uganda), +0.0032 °C·y-1 in the Virunga Mountains (Rwanda-Uganda-Democratic Republic of the Congo) and +0.0023 °C·y-1 in the Udzungwa Mountains (Tanzania). Distinct from other forests, both recruitment and mortality were important drivers of thermophilzation in the African plots. The forests studied currently act as a carbon sink, but the consequences of further thermophilization are unclear.

Landform and lithospheric development contribute to the assembly of mountain floras in China

Although it is well documented that mountains tend to exhibit high biodiversity, how geological processes affect the assemblage of montane floras is a matter of ongoing research. Here, we explore landform-specific differences among montane floras based on a dataset comprising 17,576 angiosperm species representing 140 Chinese mountain floras, which we define as the collection of all angiosperm species growing on a specific mountain. Our results show that igneous bedrock (granitic and karst-granitic landforms) is correlated with higher species richness and phylogenetic overdispersion, while the opposite is true for sedimentary bedrock (karst, Danxia, and desert landforms), which is correlated with phylogenetic clustering. Furthermore, we show that landform type was the primary determinant of the assembly of evolutionarily older species within floras, while climate was a greater determinant for younger species. Our study indicates that landform type not only affects montane species richness, but also contributes to the composition of montane floras. To explain the assembly and differentiation of mountain floras, we propose the 'floristic geo-lithology hypothesis', which highlights the role of bedrock and landform processes in montane floristic assembly and provides insights for future research on speciation, migration, and biodiversity in montane regions.

Regional uniqueness of tree species composition and response to forest loss and climate change

The conservation and restoration of forest ecosystems require detailed knowledge of the native plant compositions. Here, we map global forest tree composition and assess the impacts of historical forest cover loss and climate change on trees. The global occupancy of 10,590 tree species reveals complex taxonomic and phylogenetic gradients determining a local signature of tree lineage assembly. Species occupancy analyses indicate that historical forest loss has significantly restricted the potential suitable range of tree species in all forest biomes. Nevertheless, tropical moist and boreal forest biomes display the lowest level of range restriction and harbor extremely large ranged tree species, albeit with a stark contrast in richness and composition. Climate change simulations indicate that forest biomes are projected to differ in their response to climate change, with the highest predicted species loss in tropical dry and Mediterranean ecoregions. Our findings highlight the need for preserving the remaining large forest biomes while regenerating degraded forests in a way that provides resilience against climate change.

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.

The global pattern of epiphytic liverwort disparity: insights from Frullania

The geographical and ecological patterns of morphological disparity are crucial to understand how species are assembled within communities in the context of the evolutionary history, morphological evolution and ecological interactions. However, with limited exceptions, rather few studies have been conducted on the global pattern of disparity, particularly in early land plants. Here we explored the spatial accumulation of disparity in a morphologically variable and species rich liverwort genus Frullania in order to test the hypothesis of latitude disparity gradient. We compiled a morphological data set consisting of eight continuous traits for 244 currently accepted species, and scored the species distribution into 19 floristic regions worldwide. By reconstructing the morphospace of all defined regions and comparisons, we identified a general Gondwana-Laurasia pattern of disparity in Frullania. This likely results from an increase of ecological opportunities and / or relaxed constraints towards low latitudes. The lowest disparity occurred in arid tropical regions, largely due to a high extinction rate as a consequence of paleoaridification. There was weak correlation between species diversity and disparity at different spatial scales. Furthermore, long-distance dispersal may have partially shaped the present-day distribution of Frullania disparity, given its frequency and the great contribution of widely distributed species to local morphospace. This study not only highlighted the crucial roles of paleoenvironmental changes, ecological opportunities, and efficient dispersal on the global pattern of plant disparity, but also implied its dependence on the ecological and physiological function of traits.

Ecological niche conservatism spurs diversification in response to climate change

Lengthy debate has surrounded the theoretical and empirical science of whether climatic niche evolution is related to increased or decreased rates of biological diversification. Because species can persist for thousands to millions of years, these questions cross broad scales of time and space. Thus, short-term experiments may not provide comprehensive understanding of the system, leading to the emergence of contrasting opinions: niche evolution may increase diversity by allowing species to explore and colonize new geographic areas across which they could speciate; or, niche conservatism might augment biodiversity by supporting isolation of populations that may then undergo allopatric speciation. Here, we use a simulation approach to test how biological diversification responds to different rates and modes of niche evolution. We find that niche conservatism promotes biological diversification, whereas labile niches-whether adapting to the conditions available or changing randomly-generally led to slower diversification rates. These novel results provide a framework for understanding how Earth-life interactions produced such a diverse biota.

Deep biogeographic barriers explain divergent global vertebrate communities

Biogeographic history can lead to variation in biodiversity across regions, but it remains unclear how the degree of biogeographic isolation among communities may lead to differences in biodiversity. Biogeographic analyses generally treat regions as discrete units, but species assemblages differ in how much biogeographic history they share, just as species differ in how much evolutionary history they share. Here, we use a continuous measure of biogeographic distance, phylobetadiversity, to analyze the influence of biogeographic isolation on the taxonomic and functional diversity of global mammal and bird assemblages. On average, biodiversity is better predicted by environment than by isolation, especially for birds. However, mammals in deeply isolated regions are strongly influenced by isolation; mammal assemblages in Australia and Madagascar, for example, are much less diverse than predicted by environment alone and contain unique combinations of functional traits compared to other regions. Neotropical bat assemblages are far more functionally diverse than Paleotropical assemblages, reflecting the different trajectories of bat communities that have developed in isolation over tens of millions of years. Our results elucidate how long-lasting biogeographic barriers can lead to divergent diversity patterns, against the backdrop of environmental determinism that predominantly structures diversity across most of the world.

Variation of floristic diversity, community composition, endemism, and conservation status of tree species in tropical rainforests of Sri Lanka across a wide altitudinal gradient

Tropical rainforests in Sri Lanka are biodiversity hotspots, which are sensitive to anthropogenic disturbance and long-term climate change. We assessed the diversity, endemism and conservation status of these rainforests across a wide altitudinal range (100-2200 m above sea level) via a complete census of all trees having ≥ 10 cm diameter at breast height in ten one-hectare permanent sampling plots. The numbers of tree families, genera and species and community-scale tree diversity decreased with increasing altitude. Tree diversity, species richness and total basal area per ha across the altitudinal range were positively associated with long-term means of maximum temperature, annual rainfall and solar irradiance. Percentage of endangered species increased with increasing altitude and was positively associated with cumulative maximum soil water deficit, day-night temperature difference and high anthropogenic disturbance. Percentage of endemic species was greater in the lowland rainforests than in high-altitude montane forests. Nearly 85% of the species were recorded in three or less plots, which indicated substantial altitudinal differentiation in their distributions. Less than 10 individuals were recorded in 41% of the endemic species and 45% of the native species, which underlined the need for urgent conservation efforts across the whole altitudinal range.

Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone

Background

The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.

Methods

We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge.

Results

Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.

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.

Geographical and life-history traits associated with low and high species richness across angiosperm families

Introduction

The phenomenal expansion of angiosperms has prompted many investigations into the factors driving their diversification, but there remain significant gaps in our understanding of flowering plant species diversity.

Methods

Using the crown age of families from five studies, we used a maximum likelihood approach to classify families as having poor, predicted or high species richness (SR) using strict consensus criteria. Using these categories, we looked for associations between family SR and i) the presence of an inferred familial ancestral polyploidization event, ii) 23 life history and floral traits compiled from previously published datasets and papers, and iii) sexual system (dioecy) or genetically determined self-incompatibility (SI) mating system using an updated version of our own database and iv) geographic distribution using a new database describing the global distribution of plant species/families across realms and biomes and inferred range.

Results

We find that more than a third of angiosperm families (65%) had predicted SR, a large proportion (30.2%) were species poor, while few (4.8%) had high SR. Families with poor SR were less likely to have undergone an ancestral polyploidization event, exhibited deficits in diverse traits, and were more likely to have unknown breeding systems and to be found in only one or few biomes and realms, especially the Afrotropics or Australasia. On the other hand, families with high SR were more likely to have animal mediated pollination or dispersal, are enriched for epiphytes and taxa with an annual life history, and were more likely to harbour sporophytic SI systems. Mapping the global distribution of georeferenced taxa by their family DR, we find evidence of regions dominated by taxa from lineages with high vs low SR.

Discussion

These results are discussed within the context of the literature describing "depauperons" and the factors contributing to low and high biodiversity in angiosperm clades.

Angiosperm phylogenetic diversity is lower in Africa than South America

Although originating from a common Gondwanan flora, the diversity and composition of the floras of Africa and South America have greatly diverged since continental breakup of Africa from South America now having much higher plant species richness. However, the phylogenetic diversity of the floras and what this tells us about their evolution remained unexplored. We show that for a given species richness and considering land surface area, topography, and present-day climate, angiosperm phylogenetic diversity in South America is higher than in Africa. This relationship holds regardless of whether all climatically matched areas or only matched areas in tropical climates are considered. Phylogenetic diversity is high relative to species richness in refugial areas in Africa and in northwestern South America, once the gateway for immigration from the north. While species richness is strongly influenced by massive plant radiations in South America, we detect a pervasive influence of historical processes on the phylogenetic diversity of both the South American and African floras.

Africa as an evolutionary arena for large fruits

Strong paleoclimatic change and few Late Quaternary megafauna extinctions make mainland Africa unique among continents. Here, we hypothesize that, compared with elsewhere, these conditions created the ecological opportunity for the macroevolution and geographic distribution of large fruits. We assembled global phylogenetic, distribution and fruit size data for palms (Arecaceae), a pantropical, vertebrate-dispersed family with > 2600 species, and integrated these with data on extinction-driven body size reduction in mammalian frugivore assemblages since the Late Quaternary. We applied evolutionary trait, linear and null models to identify the selective pressures that have shaped fruit sizes. We show that African palm lineages have evolved towards larger fruit sizes and exhibited faster trait evolutionary rates than lineages elsewhere. Furthermore, the global distribution of the largest palm fruits across species assemblages was explained by occurrence in Africa, especially under low canopies, and extant megafauna, but not by mammalian downsizing. These patterns strongly deviated from expectations under a null model of stochastic (Brownian motion) evolution. Our results suggest that Africa provided a distinct evolutionary arena for palm fruit size evolution. We argue that megafaunal abundance and the expansion of savanna habitat since the Miocene provided selective advantages for the persistence of African plants with large fruits.

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927. Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the 'odd man out' pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER, here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.

Global determinants of insect mitochondrial genetic diversity

Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.

Explanations for latitudinal diversity gradients must invoke rate variation

The latitudinal diversity gradient (LDG) describes the pattern of increasing numbers of species from the poles to the equator. Although recognized for over 200 years, the mechanisms responsible for the largest-scale and longest-known pattern in macroecology are still actively debated. I argue here that any explanation for the LDG must invoke differential rates of speciation, extinction, extirpation, or dispersal. These processes themselves may be governed by numerous abiotic or biotic factors. Hypotheses that claim not to invoke differential rates, such as 'age and area' or 'time for diversification', eschew focus from rate variation that is assumed by these explanations. There is still significant uncertainty in how rates of speciation, extinction, extirpation, and dispersal have varied regionally over Earth history. However, to better understand the development of LDGs, we need to better constrain this variation. Only then will the drivers of such rate variation - be they abiotic or biotic in nature - become clearer.

Speciation across the Earth driven by global cooling in terrestrial orchids

Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.

Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line

Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.

Global patterns and climatic determinants of phylogenetic structure of regional fern floras

Knowledge of relationships between phylogenetic structure of a biological assemblage and ecological factors that drive the variation of phylogenetic structure among regions is crucial for understanding the causes of variation in taxonomic composition and richness among regions, but this knowledge is lacking for the global flora of ferns. Here, we fill this critical knowledge gap. We divided the globe into 392 geographic units on land, collated species lists of ferns for each geographic unit, and used different phylogenetic metrics (tip- vs basal-weighted) reflecting different evolutionary depths to quantify phylogenetic structure. We then related taxonomic and phylogenetic structure metrics to six climatic variables for ferns as a whole and for two groups of ferns (old clades vs polypods) reflecting different evolutionary histories across the globe and within each continental region. We found that when old clades and polypods were considered separately, temperature-related variables explained more variation in these metrics than did precipitation-related variables in both groups. When analyses were conducted for continental regions separately, this pattern holds in most cases. Climate extremes have a stronger relationship with phylogenetic structure of ferns than does climate seasonality. Climatic variables explained more variation in phylogenetic structure at deeper evolutionary depths.

The build-up of the present-day tropical diversity of tetrapods

The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.

Landscapes through time

Changes to the landscape over millions of years are a driver of Earth system processes.

Cross-disciplinary information for understanding macroevolution

Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.

Genome-wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa

Although Synsepalum dulcificum is viewed as one of the most economically promising orphan tree crops worldwide, its genetic improvement and sustainable conservation are hindered by a lack of understanding of its evolutionary history and current population structure. Here, we report for the first time the application of genome-wide single nucleotide polymorphism genotyping to a diverse panel of S. dulcificum accessions to depict the genetic diversity and population structure of the species in the Dahomey Gap (DG) and Upper Guinea (UG) regions to infer its evolutionary history. Our findings suggest low overall genetic diversity but strong population divergence within the species. Neighbor-joining analysis detected two genetic groups in the UG and DG regions, while STRUCTURE distinguished three genetic groups, corresponding to the UG, Western DG, and Central DG regions. Application of Monmonier's algorithm revealed the existence of a barrier disrupting connectivity between the UG and DG groups. The Western DG group consistently exhibited the highest levels of nucleotide and haplotype diversities, while that of the Central DG exhibited the lowest. Analyses of Tajima's D, Fu's Fs, and Achaz Y* statistics suggest that while both UG and Central DG groups likely experienced recent expansions, the Western DG group is at equilibrium. These findings suggest a geographical structuring of genetic variation which supports the conclusion of differential evolutionary histories among West African groups of S. dulcificum. These results provide foundational insights to guide informed breeding population development and design sustainable conservation strategies for this species.

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Global models and predictions of plant diversity based on advanced machine learning techniques

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is still incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, and neural networks) and conventional statistical methods (generalized linear models and generalized additive models) to test environment-related hypotheses of broad-scale vascular plant diversity gradients and to model and predict species richness and phylogenetic richness worldwide. To this end, we used 830 regional plant inventories including c. 300 000 species and predictors of past and present environmental conditions. Machine learning showed a superior performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness, illustrating the great potential of such techniques for disentangling complex and interacting associations between the environment and plant diversity. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modeling techniques (ensemble predictions) to reveal global patterns and centers of plant diversity at multiple resolutions down to 7774 km² . Our predictive maps provide accurate estimates of global plant diversity available at grain sizes relevant for conservation and macroecology.

Linking human impacts to community processes in terrestrial and freshwater ecosystems

Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to four fundamental processes that structure communities: dispersal, speciation, species-level selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and responses to impacts, may differ across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesise (i) how the four processes influence diversity and dynamics in terrestrial versus freshwater communities, specifically whether the relative importance of each process differs among ecosystems, and (ii) the pathways by which human impacts can produce divergent responses across ecosystems, due to differences in the strength of processes among ecosystems we identify. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.

Why we should be looking for longitudinal patterns in biodiversity

Our understanding of global diversity patterns relies overwhelmingly on ecological and evolutionary correlates of latitude, and largely ignores longitude. However, the two major explanations of biodiversity patterns – energy and stability – are confounded across latitudes, and longitude offers potential solutions. Recent literature shows that the global biogeography of the Cenozoic world is structured by longitudinal barriers. In a few well-studied regions, such as South Africa’s Cape, the Himalayas and the Amazon-Andes continuum, there are strong longitudinal gradients in biodiversity. Often, such gradients occur where high and low past climatic velocities are juxtaposed, and there is clear evidence of higher biodiversity at the climatically-stable end. Understanding longitudinal biodiversity variations more widely can offer new insights towards biodiversity conservation in the face of anthropogenic climatic change.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

Climate windows of opportunity for plant expansion during the Phanerozoic

Earth's long-term climate may have profoundly influenced plant evolution. Local climatic factors, including water availability, light, and temperature, play a key role in plant physiology and growth, and have fluctuated substantially over geological time. However, the impact of these key climate variables on global plant biomass across the Phanerozoic has not yet been established. Linking climate and dynamic vegetation modelling, we identify two key 'windows of opportunity' during the Ordovician and Jurassic-Paleogene capable of supporting dramatic expansions of potential plant biomass. These conditions are driven by continental dispersion, paleolatitude of continental area and a lack of glaciation, allowing for an intense hydrological cycle and greater water availability. These windows coincide with the initial expansion of land plants and the later angiosperm radiation. Our findings suggest that the timing and expansion of habitable space for plants played an important role in plant evolution and diversification.

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 diversity dynamics in the fossil record are regionally heterogeneous

Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.

Global diversity trends in the fossil record vary regionally through time and space, affecting our ability to interpret macroevolutionary history. Here, the authors propose a method to eliminate spatial sampling bias, estimate origination and extinction rates, and generate diversity estimates, applying this method to the Late Permian to Early Jurassic marine fossil record.

Distribution and Assemblage Variation of Benthic Macroinvertebrates: A Uniform Elevational Biodiversity Pattern Among Different Groups?

Biodiversity patterns along the elevational gradient of vertebrates have been widely focused on in previous studies, but they are still insufficient on invertebrates in lakes to a wide elevational extent. Based on field samplings and literature, we compared biodiversity patterns among different taxonomic groups of benthic macroinvertebrates in 104 lakes of China and India along an elevational gradient of 2–5,010 m a.s.l. and revealed the key driving factors, and then, we discussed the key mechanisms underlying elevational biodiversity patterns. We found that elevational biodiversity patterns of different taxonomic groups were not uniform, e.g., an exponentially decreasing pattern of Bivalvia, a first horizontal and then decreasing pattern of Gastropoda, and a linear decreasing pattern of Oligochaeta and Insecta. Elevation and elevation-controlled variables (temperature and salinity) were the key driving factors to biodiversity patterns. Their effects were strongest on Bivalvia and less on Gastropoda, whereas they were relatively weak on Oligochaeta and Insecta. Finally, we discussed three important mechanisms that shaped elevational biodiversity patterns and assemblage variations of benthic macroinvertebrates by linking our results with the classic hypotheses about biodiversity patterns, including climate/productivity, environmental heterogeneity, and dispersal/history. These results could improve our understanding of biodiversity patterns and biodiversity conservation.