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

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

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

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

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

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

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

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

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

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

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

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

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

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

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,

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

Populations that experience severe stress may avoid extinction through adaptation by natural selection. This process is called evolutionary rescue and has been studied under different names in medicine, agriculture, and conservation biology. It is a component of the emerging field of eco-evolutionary dynamics, which investigates how the ecological attributes of species may evolve rapidly under strong

Receiver bias in plant–animal interactions is here defined as “selection mediated by behavioral responses of animals, where those responses have evolved in a context outside the interactions.” As a consequence, the responses are not necessarily linked to fitness gains in interacting animals. Thus, receiver bias can help explain seemingly maladaptive patterns of behavior in interacting animals and the

Ecological networks depict the interactions between species, mainly based on observations in the field. The information contained in such interaction matrices depends on the sampling design, and typically, compounds preferences (specialization) and abundances (activity). Null models are the primary vehicles to disentangle the effects of specialization from those of sampling and abundance, but they

We give an overview of recently developed methods to reconstruct phylog-enies of taxa that include allopolyploids that have originated in relatively recent times—in other words, taxa for which at least some of the parental lineages of lower ploidy levels are not extinct and for which ploidy information is clearly shown by variation in chromosome counts. We review how these methods have been applied

Most ecosystems have multiple-plant invaders rather than single-plant invaders, yet ecological studies and management actions focus largely on single invader species. There is a need for general principles regarding invader interactions across varying environmental conditions, so that secondary invasions can be anticipated and managers can allocate resources toward pretreatment or postremoval actions

Secondary tropical forests that are in a state of regeneration following clearing for agriculture are now more abundant than primary forests. Yet, despite their large spatial extent and important role in the global carbon (C) cycle, secondary tropical forests are understudied, which challenges our ability to predict how tropical landscapes will respond to future disturbance and global change. We summarize

To put marine disease impacts in context requires a broad perspective on the roles infectious agents have in the ocean. Parasites infect most marine vertebrate and invertebrate species, and parasites and predators can have comparable biomass density, suggesting they play comparable parts as consumers in marine food webs. Although some parasites might increase with disturbance, most probably decline

Most species have one or more natural enemies, e.g., predators, parasites, pathogens, and herbivores, among others. These species in turn typically attack multiple victim species. This leads to the possibility of indirect interactions among those victims, both positive and negative. The term apparent competition commonly denotes negative indirect interactions between victim species that arise because

Soil organic matter (SOM) anchors global terrestrial productivity and food and fiber supply. SOM retains water and soil nutrients and stores more global carbon than do plants and the atmosphere combined. SOM is also decomposed by microbes, returning CO2, a greenhouse gas, to the atmosphere. Unfortunately, soil carbon stocks have been widely lost or degraded through land use changes and unsustainable

Evolutionary biologists often predict the outcome of natural selection on an allele by measuring its effects on lifetime survival and reproduction of individual carriers. However, alleles affecting traits like sex, evolvability, and cooperation can cause fitness effects that depend heavily on differences in the environmental, social, and genetic context of individuals carrying the allele. This variability

Nervous systems are among the most spectacular products of evolution. Their provenance and evolution have been of interest and often the subjects of intense debate since the late nineteenth century. The genomics era has provided researchers with a new set of tools with which to study the early evolution of neurons, and recent progress on the molecular evolution of the first neurons has been both exciting

By facilitating plant reproduction, pollinators perform a crucial ecological function that supports the majority of the world's plant diversity, and associated organisms, and a significant fraction of global agriculture. Thus, pollinators are simultaneously vital to supporting both natural ecosystems and human food security, which is a unique position for such a diverse group of organisms. The past