AbstractA prevailing problem in evolutionary biology is elucidating the genotype-to-phenotype map that characterizes how genomic activities regulate different aspects of organismal morphology and their variability in both space and time. Here, we explore potential causality between genome content and both morphological complexity and disparity by compiling the regulatory components (i.e., transcription factors, RNA-binding proteins, and microRNA families) as well as a representative set of nonregulatory housekeeping genes in 32 species belonging to a wide variety of animal phyla spanning a range of morphological, ecological, and genomic characteristics. A principal component analysis of these four nonoverlapping genomic components from each of these 32 species in relation to their last common ancestor revealed that no relationship exists between genome space and disparity, as changes to animal body plans appear to be largely the result of changes to the regulatory networks that govern animal development rather than gaining or losing specific sets of regulatory genes. However, using both phylogenetically correlated and phylogenetically uncorrelated statistical tests, we find a strong relationship between the loss of all considered gene types in some parasitic taxa, an exacerbation of a trend that characterizes animal genomes in general. We also find a strong correlation, and a likely causal relationship, between microRNA innovations and organismal complexity. While this analysis of genomic features suggests how complexity and disparity are each encoded in the genome, further analysis of the regulatory networks in which they participate should provide a more comprehensive description of how organisms diversify their morphologies through time.

Parasitism has independently evolved hundreds of times among metazoans. Nonetheless, parasites have explored only a limited range of ecologies, and they display frequent convergence in morphological, behavioral, and life-history traits. Although gene loss in particular parasitic species has been documented, it is not known if gene loss converges along the same lines as these other traits. To test for convergent gene loss, we characterized the housekeeping, regulatory, and DNA-repair complements of 48 bilaterian species, including 20 parasites belonging to 6 different bilaterian phyla. We found that different parasitic strategies do not display characteristic tempos or modes of gene loss. Further, the accelerated rates of gene loss seen in some parasites were almost always shared with their free-living relatives, indicating that the increased rate of loss preceded the rise of parasitism. Therefore, the convergent ecological strategies and adaptations that have arisen in distantly related parasitic lineages overlay contingent gene losses, which largely reflect their phylogenetic history. These results have important implications for how ecologists and evolutionary biologists should model the acquisition of parasitism, especially regarding the long-held assumption that reversion from a parasitic to a free-living state is impossible.

Abstract The need for niche differentiation among resource competitors to coexist is a universally accepted principle in ecology. However, this principle is derived from models with one or two resources or no resource dynamics at all. Graphical analysis of a consumer‐resource model including three resources shows that a consumer that is not the best competitor for any single resource can coexist with two consumers that are the best competitors for one and two resources, respectively, if it has high diet/niche overlap and so strongly competes with one or both other competitors for two of the resources. The same community structure emerges in randomly assembled communities with up to six consumers feeding on six resources: Up to half of the consumers can be the best competitor on no available resource. Specifically, consumers that are the best competitor for at least one available resource have low diet overlap with one another, and consumers that are the best competitor for no resource have high diet overlap with the best competitors on at least one resource and among themselves. Coexistence of these consumers requires higher niche overlap with competitors that are the best competitors for multiple resources and permits even higher niche overlap among themselves.

Assisted colonization (AC), translocating a species outside its indigenous range to avoid its extinction, is one of the few conservation options for some species. It is also controversial because of the history of ecological impacts of invasive species, including the extinction of native species as a result of novel ecological interactions resulting from the introduction. Although several national and international organizations have issued guidelines related to AC, none allow case-specific decision-making based on risks and benefits to biodiversity. We propose a two-pronged approach to fill this gap. The first step aims to separate clear-cut cases of AC from those that require an in-depth risk analysis. We propose a set of seven qualitative criteria to identify AC projects that are clearly low-risk and high-benefit, and therefore should not be controversial, and those that are clearly high-risk or low-benefit and therefore should not be attempted. This identifies only the most obvious cases, leaving out many cases to be determined through a quantitative analysis to estimate the probabilities of extirpation of the resident species because of AC, which is the second step of our approach. We propose a roadmap for developing such a system based on community ecology theory, and a framework for considering the estimated probabilities in a global context. Our framework recommends an AC project only if it would result in a larger number of globally extant species than a scenario of no action. We propose large-scale testing of the clear-cut approach, further development of the quantitative approach, and wide consultation for adopting international guidelines for risk assessment of AC projects.

The evolutionary and ecological dynamics of each species are simultaneously shaped by interactions with abiotic resources and many other species: prey, herbivores, predators, pathogens, and mutualists. In this review, I explore the conceptual linkages and empirical evidence for how ecological and evolutionary dynamics jointly assemble communities across the landscape and foster coexistence among species within communities. The abundances and traits of interacting species jointly shape the dynamics of population regulation and the regimes of natural selection that those interacting species face. While theory focuses primarily on competition, empirical studies on many taxa demonstrate that all types of species interactions play critical roles in excluding some species, fostering the coexistence of other species in various communities, and imposing natural selection that shapes these ecological outcomes. These empirical studies make clear the synergy that emerges from understanding the fitness and trait differences that foster coexistence and impose natural selection between interacting species.

We present a mechanistic model of coexistence among a mycorrhizal fungus and one or two plant species that compete for a single nutrient. Plant-fungal coexistence is more likely if the fungus is better at extracting the environmental nutrient than the plant and the fungus acquires carbon from the plant above a minimum rate. When they coexist, their interaction can shift from mutualistic to parasitic at high nutrient availability. The fungus is a second nutrient source for plants and can promote the coexistence of two plant competitors if one is better at environmental nutrient extraction and the other is better at acquiring the nutrient from the fungus. Because it extracts carbon from both plants, the fungus also serves as a conduit of apparent competition between the plants. Consequently, the plant with the lower environmental nutrient extraction rate can drive the plant with the higher environmental nutrient extraction rate extinct at high carbon supply rates. This model illustrates mechanisms to explain several observed patterns, including shifts in plant-mycorrhizal growth responses and coexistence along nutrient gradients, equivocal results among experiments testing the effect of mycorrhizal fungi on plant diversity, and differences in plant diversity among ecosystems dominated by different mycorrhizal groups.

A prevailing problem in evolutionary biology is elucidating the genotype-phenotype map that characterizes how genomic activities regulate different aspects of organismal morphology and their variability in both space and time. Here, we explore potential causality between genome content and both morphological complexity and disparity by compiling the regulatory components (i.e., transcription factors, RNA binding proteins, and microRNA families) as well as a representative set of non-regulatory housekeeping genes in 32 species belonging to a wide variety of animal phyla, altogether encapsulating a number of varying genomic characteristics and morphological diversities. A principal component analysis of these four non-overlapping genomic components from each of these 32 species in relation to their last common ancestor revealed that no relationship exists between genome space and disparity, as changes to animal body plans appear to be largely the result of changes to the gene regulatory networks that govern animal development rather than gaining or losing specific sets of regulatory genes. However, using both phylogenetically correlated as well as phylogenetically uncorrelated statistical tests, we find a strong relationship between the loss of all considered gene types and the advent of some parasitic taxa, as well as between microRNA innovations and organismal complexity. While this analysis of genomic features suggests how complexity and disparity are each encoded in the genome, further analysis of the regulatory networks in which they participate should provide a more comprehensive description of how organisms diversify their morphologies over time through alterations in their genomic components. ### Competing Interest Statement The authors have declared no competing interest.

Dispersal among local communities is fundamental to the metacommunity concept but is only important to the metacommunity structure if dispersal causes distortions of species abundances away from what local ecological conditions favour. We know from much previous work that dispersal can cause such abundance distortions. However, almost all previous theoretical studies have only considered one species alone or two interacting species (e.g. competitors or predator and prey). Moreover, a systematic analysis is needed of whether different dispersal strategies (e.g. passive dispersal versus demographic habitat selection) result in different abundance distortion patterns, how these distortion patterns change with local food web structure, and how the dispersal propensities of the interacting species might evolve in response to one another. In this article, we show using computer simulations and analytical models that abundance distortions occur in simple food webs with both passive dispersal and habitat selection, but habitat selection causes larger distortions. Additionally, patterns in the evolution of dispersal propensity in interacting species are very different for these two dispersal strategies. This study identifies that the dispersal strategies employed by interacting species critically shape how dispersal will influence metacommunity structure. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Parasite-driven population divergence in hosts can be exacerbated by environmental factors affecting host parasitism, as well as by increasing sexual selection against parasitized hosts. Environmental factors can influence parasitism directly by affecting parasite survival, and indirectly by affecting host condition, which can in turn shape host sexual selection. To disentangle these potential alternative paths, we used a damselfly (host) - water mite (parasite) system to examine how environmental factors directly and indirectly drive heterogeneity in parasitism across populations and influence the strength of sexual selection acting against parasitized males. We found substantial heterogeneity in parasitism across populations, driven mainly by lake pH, and damselfly density. Although this heterogeneity in parasitism did not translate directly into variation in sexual selection, the density of predatory fish increased sexual selection strength, likely through the effects on damselfly condition. These results imply that parasitism alone may not cause differences in sexual selection across populations, but when linked with underlying environmental conditions, parasitism can increase the strength of selection. More broadly, these results suggest that elucidating how parasitism may drive sexual selection requires consideration of the intwined effects of ecological processes.

AbstractThis book explores how mathematical models can illuminate the interaction known as interspecific competition. Competition occurs whenever two or more species share at least some of the same limiting resources. It is likely to affect all species, as well as many higher-level aspects of community and ecosystem dynamics. Interspecific competition shares many of the same features as density dependence (intraspecific competition) and evolution (competition between genotypes). In spite of this, a robust theoretical framework for understanding its outcomes and many potential effects on ecological communities is lacking. Despite its prominence in the ecological literature, the theory seems to have lost direction in recent decades, with many synthetic papers promoting outdated ideas, failing to use resource-based models, and having little utility in applied fields such as conservation and environmental management. The book examines how theory that began to be developed half a century ago can be extended to illuminate the effects of environmental change on the abundances of competing species. Current competition theory needs to incorporate findings regarding consumer–resource interactions in the context of larger food webs containing behaviourally or evolutionarily adapting components. Overly simple models and methods of analysis have led to past theory contributing less than it should have to practical applications. The book also discusses the related interactions of intraspecific competition and apparent competition, and examines the evolutionary as well as the ecological effects of this important process.

Eco-evolutionary feedbacks among multiple species occur when one species affects another species' evolution via its effects on the abundance and traits of a shared partner species. What happens if those two species enact opposing effects on their shared partner's population growth? Furthermore, what if those two kinds of interactions involve separate traits? For example, many plants produce distinct suites of traits that attract pollinators (mutualists) and deter herbivores (antagonists). Here, we develop a model to explore how pollinators and herbivores may influence each other's interactions with a shared plant species via evolutionary effects on the plant's nectar and toxin traits. The model results predict that herbivores indirectly select for the evolution of increased nectar production by suppressing plant population growth. The model also predicts that pollinators indirectly select for the evolution of increased toxin production by plants and increased counterdefenses by herbivores via their positive effects on plant population growth. Unless toxins directly affect pollinator foraging, plants always evolve increases in attraction and defense traits when they interact with both kinds of foragers. This work highlights the value of incorporating ecological dynamics to understand the entangled evolution of mutualisms and antagonisms in natural communities.

The usual conception of character displacement is of resource competitors differentiating to specialize on different prey in order to reduce competition. However, traits that underlie many predator-prey interactions, such as chase-evade speeds, gape limitation, and toxin concentrations, do not permit such specialization, but instead result in unidirectional evolutionary arms races. Here, we develop and analyze an evolutionary model of predator-prey interactions to explore whether character displacement will still occur when such unidirectional traits define the species interactions, and if so, what environmental conditions foster or retard differentiation. Character displacement in predators and prey does occur, and this differentiation is driven by fitness component trade-offs. Instead of specialization or compartmentalization in which different sets of species have strong interactions, differentiation in this model causes a nested community structure in which species of predators and prey have the same rank interaction strengths with species at the other trophic level. Also, analyses of the model predict that character displacement is fostered in environments with higher productivity, weaker stressors, and lower structural complexity. Model comparisons suggest that character displacement should occur over a broader set of environmental conditions when traits permit prey specialization than when traits foster arms races. These results highlight how different types of phenotypic traits that underlie species interactions shape the species diversification and the structure of the resulting community.

Many different analyses have shown how antagonistic interactions (e.g. predation, disease, interference competition) can foster the coexistence of two species that compete for a single resource. In contrast, whether interactions with mutualist partners can similarly foster coexistence between resource competitors has been little considered. Here, we derive a mechanistic model of two plant species that compete for a single abiotic resource and that each produce nectar that supports a single shared pollinator species. In our model, plant coexistence requires three relationships: 1) one plant species must be better at utilizing the abiotic resource to produce more ovules; 2) this better resource competitor must also be more pollen‐limited in the absence of the pollinator; and 3) this species must produce much less nectar, such that pollinator abundance depends primarily on nectar produced by the less pollen‐limited species. Pollinators can also shape the competitive hierarchy among plant species without promoting coexistence, an influence determined by the amount of nectar produced by the entire plant assemblage that supports pollinator abundance. Our results show that patterns of pollen limitation and nectar production across competing plant species will be essential data to evaluating whether pollinators may foster the plants' coexistence.

Sexual selection can be shaped by spatial variation in environmental features among populations. Differences in sexual selection among populations generated through the effects of the environment could be shaped via four paths: differences in mean absolute fitness, differences in the means or variances of phenotypes, or differences in the absolute fitness-trait function relationship. Because sexual selection occurs only during the adult life stage, most studies have focused on identifying environmental features that influence these metrics of fitness and trait distributions among adults. However, these adult features could also be affected by environmental factors experienced in early life stages that then shape the trajectory for sexual selection during the adult life stage. Here we investigated how among-population variation in environmental conditions during the juvenile (larval) stage of two species of Enallagma damselflies shapes sexual selection on male body size. We found that environmental factors related to predation pressures, lake primary productivity, and habitat availability play a role in shaping spatial variation in sexual selection. This acts mainly through how the environment affects absolute fitness-body size associations, not spatial variation in mean fitness or body size means and variances. These results demonstrate that the underpinnings of sexual selection in the wild can arise from environmental conditions during prereproductive life stages.

1. Recent studies demonstrate that ecological and evolutionary processes can occur over similar temporal and spatial scales and might thus frequently interact. Although concepts such as the evolving metacommunity, diffuse (co)evolution and community genetics integrate multi-species dynamics, most experimental studies usually consider how evolution affects only one focal species. Hence, our understanding of evolution in multi-species communities is still underdeveloped. 2. We highlight key community and evolutionary mechanisms and their interactions to facilitate a broader understanding of evolution in multi-species communities. We propose a framework that explicitly considers interactions between each of the four analogous processes of evolutionary biology (selection, gene flow, genetic drift and mutation) and community ecology (species sorting, dispersal, ecological drift and speciation). 3. Focusing on interactions between processes of evolutionary biology and community ecology enables explorations of the full range of eco-evolutionary dynamics in multi-species communities and guides the design of novel experiments. Furthermore, the proposed framework develops a shared language between evolutionary biologists and community ecologists and indicates new research avenues. 4. Overall, we propose that explicitly incorporating interactions between these evolutionary and community processes to study eco-evolutionary dynamics in multi-species communities will better inform broader questions about the maintenance of diversity and the resilience of diverse communities to disturbances, both natural and manmade.

Whole genome duplications (WGDs) have long been considered the causal mechanism underlying the dramatic increase in vertebrate morphological complexity relative to invertebrates. This is due to the retention and neo-functionalization of paralogues generated during these events, evolving new regulatory circuits, and ultimately morphological novelty. Nonetheless, an alternative hypothesis suggests that behind the retention of most paralogues is not neo-functionalization, but instead the degree of the inter-connectivity of the intended gene product, as well as the mode of the WGD itself. Here, we explore both the causes and consequences of WGD by examining the distribution, expression, and molecular evolution of microRNAs (miRNAs) in both gnathostome vertebrates as well as chelicerate arthropods. We find that although the number of miRNA paralogues tracks the number of WGDs experienced within the lineage, few of these paralogues experienced changes to the seed sequence, and thus are functionally equivalent relative to their mRNA targets. Nonetheless, the paralogues generated by the gnathostome 2R allotetraploidization event are retained in higher numbers on one sub-genome relative the second, with the miRNAs found on the preferred set of paralogons showing both higher expression of mature miRNA transcripts and slower molecular evolution of the precursor miRNA sequences. Importantly, WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.

That species must differ ecologically is often viewed as a fundamental condition for their stable coexistence in biological communities. Yet, recent work has shown that ecologically equivalent species can coexist when reproductive interactions and sexual selection regulate population growth. Here, we review theoretical models and highlight empirical studies supporting a role for reproductive interactions in maintaining species diversity. We place reproductive interactions research within a burgeoning conceptual framework of coexistence theory, identify four key mechanisms in intra- and interspecific interactions within and between sexes, speculate on novel mechanisms, and suggest future research. Given the preponderance of sexual reproduction in nature, our review suggests that this is a neglected path towards explaining species diversity when traditional ecological explanations have failed.