Community ecology has developed a rich and increasingly diverse body of theory, but its rapid expansion has outpaced efforts to compare and synthesize competing frameworks. As a result, semantic ambiguity often masks genuine scientific disagreement. Using theories of species interactions as a lens, I organize this landscape along two axes: formalization (how theories are built) and function (why they are used). Within formalization, I contrast the model-driven culture (which imposes structure) with the data-driven culture (which discovers it), highlighting the distinct forms of misspecification that plague each. Within function, I distinguish three goals: building predictive heuristics, developing definitional frameworks, and running experiments in model worlds. I use this mapping to identify where and why distinct traditions talk past one another, drawing on examples from modern coexistence theory, diversity–stability relationships, niche theory, and network ecology. This analysis provides a diagnostic roadmap for pinpointing why models disagree, justifying the choice of formalization, and aligning questions with appropriate theoretical tools. Beyond diagnosis, I survey current integration efforts and outline practical steps toward synthesis. Finally, I address the human dimension of theoretical practice, arguing that artificial intelligence offers a major opportunity to democratize access to theory if training pivots from derivation to verification. This review lays the groundwork for a conceptual commons where diverse theories can be rigorously compared and productively combined.
Fossil biotic interactions (fBIs) provide a critical but underutilized window into the ecological and evolutionary dynamics of life through time. Unlike modern ecological data, the fossil record captures the long-term consequences of short-term and local interactions, offering insights into biodiversity, extinction, adaptation, and ecosystem function. We review the contributions of the fossil record to studies of biotic interactions, propose a unified framework for reporting fBI data, and outline the interpretative challenges unique to fossils, including taphonomy and the inability to directly observe behavior. This review traces the process of knowledge creation from specimen-level evidence to inferred interactions, highlights insights gained from different fBI types, and advocates for standardized nomenclature and reporting. The fossil record is indispensable for understanding how interactions evolve, collapse, or persist across environmental crises, providing the foundation for linking organismal observations to evolutionary insights on how life has shaped—and been shaped by—biotic interactions.
Eukaryotes show extraordinary diversity in form, function, and behavior, underpinned by a vast range of life history strategies shaped by selection, ancestry, and ecological constraints. Life history theory explains how organisms allocate limited energy and time to survival, growth, and reproduction. Finite resources impose unavoidable trade-offs, preventing the evolution of any single universally optimal life history strategy. Instead, eukaryotes have evolved manifold approaches to solve the problem of persistence. This review explores life history variation across eukaryotes, tracing key developments in life history theory. We synthesize core concepts including trade-offs, environmental variability, and major evolutionary innovations, including multicellularity, sexual reproduction, and life-cycle compartmentalization. To conclude, we highlight critical knowledge gaps and propose future research directions, emphasizing the value of comparative and experimental approaches that more fully span eukaryotic diversity. Integrating micro- and macroevolutionary perspectives, our review provides a concise synthesis of the principles governing life history variation in eukaryotes.
Resolving the ecological and evolutionary processes affecting biodiversity requires long-term community data. By separating short-term variability from directional change and by revealing lags spanning years to decades, these records expose the relative roles of dispersal, environmental filtering, species interactions, and drift, as well as the relevant timescales involved. Across realms, such records show that biodiversity change will frequently concern composition rather than species richness. Across time, the records resolve dynamics such as cycles and evolutionary change invisible to short studies. Long-term records also provide rare windows into eco-evolutionary change, from climate-driven selection on phenology to trait shifts feeding back to coexistence. We integrate insights from flagship sites, monitoring networks, and global databases, highlighting statistical advances that strengthen inference despite imperfect designs. However, the full potential of long-term community data remains underused. Comparative analyses across taxa and regions, together with harmonized sampling and the initiation of new long-term monitoring, are essential to overcome existing biases.
Effective population size ( N e ) is a crucial parameter in the fields of evolutionary biology, conservation biology of endangered species, and selective breeding of domestic animals and crops, as it quantifies the magnitude of genetic drift and inbreeding occurring in a population. Because genetic drift is responsible for the loss of genetic variation and adaptive potential of populations, and inbreeding is known to cause the deterioration of fitness (i.e., inbreeding depression), N e is considered one of the key indicators for assessing the genetic status, adaptive potential, and extinction risks of populations. Different methods have been developed to estimate this parameter, with recent advances made possible using genomic markers generated through genotyping and sequencing projects. This review aims to provide an overview of the methods currently employed to estimate contemporary and recent N e from genomic data and to exemplify these methods by analyzing some simulated and empirical datasets.
The evolution of new genes is a general process across organisms. New genes often have adaptive functions that underlie evolutionary novelties, as suggested by strong signals of positive selection. We review new evidence for a pervasive role of sex-dependent effects in new gene evolution. Recent studies in Drosophila have revealed that intralocus sexual conflict (IASC) is prevalent in the evolution of both new and old genes. Large-scale knockdown experiments in somatic tissues have revealed that most new genes benefit males but harm females, while germline knockdowns have shown that less than half of new genes benefit both sexes. New experimental approaches demonstrate that new genes expressing IASC have become fixed in natural populations and have evolved new reproductive functions. Here, we review recent literature to discuss how IASC, sexual antagonism, germline–soma conflict, and natural selection together drive new gene evolution. We discuss patterns of sequence and functional divergence between new and old genes that underlie broad patterns of genome evolution.
Complex systems are characterized not only by their components but also by the interactions linking them, with megadiverse ecosystems shaping intricate and functionally coupled webs. Yet, Earth's ecological interactome—the whole network of interspecific interactions—remains unexplored, despite efforts at biodiversity monitoring. This interactome, the functional scaffold of the biosphere, sustains crucial ecological processes resulting from interactions of many different types at individual, ecosystem, and global scales. Interactions, governed by species traits, phylogeny, and ecological context, play a stronger role than species identity in maintaining ecosystem functionality. This review synthesizes theory and data on interaction richness, sampling effects, interaction outcomes, and integration of multiple interaction types in multilayer networks at different scales. Emerging approaches aim to infer probabilistic networks with conditional variables (e.g., traits, phylogenetic relationships), accounting for uncertainty arising from spatial and temporal variability. Recognizing that interaction extinctions often precede species loss, conservation strategies must address interaction loss to safeguard network integrity alongside taxonomic diversity.
Kin selection may act directly on individuals expressing a particular trait as well as indirectly through the trait's effect on the fitness of their relatives. This insight has fundamentally transformed our understanding of the evolution of animal behavior—especially social behavior—but it is relevant to any organism in which individuals interact with their relatives, including plants. We here explore how and when kin selection might occur in plants, both through reducing the effects of competition among kin and through promoting the improved performance of kin. We survey plant traits likely to be affected by kin selection, including sex allocation, ovule number, dispersal, seed dormancy, and traits affecting competition. We point to opportunities for future research on kin selection in plants, explain what such research needs to accomplish, and identify limits on the action of kin selection. To conclude, we discuss approaches for detecting kin selection in nature.
Supergenes are clusters of linked loci that control alternative phenotypes involving multiple traits. While an increasing number of supergenes persisting as balanced polymorphisms within populations are being discovered, researchers have more to learn about the forces governing their evolution and long-term maintenance. Historically, supergenes were described as coadapted gene complexes that evolved because suppressed recombination locked beneficial allele combinations together while preventing maladaptive ones. A well-known byproduct of suppressed recombination is the accumulation of deleterious mutations. A less widely recognized consequence of suppressed recombination is that it can protect selfish genetic elements, including various types of transmission ratio distorters. In this review, we synthesize conceptual and empirical evidence connecting supergenes and selfish genetic elements. We show that selfish genetic elements frequently occur in supergenes, potentially promoting their spread but also destabilizing the genetic polymorphism. We conclude that intragenomic conflict plays a major role in the dynamics of supergenes.
Drought, wildfire, wind, insects, and pathogens can interact across space and time to shape forest ecosystems. Although subdisciplines in ecology have long studied individual disturbances, their interactions remain poorly understood, particularly under climate change. Further, inconsistent terminology used to describe these interactions compounds this gap. To address this challenge, we first develop a unifying framework and then review the literature to synthesize climate change effects on the seven classes of forest disturbance interactions. Climate change alters the impacts of disturbance interactions by shifting ( a ) the characteristics of disturbances and ( b ) the effects of interactions when they occur. Many studies document amplifying effects of climate change, and disturbance interactions governed by nonlinearities and positive feedbacks can be particularly transformative in forest ecosystems. In some cases, however, climate change can dampen outcomes of disturbance interactions, which may buffer forests from disturbance impacts. Critically, climate change is expected to increase the frequency of ecosystem transitions worldwide by amplifying the outcomes of complex interactions, particularly coupled feedbacks and network effects. Although there is strong evidence that climate change is modifying some disturbance interactions, they remain an important, yet understudied frontier in ecology.
Kelp forests are under threat worldwide due to a variety of biological and physical factors that include climate change, marine heat waves, storms, coastal development, and overgrazing by sea urchins. This is leading to widespread losses of the important services they provide and an overall reduction in ecosystem value. Chief among these are reductions in the biodiversity of many ecologically and commercially important fishes and invertebrates; lower rates of primary production; altered patterns of seawater chemistry and carbon sequestration; and the loss of biomass that is used for human food, medicine, and industrial and cultural purposes. Therefore, understanding how kelp loss affects these important services and identifying ways to better conserve and restore these iconic forests is of significant economic, social, and ecological concern. This review examines the ecosystem services kelp forests provide and how the loss of these forests affects them. It discusses kelp aquaculture as a potential solution to restore many of these services and explores how advances in our understanding of the kelp microbiome can enhance farming and restoration efforts. It ends with a call for international collaboration in the conservation and restoration of these iconic forests.
Looking back on the Endangered Species Act (ESA) after 50-plus years of implementation reveals a substantial influence on conservation science. The ESA catalyzed science to support listing decisions, species status assessments, a shared understanding of species’ habitats and ranges, threat assessment and recovery planning. However, rising threats to species and limited resources to support recovery have resulted in increasing numbers of imperiled species. Prioritizing investment in biodiversity management requires more interdisciplinary approaches. Emerging research is shifting from objective solution seeking to supporting complex listing decisions based on increasingly complex genetic data to nontraditional management measures like assisted migration. Conservation science has evolved to focus on scales beyond a single species, leading to both new challenges and opportunities in how the ESA can support ecosystem and landscape-scale conservation. The importance of increasingly inclusive management also presents challenges and opportunities for more integrative research to support ESA decision-making.
Understanding the relationships between organism traits and ecosystem processes is crucial for advancing ecological theory and predicting ecosystem responses to environmental change. Fundamental biological functions—metabolism, growth, reproduction—scale predictably with organism size across diverse taxa. Moreover, scaling relationships are pervasive across organizational levels, governing population density, competitive interactions, and trophic food webs. This review synthesizes theoretical and empirical evidence linking organism size to ecosystem processes, highlighting the significance of allometric scaling laws, including the metabolic scaling theory and the energy equivalence rule. It discusses deviations from these predictions due to environmental heterogeneity, biotic interactions, and evolutionary dynamics. By exploring the role of size in modulating functional traits and ecosystem-level outcomes, we emphasize the need for integrated approaches to refine predictive models. This review underscores the centrality of size as a key driver of ecological processes and its implications for biodiversity conservation.
For over 100 years, the deuterostome clade has been one of the few unchallenged branches in the phylogeny of the animal phyla. Deuterostomia includes the echinoderms and hemichordate worms and also our own phylum of chordates. Molecular phylogenies have shown that some other phyla previously linked to deuterostomes by shared morphology and embryology (most notably the chaetognaths or arrow worms) are in fact members of the second major branch of bilaterian animals: the protostomes. Several supposedly deuterostomian characters found in chaetognaths are therefore common to both branches of bilaterian animals, weakening the support for Deuterostomia. Recent studies of molecular data show equivocal support for the deuterostome clade. The deuterostome clade even seems to get some artefactual support from well-known sources of systematic error. The weak and possibly nonexistent support for Deuterostomia has important consequences for our understanding of bilaterian evolution and the origins of the chordates.
Squamates (lizards, including snakes) are the most diverse group of terrestrial vertebrates on Earth today and have an evolutionary history dating back to at least the Middle Triassic (ca. 242 Mya). Despite their vast taxonomic, morphological, and ecological diversity, understanding their origin has remained a challenging and controversial topic for over a century. Initial studies focused on their patchy early fossil record using morphological data, yielding strongly contrasting hypotheses on squamate early evolutionary trajectories. The past decade has seen a massive overhaul of the subject, due to rapid advances in the areas studying phylogenomics, comparative genomics, phenotypic evolution, and new fossil discoveries. Here, we review advances across all of these fields and how they have been bridging hypotheses previously considered irreconcilable, providing a renewed and synthetic understanding of early squamate evolution. We conclude by discussing new datasets and methods behind these advances and perspectives on how the field will move forward for the next decade.
Throughout geological time, an intertwined relationship between ecology and evolution has enabled distant clades to attain gigantism. By synthesizing fossil and modern data, we identify key tipping points in the rise of extreme-sized ocean animals—from early Cambrian arthropods and Ordovician mollusks to Triassic ichthyosaurs, Neogene sharks, and Quaternary whales. We show that ecological opportunities—from vacant niches to shifts in ocean productivity—have promoted the evolution of key adaptations to enhance prey intake, such as predatory appendages, specialized dentition, and baleens, ultimately enabling species to reach extreme sizes. The presence of ocean giants, in turn, has reshaped marine food webs, energy flow, nutrient cycling, and overall ecosystem structure. As such, their extinction or decline can have profound and lasting ecological consequences. Understanding the coevolutionary dynamics between marine giants and their environments is essential for predicting their resilience and conserving their critical roles in ocean ecosystems.
Though previously considered an amniote order of their own, pelycosaurs are now recognized as a basalmost paraphyletic grouping within the Synapsida—the lineage that ultimately led to modern-day mammals. Although they are no longer considered a monophyletic taxon, pelycosaurian-grade synapsids still provide critical insight into the basal amniote condition, including our understanding of the systematics, biology, and ecology of those vertebrates that ultimately completed the water-to-land transition. Whereas the familial designations made almost a century ago have not changed dramatically, interfamilial relationships among pelycosaurs have changed significantly. Recent descriptions of new pelycosaurian taxa demonstrate greater similarity in skull morphology between the most basal members of each family. Paleohistology and craniodental analyses suggest that many features previously thought to be those of the more derived synapsids, the therapsids and mammals, began their development much earlier in pelycosaurs. Furthermore, pelycosaurs have also played key roles in determining that the earliest examples of modern vertebrate terrestrial food webs and ecosystems originated in the early Permian, as long 290 million years ago, and well before the previously suggested middle to late Permian and Mesozoic.
The unique mutualism between male euglossine bees and the perfume flowers they pollinate in tropical America is one of the most iconic plant–pollinator associations, with a rich body of research incorporating chemical ecology, speciation, and natural history. Male bees collect species-specific blends of compounds from the environment to subsequently use during courtship display. As bees exhibit rapidly evolving olfactory preferences, divergence in floral scent causing visitation by different sets of bee species is thought to drive speciation of the plants via pollinator isolation. Here, we synthesize our current understanding of this specialized system, reviewing the extensive literature on chemical production and diversity in these plants with implications for speciation, and discuss broader patterns from biogeographic and macroevolutionary studies in the group. We highlight gaps in knowledge and propose promising future avenues of research.
Hybridization of individuals from genetically differentiated populations causes their genomes to become a mosaic of population ancestries. Widespread availability of genetic markers during the late twentieth century stimulated the development of statistical methods for inferring both recent hybrids and population admixture proportions in individuals. Newer methods focus on population ancestries of chromosomal segments in individuals (local ancestry inference or chromosome painting). We first review established statistical methods for inferring recent hybrids (specifically F 1 , F 2 , and first-generation backcrosses), individual population admixture proportions, and population ancestry of chromosome segments in individuals, focusing on the biological assumptions underlying different methods. We then discuss a canonical population genetic model, the multispecies coalescent with introgression and recombination, that connects the inference of admixture proportions with population ancestries of chromosomes. Finally, we discuss new approaches with prospects for increasing the biological realism of admixture models and improving population ancestry inference on chromosomes using techniques such as deep learning.
Within seasonal temperate forests, changes in precipitation structure—its form, duration, and seasonal timing—is a dominant characteristic of climate change. While past research has focused primarily on annual precipitation totals, emerging evidence shows that short-duration extreme precipitation can impact ecosystem carbon, water, and biogeochemical cycling when it coincides with key phenological and physiological transitions. These impacts are mediated by the responses of plant and microbial physiology, aboveground–belowground interactions, and lagged feedbacks as organisms and communities adjust to these extremes. This review focuses on shifts ( a ) within ecosystem water cycling, ( b ) within tree growth dynamics (carbon uptake and aboveground–belowground allocation and coordination), ( c ) within soil biogeochemical cycling, ( d ) from the loss of winter snow, and ( e ) in forest structure and community composition. Together, these concepts highlight the urgent need to understand how changes in all aspects of precipitation structure reshape the functioning and resilience of mesic temperate forests.
