Community ecology is often perceived as a mess, given the seemingly vast number of processes that can underlie the many patterns of interest, and the apparent uniqueness of each study system. However, at the most general level, patterns in the composition and diversity of speciesthe subject matter of community ecologyare influenced by only four classes of process: selection, drift, speciation, and dispersal. Selection represents deterministic fitness differences among species, drift represents stochastic changes in species abundance, speciation creates new species, and dispersal is the movement of organisms across space. All theoretical and conceptual models in community ecology can be understood with respect to their emphasis on these four processes. Empirical evidence exists for all of these processes and many of their interactions, with a predominance of studies on selection. Organizing the material of community ecology according to this framework can clarify the essential similarities and differences among the many conceptual and theoretical approaches to the discipline, and it can also allow for the articulation of a very general theory of community dynamics: species are added to communities via speciation and dispersal, and the relative abundances of these species are then shaped by drift and selection, as well as ongoing dispersal, to drive community dynamics.
This review describes new developments in the study of transgenerational epigenetic inheritance, a component of epigenetics. We start by examining the basic concepts of the field and the mechanisms that underlie epigenetic inheritance. We present a comprehensive review of transgenerational cellular epigenetic inheritance among different taxa in the form of a table, and discuss the data contained therein. The analysis of these data shows that epigenetic inheritance is ubiquitous and suggests lines of research that go beyond present approaches to the subject. We conclude by exploring some of the consequences of epigenetic inheritance for the study of evolution, while also pointing to the importance of recognizing and understanding epigenetic inheritance for practical and theoretical issues in biology.
The notion of the “biological individual” is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both present and functional in completing metabolic pathways and serving other physiological functions. Similarly, these new studies have shown that animal development is incomplete without symbionts. Symbionts also constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. The immune system also develops, in part, in dialogue with symbionts and thereby functions as a mechanism for integrating microbes into the animal-cell community. Recognizing the “holobiont”—the multicellular eukaryote plus its colonies of persistent symbionts—as a critically important unit of anatomy, development, physiology, immunology, and evolution opens up new investigative avenues and conceptually challenges the ways in which the biological subdisciplines have heretofore characterized living entities.
Although invasive species are viewed as major threats to ecosystems worldwide, few such species have been studied in enough detail to identify the pathways, magnitudes, and timescales of their impact on native fauna. One of the most intensively studied invasive taxa in this respect is the cane toad ( ), which was introduced to Australia in 1935. A review of these studies suggests that a single pathwaylethal toxic ingestion of toads by frog-eating predatorsis the major mechanism of impact, but that the magnitude of impact varies dramatically among predator taxa, as well as through space and time. Populations of large predators (e.g., varanid and scincid lizards, elapid snakes, freshwater crocodiles, and dasyurid marsupials) may be imperilled by toad invasion, but impacts vary spatially even within the same predator species. Some of the taxa severely impacted by toad invasion recover within a few decades, via aversion learning and longer-term adaptive changes. No native species have gone extinct as a result of toad invasion, and many native taxa widely imagined to be at risk are not affected, largely as a result of their physiological ability to tolerate toad toxins (e.g., as found in many birds and rodents), as well as the reluctance of many native anuran-eating predators to consume toads, either innately or as a learned response. Indirect effects of cane toads as mediated through trophic webs are likely as important as direct effects, but they are more difficult to study. Overall, some Australian native species (mostly large predators) have declined due to cane toads; others, especially species formerly consumed by those predators, have benefited. For yet others, effects have been minor or have been mediated indirectly rather than through direct interactions with the invasive toads. Factors that increase a predator's vulnerability to toad invasion include habitat overlap with toads, anurophagy, large body size, inability to develop rapid behavioral aversion to toads as prey items, and physiological vulnerability to bufotoxins as a result of a lack of coevolutionary history of exposure to other bufonid taxa.
Niche construction theory (NCT) explicitly recognizes environmental modification by organisms (“niche construction”) and their legacy over time (“ecological inheritance”) to be evolutionary processes in their own right. Here we illustrate how niche construction theory provides useful conceptual tools and theoretical insights for integrating ecosystem ecology and evolutionary theory. We begin by briefly describing NCT, and illustrating how it differs from conventional evolutionary approaches. We then distinguish between two aspects of niche construction—environment alteration and subsequent evolution in response to constructed environments—equating the first of these with “ecosystem engineering.” We describe some of the ecological and evolutionary impacts on ecosystems of niche construction, ecosystem engineering, and ecological inheritance, and illustrate how these processes trigger ecological and evolutionary feedbacks and leave detectable ecological signatures that are open to investigation. Finally, we provide a practical guide to how NCT could be deployed by ecologists and evolutionary biologists to explore eco-evolutionary dynamics. We suggest that, by highlighting the ecological and evolutionary ramifications of changes that organisms bring about in ecosystems, NCT helps link ecosystem ecology to evolutionary biology, potentially leading to a deeper understanding of how ecosystems change over time.
Interactions between individual consumer and resource organisms can be modified by neighbors, e.g., when herbivory depends on the identity or diversity of neighboring plants. Effects of neighbors on consumer-resource interactions (“associational effects”) occur in many systems, including plant-herbivore interactions, predator-prey interactions (mimicry), and plant-pollinator interactions. Unfortunately, we know little about how ecologically or evolutionarily important these effects are because we lack appropriate models and data to determine how neighbor effects on individuals contribute to net interactions at population and community levels. Here we supply a general definition of associational effects, review relevant theory, and suggest strategies for future theoretical and empirical work. We find that mathematical models from a variety of fields suggest that individual-level associational effects will influence population and community dynamics when associational effects create local frequency dependence. However, there is little data on how local frequency dependence in associational effects is generated, or on the form or spatial scale of that frequency dependence. Similarly, existing theory lacks consideration of nonlinear and spatially explicit frequency dependence. We outline an experimental approach for producing data that can be related to models to advance our understanding of how associational effects contribute to population and community processes.
Although sexual interactions between species (reproductive interference) have been reported from a wide range of animal taxa, their potential for determining species coexistence is often disregarded. Here, we review evidence from laboratory and field studies illustrating that heterospecific sexual interactions are frequently associated with fitness loss and can have severe ecological and evolutionary consequences. We define reproductive interference as any kind of interspecific interaction during the process of mate acquisition that adversely affects the fitness of at least one of the species involved and that is caused by incomplete species recognition. We distinguish seven types of reproductive interference: signal jamming, heterospecific rivalry, misdirected courtship, heterospecific mating attempts, erroneous female choice, heterospecific mating, and hybridization. We then discuss the sex-specific costs of these types and highlight two typical features of reproductive interference: density-dependence and asymmetry. Similar to competition, reproductive interference can lead to displacement of one species (sexual exclusion), spatial, temporal, or habitat segregation, changes in life history parameters, and reproductive character displacement. In many cases, patterns of coexistence might be shaped by reproductive interference rather than by resource competition, as the presence of a few heterospecifics might substantially decrease reproductive success. Therefore, interspecific sexual interactions should receive more attention in ecological research. Reproductive interference has mainly been discussed in the context of invasive species or hybrid zones, whereas its influence on naturally-occurring sympatric species pairs has rarely been addressed. To improve our knowledge of the ecological significance of reproductive interference, findings from laboratory experiments should be validated in the field. Future studies should also focus on ecological mechanisms, such as temporal, spatial, or habitat partitioning, that might enable sexually interacting species to coexist. Reproductive interference also has implications for the management of endangered species, which can be threatened by sexual interactions with invasive or common species. Studies of reproductive interference might even provide new insights for biological pest control.
A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.
We propose that plant foods containing high quantities of starch were essential for the evolution of the human phenotype during the Pleistocene. Although previous studies have highlighted a stone tool-mediated shift from primarily plant-based to primarily meat-based diets as critical in the development of the brain and other human traits, we argue that digestible carbohydrates were also necessary to accommodate the increased metabolic demands of a growing brain. Furthermore, we acknowledge the adaptive role cooking played in improving the digestibility and palatability of key carbohydrates. We provide evidence that cooked starch, a source of preformed glucose, greatly increased energy availability to human tissues with high glucose demands, such as the brain, red blood cells, and the developing fetus. We also highlight the auxiliary role copy number variation in the salivary amylase genes may have played in increasing the importance of starch in human evolution following the origins of cooking. Salivary amylases are largely ineffective on raw crystalline starch, but cooking substantially increases both their energy-yielding potential and glycemia. Although uncertainties remain regarding the antiquity of cooking and the origins of salivary amylase gene copy number variation, the hypothesis we present makes a testable prediction that these events are correlated.
Machine learning methods, a family of statistical techniques with origins in the field of artificial intelligence, are recognized as holding great promise for the advancement of understanding and prediction about ecological phenomena. These modeling techniques are flexible enough to handle complex problems with multiple interacting elements and typically outcompete traditional approaches (e.g., generalized linear models), making them ideal for modeling ecological systems. Despite their inherent advantages, a review of the literature reveals only a modest use of these approaches in ecology as compared to other disciplines. One potential explanation for this lack of interest is that machine learning techniques do not fall neatly into the class of statistical modeling approaches with which most ecologists are familiar. In this paper, we provide an introduction to three machine learning approaches that can be broadly used by ecologists: classification and regression trees, artificial neural networks, and evolutionary computation. For each approach, we provide a brief background to the methodology, give examples of its application in ecology, describe model development and implementation, discuss strengths and weaknesses, explore the availability of statistical software, and provide an illustrative example. Although the ecological application of machine learning approaches has increased, there remains considerable skepticism with respect to the role of these techniques in ecology. Our review encourages a greater understanding of machine learning approaches and promotes their future application and utilization, while also providing a basis from which ecologists can make informed decisions about whether to select or avoid these approaches in their future modeling endeavors.
Character displacement is the process by which traits evolve in response to selection to lessen resource competition or reproductive interactions between species. Although character displacement has long been viewed as an important mechanism for enabling closely related species to coexist, the causes and consequences of character displacement have not been fully explored. Moreover, character displacement in traits associated with resource use (ecological character displacement) has been largely studied independently of that in traits associated with reproduction (reproductive character displacement). In this review, we underscore the commonalities of these two forms of character displacement and discuss how they interact. We focus on the causes of character displacement and explore how character displacement can have downstream effects ranging from speciation to extinction. In short, understanding how organisms respond to competitive and reproductive interactions with heterospecifics offers key insights into the evolutionary causes and consequences of species coexistence and diversification.
Secondary injury is a term applied to the destructive and self-propagating biological changes in cells and tissues that lead to their dysfunction or death over hours to weeks after the initial insult (the “primary injury”). In most contexts, the initial injury is usually mechanical. The more destructive phase of secondary injury is, however, more responsible for cell death and functional deficits. This subject is described and reviewed differently in the literature. To biomedical researchers, systemic and tissue-level changes such as hemorrhage, edema, and ischemia usually define this subject. To cell and molecular biologists, “secondary injury” refers to a series of predominately molecular events and an increasingly restricted set of aberrant biochemical pathways and products. These biochemical and ionic changes are seen to lead to death of the initially compromised cells and “healthy” cells nearby through necrosis or apoptosis. This latter process is called “bystander damage.” These viewpoints have largely dominated the recent literature, especially in studies of the central nervous system (CNS), often without attempts to place the molecular events in the context of progressive systemic and tissue-level changes. Here we provide a more comprehensive and inclusive discussion of this topic.
Dispersal is central in ecology and evolution because it influences population regulation, adaptation, and speciation. In many species, dispersal is different between genders, leading to sex-biased dispersal. Several theoretical hypotheses have been proposed to explain the evolution of this bias: the resource competition hypothesis proposed by Greenwood, the local mate competition hypothesis, and the inbreeding avoidance hypothesis. Those hypotheses argued that the mating system should be the major factor explaining the direction of such bias. Sociality and the presence of handicap in genders (exaggerated sexual characters or parental care) have recently been proposed to be linked with the direction of this bias. We tested these expected coevolutions using a database of 257 species. Based on phylogenetic approaches, our findings marginally corroborated Greenwood's hypothesis by showing relationships between the direction of sex-biased dispersal, mating systems, and territoriality. More importantly, our results highlighted that the evolution of this bias was more linked to parental care and sexual dimorphism. These traits were also found to be associated with mating systems, suggesting that sexual asymmetry in morphology and parental care might be the main determinant of the evolution of sex-biased dispersal across species and not mating systems per se, as proposed in Greenwood's hypothesis.
Measurement—the assignment of numbers to attributes of the natural world—is central to all scientific inference. Measurement theory concerns the relationship between measurements and reality; its goal is ensuring that inferences about measurements reflect the underlying reality we intend to represent. The key principle of measurement theory is that theoretical context, the rationale for collecting measurements, is essential to defining appropriate measurements and interpreting their values. Theoretical context determines the scale type of measurements and which transformations of those measurements can be made without compromising their meaningfulness. Despite this central role, measurement theory is almost unknown in biology, and its principles are frequently violated. In this review, we present the basic ideas of measurement theory and show how it applies to theoretical as well as empirical work. We then consider examples of empirical and theoretical evolutionary studies whose meaningfulness have been compromised by violations of measurement-theoretic principles. Common errors include not paying attention to theoretical context, inappropriate transformations of data, and inadequate reporting of units, effect sizes, or estimation error. The frequency of such violations reveals the importance of raising awareness of measurement theory among biologists.
Our best hope of developing innovative methods to combat invasive species is likely to come from the study of high-profile invaders that have attracted intensive research not only into control, but also basic biology. Here we illustrate that point by reviewing current thinking about novel ways to control one of the world’s most well-studied invasions: that of the cane toad in Australia. Recently developed methods for population suppression include more effective traps based on the toad’s acoustic and pheromonal biology. New tools for containing spread include surveillance technologies (e.g., eDNA sampling and automated call detectors), as well as landscape-level barriers that exploit the toad’s vulnerability to desiccation—a strategy that could be significantly enhanced through the introduction of sedentary, range-core genotypes ahead of the invasion front. New methods to reduce the ecological impacts of toads include conditioned taste aversion in free-ranging predators, gene banking, and targeted gene flow. Lastly, recent advances in gene editing and gene drive technology hold the promise of modifying toad phenotypes in ways that may facilitate control or buffer impact. Synergies between these approaches hold great promise for novel and more effective means to combat the toad invasion and its consequent impacts on biodiversity.
In recent decades, malaria has become established in zones at the margin of its previous distribution, especially in the highlands of East Africa. Studies in this region have sparked a heated debate over the importance of climate change in the territorial expansion of malaria, where positions range from its neglect to the reification of correlations as causes. Here, we review studies supporting and rebutting the role of climatic change as a driving force for highland invasion by malaria. We assessed the conclusions from both sides of the argument and found that evidence for the role of climate in these dynamics is robust. However, we also argue that over-emphasizing the importance of climate is misleading for setting a research agenda, even one which attempts to understand climate change impacts on emerging malaria patterns. We review alternative drivers for the emergence of this disease and highlight the problems still calling for research if the multidimensional nature of malaria is to be adequately tackled. We also contextualize highland malaria as an ongoing evolutionary process. Finally, we present Schmalhausen's law, which explains the lack of resilience in stressed systems, as a biological principle that unifies the importance of climatic and other environmental factors in driving malaria patterns across different spatio-temporal scales.
How cooperation originates and persists in diverse species, from bacteria to multicellular organisms to human societies, is a major question in evolutionary biology. A large literature asks: what prevents selection for cheating within cooperative lineages? In mutualisms, or cooperative interactions between species, feedback between partners often aligns their fitness interests, such that cooperative symbionts receive more benefits from their hosts than uncooperative symbionts. But how do these feedbacks evolve? Cheaters might invade symbiont populations and select for hosts that preferentially reward or associate with cooperators (often termed sanctions or partner choice); hosts might adapt to variation in symbiont quality that does not amount to cheating (e.g., environmental variation); or conditional host responses might exist before cheaters do, making mutualisms stable from the outset. I review evidence from yucca-yucca moth, fig-fig wasp, and legume-rhizobium mutualisms, which are commonly cited as mutualisms stabilized by sanctions. Based on the empirical evidence, it is doubtful that cheaters select for host sanctions in these systems; cheaters are too uncommon. Recognizing that sanctions likely evolved for functions other than retaliation against cheaters offers many insights about mutualism coevolution, and about why mutualism evolves in only some lineages of potential hosts.
The number of species on Earth is one of the most fundamental numbers in science, but one that remains highly uncertain. Clearly, more species exist than the present number of formally described species (approximately 1.5 million), but projected species numbers differ dramatically among studies. Recent estimates range from about 2 million species to approximately 1 trillion, but most project around 11 million species or fewer. Numerous studies have focused on insects as a major component of overall richness, and many have excluded other groups, especially non-eukaryotes. Here, we re-estimate global biodiversity. We also estimate the relative richness of the major clades of living organisms, summarized as a “Pie of Life.” Unlike many previous estimates, we incorporate morphologically cryptic arthropod species from molecular-based species delimitation. We also include numerous groups of organisms that have not been simultaneously included in previous estimates, especially those often associated with particular insect host species (including mites, nematodes, apicomplexan protists, microsporidian fungi, and bacteria). Our estimates suggest that there are likely to be at least 1 to 6 billion species on Earth. Furthermore, in contrast to previous estimates, the new Pie of Life is dominated by bacteria (approximately 70–90% of species) and insects are only one of many hyperdiverse groups.
For almost 40 years, studies of whole-organism performance have formed a cornerstone of evolutionary physiology. Although its utility as a heuristic guide is beyond question, and we have learned much about morphological evolution from its application, the ecomorphological paradigm has frequently been applied to performance evolution in ways that range from unsatisfactory to inappropriate. More importantly, the standard ecomorphological paradigm does not account for tradeoffs among performance and other traits, nor between performance traits that are mediated by resource allocation. A revised paradigm that includes such tradeoffs, and the possible ways that performance and fitness-enhancing traits might affect each other, could potentially revivify the study of phenotypic evolution and make important inroads into understanding the relationships between morphology and performance and between performance and Darwinian fitness. We describe such a paradigm, and discuss the various ways that performance and key life-history traits might interact with and affect each other. We emphasize both the proximate mechanisms potentially linking such traits, and the likely ultimate factors driving those linkages, as well as the evolutionary implications for the overall, multivariate phenotype. Finally, we highlight several research directions that will shed light on the evolution and ecology of whole-organism performance and related life-history traits.