I survey the 50-year history of the Annual Review of Ecology and Systematics, retitled Annual Review of Ecology, Evolution, and Systematics in 2003. An overview of reviews up through 2009 portrays much of the history of the series’ subject areas, revealing both lasting themes and great changes in emphasis, theory, evidence, and understanding. Much of the progress has resulted from conceptual innovation and from momentous advances in computation, data analysis, and molecular methodology, some of which have been reviewed in these volumes. Some of the most significant changes entail intercourse between formerly separate realms of study. If the remarkably long citation life of many reviews is any indication, contributions to this series have helped to shape research questions and conceptual development in ecology, evolution, and systematics and their applications to social concerns that range from antibiotic resistance to the ecological consequences of human actions.

In recent decades, a burgeoning literature has documented the cultural transmission of behavior through social learning in numerous vertebrate and invertebrate species. One meaning of “cultural evolution in animals” refers to these discoveries, and I present an overview of key findings. I then address the other meaning of the term focused on cultural changes within a lineage. Such changes in humans, described as “cumulative cultural evolution,” have been spectacular, but relatively little attention has yet been paid to the topic in nonhuman animals, other than asserting that the process is unique to humans. A variety of evidence including both controlled experiments and field observations has begun to challenge this view, and in some behavioral domains, notably birdsong, cultural evolution has been studied for many years. In this review, I dissect concepts of cultural evolution and cumulative culture and appraise the accumulating evidence bearing on their nature and significance for evolutionary biology at large.

Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.

Studies of speciation typically investigate the evolution of reproductive isolation between populations, but several other processes can serve as key steps limiting the formation of species. In particular, the probability of successful speciation can be influenced by factors that affect the frequency with which population isolates form as well as their persistence through time. We suggest that population isolation and persistence have an inherently spatial dimension that can be profitably studied using a conceptual framework drawn from metapopulation ecology. We discuss models of speciation that incorporate demographic processes and highlight the need for a broader application of phylogenetic comparative approaches to evaluate the general importance of population isolation, persistence, and reproductive isolation in speciation. We review diverse and nontraditional data sources that can be leveraged to study isolation and persistence in a comparative framework. This incorporation of spatial demographic information facilitates the integration of perspectives on speciation across disciplines and timescales.

Transgenerational plasticity (TGP) occurs when the environment experienced by a parent influences the development of their offspring. In this article, we develop a framework for understanding the mechanisms and multigenerational consequences of TGP. First, we conceptualize the mechanisms of TGP in the context of communication between parents (senders) and offspring (receivers) by dissecting the steps between an environmental cue received by a parent and its resulting effects on the phenotype of one or more future generations. Breaking down the problem in this way highlights the diversity of mechanisms likely to be involved in the process. Second, we review the literature on multigenerational effects and find that the documented patterns across generations are diverse. We categorize different multigenerational patterns and explore the proximate and ultimate mechanisms that can generate them. Throughout, we highlight opportunities for future work in this dynamic and integrative area of study.

Unraveling the origins of Malesia's once vast, hyperdiverse rainforests is a perennial challenge. Major contributions to rainforest assembly came from floristic elements carried on the Indian Plate and montane elementsfrom the Australian Plate (Sahul). The Sahul component is now understood to include substantial two-way exchanges with Sunda inclusive of lowland taxa. Evidence for the relative contributions of the great Asiatic floristic interchanges (GAFIs) with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic diversity. Functional-trait and biome conservatism are noted features of montane austral lineages from Sahul (e.g., diverse Podocarpaceae), whereas the abundance and diversity of lowland lineages, including Syzygium (Myrtaceae) and the Asian dipterocarps (Dipterocarpoideae), reflect a less well understood combination of dispersal, ecology, and adaptive radiations. Thus, Malesian rainforest assembly has been shaped by sharply contrasting evolutionary origins and biogeographic histories.

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

The rate of non-native species introductions continues to increase, with directionality from continents to islands. It is no longer single species but entire networks of coevolved and newly interacting continental species that are establishing on islands. The consequences of multispecies introductions on the population dynamics and interactions of native and introduced species will depend on the form of trophic limitation on island ecosystems. Freed from biotic constraints in their native range, species introduced to islands no longer experience top-down limitation, instead becoming limited by and disrupting bottom-up processes that dominate on resource-limited islands. This framing of the ecological and evolutionary relationships among introduced species with one another and their ecosystem has important consequences for conservation. Whereas on continents the focus of conservation is on restoring native apex species and top-down limitation, on islands the focus must instead be on removing introduced animal and plant species to restore bottom-up limitation.

Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.

Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.

Inhabiting the interface between plant roots and soil, mycorrhizal fungi play a unique but underappreciated role in soil organic matter (SOM) dynamics. Their hyphae provide an efficient mechanism for distributing plant carbon throughout the soil, facilitating its deposition into soil pores and onto mineral surfaces, where it can be protected from microbial attack. Mycorrhizal exudates and dead tissues contribute to the microbial necromass pool now known to play a dominant role in SOM formation and stabilization. While mycorrhizal fungi lack the genetic capacity to act as saprotrophs, they use several strategies to access nutrients locked in SOM and thereby promote its decay, including direct enzymatic breakdown, oxidation via Fenton chemistry, and stimulation of heterotrophic microorganisms through carbon provision to the rhizosphere. An additional mechanism, competition with free-living saprotrophs, potentially suppresses SOM decomposition, leading to its accumulation. How these various nutrient acquisition strategies differentially influence SOM formation, stabilization, and loss is an area of critical research need.

Long-term studies have been crucial to the advancement of population biology, especially our understanding of population dynamics. We argue that this progress arises from three key characteristics of long-term research. First, long-term data are necessary to observe the heterogeneity that drives most population processes. Second, long-term studies often inherently lead to novel insights. Finally, long-term field studies can serve as model systems for population biology, allowing for theory and methods to be tested under well-characterized conditions. We illustrate these ideas in three long-term field systems that have made outsized contributions to our understanding of population ecology, evolution, and conservation biology. We then highlight three emerging areas to which long-term field studies are well positioned to contribute in the future: ecological forecasting, genomics, and macrosystems ecology. Overcoming the obstacles associated with maintaining long-term studies requires continued emphasis on recognizing the benefits of such studies to ensure that long-term research continues to have a substantial impact on elucidating population biology.

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.

Climate change is affecting every ecosystem on Earth. Though climate change is global in scope, literature reviews on the biotic impacts of climate change have focused on temperate and polar regions. Tropical species have distinct life histories and physiologies, and ecological communities are assembled differently across latitude. Thus, tropical species and communities may exhibit different responses to climate change compared with those in temperate and polar regions. What are the fingerprints of climate change in the tropics? This review summarizes the current state of knowledge on impacts of climate change in tropical regions and discusses research priorities to better understand the ways in which species and ecological communities are responding to climate change in the most biodiverse places on Earth.

Guppies in Trinidad range across aquatic environments with fish communities that vary in risk of predation. These communities are often discrete, separated by waterfalls, with high-predation communities downstream and low-predation communities upstream. This gradient is repeated in many rivers; in each one, we see the same divergence between guppy populations in life history, behavior, morphology, and physiology. We have shown that the agent of selection on the life history, behavior, and physiology in low-predation communities is high population density and the cascade of ecological effects that stems from it. In effect, guppy populations modify their ecosystem and, in so doing, impose selection on themselves and shape their own evolution, which further changes the ecosystem. Evolution unfolds rapidly in this system, which has enabled us to study the dynamics of the process, not just its end points. Those studies enable us to answer some very general questions in ecology and evolutionary biology.

Species invasions are pervasive in Earth history, yet the ecological and evolutionary consequences vary greatly. Ancient invasion events can be organized in a hierarchy of increasing invasion intensity from ephemeral invasions to globally pervasive invasive regimes. Each level exhibits emergent properties exceeding the sum of interactions at lower levels. Hierarchy levels correspond to, but do not always exactly correlate with, geographic extent of invasion success. The ecological impacts of lower-level impacts can be negligible or result in temporary community accommodation. Invasion events at moderate to high levels of the hierarchy permanently alter ecological communities, regional faunas, and global ecosystems. The prevalence of invasive species results in evolutionary changes by fostering niche evolution, differential survival of ecologically generalized taxa, faunal homogenization, and suppressing speciation. These impacts can contribute to mass extinctions and biodiversity crises that alter the trajectory of ecological and evolutionary patterns of life. The fossil record provides a long-term record of how invasion impacts may scale up through time, which can augment ecological studies of modern species invasions.

Pathogens and insect pests are important drivers of tree mortality and forest dynamics, but global change has rapidly altered or intensified their impacts. Predictive understanding of changing disease and outbreak occurrence has been limited by two factors: (a) tree mortality and morbidity are emergent phenomena determined by interactions between plant hosts, biotic agents (insects or pathogens), and the environment; and (b) disparate global change drivers co-occur, obscuring net impacts on each of these components. To expand our understanding of changing forest diseases, declines, and outbreaks, we adopt a framework that identifies and organizes observed impacts of diverse global change drivers on the primary mechanisms underlying agent virulence and host susceptibility. We then discuss insights from ecological theory that may advance prediction of forest epidemics and outbreaks. This approach highlights key drivers of changing pest and pathogen dynamics, which may inform forest management aimed at mitigating accelerating rates of tree mortality globally.

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

Many important questions about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years ago, and where were the ancestors of a particular individual alive today? Answers to these questions can have profound consequences for our understanding of history, ecology, and the evolutionary process. In this review, we discuss how geographic aspects of the distribution, movement, and reproduction of organisms are reflected in their pedigree across space and time. Because the structure of the pedigree is what determines patterns of relatedness in modern genetic variation, our aim is to thus provide intuition for how these processes leave an imprint in genetic data. We also highlight some current methods and gaps in the statistical toolbox of spatial population genetics.

Animals are distinguished by having guts—organs that must extract nutrients from food yet also bar invasion by pathogens. Most guts are colonized by nonpathogenic microorganisms, but the functions of these microbes, or even the reasons why they occur in the gut, vary widely among animals. Sometimes these microorganisms have codiversified with hosts; sometimes they live mostly elsewhere in the environment. Either way, gut microorganisms often benefit hosts. Benefits may reflect evolutionary addiction, whereby hosts incorporate gut microorganisms into normal developmental processes. But benefits often include novel ecological capabilities; for example, many metazoan clades exist by virtue of gut communities enabling new dietary niches. Animals vary immensely in their dependence on gut microorganisms, from lacking them entirely to using them as food or to obligate dependence for development, nutrition, or protection. Many consequences of gut microorganisms for hosts can be ascribed to microbial community processes and the host's ability to shape these processes.

Nectarivorous birds and bird-pollinated plants are linked by a network of interactions. Here I ask how these interactions influence evolution and community composition. I find near complete evidence for the effect of birds on plant evolution. Experiments show the process in action—birds select among floral phenotypes in a population—and comparative studies find the resulting pattern—bird-pollinated species have long-tubed, red flowers with large nectar volumes. Speciation is accomplished in one “magical” step when adaptation for bird pollination brings about divergent morphology and reproductive isolation. In contrast, evidence that plants drive bird evolution is fragmentary. Studies of selection on population-level variation are lacking, but the resulting pattern is clear—nectarivorous birds have evolved a remarkable number of times and often have long bills and brush-tipped or tubular tongues. At the level of the ecological guild, birds select among plant species via an effect on seed set and thus determine plant community composition. Plants simultaneously influence the relative fitness of bird species and thus determine the composition of the bird guild. Interaction partners may give one guild member a constant fitness advantage, resulting in competitive exclusion and community change, or may act as limiting resources that depress the fitness of frequent species, thus stabilizing community composition and allowing the coexistence of diversity within bird and plant guilds.

To cope with the reduced availability of O2 at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O2 delivery with metabolic O2 demand. We explain how changes at interacting steps of the O2 transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environmentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to hypoxia, resulting in counter-gradient patterns of altitudinal variation for key physiological phenotypes. For traits that exhibit counteracting environmental and genetic effects, evolved changes in phenotype may be cryptic under field conditions and can only be revealed by rearing representatives of high- and low-altitude populations under standardized environmental conditions to control for plasticity.

The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: (a) evolutionary feedbacks, (b) maintaining resilience, (c) alleviating constraints, (d) coevolutionary disruption, and (e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.

As terrestrial leaf litter decomposes in rivers, its constituent elements follow multiple pathways. Carbon leached as dissolved organic matter can be quickly taken up by microbes, then respired before it can be transferred to the macroscopic food web. Alternatively, this detrital carbon can be ingested and assimilated by aquatic invertebrates, so it is retained longer in the stream and transferred to higher trophic levels. Microbial growth on litter can affect invertebrates through three pathways, which are not mutually exclusive. First, microbes can facilitate invertebrate feeding, improving food quality by conditioning leaves and making them more palatable for invertebrates. Second, microbes can be prey for invertebrates. Third, microbes can compete with invertebrates for resources bound within litter and may produce compounds that retard carbon and nitrogen fluxes to invertebrates. As litter is broken down into smaller particles, there are many opportunities for its elements to reenter the stream food web. Here, I describe a conceptual framework for evaluating how traits of leaf litter will affect its fate in food webs and ecosystems that is useful for predicting how global change will alter carbon fluxes into and out of streams.

Rapid adaptive radiation poses two distinct questions apart from speciation and adaptation: What happens after one speciation event and how do some lineages continue speciating through a rapid burst? We review major features of rapid radiations and their mismatch with theoretical models and speciation mechanisms. The paradox is that the hallmark rapid burst pattern of adaptive radiation is contradicted by most speciation models, which predict continuously decelerating diversification and niche subdivision. Furthermore, it is unclear if and how speciation-promoting mechanisms such as magic traits, phenotype matching, and physical linkage of coadapted alleles promote rapid bursts of speciation. We review additional mechanisms beyond ecological opportunity to explain rapid radiations: (a) ancient adaptive alleles and the transporter hypothesis, (b) sexual signal complexity, (c) fitness landscape connectivity, (d) diversity begets diversity, and (e) plasticity first. We propose new questions and predictions connecting microevolutionary processes to macroevolutionary patterns through the study of rapid radiations.

The accumulation of data on the genomic bases of adaptation has triggered renewed interest in theoretical models of adaptation. Among these models, Fisher Geometric Model (FGM) has received a lot of attention over the last two decades. FGM is based on a continuous multidimensional phenotypic landscape, but it is for the emerging properties of individual mutation effects that it is mostly used. Despite an apparent simplicity and a limited number of parameters, FGM integrates a full model of mutation and epistatic interactions that allows the study of both beneficial and deleterious mutations, and subsequently the fate of evolving populations. In this review, I present the different properties of FGM and the qualitative and quantitative support they have received from experimental evolution data. I later discuss how to estimate the different parameters of the model and outline some future directions to connect FGM and the molecular determinants of adaptation.

Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.

There is a growing appreciation that chromosome inversions affect rates of adaptation, speciation, and the evolution of sex chromosomes. Comparative genomic studies have identified many new paracentric inversion polymorphisms. Population models suggest that inversions can spread by reducing recombination between alleles that independently increase fitness, without epistasis or coadaptation. Areas of linkage disequilibrium extend across large inversions but may be interspersed by areas with little disequilibrium. Genes located within inversions are associated with a variety of traits including those involved in climatic adaptation. Inversion polymorphisms may contribute to speciation by generating underdominance owing to inviable gametes, but an alternative view gaining support is that inversions facilitate speciation by reducing recombination, protecting genomic regions from introgression. Likewise, inversions may facilitate the evolution of sex chromosomes by reducing recombination between sex determining alleles and alleles with sex-specific effects. However, few genes within inversions responsible for fitness effects or speciation have been identified.

We examine how aging is impacted by various chemical challenges that organisms face and by the molecular mechanisms that have evolved to regulate lifespan in response to them. For example, environmental information, which is detected and processed through sensory systems, can modulate lifespan by providing information about the presence and quality of food as well as presence and density of conspecifics and predators. In addition, the diverse forms of molecular damage that result from constant exposure to damaging chemicals that are generated from the environment and from metabolism pose an informatic and energetic challenge for detoxification systems, which are important in ensuring longevity. Finally, systems of innate immunity are vital for recognizing and combating pathogens but are also seen as of increasing importance in causing the aging process. Integrating ideas of molecular mechanism with context derived from evolutionary considerations will lead to exciting new insights into the evolution of aging.

Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci.

Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, in particular, are known for their great diversity in these behaviors, and so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence to evaluate the importance of behavioral isolation in the early stages of avian speciation. Experimentally measured mating preferences indicate that changes in mating behavior can result in premating barriers, with their strength depending on the extent of divergence in mating signals. Differences in migratory and foraging behavior also can play important roles in generating reproductive barriers in the early stages of speciation. However, because premating behavioral isolation is imperfect, extrinsic postzygotic barriers, in the form of selection against hybrids having intermediate phenotypes, also play an important role in avian diversification, especially in completing the speciation process.

We review the state of the art of alien plant research with emphasis on conceptual advances and knowledge gains on general patterns and drivers, biotic interactions, and evolution. Major advances include the identification of different invasion stages and invasiveness dimensions (geographic range, habitat specificity, local abundance) and the identification of appropriate comparators while accounting for propagule pressure and year of introduction. Developments in phylogenetic and functional trait research bear great promise for better understanding of the underlying mechanisms. Global patterns are emerging with propagule pressure, disturbance, increased resource availability, and climate matching as major invasion drivers, but species characteristics also play a role. Biotic interactions with resident communities shape invasion outcomes, with major roles for species diversity, enemies, novel weapons, and mutualists. Mounting evidence has been found for rapid evolution of invasive aliens and evolutionary responses of natives, but a mechanistic understanding requires tighter integration of molecular and phenotypic approaches. We hope the open questions identified in this review will stimulate further research on the ecology and evolution of alien plants.

Mesophotic coral reefs, currently defined as deep reefs between 30 and 150 m, are linked physically and biologically to their shallow water counterparts, have the potential to be refuges for shallow coral reef taxa such as coral and sponges, and might be a source of larvae that could contribute to the resiliency of shallow water reefs. Mesophotic coral reefs are found worldwide, but most are undescribed and understudied. Here, we review our current knowledge of mesophotic coral reefs and their functional ecology as it relates to their geomorphology, changes in the abiotic environment along depth gradients, trophic ecology, their reproduction, and their connectivity to shallow depths. Understanding the ecology of mesophotic coral reefs, and the connectivity between them and their shallow water counterparts, is now a primary focus for many reef studies as the worldwide degradation of shallow coral reefs, and the ecosystem services they provide, continues unabated.

Evolutionary conflict occurs when two parties can each affect a joint phenotype, but they gain from pushing it in opposite directions. Conflicts occur across many biological levels and domains but share many features. They are a major source of biological maladaptation. They affect biological diversity, often increasing it, at almost every level. Because opponents create selection that can be strong, persistent, and malevolent, conflict often leads to accelerated evolution and arms races. Conflicts might even drive the majority of adaptation, with pathogens leading the way as selective forces. The evolution of conflicts is complex, with outcomes determined partly by the relative evolvability of each party and partly by the kinds of power that each evolves. Power is a central issue in biology. In addition to physical strength and weapons, it includes strength from numbers and complexity; abilities to bind and block; advantageous timing; and abilities to acquire, use, and distort information.

Many fields of evolutionary biology now depend on stochastic mathematical models. These models are valuable for their ability to formalize predictions in the face of uncertainty and provide a quantitative framework for testing hypotheses. However, no mathematical model will fully capture biological complexity. Instead, these models attempt to capture the important features of biological systems using relatively simple mathematical principles. These simplifications can allow us to focus on differences that are meaningful, while ignoring those that are not. However, simplification also requires assumptions, and to the extent that these are wrong, so is our ability to predict or compare. Here, we discuss approaches for evaluating the performance of evolutionary models in light of their assumptions by comparing them against reality. We highlight general approaches, how they are applied, and remaining opportunities. Absolute tests of fit, even when not explicitly framed as such, are fundamental to progress in understanding evolution.

Ever since the first plant secondary metabolites (PSMs) were isolated and identified, questions about their ecological functions and diversity have been raised. Recent advances in analytical chemistry and complex data computation, as well as progress in chemical ecology from mechanistic to functional and evolutionary questions, open a new box of hypotheses. Addressing these hypotheses includes the measurement of complex traits, such as chemodiversity, in a context-dependent manner and allows for a deeper understanding of the multifunctionality and functional redundancy of PSMs. Here we review a hypothesis framework that addresses PSM diversity on multiple ecological levels (α, β, and γ chemodiversity), its variation in space and time, and the potential agents of natural selection. We use the concept of chemical information transfer as mediator of antagonistic and mutualistic interaction to interpret functional and microevolutionary studies and create a hypothesis framework for understanding chemodiversity as a factor driving ecological processes.

Function-valued traits—phenotypes whose expression depends on a continuous index (such as age, temperature, or space)—occur throughout biology and, like any trait, it is important to understand how they vary and evolve. Although methods for analyzing variation and evolution of function-valued traits are well developed, they have been underutilized by evolutionists, especially those who study natural populations. We seek to summarize advances in the study of function-valued traits and to make their analyses more approachable and accessible to biologists who could benefit greatly from their use. To that end, we explain how curve thinking benefits conceptual understanding and statistical analysis of functional data. We provide a detailed guide to the most flexible and statistically powerful methods and include worked examples (with R code) as supplemental material. We review ways to characterize variation in function-valued traits and analyze consequences for evolution, including constraint. We also discuss how selection on function-valued traits can be estimated and combined with estimates of heritable variation to project evolutionary dynamics.

Phenological mismatch results when interacting species change the timing of regularly repeated phases in their life cycles at different rates. We review whether this continuously ongoing phenomenon, also known as trophic asynchrony, is becoming more common under ongoing rapid climate change. In antagonistic trophic interactions, any mismatch will have negative impacts for only one of the species, whereas in mutualistic interactions, both partners are expected to suffer. Trophic mismatch is therefore expected to last for evolutionarily short periods, perhaps only a few seasons, adding to the difficulty of attributing it to climate change, which requires long-term data. So far, the prediction that diverging phenologies linked to climate change will cause mismatch is most clearly met in antagonistic interactions at high latitudes in the Artic. There is limited evidence of phenological mismatch in mutualistic interactions, possibly because of strong selection on mutualists to have co-adapted phenological strategies. The study of individual plasticity, population variation, and the genetic bases for phenological strategies is in its infancy. Recent work on woody plants revealed the large imprint of historic climate change on temperature, chilling, and day-length thresholds used by different species to synchronize their phenophases, which in the Northern Hemisphere has led to biogeographic phenological regions in which long-lived plants have adapted to particular interannual and intermillennial amplitudes of climate change.

Bivalve molluscs are abundant in marine and freshwater ecosystems and perform important ecological functions. Bivalves have epifaunal or infaunal lifestyles but are largely filter feeders that couple the water column and benthos. Bivalve ecology is a large field of study, but few comparisons among aquatic ecosystems or lifestyles have been conducted. Bivalves impact nutrient cycling, create and modify habitat, and affect food webs directly (i.e., prey) and indirectly (i.e., movement of nutrients and energy). Materials accumulated in soft tissue and shells are used as environmental monitors. Freshwater mussel and oyster aggregations in rivers and estuaries are hot spots for biodiversity and biogeochemical transformations. Historically, human use includes food, tools, currency, and ornamentation. Bivalves provide direct benefits to modern cultures as food, building materials, and jewelry and provide indirect benefits by stabilizing shorelines and mitigating nutrient pollution. Research on bivalve-mediated ecological processes is diverse, and future synthesis will require collaboration across conventional disciplinary boundaries.

The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.

This review of metapopulation biology has a special focus on Professor Ilkka Hanski's (1953–2016) research. Hanski made seminal contributions to both empirical and theoretical metapopulation biology throughout his scientific career. Hanski's early research focused on ecological aspects of metapopulation biology, in particular how the spatial structure of a landscape influences extinction thresholds and how habitat loss and fragmentation can result in extinction debt. Hanski then used the Glanville fritillary system as a natural laboratory within which he studied genetic and evolutionary processes, such as the influence of inbreeding on extinction risk and variation in selection for dispersal traits generated by landscape variation. During the last years of his career, Hanski's work was in the forefront of the rapidly developing field of eco-evolutionary dynamics. Hanski was a pioneer in showing how molecular-level underpinnings of trait variation can explain why evolutionary change can occur rapidly in natural populations and how these changes can subsequently influence ecological dynamics.

Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.

The Arctic may seem remote, but the unprecedented environmental changes occurring there have important consequences for global society. Of all Arctic system components, changes in permafrost (perennially frozen ground) are one of the least documented. Permafrost is degrading as a result of climate warming, and evidence is mounting that changing permafrost will have significant impacts within and outside the region. This review asks: What are key structural and functional properties of ecosystems that interact with changing permafrost, and how do these ecosystem changes affect local and global society? Here, we look beyond the classic definition of permafrost to include a broadened focus on the composition of frozen ground, including the ice and the soil organic carbon content, and how it is changing. This ecological perspective of permafrost serves to identify areas of both vulnerability and resilience as climate, ecological disturbance regimes, and the human footprint all continue to change in this sensitive and critical region of Earth.

Parallel evolution across replicate populations has provided evolutionary biologists with iconic examples of adaptation. When multiple populations colonize seemingly similar habitats, they may evolve similar genes, traits, or functions. Yet, replicated evolution in nature or in the laboratory often yields inconsistent outcomes: Some replicate populations evolve along highly similar trajectories, whereas other replicate populations evolve to different extents or in distinct directions. To understand these heterogeneous outcomes, biologists are increasingly treating parallel evolution not as a binary phenomenon but rather as a quantitative continuum ranging from parallel to nonparallel. By measuring replicate populations’ positions along this (non)parallel continuum, we can test hypotheses about evolutionary and ecological factors that influence the extent of repeatable evolution. We review evidence regarding the manifestation of (non)parallel evolution in the laboratory, in natural populations, and in applied contexts such as cancer. We enumerate the many genetic, ecological, and evolutionary processes that contribute to variation in the extent of parallel evolution.

Adaptive phenotypic plasticity provides a mechanism of developmental rescue in novel and rapidly changing environments. Understanding the underlying mechanism of plasticity is important for predicting both the likelihood that a developmental response is adaptive and associated life-history trade-offs that could influence patterns of subsequent evolutionary rescue. Although evolved developmental switches may move organisms toward a new adaptive peak in a novel environment, such mechanisms often result in maladaptive responses. The induction of generalized physiological mechanisms in new environments is relatively more likely to result in adaptive responses to factors such as novel toxins, heat stress, or pathogens. Developmental selection forms of plasticity, which rely on within-individual selective processes, such as shaping of tissue architecture, trial-and-error learning, or acquired immunity, are particularly likely to result in adaptive plasticity in a novel environment. However, both the induction of plastic responses and the ability to be plastic through developmental selection come with significant costs, resulting in delays in reproduction, increased individual investment, and reduced fecundity. Thus, we might expect complex interactions between plastic responses that allow survival in novel environments and subsequent evolutionary responses at the population level.

Antarctica is enormous, cold, remote, and particularly sensitive to climate change. Most biological research below 60°S has focused on the isolated nature of the biota and how organisms have adapted to the cold and ice. However, biogeographic patterns in Antarctica and the Southern Ocean, and the processes explaining how those patterns came about, still await adequate explanation. Both terrestrial and marine organisms have been influenced by climatic change (e.g., glaciation), physical phenomena (e.g., oceanic currents), and/or potential barriers to gene flow (e.g., steep thermal gradients). Whereas the Antarctic region contains diverse and complex marine communities, terrestrial systems tend to be comparatively simple with limited diversity. Here, we challenge the current dogma used to explain the diversity and biogeographic patterns present in the Antarctic. We assert that relatively modern processes within the last few million years, rather than geo-logical events that occurred in the Eocene and Miocene, account for present patterns of biodiversity in the region. Additionally, reproductive life history stages appear to have little influence in structuring genetic patterns in the Antarctic, as currents and glacial patterns are noted to be more important drivers of organismal patterns of distribution. Finally, we highlight the need for additional sampling, high-throughput genomic approaches, and broad, multinational cooperation for addressing outstanding questions of Antarctic biogeography and biodiversity.

Dinosaurs were large-bodied land animals of the Mesozoic that gave rise to birds. They played a fundamental role in structuring Jurassic–Cretaceous ecosystems and had physiology, growth, and reproductive biology unlike those of extant animals. These features have made them targets of theoretical macroecology. Dinosaurs achieved substantial structural diversity, and their fossil record documents the evolutionary assembly of the avian body plan. Phylogeny-based research has allowed new insights into dinosaur macroevolution, including the adaptive landscape of their body size evolution, patterns of species diversification, and the origins of birds and bird-like traits. Nevertheless, much remains unknown due to incompleteness of the fossil record at both local and global scales. This presents major challenges at the frontier of paleobiological research regarding tests of macroecological hypotheses and the effects of dinosaur biology, ecology, and life history on their macroevolution.

Throughout Earth's history, drought has been a common crisis in terrestrial ecosystems; in human societies, it can cause famine, one of the Four Horsemen of the apocalypse. As the global hydrological cycle intensifies with global warming, deeper droughts and rewetting will alter, and possibly transform, ecosystems. Soil communities, however, seem more tolerant than plants or animals are to water stress—the main effects, in fact, on soil processes appear to be limited diffusion and the limited supply of resources to soil organisms. Thus, the rains that end a drought not only release soil microbes from stress but also create a resource pulse that fuels soil microbial activity. It remains unclear whether the effects of drought on soil processes result from drying or rewetting. It is also unclear whether the flush of activity on rewetting is driven by microbial growth or by the physical/chemical processes that mobilize organic matter. In this review, I discuss how soil water, and the lack of it, regulates microbial life and biogeochemical processes. I first focus on organismal-level responses and then consider how these influence whole-soil organic matter dynamics. A final focus is on how to incorporate these effects into Earth System models that can effectively capture dry–wet cycling.

Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.

The rate of evolution of population mean fitness informs how selection acting in contemporary populations can counteract environmental change and genetic degradation (mutation, gene flow, drift, recombination). This rate influences population increases (e.g., range expansion), population stability (e.g., cryptic eco-evolutionary dynamics), and population recovery (i.e., evolutionary rescue). We review approaches for estimating such rates, especially in wild populations. We then review empirical estimates derived from two approaches: mutation accumulation (MA) and additive genetic variance in fitness (IAw). MA studies inform how selection counters genetic degradation arising from deleterious mutations, typically generating estimates of <1% per generation. IAw studies provide an integrated prediction of proportional change per generation, nearly always generating estimates of <20% and, more typically, <10%. Overall, considerable, but not unlimited, evolutionary potential exists in populations facing detrimental environmental or genetic change. However, further studies with diverse methods and species are required for more robust and general insights.

Coexisting species may be evolutionarily proximate or distant, resulting in phylogenetically poor or rich communities. This variation is often considered to result from present assembly processes. We argue that, under certain conditions, deep-past processes might control the phylogenetic diversity of communities. First, deep-past effects involve macroevolutionary processes, such as diversification rate, niche conservatism, or dispersal, in the lineages that constitute communities. Second, deep-past processes in the respective region or in the habitat type play a role, for instance, through age, area, stability, or connectivity. Third, the deep past may affect communities via trophic interactions (i.e., communities of enemies or mutualists or communities of hosts). We suggest that deep-past effects can be identified in local communities by measuring phylogenetic diversity in different species pools. We also show how community phylogenetic diversity results in positive or negative eco-evolutionary feedback, and we identify present-day conservation challenges that may profit from a deep-time perspective.

We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution.

For this article, I reviewed empirical studies finding significant ecological responses to habitat fragmentation per se—in other words, significant responses to fragmentation independent of the effects of habitat amount (hereafter referred to as habitat fragmentation). I asked these two questions: Are most significant responses to habitat fragmentation negative or positive? And do particular attributes of species or landscapes lead to a predominance of negative or positive significant responses? I found 118 studies reporting 381 significant responses to habitat fragmentation independent of habitat amount. Of these responses, 76% were positive. Most significant fragmentation effects were positive, irrespective of how the authors controlled for habitat amount, the measure of fragmentation, the taxonomic group, the type of response variable, or the degree of specialization or conservation status of the species or species group. No support was found for predictions that most significant responses to fragmentation should be negative in the tropics, for species with larger movement ranges, or when habitat amount is low; most significant fragmentation effects were positive in all of these cases. Thus, although 24% of significant responses to habitat fragmentation were negative, I found no conditions in which most responses were negative. Authors suggest a wide range of possible explanations for significant positive responses to habitat fragmentation: increased functional connectivity, habitat diversity, positive edge effects, stability of predator–prey/host–parasitoid systems, reduced competition, spreading of risk, and landscape complementation. A consistent preponderance of positive significant responses to fragmentation implies that there is no justification for assigning lower conservation value to a small patch than to an equivalent area within a large patch—instead, it implies just the opposite. This finding also suggests that land sharing will usually provide higher ecological value than land sparing.

Ecological networks have a long history in ecology, and a recent increase in network analyses across environmental gradients has revealed important changes in their structure, dynamics, and functioning. These changes can be broadly grouped according to three nonexclusive mechanisms: (a) changes in the species composition of the networks (driven by interaction patterns of invaders, nonrandom extinction of species according to their traits, or differences among species in population responses across gradients); (b) changes that alter interaction frequencies via changes in search efficiency (driven by altered habitat structure or metabolic rates) or changes in spatial and temporal overlap; and (c) changes to coevolutionary processes and patterns. Taking spatial and temporal processes into account can further elucidate network variation and improve predictions of network responses to environmental change. Emerging evidence links network structure to ecosystem functioning; however, scaling up to metanetworks or multilayer networks may modify interpretations of network structure, stability, and functioning.

The use of artificial lighting to illuminate the night has provided substantial benefits to humankind. It has also disrupted natural daily, seasonal, and lunar light cycles as experienced by a diversity of organisms, and hence it has also altered cues for the timings of many biological activities. Here we review the evidence for impacts of artificial nighttime lighting on these timings. Although the examples are scattered, concerning a wide variety of species and environments, the breadth of such impacts is compelling. Indeed, it seems reasonable to conclude that the vast majority of impacts of artificial nighttime lighting stem from effects on biological timings. This adds support to arguments that artificial nighttime lighting has a quite pervasive and marked impact on ecological systems, that the rapid expansion in the global extent of both direct illuminance and skyglow is thus of significant concern, and that a widespread implementation of mitigation measures is required.

Resolving the genealogy of life—the phylogenetic relationships that describe the evolutionary history of species—remains one of the great challenges of systematic biology. The recent proliferation of DNA sequencing technologies has sparked a rapid increase in the volume of genetic data being applied to phylogenetic studies. Single nucleotide polymorphism (SNP) data, ubiquitous genetic markers once considered reserved for population genetic studies, are now being applied in phylogenetics research at deep evolutionary timescales. The potential for SNPs to resolve contentious phylogenetic problems while researchers also investigate population demographics is promising, yet serious challenges remain with respect to data collection, assembly, modeling, and analysis. The low cost and ease of collecting SNPs suggest that they will remain an important source of genetic information for inferring phylogenies across time periods ranging from the Anthropocene to the Cretaceous.

Sexual selection plays several intricate and complex roles in the related processes of local adaptation and speciation. In some cases sexual selection can promote these processes, but in others it can be inhibitory. We present theoretical and empirical evidence supporting these dual effects of sexual selection during local adaptation, allopatric speciation, and speciation with gene flow. Much of the empirical evidence for sexual selection promoting speciation is suggestive rather than conclusive; we present what would constitute strong evidence for sexual selection driving speciation. We conclude that although there is ample evidence that sexual selection contributes to the speciation process, it is very likely to do so only in concert with natural selection.

Ongoing increases in air temperature and changing precipitation patterns are altering water temperatures and flow regimes in lotic freshwater systems, and these changes are expected to continue in the coming century. Freshwater taxa are responding to these changes at all levels of biological organization. The generation of appropriate hydrologic and water temperature projections is critical to accurately predict the impacts of climate change on freshwater systems in the coming decade. The goal of this review is to provide an overview of how changes in climate affect hydrologic processes and how climate-induced changes in freshwater habitat can impact the life histories and traits of individuals, and the distributions of freshwater populations and biodiversity. Projections of biological responses during the coming century will depend on accurately representing the spatially varying sensitivity of physical systems to changes in climate, as well as acknowledging the spatially varying sensitivity of freshwater taxa to changes in environmental conditions.

Mating in seed plants arises from interactions between plant traits and the environmental and demographic context in which individuals reside. These interactions commonly cause nonrandom mating, including selfing and promiscuous outcrossing within local neighborhoods. Shared features of seed plants, specifically immobility, hermaphroditism, and modularity, shape the essential character of mating mediated by animals, wind, and water. In addition, diverse floral strategies promote cross- and self-mating, depending on environmental circumstances. Extrinsic ecological factors influence all stages of the mating process—pollination, pollen-tube growth, ovule fertilization—as well as seed development, determining offspring quantity and quality. Traditionally, measures of plant mating systems have focused on a single axis of variation, the maternal outcrossing rate. Instead, we argue for an expanded perspective encompassing mating portfolios, which include all offspring to which individuals contribute genetically as maternal or paternal parents. This approach should expose key ecological determinants of mating-system variation and their evolutionary consequences.

Phenology is a key aspect of plant and animal life strategies that determines the ability to capture seasonally variable resources. It defines the season and duration of growth and reproduction and paces ecological interactions and ecosystem functions. Phenology models have become a key component of models in agronomy, forestry, ecology, and biogeosciences. Plant and animal process-based phenology models have taken different paths that have so far not crossed. Yet, they share many features because plant and animal annual cycles also share many characteristics, from their stepwise progression, including a resting period, to their dependence on similar environmental factors. We review the strengths and shortcomings of these models and the divergences in modeling approaches for plants and animals, which are mostly due to specificities of the questions they tackle. Finally, we discuss the most promising avenues and the challenges phenology modeling needs to address in the upcoming years.