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bioRxiv2023

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,049 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation. One-Sentence SummaryA nearly complete genomic catalog of the yeast subphylum illuminates the evolution of their diverse ecologies and metabolisms.

evolutionary biology↗

bioRxiv2023

Ecological network inference is not consistent across sales or approaches

Identifying the most suitable method of ecological network inference in line with individual research considerations is a non-trivial task, which significantly hinders adoption of network approaches to forest management applications. To advance the study of ecological networks and better guide their use in managing forest ecosystems, we propose a framework that aligns pairwise species-association inference methods with specific research questions, biological interaction types, data availability, and spatial scales of study. We motivate the adoption of this framework through an empirical comparison of multiple inference methods, highlighting substantial inconsistencies that arise across scales and methodologies. Using data on species distributions and attributes at local, regional, and continental scales for temperate conifer forests in North America, we show that network inference varies significantly depending on whether occurrence, abundance, or performance data are used and the degree to which confounding factors are accounted for. Across four widely used and/or cutting-edge inference methods (COOCCUR, NETASSOC, HMSC, NDD-RIM), we find notable disparities in both whole-network metrics and pairwise species associations, particularly at continental scales. These findings underscore that no single method is likely to universally outperforms others across scales, emphasizing the importance of choosing an inference approach that aligns with specific ecological and spatial contexts. Our framework aids in interpreting network topologies and interactions in light of these method- and datatype-driven variances, providing a structured approach to more reliably infer ecological associations and address complex network dynamics in forest management practices.

bioinformatics↗

bioRxiv2023

Ecological predictors of organelle genome evolution: Phylogenetic correlations with taxonomically broad, sparse, unsystematized data

Comparative analysis of variables across phylogenetically linked observations can reveal mechanisms and insights in evolutionary biology. As the taxonomic breadth of the sample of interest increases, challenges of data sparsity, poor phylogenetic resolution, and complicated evolutionary dynamics emerge. Here, we investigate a cross-eukaryotic question where all these problems exist: which organismal ecology features are correlated with gene retention in mitochondrial and chloroplast DNA (organelle DNA or oDNA). Through a wide palette of synthetic control studies, we characterize the specificity and sensitivity of a collection of parametric and non-parametric phylogenetic comparative approaches to identify relationships in the face of such sparse and awkward datasets. We combine and curate ecological data coupled to oDNA genome information across eukaryotes, including a new semi-automated approach for gathering data on organismal traits from less systematized open-access resources including encyclopedia articles on species and taxa. Combining this unique dataset with our benchmarked comparative approaches, we confirm support for several known links between organismal ecology and organelle gene retention, identify several previously unidentified relationships constituting possible ecological contributors to oDNA genome evolution, and provide support for a recently hypothesized link between environmental demand and oDNA retention. We, with caution, discuss the implications of these findings for organelle evolution and of this pipeline for broad comparative analyses in other fields.

evolutionary biology↗

bioRxiv2023

Stability of Ecologically Scaffolded Traits During Evolutionary Transitions in Individuality

Evolutionary transitions in individuality (ETIs), such as the emergence of multicellularity, are events in the history of life during which entities at one level of organisation (particles) form collective-level entities that subsequently become individuals in their own right. Recent empirical and theoretical studies advocate the importance of an externally imposed meta-population structure or "ecological scaffold" for the emergence of new levels of individuality. Such a scaffold enables survival and reproduction at the collective level and thus the possibility of selection for beneficial traits on that level. However, a long-standing difficulty for the ecological scaffolding approach has been its inability to adequately explain how collective-level trait values that evolved under scaffolding conditions can be retained once these conditions are lifted. We call this difficulty "the problem of endogenisation." Here, we derive general conditions for the possibility of endogenisation. Key to endogenisation is the existence of a fitness valley that can be circumvented when scaffolding occurs. Using a stochastic meta-population model, we implement two versions of ecological scaffolding (one temporal and one spatial) and study subsequent evolutionary trajectories using the modelling techniques of adaptive dynamics. Our analysis yields several important results. The temporal model reveals that only collective traits based on particle-particle interactions can be endogenised when a temporary scaffold is applied to the entire population. The spatial model shows that, given the presence of an environmental gradient of externally imposed meta-population structure, ecological scaffolding can only occur in a limited "Goldilocks" zone of the environment. Further, if endogenisation conditions are also fulfilled, scaffolded collectives can colonise non-scaffolding areas of the environment. We conjecture that Goldilocks zones could act as initiators of ETIs and help explain the near ubiquity of collective-level individuality even if the conditions that promote it prove to be rare.

evolutionary biology↗

bioRxiv2023

The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean

Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on the Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related with B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomy of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and their carrying taxa in the global ocean, in light of the limitation to detect de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating epipelagic from mesopelagic zones. The functional genes were relatively stably distributed across different oceans, but their carrying taxa varied considerably, showing clear functional redundancy of microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen and nitrate. However, the composition of functional genes was weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the compositional variation of B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between chlorophyll a concentration and B12 biosynthesis traits, indicating their importance in global ocean primary production. Conclusively, this study revealed an essential ecological mechanism governing the assembly of microbes in nature: the environment selects function rather than taxonomy; functional redundancy underlies stochastic community assembly. Impact StatementA central question in ecology is how a galaxy of microbial taxa is assembled and distributed across space and through time, executing essential ecosystem functions. By anchoring microbial functional traits potentially involved in B12 biosynthesis and their carrying microbial taxa in the global ocean, this study addresses essential ecological questions from functional and taxonomic angles. Integrating multiple lines of evidence, we show that the ecosystem selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. Also, microbial communities potentially involved in B12 biosynthesis are significantly associated with chlorophyll a concentration, demonstrating their importance in global ocean primary production. This study provides valuable mechanistic insights into the complex microbial community assembly in natural ecosystems.

microbiology↗

bioRxiv2023

How to define, use, and interpret Pagel's lambda (lambda) in ecology and evolution

1Pagels {lambda} (lambda) is a critical tool in ecology and evolution for describing trait evolution, imputing missing species data, and generalising ecological relationships beyond their study system. Yet the interpretation of {lambda} depends on context, and there are many misconceptions about metrics that are similar but not identical to {lambda}. As an index of phylogenetic signal applied to continuous traits, {lambda} typically (but not always) ranges between 0 and 1, and is a rate-independent measure of the degree to which closely-related species resemble one-another relative to a Brownian motion expectation. But this measure is biased by non-random species sampling--a common characteristic of ecological data--which also makes phylogenetic imputation of missing traits challenging. The {lambda} estimated in regression models has little to do with the phylogenetic signal of measured traits and is better considered as either a statistical correction or a measure of the impact of unmeasured (latent) traits in the model. In other contexts, such as hierarchical models including intra-specific variation, {lambda} is frequently confused with distinct metrics such as h2. We show how confusion in defining and using {lambda} can mislead our interpretation of ecological and evolutionary processes. Open research statementNo data were used or collected as part of this work.

evolutionary biology↗

bioRxiv2023

Ecological specialization and local adaptation in sympatric sexual and asexual grass thrips species

The maintenance of sex is difficult to explain in the face of the demographic advantages of asexuality, especially when sexual and asexual lineages co-occur and compete. Here, we test if niche divergence and specialization can contribute to the maintenance of sympatric populations of two closely related, sexual and asexual Aptinothrips grass thrips species. In mesocosm experiments, ecological niches and ecological specialization were inferred from thrips performances on different grass species used as hosts in natural populations. Sexual and asexual thrips performed best on different grass hosts, indicating niche differentiation. The asexual species was also characterized by a broader fundamental ecological niche than the sexual one. However, niche differentiation is unlikely to explain the maintenance of the two species in sympatry because the reproductive rate of asexual females generally exceeded that of sexual ones. Surprisingly, the asexual but not sexual species showed geographic variation in the fundamental niche. This geographic variation likely stems from different clonal assemblages at different locations because different asexual genotypes have different ecological niches. Across natural populations, the performance of asexual females on a specific grass species was further positively correlated with the frequency of that grass species, consistent with adaptation to locally abundant grasses. Altogether, our results suggest that niche differentiation contributes little to the maintenance of grass thrips species with different reproductive modes and that asexuality facilitates adaptation to a diversity of co-occurring host plants.

evolutionary biology↗

bioRxiv2023

Computer simulation and mathematical modeling of the interactions between ecological and sexual selection to reveal the mechanism of sympatric speciation

In modern evolutionary theory, the mechanism of sympatric speciation is still an unsolved mystery. Ecological niche specialization and the subsequent premating reproductive isolation (RI) are the putative initial steps of sympatric speciation, even though the exact mechanism of how the former leads to the latter remains unclear. This study aims to develop a simple, intuitive, and realistic model ecosystem that uses the fewest variables possible but is still comprehensive enough to uncover the fundamental mechanisms of sympatric speciation. Applying the concept of an adaptive fitness landscape, the study used an individual-based computer simulation to investigate how ecological selection and sexual selection may interact to produce sympatric premating RI. Mathematical models were derived to describe the nonlinear adaptive dynamics of the system. A user-friendly computer application was able to solve, numerically, all the trajectories, fixed points, and bifurcation points of the models and display the solutions as phase portraits. The findings reveal that under favorable conditions, fixed points may emerge in the systems phase portraits to create stable mating-bias-allele polymorphisms and varying degrees of premating RI between niche ecotypes. Solving the nonlinear equations of the mathematical models establishes the precise parametric values required to produce such fixed points. It also specifies the conditions necessary for high-mating-bias mutant alleles to invade and produce, or enhance, premating RI. Restricting migration between niches impedes mutant invasion in parapatric and allopatric populations. Multi-locus mating traits may produce hybrids that prevent speciation. Simulation results of a gonochoric, multi-niche system demonstrate that linkage disequilibrium can emerge spontaneously among ecological, male-trait, and female-preference genotypes to produce premating RI. From these results, a five-stage mechanism of sympatric speciation is formulated: Initially, disruptive ecological selection creates selection pressure for high-mating-bias alleles to invade and rapidly establish premating RI. This then paves the way for the recruitment of late-stage mechanisms, such as adaptive coupling and post-zygotic isolation, to complete the speciation process. Applying nonlinear dynamics theories to model and analyze sympatric speciation has yielded novel findings that support and extend the results of prior studies. These new discoveries may help to overcome the theoretical objections to sympatric speciation and establish it as a prevalent mode of speciation in nature.

evolutionary biology↗

bioRxiv2023

Mechanics limit ecological diversity and promote heterogeneity in confined bacterial communities

Multi-species bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here we study a model system consisting of two populations of non-motile E. coli bacteria competing within open, monolayer micro-channels. The competitive dynamics is observed to be bi-phasic: after seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Polya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.

biophysics↗

bioRxiv2024

Ecological diversification in sexual and asexual lineages

The presence or absence of sex can have a strong influence on the processes whereby species arise. Yet, the mechanistic underpinnings of this influence are poorly understood. To gain insights into the mechanisms whereby the reproductive mode may influence diversification, we investigate how natural selection, genetic mixing and the reproductive mode interact and how this interaction affects the evolutionary dynamics of diversifying lineages. To do so, we formulate and analyze trait-based eco-evolutionary models of ecological diversification for sexual and asexual lineages, in which diversification is driven by intraspecific resource competition. We find that the reproductive mode strongly influences the diversification rate and thus the ensuing diversity of a lineage. Our results reveal that natural selection is stronger in asexual lineages because asexual organisms have a higher reproductive potential than sexual ones. As a consequence, an asexual population can reach a higher population density than a sexual population under the very same ecological conditions. This causes competition, and thus ecologically-based selection, to be stronger in asexual lineages, promoting faster diversification. However, a small amount of genetic mixing accelerates the trait expansion process in sexual lineages, overturning the effect of selection alone and enabling a faster niche occupancy than asexual lineages. As a consequence, sexual lineages can occupy more ecological niches, eventually resulting in higher diversity. This suggests that sexual reproduction may be widespread among species because it increases rates of diversification.

evolutionary biology↗

bioRxiv2024

Cause and effect in the natural selection of the population ecological life histories of mammals

The inter-specific life history and ecological variation of mammals is often explained as allometric consequences of physiological adaptations to unexplained body mass variation. But these hypotheses are unnecessary because the allometric scaling is explained already by the natural selection that explains the variation in mass. I decompose the population ecological life histories of 4,936 species of mammals to show how the selection of mass accounts for the life history and population ecological variation in mammals. This shows that 55% of the within order variance, and 91% of the between order differences, in the body mass, demography, and population ecological traits are reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.

evolutionary biology↗

bioRxiv2024

Ancient secretory pathways contributed to the evolutionary origin of an ecologically impactful bioluminescence system

Evolutionary innovations in chemical secretion - such as the production of secondary metabolites, pheromones, and toxins - profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochemical pathways are integrated with conserved secretory processes to create novel products. Among secretory innovations, bioluminescence is important because it evolved convergently many times to influence predator-prey interactions, while often producing courtship signals linked to increased rates of speciation. However, whether or not deeply conserved secretory genes are used in secretory bioluminescence remains unexplored. Here, we show that in the ostracod Vargula tsujii, the evolutionary novel c-luciferase gene is co-expressed with many conserved genes, including those related to toxin production and high-output protein secretion. Our results demonstrate that the legacy-plus-innovation mode of secretory evolution, previously applied to sensory modalities of olfaction, gustation, and nociception, also encompasses light-producing signals generated by bioluminescent secretions. This extension broadens the paradigm of secretory diversification to include not only chemical signals but also bioluminescent light as an important medium of ecological interaction and evolutionary innovation. Significance StatementAnimals produce an enormous diversity of secreted chemical products, like toxins and pheromones, with wide-ranging impacts on ecological interactions. Although a deeply conserved toolkit of secretory genes may often underlie chemical interactions mediated through smell, taste, and sensing pain, whether or not this evolutionary mode generalizes to sensing light is unknown. Here we show that a bioluminescence secretion system, which creates light for anti-predator and courtship interactions, also uses genes of a deeply conserved secretory toolkit. Therefore, secretory innovations may act through all sensory modalities by integrating conserved genes with novel biosynthesis pathways, to serve as crucibles of evolutionary and ecological diversity.

evolutionary biology↗

bioRxiv2024

Microbial species exist and are maintained by ecological cohesiveness coupled to high homologous recombination.

Recent analyses of metagenomes and genomes have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars). To advance the species concept the underlying genetic or ecological mechanisms that maintain these discrete units need to be elucidated. By analyzing closely related isolate genomes from the same or related samples we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on higher similarity in abundance patterns of genomes of the same vs. different units, while recombination frequency was shown to have two times or more impact on sequence evolution than point mutation. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or selection-driven recombination, but not their synergistic effect, as the mechanism of unit cohesion. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results have strong implications for how to identify and regulate microbial species and genomovars of clinical or environmental importance and answer an important question for microbiology: what a species is. SIGNIFICANCEA highly pressing issue to resolve toward advancing the species concept for microbes (i.e., "what a species is") is to elucidate the underlying mechanisms for creating and maintaining species- and intraspecies-level gaps in diversity, or simply "clusters". In this study, we provide a novel methodology and the appropriate data to elucidate these mechanisms, and thus provide a mechanistic explanation of how the evolution of species- and strain-level clusters takes place. Specifically, our results show that several bacteria may be evolving and speciating much more sexually than previously thought, even under conditions of no strong positive selection for DNA exchange (i.e., neutral conditions). These results have major implications for better understanding and modeling microbial diversity on the planet.

microbiology↗

bioRxiv2024

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

BackgroundViruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. ResultsHere we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. ConclusionProphages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.

bioinformatics↗

bioRxiv2025

From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning

The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organisms and their ecologies. However, access to and extraction of relevant data from this extensive resource remain challenging. Advances in text and data mining (TDM) and Natural Language Processing (NLP) techniques offer new opportunities for liberating such information from the literature. Testing and using such approaches to annotate articles in machine actionable formats is therefore necessary to enable the exploitation of existing knowledge in new biology, ecology, and evolution research. Here we explore the potential of these methods to annotate and extract organismal and ecological trait data for the most diverse animal group on Earth, the arthropods. The article processing workflow uses manually curated trait dictionaries with trained NLP models to perform labelling of entities and relationships of thousands of articles. A subset of manually annotated documents facilitated the formal evaluation of the performance of the workflow in terms of entity recognition and normalisation, and relationship extraction, highlighting several important technical challenges. The results are made available to the scientific community through an interactive web tool and queryable resource, the ArTraDB Arthropod Trait Database. These methodological explorations provide a framework that could be extended beyond the arthropods, where TDM and NLP approaches applied to the taxonomy and biodiversity literature will greatly facilitate data synthesis studies and literature reviews, the identification of knowledge gaps and biases, as well as the data-informed investigation of ecological and evolutionary trends and patterns.

bioinformatics↗

bioRxiv2025

Tumor Landscape Analysis: An Ecologically Informed Framework to Understand Tumor Microenvironments

Tumor microenvironments (TMEs) are spatially complex and dynamic systems shaped by evolutionary pressures, tissue architecture, and cellular interactions. To capture this complexity, we developed the Tumor Landscape Analysis (TLA) pipeline, a computational framework applying principles from landscape ecology and spatial statistics to quantitatively characterize tumor spatial heterogeneity. TLA integrates spatially resolved pathology data, including whole-cell, point-based, and region-level formats, and computes multiscale metrics to assess cell distributions, neighborhood relationships, and tissue-level organization. The framework leverages ecological indices such as the Morisita-Horn index, Ripleys H function, and Shannon diversity to quantify intercellular proximity, spatial clustering, and cellular diversity. It also uses the concept of local microenvironments (LMEs), data-driven ecological niches defined by local cell-type abundance and spatial uniformity, enabling unsupervised and reproducible classification of tumor regions. The use of fragmentation metrics, including patch density, shape complexity, and interspersion, provide further insight into spatial disorganization and emergent tissue architecture. TLA is agnostic to imaging modality and biological context, supporting broad applicability across tumor types and sample formats. By translating complex tissue architectures into interpretable spatial metrics, the pipeline enables integrative analyses that link spatial ecology to clinical and molecular phenotypes. This approach facilitates a deeper understanding of how spatial features contribute to tumor progression, therapeutic resistance, and clinical outcomes, offering new opportunities for precision oncology rooted in spatial systems biology.

cancer biology↗

bioRxiv2025

Divergent paths, convergent heads: morphological adaptation of head shape to ecological niches in snakes.

Morphological convergence--where distantly related species evolve similar traits in response to shared ecological pressures--is a hallmark of adaptive evolution. In snakes, head shape is a key functional trait linked to habitat use and diet, yet the extent and drivers of its convergence across habitat types and diet remain poorly understood. Here, we used geometric morphometric analyses to analyze dorsal head shape from photographs of over 266 snake species, representing [~]5% of global snake diversity. Our analyses reveal that head shape variation is only weakly structured by phylogeny and allometry, but shaped by ecological specialization. Morphospace patterns reflect distinct differences in species with different ecologies: fossorial species exhibit compact, posteriorly wider heads suited for burrowing; aquatic species show streamlined profiles for hydrodynamic efficiency; and arboreal snakes tend to possess elongated heads for maneuvering in complex habitats. Terrestrial and semi-fossorial snakes display broad morphospace overlap and an elevated shape disparity highlighting morphological versatility. While diet covaried significantly with head shape, species with similar diets did not exhibit strong morphological convergence. These findings underscore the dominant role of ecology over phylogeny in shaping the evolution of head shape in gape-limited predators like snakes.

evolutionary biology↗

bioRxiv2025

Ecological inheritance facilitates the coexistence of environmental helpers and free-riders

Variation in social traits and behaviours is widespread in nature and can be maintained by selection. Many social traits influence fitness indirectly by modifying shared environments that are transmitted across generations, a process known as ecological inheritance. Here, we investigate how variation in environmentally mediated social behaviour, such as helping to improve shared resources, can emerge and persist in spatially subdivided populations where locally modified environments are transmitted across generations. Using mathematical and computational modelling, we show that ecological inheritance, when combined with limited dispersal, readily leads to the stable coexistence of two types with opposite environmental legacies: helpers, who improve the local environment for the future at a personal cost, and environmental free-riders, who benefit without contributing to the detriment of future generations. In turn, this polymorphism generates lasting spatial heterogeneity in environmental quality and, consequently, in survival and reproduction--particularly under isolation-by-distance, creating stable clusters of high- and low-quality habitats across an otherwise homogeneous landscape. These findings reveal how ecological inheritance and spatial structure interact to stabilise polymorphism, potentially driving long-term behavioural, ecological, and fitness variation across diverse biological systems.

evolutionary biology↗