Nature Ecology & Evolution

Global changes are altering patterns of biodiversity on Earth and species interactions are essential for maintaining this biodiversity. Understanding how interaction networks are shifting in structure and function across time and space provides important insights about the underlying drivers of biodiversity, ultimately improving predictions across scales. Yet lack of interaction data across broad geographic areas and taxa has hindered progress. Birds are ideal taxa to address this shortfall because they are involved in numerous types of positive, negative, and neutral interactions that provide essential ecosystem functions and services. Here we leverage AvianMetaNetwork, a novel and comprehensive database of avian interactions in North America, to quantify six types of network layers using 13,762 pairwise interactions among 687 species from the North American Breeding Bird Survey. Using network modelling, we quantify six decades of bird interaction network shifts, at regional to continental scales. We find that turnover of species abundance since 1970 accounts for the vast majority of changes in trophic and non-trophic interaction networks, and that this turnover results in large changes in network structure and function, especially in eastern North America. Increased human pressures over multiple decades are highly correlated with these trends (especially human intrusion into habitat, infrastructure, and pollution), suggesting that humans are driving these changes. With this metanetwork, we uncovered more than a half century of previously undocumented shifts in the structure of all avian networks at a continental scale, with large implications for the functioning of bird communities and the ecosystems that rely on them.

Nutrient resorption is a key plant strategy for nutrient conservation, yet whether it responds plastically to non-nutrient stressors such as salinity remains unresolved. Using a common garden experiment with 110 genotypes of the cosmopolitan grass Phragmites australis, we first established that the imposed salinity treatment induced strong multi-level stress responses: above-ground biomass declined by >60%, sodium accumulated 3- to 5-fold across all leaf stages, and 484 metabolites showed significant differential accumulation, including canonical markers of osmotic and oxidative stress. Against this backdrop of confirmed stress, we found that nutrient resorption efficiency (NuRE) remained largely unaffected by salinity. Instead, NuRE was strongly correlated with phylogeographic lineage, ecotype, and latitude of origin, demonstrating evolutionary canalization rather than short-term acclimation. Element-specific regulatory patterns were also evident: while phosphorus resorption followed concentration-dependent control regardless of stress, nitrogen control was disrupted under salinity, and potassium resorption showed no such dependence. Our findings reveal that intraspecific variation in nutrient resorption is predominantly shaped by historical adaptation and geographic context, not by plasticity to salinity. This genetic canalization of a key functional trait implies that predictions of nutrient cycling under global change must account for the phylogeographic composition of plant populations.

Nautiloids, the only surviving externally shelled cephalopods, persist in isolated Indo-Pacific reef slopes despite life-history traits that limit dispersal and recovery. Yet the ecological basis of their persistence remains poorly understood. Here, we compare carbon ({delta}13C) and nitrogen ({delta}15N) isotope values from seven nautiloid populations (including Nautilus and Allonautilus) spanning the Pacific. Isotopic niches varied strongly among locations, but only weakly among species, suggesting that geographic context rather than phylogenetic identity is the primary driver of trophic differentiation. Populations from the Bismarck Sea and American Samoa exhibited elevated {delta}15N, consistent with regional nutrient cycling and nitrogen fixation, whereas Great Barrier Reef (GBR) nautiloids displayed unusually broad {delta}13C ranges linked to possible reef-derived carbon subsidies. These results reveal how local oceanography and resource availability shape isotopic niches in long-isolated populations, providing a framework for understanding both the ecological resilience and evolutionary divergence of ancient cephalopods in modern oceans.

The evolution of antibiotic resistance is traditionally understood as a selective sweep to fixation, yielding easily detectable, population-wide resistance. Many clinical isolates, however, exhibit a subtle phenotype in which resistance remains hidden within a susceptible majority despite a clonal genetic background: a phenomenon clinically recognized as heteroresistance (HR). Treatment failure driven by HR has been widely reported across bacterial and fungal infections and in cancer therapy. To understand when and how HR evolves, and why it is selected over classical population-wide resistance, we conducted de novo evolution experiments starting from susceptible Escherichia coli and analyzed the genetic changes and fitness effects in the evolved strains. Prolonged gaps in antibiotic exposure are required for HR to evolve, implicating treatment interruptions as a key driver. HR emerges rapidly and reproducibly with minimal antibiotic use, yet its emergence is not readily detected by routine susceptibility testing. Unlike classical resistance, an evolved HR population partitions at the single-cell level into multiple phenotypes with distinct growth-resistance trade-offs. Their relative abundance shifts dynamically with antibiotic exposure, enabling robust population survival while avoiding the constitutive fitness burden associated with classical resistance. Despite this phenotypic flexibility, stable single mutations including a missense substitution and a short in-frame deletion are sufficient to generate HR, indicating a low evolutionary barrier. Additionally, we found that clinical isolates exhibit genetic and fitness signatures resembling those of our lab-evolved strains, suggesting that clinical HR emerges through the selective mechanism uncovered in our experiments. Together, our results establish HR as a readily evolvable adaptive strategy under treatment interruptions that leverages phenotypic flexibility to maintain resistance at minimal fitness cost, providing mechanistic insight into its emergence and prevalence.

Hybridisation between species was once considered a relatively uncommon occurrence but is now recognised to occur frequently across many different taxa. It can result in homogenisation of previously distinct forms, a potential conservation issue, but can also act as a catalyst for diversification through introgression and sharing of favourable genes. Repeated rounds of island colonisation followed by speciation result in secondary sympatry, with the potential for hybridisation between early and late arrivers. In the southwest Pacific, this situation has arisen in the avian family Zosteropidae (the white-eyes). Here we use whole genome sequencing of live birds and historical specimens to characterise hybridisation between three white-eye species on Norfolk Island: two island endemics, Zosterops tenuirostris and the now-extinct Zosterops albogularis, and Zosterops lateralis, which colonised the island in 1904. Despite over two million years of divergence between Z. lateralis and the two endemics, we provide genomic evidence of their hybridisation. First, we confirm the identities of three Z. lateralis x Z. tenuirostris hybrids and additionally identify one Z. lateralis x Z. albogularis hybrid. We also report asymmetric, genome-wide introgression from both endemics into Z. lateralis, with introgressed regions enriched for a range of potential functions. However, despite this introgression, species boundaries have been maintained, and the extant endemic Z. tenuirostris does not appear to be at risk of genetic extinction. Our work additionally demonstrates an unusual case of recent ghost introgression from the extinct Z. albogularis into Z. lateralis. This study sheds light on the genomic outcomes of secondary sympatry and its potential consequences for single-island endemics.

Our biosphere exhibits remarkable diversity yet is constrained by universal organizational principles, including molecular homochirality. Advances in synthetic biology have raised the possibility of engineering alternative life forms based on mirror-image biomolecules, prompting both technological interest and biosecurity concerns. While current discussions of mirror life largely emphasize molecular feasibility and cellular function, its potential establishment in natural environments remains poorly understood. Here, we develop a theoretical framework to assess the invasion potential of mirror organisms within existing ecosystems. Using population-level models that incorporate resource competition, metabolic constraints, and ecological network interactions, we show that mirror life faces severe limitations arising from both nutrient incompatibility and competitive exclusion by established biota. In particular, the reliance on rare or achiral substrates and the asymmetry of interactions with natural organisms constrain growth and persistence across a broad range of ecological conditions. These results indicate that, beyond engineering challenges, the structure and dynamics of the biosphere itself act as a strong barrier to the spread of mirror life. We conclude that the widespread establishment of mirror organisms in the extant biosphere is highly unlikely, highlighting the importance of ecological constraints in evaluating the risks and feasibility of synthetic life.

All organisms interact with other organisms, directly, and indirectly through different ecological relationships involving multiple types of interactions. Yet at broad continental scales, we lack comprehensive information on biotic interactions, which has hindered our ability to answer macroecological and eco-evolutionary questions across scales and to fully quantify the diversity of biotic interactions as an important dimension of biodiversity. Here, we help fill these gaps with an open and comprehensive dataset and data workflow of 25,907 pairwise, directional interspecific interactions among birds spanning a continental scale. All data are empirically documented and comprise bird-bird interactions across both breeding and non-breeding ranges of 731 focal avian taxa, covering all birds in the focal region of Canada and the continental United States, including Alaska. These data also include 1,258 additional avian taxa interacting with the focal taxa outside the focal region, resulting in 1,989 avian taxa altogether. The continental scale and breadth of interspecific interactions within these data fill fundamental knowledge gaps and enable scientists and practitioners to address a myriad of questions at broader scales than were previously possible.

Forecasting zoonotic risk requires identifying which host species are biologically susceptible to infection, yet susceptibility is rarely predicted using frameworks that integrate molecular mechanisms with macroecology. Filoviruses, a diverse group of bat-associated viruses that include Ebola and Marburg viruses, illustrate this challenge: viral entry depends on interactions between viral glycoproteins and the host receptor NPC1, and host ecology and distribution determine opportunity of viral entry. Additionally, receptor sequence data used for informing viral entry are available for only a small fraction of bat species. Here, we extend virus-specific susceptibility prediction across the global diversity of bats by integrating experimentally measured and physicochemically inferred virus-receptor binding strengths with phylogenetic, ecological, and environmental data. Using boosted regression models trained on binding assay labels, we generate predictions of NPC1-mediated binding strength for more than 1,300 bat species. Predicted susceptibility is strongly structured by evolutionary relationships, with high binding concentrated in particular bat lineages, but is further differentiated within clades by morphology, life-history strategy, and environmental context. Strikingly, macroevolutionary structure alone recovers interaction patterns originally derived from amino acid-level physicochemistry, indicating that information about receptor-mediated compatibility is recoverable from host evolutionary history and ecological traits. Predicted high binding strength extends well beyond historically recognized outbreak regions, suggesting that the fundamental host range of filoviruses may be substantially broader than their currently realized distribution. By scaling receptor biology to global host diversity, this multi-scale framework expands mechanistic susceptibility forecasting beyond species with available molecular data and provides a generalizable approach for integrating molecular and ecological information in zoonotic prediction.

Innovation of the avian beak has facilitated a grand radiation of >11,000 species, with vast morphological disparity suggesting limited developmental constraints on beak diversification. We assess four macroevolutionary currencies - integration, disparity, phenotypic evolutionary rates, and ecological specialization - using 3D beak landmarks for 8,627 species mapped to a complete avian supertree with a resolved genomic backbone. We introduce a Gini coefficient-based metric of ecological specialization, measuring evolutionary time spent across trophic niches. Phylogenetic regressions show that lineages with faster phenotypic rates exhibit stronger beak integration (landmark covariation) and more generalised diets, while beak disparity declines with greater trophic specialization. These results suggest that integration facilitates, rather than constrains, phenotypic evolution, by channeling variation along lines of least resistance. Future work should explore modular structure of the bird beak, which arises from multiple genetic and developmental factors.

Ecological specialization emerges when adaptation to a focal context increases fitness in that context relative to others. Experimental evolution has been widely used to study microbial specialization in abiotic environments but not predatory specialization. Here we demonstrate evolutionary specialization by a bacterial predator and characterize associated diversification of its predation profile. Populations of the bacterium Myxococcus xanthus evolving on single, non-evolving prey species diverged in predatory performance, showing increased performance on their home prey relative to their common ancestor, and relative to foreign prey not encountered during adaptation. Adaptation to the single-prey environments resulted in striking radiation of performance profiles across a diverse panel of foreign prey that was shaped interactively by selection, chance, and indirect effects, with home-prey identity modulating the degree of stochastic indirect diversification. Despite a great diversity of indirect evolutionary effects, correlated evolution was net-positive, yielding positive predatory specialization as the general outcome. Genomic evolution mirrored phenotypic evolution in that degrees of genomic parallelism differed as a function of home-prey identity. These findings show that adaptation to even simple biotic conditions can generate great ecological and behavioral diversity, linking direct selection, deterministic indirect effects of adaptation, stochasticity, and the origins of predator specialization and diversification.

As global temperatures rise, ecological communities are increasingly dominated by warm-affiliated species, a process known as community warming or thermophilisation. Yet, why different taxa exhibit different rates of community warming remains unclear. Habitat composition and structure are likely drivers of this variation, as the ecological consequences of warming are filtered by local environmental conditions. Using over 40 years of monitoring data spanning terrestrial (birds, insects, plants) and freshwater (phytoplankton) communities, we show that habitat structure determines how strongly communities track warming. Forest cover systematically slows thermophilisation by reducing communities sensitivity to temperature change, whereas habitat heterogeneity has weak and variable effects that differ among ecosystems. Together, these results demonstrate that uneven thermophilisation arises from habitat-mediated differences in how communities respond to a shared climatic signal. Incorporating these effects is essential for improving predictions of biodiversity change under ongoing climate warming.

Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, and complex behaviors. Most evolutionary studies of cephalopods have compared individual genomes of taxa that diverged tens to hundreds of millions of years ago, yet very few have examined more recent evolution from a population genetics perspective. Here we present a comparative population genomic analysis of the sympatric sister species Octopus bimaculatus and Octopus bimaculoides using whole-genome resequencing. Despite similar morphologies, these species differ substantially in their life histories, ecologies, and geographic distributions. Using demographic inference, we estimated that the two species diverged approximately one million years ago and that O. bimaculatus has maintained a consistently larger effective population size since divergence. Consistent with these demographic histories, we found stronger signatures of positive selection in O. bimaculatus, including a positive correlation between recombination rate and nucleotide diversity, more selective sweeps, and a higher proportion of mutations fixed by adaptation--all consistent with more efficient natural selection in larger populations. Protein-coding genes overlapping with selective sweeps were enriched for various functions that included many related to brain and eye development, suggesting that traits characteristic of coleoid cephalopods continue to be shaped by positive selection on recent timescales in these species. Comparing coding-sequence divergence on the Z chromosome to the autosomes, we also find evidence for a female-biased mutation rate, consistent with an independent estimate from a deeper-timescale cephalopod comparison.

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

Auxotrophy, the absence of biosynthetic capacity for essential metabolites, is widespread in microbes and is thought to shape interactions within communities. Auxotrophies are often treated as fixed properties of organisms; however, recent evidence indicates that auxotrophic phenotypes can depend on environmental context, thereby affecting community assembly or cross-feeding. Here, we systematically quantify how nutrient environments shape both auxotrophy and cross-feeding. Using matched sets of six amino acid auxotrophs in Escherichia coli and Bacillus subtilis, we measured monoculture and pairwise coculture growth across 40 carbon and nitrogen environments. We find that auxotrophy itself is highly environment dependent, with strains growing in a substantial fraction of amino acid-free conditions despite lacking key biosynthetic enzymes. Cross-feeding likewise varies widely across species, environments, and auxotroph pairs. Despite this variability, cross-feeding outcomes exhibit consistent patterns across species. In particular, cross-feeding growth is better predicted by auxotroph type (i.e., which amino acids the strain requires) than by environmental context. A machine-learning model recapitulates this pattern, identifying auxotroph type as the strongest predictor of cross-feeding growth, exceeding the contributions of nutrient environment, prototroph growth, and species identity. Together, these results show that environmental context reshapes both metabolic need and exchange, yet cross-feeding follows emergent patterns linked to auxotrophy. More broadly, our findings suggest that metabolic interdependence is shaped by both gene essentiality in an environmental context and intrinsic constraints of metabolic pathways, with implications for community assembly and the evolution of gene loss.

Genetic variation is the raw material for evolution. One source of variation is chromosomal rearrangements, which can bring genes together and form genetic linkage. Rearrangements can also suppress recombination and gene flow, as in the case of sex chromosome evolution. We conducted the first population genomic study of the red harvester ant Pogonomyrmex barbatus to investigate genomic rearrangements that differentiate the lineages J1 and J2 in the "dependent-lineage system" (also known as "social hybridogenesis"). In this unusual reproductive system, males and females from different lineages mate to create hybrids, yet these hybrids develop into sterile offspring (workers), and so the two lineages remain reproductively isolated. We sequenced high-quality reference genomes for the two lineages to search for a potential explanation of the suppression of gene flow between them. Comparison of the two genome assemblies revealed multiple large-scale genomic rearrangements, all of which occurred in the J1 lineage. The rearrangements formed some of the largest J1 chromosomes, including the largest scaffold in the assembly that was formed by at least two translocation events and additional intra-chromosomal rearrangements. The translocations brought together 118 odorant receptor (OR) genes on this rearranged chromosome, 44 of which are 9-exon ORs, which are implicated in chemical communication in ants. We also identified an enrichment of transposable elements in a large synteny gap between the translocated segments. The discovery of multiple translocations that formed large rearranged chromosomes provides a potential explanation for the reproductive isolation between the pair of dependent lineages in this system, and opens the way for the study of the molecular genetic basis of an intriguing evolutionary phenomenon in these and in other ant lineages.

Beetles (Coleoptera) represent the most species-rich group of organisms, yet the macroevolutionary processes underlying their exceptional diversification remain unresolved. Here, we estimated their origination and extinction dynamics as well as the potential drivers shaping these patterns, using Bayesian birth-death models applied to a comprehensive fossil occurrence dataset. We find that beetles have experienced low extinction rates and exhibited high resilience through major extinction events. Vascular plant diversities emerge as a key driver of beetle diversification, with origination rates positively correlated with angiosperms, and extinction rates negatively correlated, especially for Polyphaga, the most diverse beetle clade. Together, our results provide quantitative evidence that the angiosperm radiation not only promoted beetle origination, but also buffered them against extinction, illustrating how ecological interactions can shape macroevolution.

Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a [~]20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system (CNTNAP2) and reproductive development (FSHR). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

The 36 global biodiversity hotspots harbor a disproportionate share of the worlds endemic species, making their conservation critical for planetary health. Traditionally hotspots were defined as ecoregions with [≥]1,500 endemic vascular plant species and >70% natural habitat loss; this relied heavily on expert judgment, with subjective assessments of endemism and habitat loss applied. Challenges in defining endemism, quantifying habitat loss, and the global unevenness in available vascular plant data have hindered hotspot identification over the past decades. Here, we built a global dataset of 150,487 rare vascular plants, identified from 88.1% of the worlds known vascular species, and recognize hotspots based on their richness using three complementary conservation targets and algorithms. We then quantified natural habitat loss and habitat fragmentation using high-resolution remote sensing data and assessed the diversity and distribution of terrestrial vertebrates within these newly identified hotspots. Our data-driven method recovered all the 36 established global biodiversity hotspots, revised 17, and identified 11 new hotspots spanning diverse ecosystems across six continents. These 47 hotspots cover 26.63% of global land area, yet contain 83.8% of rare vascular plants, 92.4% of mammals, 96.1% of birds, 87.8% of reptiles, and 95.0% of amphibians. Collectively, they encompass >89% of terrestrial vertebrates classified as IUCN threatened species. Only 10 hotspots have undergone [≥]70% habitat loss, and the lack of a consistent relationship with habitat fragmentation suggests that this criterion is not globally applicable. Effectively protecting [~]27% of Earths land could theoretically safeguard >89.8% of threatened terrestrial species and >67% of threatened terrestrial species hotspot area, assuming effective protection of the identified biodiversity hotspots. Targeted conservation efforts within these global biodiversity hotspots can meet the established biodiversity targets of the Kunming-Montreal Global Biodiversity Framework as well as post-2030 biodiversity targets. Most importantly, our framework enables conservation scientists to iteratively identify and update global biodiversity hotspots in step with growing global biodiversity data.

Understanding how genome-wide divergence translates to barriers to gene flow is a central question in speciation research, particularly in marine environments where interconnected habitats frequently accommodate cryptic diversity. Using linked-read whole-genome data from the brown alga Ectocarpus, we investigated genome-wide reproductive isolation between two cryptic brown algal species E. siliculosus and E. crouaniorum across replicated hybrid zones in Europe and Chile. We first uncover deep genetic structure within E. crouaniorum, revealing a more intricate species complex than previously recognized. Despite this complexity, we found parallel patterns of asymmetric introgression that emerged independently in Europe and Chile, where we detected both, F1 and low-level introgressed individuals. However, the specific lineage pairs involved in hybridization depended on local demographic history. Demographic modeling further indicated that reproductive isolation strengthens gradually with divergence time and differs markedly between geographic regions, with ongoing asymmetric gene flow even between lineage pairs where hybrids were not detected in the field. In all cases, the genomic landscape of hybridization is consistent with a polygenic, genome-wide barrier to gene flow rather than a few large-effect regions. Our results show that cryptic speciation in brown algae is driven by repeatable, regionally parallel architectures of genome-wide reproductive isolation which is shaped by ecological and demographic context.

Effective biodiversity conservation requires tools that can identify priority areas under growing human pressures. Building on the concept of global biodiversity hotspots, we present a transparent and repeatable approach to mapping conservation priorities using data for 33,604 species of terrestrial vertebrates from the IUCN Red List. This framework expands the taxonomic scope of previous efforts and integrates updated information on key human-driven threats to biodiversity. We identify that around 13% of Earths terrestrial surface qualifies as vertebrate conservation hotspots, often shaped by distinct combinations of species groups and threats. These results highlight the need for tailored, context-specific conservation strategies. By providing a robust method to guide spatial prioritization, our work supports more effective implementation of conservation targets in a rapidly changing world.