Nature Ecology & Evolution

The sprawling-parasagittal postural transition is a key part of mammalian evolution, associated with sweeping reorganization of the postcranial skeleton in mammals compared to their forebears, the non-mammalian synapsids. However, disputes over forelimb function in fossil synapsids render the precise nature of the sprawling-parasagittal transition controversial. We shed new light on the origins of mammalian posture, using evolutionary adaptive landscapes to integrate 3D humerus shape and functional performance data across a taxonomically comprehensive sample of fossil synapsids and extant comparators. We find that the earliest pelycosaur-grade synapsids had a unique mode of sprawling, intermediate between extant reptiles and monotremes. Subsequent evolution of synapsid humerus form and function showed little evidence of a direct progression from sprawling pelycosaurs to parasagittal mammals. Instead, posture was evolutionarily labile, and the ecological diversification of successive synapsid radiations was accompanied by variation in humerus morphofunctional traits. Further, synapsids frequently evolve towards parasagittal postures, diverging from the reconstructed optimal evolutionary path; the optimal path only aligns with becoming increasingly mammalian in derived cynodonts. We find the earliest support for habitual parasagittal postures in stem therians, implying that synapsids evolved and radiated with distinct forelimb trait combinations for most of their recorded history.

Virulent pathogens commonly circulate in wildlife populations without causing mass mortality; the triggers of die-offs remain poorly understood. Prevailing frameworks emphasize individual host susceptibility, yet experimental manipulations of susceptibility factors often fail to predict population-level outcomes. We tracked ranavirus epizootics across 40 wood frog breeding ponds over three years, comparing lagged viral state variables against abiotic and host predictors at each epizootic stage. Lagged viral state--environmental DNA concentration and infection prevalence--outperformed abiotic and host predictors of transmission, intensification, and viral accumulation. Infected hosts shed virus into the water column throughout epizootics, but the reciprocal pathway, environmental virus driving new and more severe infections, activated only at the transition to die-off, consistent with a self-reinforcing feedback. The rate of viral accumulation discriminated die-offs, while no static pond or host feature was predictive, reframing mass mortality as an emergent property of pathogen accumulation in shared environments rather than of individual host susceptibility.

Animals moving through landscapes need to strike a balance between finding sufficient resources to grow and reproduce while minimizing encounters with predators 1,2. Because encounter rates are determined by the average distance over which directed motion persists 1,3-5, this trade-off should be apparent in individuals movement. Using GPS data from 1,396 individuals across 62 species of terrestrial mammals, we show how predators maintained directed motion ~7 times longer than for similarly-sized prey, revealing how prey species must trade off search efficiency against predator encounter rates. Individual search strategies were also modulated by resource abundance, with prey species forced to risk higher predator encounter rates when resources were scarce. These findings highlight the interplay between encounter rates and resource availability in shaping broad patterns mammalian movement strategies.

Climate change is shifting when animals breed1,2, but it is still not clear why some populations keep pace with warming while others fall behind3,4. Differences could arise from variation in sensitivity to temperature3 or constraints on the ability to respond to temperature. Without knowing whether populations differ in sensitivity--or in their ability to act on that sensitivity--we cannot identify which are most at risk. Using 1,555 population-years from 123 populations of tree swallows (Tachycineta bicolor), we show that populations have similar sensitivity to local temperature, advancing breeding by about one day per degree of warming. However, northern populations face tighter time constraints and greater exposure to recent warming. Northern populations have advanced laying dates the most, but still experience stronger selection for earlier breeding, especially in warm years; they have also declined most in breeding abundance. These findings show that vulnerability to climate change can arise not just from different sensitivity to warming, but from when and where populations can respond effectively. By disentangling sensitivity from timing constraints, our results support a general mechanism by which even uniformly responsive species can show uneven impacts of climate change across their ranges.

Bacteriophages (phages), viruses that exclusively infect bacteria, coexist with their bacterial hosts across diverse environments at densities exceeding 107 ml-1 in marine surface waters, 108 ml-1 in soils, and 109 ml-1 in the human gut1-6. In contrast, phage lysis of bacteria populations within well-mixed in vitro environments select for the emergence of phage-resistant bacterial mutants7, which in turn select for host-range expansion phage mutants8, leading to the emergence of complex cross-infection networks9, and eventually the collapse of phage populations altogether10,11. This gap in outcome raises a question: what enables long-term phage-bacteria coexistence? Here, we show how interactions in space can facilitate stable coexistence and long-range transport of virulent phage along with migrating bacteria. Through the joint use of theory, simulation, and experiments across multiple phage-bacteria systems, we reveal a chemotaxis-driven mechanism which robustly stabilizes coexistence and dispersal of virulent phages with migrating hosts, while minimizing the potential for coevolutionary-induced collapse of either bacteria or phage. These findings suggest the ecological relevance of spatial interaction mechanisms that reinforce stability between antagonistic partners, in the absence of perpetual cycles of defense and counter-defense, that may be broadly applicable across phage-bacteria systems.

Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasites infective stages, as well as the hosts ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modeling at a regional scale, we uncovered the biotic and abiotic drivers of a lethal infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water--i.e., the propagule pressure-- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts--i.e., proxies for disease emergence--were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by compromising the hosts ability to fight the parasite. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on disease emergence.

Top-down and bottom-up controls of animal populations are well-known elements of niche and coexistence theories, but there is little empirical evidence on how these forces determine species distribution and community assemblies. In Arctic ecosystems, spring snowmelt sets the timing and duration of the snow-free period, thereby controlling food availability, while predation often imposes additional control on prey species. The relative importance of abiotic and biotic filters on distribution is also susceptible to vary with body size. Using 10-years of high-resolution data on all major members of an Arctic vertebrate community and their shared predator, we tested how snowmelt timing interacts with predation to shape species occurrence and community structure. Species occurrence declined with later snowmelt dates, with larger-bodied species being particularly constrained by short snow-free periods. Predation further modulated species occurrence, with responses varying according to body mass. Our findings highlight the combined influence of the phenology of food availability and predation as important filters shaping local community structure. Building on species contrasted responses, we propose a conceptual framework for how phenological constraints and predation jointly shape community assembly in highly seasonal environments.

Olfactory receptors (ORs), which mediate chemical detection in vertebrates, constitute a highly dynamic and ecologically responsive gene family. While OR evolution has been well studied in fully terrestrial and aquatic lineages, its dynamics in amphibious vertebrates remain less explored. Species that occupy both aquatic and terrestrial habitats span a broad phylogenetic and ecological range--from amphibians to freshwater-dwelling mammals, semi-aquatic reptiles, and shoreline birds--and are subject to the functional demands of odour detection across two chemically disparate milieus. Here, we analysed OR gene repertoires across 230 vertebrate genomes, including 138 amphibious species. Our results show that OR repertoire expansion is not a uniform feature of terrestrial adaptation but is most pronounced in amphibious lineages, particularly those inhabiting freshwater systems, where chemically variable environments likely impose stronger selective pressures on olfaction. These expansions are primarily driven by lineage-specific expansions and correlate with ecologies that require sensing a wide range of chemical cues. While amphibious marine taxa possess larger OR repertoires than their fully marine relatives, they consistently exhibit fewer ORs than freshwater amphibious vertebrates. More broadly, species that rely on other sensory modalities--such as echolocation, electroreception, or vision--tend to exhibit reduced OR repertoires. Despite this diversity, several amphibious and terrestrial species within the same clade retain a small subset of shared OR genes, reflecting the retention of conserved OR orthologs--potentially those tuned to airborne odorants--across habitat transitions. However, overlap across clades is minimal, reflecting independent evolutionary responses to similar ecological pressures. Overall, our findings highlight amphibious lifestyles as key inflection points in vertebrate olfactory evolution--driving both OR repertoire expansion and divergence through the interplay of habitat complexity, sensory trade-offs, and lineage-specific constraints.

Ecological communities are assembled by colonization and extinction events, that may be regulated by ecological niches1-5. The most parsimonious explanation of local community assembly is the Dynamic Equilibrium (DE) model, which assumes that community dynamics is shaped by random colonization and extinctions events, effectively ignoring the effects of niches1, 6. Despite its empirical success in explaining diversity patterns1, 5, 7, it is unknown to what extent the assembly dynamics of communities around the globe are consistent with this model. Using a newly developed methodology, we show that in 4989 communities from 49 different datasets, representing multiple taxa, biomes and locations, changes in richness and composition are larger than expected by DE. All the fundamental assumptions of DE are violated, but the large changes in species richness and composition primarily stem from the synchrony in the dynamics of different species. These results indicate that temporal changes in communities are predominantly driven by shared responses of co-occurring species to environmental changes, rather than by inter-specific competition. This finding is in sharp contrast to the long-term recognition of competition as a primary driver of species assembly8-12. While ecological niches are often thought to stabilize species diversity and composition4, 13, 14, we found that they promote large changes in ecological communities.

Elemental composition links organismal physiology to biogeochemical cycles, yet the relative importance of evolutionary and ecological drivers remains unresolved for insects. Integrating a global stoichiometric database with a comprehensive phylogenetic backbone, we demonstrate hierarchical control of insect stoichiometry, with phylogeny accounting for [~]50% of variation in C:N:P ratios, followed by temperature, body mass, trophic group and habitat. We also identify nutrient enrichment in terrestrial lineages relative to aquatic ones. Our work offers a general framework for partitioning evolutionary, ecological, and physiological influences on organismal stoichiometry, highlighting new avenues to link macroevolutionary patterns to underlying processes.

Introduced large herbivores have partly filled ecological gaps formed in the late Pleistocene, when many of the Earths megafauna were driven extinct. However, surviving predators are widely considered unable to influence introduced megafauna, leading them to exert unusually strong herbivory and disturbance-related effects. We report on a behaviorally-mediated trophic cascade between cougars (Puma concolor) and feral donkeys (Equus africanus asinus) at desert wetlands in North America. In response to predation of juveniles, donkeys shifted from nocturnal to almost exclusively diurnal, thereby avoiding peaks in cougar activity. Furthermore, donkeys reduced the time they spent at desert wetlands by 87%: from 5.5 hours a day to 0.7 hours at sites with predation. These shifts in activity were associated with increased activity and richness of other mammal species and reduced disturbance and herbivory-related effects on these ecologically-distinct wetland ecosystems, including 49% fewer trails, 35% less trampled bare ground, and 227% more canopy cover. Cougar predation on introduced donkeys rewires an ancient food web, with diverse implications for modern ecosystems.

How macroevolution interacts with ecological networks remains a major question in eco-evolutionary science. We investigate this interplay in the Naesiotus snail radiation of the Galapagos Islands, which encapsulates parasitic nematodes within the shell--a recently discovered gastropod defense. Using a natural history collection, we examined dry shells from 47 species across 12 islands, quantified encapsulations, and sequenced nematode DNA to reconstruct a host-parasite network. Encapsulations were widespread and revealed high nematode diversity, including in snail hosts presumed extinct. Nematode diversity was shaped by habitat, while encapsulation load was better explained by host species identity, suggesting species-specific defenses. Neither trait showed phylogenetic signal, and shell brightness was unrelated to nematode interactions. Similarly, host diversification rate did not predict network position, suggesting that macroevolution may leave a weak or obscured imprint on this host-parasite network. This snail-nematode system in islands readily enables integration of ecological networks, phylogeny, functional traits, and biogeography.

A mass extinction at the end of the Devonian is thought to have had a major influence on the evolution of actinopterygians (ray-finned fishes), which comprise half of living vertebrates. This extinction appears to have acted as a bottleneck, paring the early diversity of the group to a handful of survivors. Coupled with increases in taxonomic and morphological diversity in the Carboniferous, this contributes to a model of explosive post-extinction radiation. However, most actinopterygians from within a ~20-million-year (Myr) window surrounding the extinction remain poorly known, contributing to uncertainty about these patterns. An exceptionally preserved fossil of a diminutive fish from 7 Myr before the extinction reveals unexpected anatomical features that suggest a very different story. This new fossil nests within a clade of post-Devonian species and, in an expanded phylogenetic analysis, draws multiple lineages of Carboniferous actinopterygians into the Devonian. This suggests cryptic but extensive lineage diversification in the latest Devonian, followed by more conspicuous feeding and locomotor structure diversification in the Carboniferous. Our revised model matches more complex patterns of divergence, survival, and diversification around the Devonian-Carboniferous boundary in other vertebrate clades. It also fundamentally recalibrates the onset of diversification early in the history of this major radiation.

Earth is home to over 350,000 vascular plant species1 that differ in their traits in innumerable ways. Yet, a handful of functional traits can help explaining major differences among species in photosynthetic rate, growth rate, reproductive output and other aspects of plant performance2-6. A key challenge, coined "the Holy Grail" in ecology, is to upscale this understanding in order to predict how natural or anthropogenically driven changes in the identity and diversity of co-occurring plant species drive the functioning of ecosystems7, 8. Here, we analyze the extent to which 42 different ecosystem functions can be predicted by 41 plant traits in 78 experimentally manipulated grassland plots over 10 years. Despite the unprecedented number of traits analyzed, the average percentage of variation in ecosystem functioning that they jointly explained was only moderate (32.6%) within individual years, and even much lower (12.7%) across years. Most other studies linking ecosystem functioning to plant traits analyzed no more than six traits, and when including either only six random or the six most frequently studied traits in our analysis, the average percentage of explained variation in across-year ecosystem functioning dropped to 4.8%. Furthermore, different ecosystem functions were driven by different traits, with on average only 12.2% overlap in significant predictors. Thus, we did not find evidence for the existence of a small set of key traits able to explain variation in multiple ecosystem functions across years. Our results therefore suggest that there are strong limits in the extent to which we can predict the long-term functional consequences of the ongoing, rapid changes in the composition and diversity of plant communities that humanity is currently facing.

The drivers of community coexistence are known to vary with environment, but their consistency across latitudes and scales, and resulting conservation implications, remain little understood. Here, we combine functional and phylogenetic evidence along elevations to document strong biotic constraints on coexistence in avian communities in both benign (tropical low elevations) and severely harsh (temperate/polar highlands) environments. Assemblages in both are marked by high assemblage functional uniqueness, whereas in tropical highlands and temperate/polar low elevations there is strong functionally redundancy and pronounced environmental constraints. Only in harsh environments is phylogeny an effective surrogate for functional assemblage structure, reflecting nuanced shifts in the position, shape, and composition of measured multivariate trait space along gradients. Independent of scale and latitude, high elevation assemblages emerge as exceptionally susceptible to functional change.

Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar. Additionally, we highlight the role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique phenotypic combinations and ecology. These results highlight the role of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation.

Islands harbor a disproportionate share of global biodiversity1, yet insects, even invaluable pollinators such as bees2, remain underrepresented in island biogeography research3. Here, we present the first global checklist of island bees, recording 4,140 species across 306 islands. Although islands comprise only [~]5% of Earths land area, they support [~]20% of global bee diversity, and 43% of insular species are endemic, making up [~]8% of all known bee species. Island bee species richness, mirroring continental trends4, peaks at mid-latitudes. Native richness increases with island area and declines with isolation, consistent with patterns in other taxa5. The strength of species-area relationships varies among biomes and is steepest in mediterranean-type systems, which also support disproportionately high bee richness relative to flowering plant diversity. Endemism is highest on large tropical islands, reflecting extensive in situ diversification. Major centers of bee endemism include Madagascar, Malesia (e.g. the Greater Sundas and New Guinea), and Hawaii, where a single large radiation of Hylaeus (Nesoprosopis) dominates6. Among islands capable of supporting endemic species, endemism scales strongly with total richness. These findings highlight the need to integrate island bee diversity into global conservation planning and position bees as a model for understanding insect evolution and conservation on islands.

Ecological and evolutionary processes shape the dynamics of species interactions, yet the drivers of eco-evolutionary feedback remain elusive. Here, we developed an individual-based model of a coevolving predator-prey-parasite system, in which predators can be infected by trophically transmitted parasites. We combined host-parasite coevolution with prey-predator interactions at an individual level, hence integrating evolutionary and ecological processes. We show that species coexist more when parasite-mediated selection is weak on both the predator and the prey. Population size and genotypic diversity of the parasite are highest at intermediate parasite-mediated selection on the predator and no parasite-mediated selection on the prey. Interestingly, we show that the evolution of super-resistant genotypes, where host genotypes have resistant alleles in all loci, is driven by interspecific interactions rather than by the population size of the host species. Overall, host-parasite coevolution shapes the direction of interspecific ecological interactions which, in turn, determine species coexistence and community diversity in a complex system.

The species abundance distribution (SAD) is one of the most fundamental and best-studied macroecological patterns at the core of any biodiversity theory. Remarkably, almost every community investigated to date shows a hollow curve, indicative of the presence of many rare species and a few abundant species. While the precise nature of SAD is believed to reflect fundamental ecological processes underlying community assembly, ecologists have yet to identify a single model that comprehensively explains all SADs. Recent studies using large datasets suggested that logseries best describes animal and plant communities1,2 while lognormal is the best model for microbes3, thereby challenging the notion of a unifying SAD model across the tree of life. Using a large dataset of [~]30,000 globally distributed communities spanning animals, plants and microbes from diverse environments, here we show that powerbend distribution, predicted by a maximum information entropy-based theory of ecology, emerges as a unifying model that accurately captures SADs of all life forms, habitats and abundance scales, supporting the existence of universal ecological principles. Our findings reject the notion of pure neutrality and support the idea that community assembly is driven by both random fluctuations and deterministic mechanisms, such as interspecific trait variation and resource competition. We also show that the previously estimated one trillion microbial species existing on Earth might be orders of magnitude off.

Species vulnerability to climate change depends in part on their capacity to evolve in response to increasing heat1. Within terrestrial ectotherms, heat tolerance generally corresponds weakly to current climates, which has led many to conclude that this trait is evolutionarily constrained2-4. However, most studies have not accounted for the role of microclimates, potentially obscuring signals of local adaptation. We examined heat tolerance in 95 species of wild bees that varied in nesting behaviour across the latitudinal extent of Australia. Species nest (ground, wooden cavities, or plant stems) micro-climate temperatures predicted heat tolerance evolution, where stem nesters evolved the highest heat tolerances, and ground nesters evolved the lowest heat tolerances due to their ability to evade extreme heat. A moderate level of phylogenetic inertia in heat tolerance was explained by patterns of related species sharing nesting behaviours. This indicated repeated adaptive evolution of similar heat tolerances, rather than strong evolutionary constraints on heat tolerance. Finally, incorporating nesting behaviour into assessments of climate change vulnerability changed the rank order of which species were most at risk. This underscores the need to understand what drives the evolution of heat tolerance across species to better identify the taxa most at risk to climate change.