Annual Review of Ecology, Evolution, and Systematics - Current Issue

Species diversification—the balance between speciation and extinction—is fundamental to our understanding of how species richness varies in space and time and throughout the Tree of Life. Phylogenetic approaches provide insights into species diversification by enabling support for alternative diversification scenarios to be compared and speciation and extinction rates to be estimated. Here, we review the current toolkit available for conducting such analyses. We first highlight how modeling efforts over the past decade have fostered a notable transition from overly simplistic evolutionary scenarios to a more nuanced understanding of how and why diversification rates vary through time and across lineages. Using the latitudinal diversity gradient as a case study, we then illustrate the impact that modeling choices can have on the results obtained. Finally, we review recent progress in two areas that are still lagging behind: phylogenetic insights into microbial diversification and the speciation process.

There is broad concern that the range shifts of global flora and fauna will not keep up with climate change, increasing the likelihood of population declines and extinctions. Many populations of nonnative species already have advantages over native species, including widespread human-aided dispersal and release from natural enemies. But do nonnative species also have an advantage with climate change? Here, we review observed and potential range shifts for native and nonnative species globally. We show that nonnative species are expanding their ranges orders of magnitude faster than native species, reflecting both traits that enable rapid spread and ongoing human-mediated introduction. We further show that nonnative species have large potential ranges and range expansions with climate change, likely due to a combination of widespread introduction and broader climatic tolerances. With faster spread rates and larger potential to persist or expand, nonnative populations have a decided advantage in a changing climate.

Successful invasive species commonly depend on the establishment of mutualistic interactions with native and nonnative biota. In turn, invasive species can affect native mutualisms and community stability. Here, we examine different forms of mutualist acquisition by invasive species and the causes and consequences of mutualism abandonment for invasion processes. Additionally, we delve into the quantitative and qualitative effects of invaders on native biota via mutualism disruption that can occur through direct and diverse indirect pathways. These effects of invasive species on native biota via mutualistic interactions can often be a consequence of the invaders’ abundance, which should be considered a prime predictor when evaluating the impact of invasive species on native mutualisms and community stability. We propose that the ecological as well as the evolutionary consequences of mutualism disruption and switches caused by invasive species can play crucial roles in determining future biodiversity.

Ecological networks of species interactions are popular and provide powerful analytical tools for understanding variation in community structure and ecosystem functioning. However, network analyses and commonly used metrics such as nestedness and connectance have also attracted criticism. One major concern is that observed patterns are misinterpreted as niche properties such as specialization, whereas they may instead merely reflect variation in sampling, abundance, and/or diversity. As a result, studies potentially draw flawed conclusions about ecological function, stability, or coextinction risks. We highlight potential biases in analyzing and interpreting species-interaction networks and review the solutions available to overcome them, among which we particularly recommend the use of null models that account for species abundances. We show why considering variation across species and networks is important for understanding species interactions and their consequences. Network analyses can advance knowledge on the principles of species interactions but only when judiciously applied.

Animals with close social relationships often have similar microbiomes. These socially structured microbiomes can arise through multiple mechanisms that are often difficult to disentangle, including transmission between social partners or via socially structured, shared environments. Here, we review evidence for socially structured microbiomes and propose methods to differentiate the mechanisms that give rise to them. We discuss the evolutionary implications of these mechanisms for both hosts and their microbiomes, including the possibility that social transmission selects for host-specialized microbiomes. We conclude by identifying outstanding questions related to social microbiomes and their implications for social evolution. We identify new or underutilized approaches like longitudinal study designs, strain-sharing analysis, and culture-based characterization to address these outstanding questions.

The continuous process of decision-making in animals is crucial for their survival. For example, when deciding when, where, and with whom to forage, they need to consider their internal state, previous experience, and social information in addition to external factors such as food distribution and weather conditions. Studying animal decision-making in the wild is a complicated task due to the complexity of the process, which requires continuous monitoring of the examined individual and its environment. Here, we review the most advanced methods to examine decision-making from an individual point of view, namely tracking technologies to monitor the movement of an individual, the sensory information available to it, the presence and behavior of other animals around it, and its surrounding environment. We provide examples for studying decision-making during competition, examining the ontogeny of decision-making, and describing the importance of long-term monitoring and field manipulation for understanding decision processes throughout different life stages.

Deadwood represents a significant carbon pool and unique biodiversity reservoir in forests and savannas but has been largely overlooked until recently. Storage and release of carbon from deadwood is controlled by interacting decomposition drivers including biotic consumers (animals and microbes) and abiotic factors (water, fire, sunlight, and freeze–thaw). Although previous research has focused mainly on forests, we synthesize deadwood studies across diverse ecosystems with woody vegetation. As changing climates and land-use practices alter the landscape, we expect accelerating but variable rates of inputs and outputs from deadwood pools. Currently, Earth system models implicitly represent only microbial consumers as drivers of wood decomposition; we show that many other factors influence deadwood pools. Forest management practices increasingly recognize deadwood as an important contributor to forest dynamics, biodiversity, and carbon budgets. Together, emerging knowledge from modeling and management suggests a growing need for additional research on deadwood contributions to carbon storage and greenhouse gas emissions.

The globalization of trade and increased human mobility have facilitated the introduction and spread of nonnative species, posing significant threats to biodiversity and human well-being. As centers of global trade and human populations, cities are foci for the introduction, establishment, and spread of nonnative species. We present a global synthesis of urban characteristics that drive biological invasions within and across cities, focusing on four axes: (a) connectivity, (b) physical properties, (c) culture and socioeconomics, and (d) biogeography and climate. Urban characteristics such as increased connectivity within and among cities, city size and age, and wealth emerged as important drivers of nonnative species diversity and spread, while the relative importance of biogeographic and climate drivers varied considerably. Elaborating how these characteristics shape biological invasions in cities is crucial for designing and implementing strategies to mitigate the impacts of invasions on ecological systems and human well-being.

Phylogenetic comparative methods are important tools in biology, providing insights into the way traits evolve. There are many technical resources describing how these methods work. Our aim here is to complement these with an overview of the types of biological questions that can be addressed by different methods and to outline potential pitfalls and considerations when embarking on comparative studies. First, we introduce what comparative methods are and why they are important. Second, we outline how they can be used to understand when, where, and how frequently traits evolve. Third, we examine how the coevolution of traits within and between species can be studied, along with patterns of causality. Finally, we discuss how to approach comparative analyses and the ways in which different types of data, such as published relationships, omic, and remote sensing data, can be integrated.

Animal linguistics is an interdisciplinary field that integrates animal behavior, linguistics, and cognitive science to explore issues such as (a) what animal signals mean, (b) what cognitive abilities are necessary for the production and understanding of these signals, and (c) how communication systems have evolved. Despite the traditional belief that language evolved through a single mutation in our ancestors, accumulating evidence suggests that many cognitive abilities underlying human language have also evolved in nonhuman animals. For example, several species of birds and nonhuman primates convey conceptual meanings through specific vocalizations and/or combine multiple meaning-bearing calls into sequences using syntactic rules. Using experimental paradigms inspired by cognitive science and linguistics, animal linguistics aims to uncover the cognitive mechanisms underlying animal language and explores its evolutionary principles. This review examines previous studies exploring the meanings and cognitive abilities underlying animal language and introduces key methodologies in this emerging field.

Arctic ecosystems have long been thought to be minimal sources of volatile organic compounds (VOCs) to the atmosphere because of their low plant biomass and cold temperatures. However, these ecosystems experience rapid climatic warming that alters vegetation composition. Tundra vegetation VOC emissions have stronger temperature dependency than current emission models estimate. Thus, warming, both directly and indirectly (via vegetation changes) likely increases the release and alters the blend of emitted plant volatiles, such as isoprene, monoterpenes, and sesquiterpenes, from Arctic ecosystems. Climate change also increases the pressure of both background herbivory and insect outbreaks. The resulting leaf damage induces the production of volatile defense compounds, and warming amplifies this response. Soils function as both sources and sinks of VOCs, and thawing permafrost is a hotspot for soil VOC emissions, contributing to ecosystem emissions if the VOCs bypass microbial uptake. Overall, Arctic VOC emissions are likely to increase in the future, with implications for ecological interactions and atmospheric composition.

Early studies in coral reefs showed that simple measurements of ecosystem metabolism (primary production and ecosystem respiration) were useful for understanding complex reef dynamics at an ecosystem scale. These studies also helped establish the field of ecosystem ecology, but contemporary coral reef ecology has shifted away from these origins. In this manuscript, I describe the historical development of a theory of ecosystem metabolism that was foundational for the discipline of ecosystem ecology, and I update this theory to fully incorporate dynamics on coral reefs (and all ecosystems). I use this updated theory to (a) identify important controls on coral reef processes and (b) provide a rationale for patterns of coral reef carbon dynamics that allow me to generate hypotheses of coral reef ecosystem production. I then use existing data to broadly evaluate these hypotheses. My findings emphasize the importance of integrating measurements of ecosystem metabolism with current approaches to improve the development of theory and the efficacy of conservation and management of coral reefs.

Globally, winter temperatures are rising, and snowpack is shrinking or disappearing entirely. Despite previous research and published literature reviews, it remains unknown whether biomes across the globe will cross important thresholds in winter temperature and precipitation that will lead to significant ecological changes. Here, we combine the widely used Köppen–Geiger climate classification system with worst-case-scenario projected changes in global monthly temperature and precipitation to illustrate how multiple climatic zones across Earth may experience shifting winter conditions by the end of this century. We then examine how these shifts may affect ecosystems within corresponding biomes. Our analysis demonstrates potential widespread losses of extreme cold (<−20°C) in Arctic, boreal, and cool temperate regions. We also show the possible disappearance of freezing temperatures (<0°C) and large decreases in snowfall in warm temperate and dryland areas. We identify important and potentially irreversible ecological changes associated with crossing these winter climate thresholds.

The approximately 320 atolls of the world, scattered across the tropical oceanic basins, constitute a unique type of ecosystem in that they are each an integrated unit consisting of island, coral reef, and lagoon components. Atolls have a complex geology, ecology, and biogeography, which can be fully appreciated only by transcending the classic boundary thinking of marine and terrestrial realms. The atolls we observe today were shaped by Quaternary sea-level fluctuations, which imposed strong environmental filters on their communities. As entirely biogenic, reef-borne structures, the islands of atolls depend upon marine productivity, which catalyzes island community assembly. Island species communities exist in complex dynamic equilibria with the surrounding oceanographic conditions. Energy fluxes and element cycles of the atoll system readily cross habitat boundaries and create a productive, diverse, and biomass-rich ecosystem on land and underwater. Past human disturbances and future global change put atolls at the forefront of conservation and ecological restoration.

Beavers, Castor canadensis in North America and Castor fiber in Eurasia, are widely referred to as nature's engineers due to their ability to rapidly transform diverse landscapes into dynamic wetland ecosystems. Few other organisms exhibit the same level of control over local geomorphic, hydrologic, and ecological conditions. Though freshwater ecosystems are particularly vulnerable to changing climate, beavers and their wetland homes have persisted throughout the Northern Hemisphere during numerous prior periods of climatic change. Some research suggests that the need to create stable, climate-buffered habitats at high latitudes during the Miocene directly led to the evolution of dam construction. As we follow an unprecedented trajectory of anthropogenic warming, we have the unique opportunity to describe how beaver ecosystem engineering ameliorates climate change today. Here, we review how beavers create and maintain local hydroclimatic stability and influence larger-scale biophysical ecosystem processes in the context of past, present, and future climate change.

Kin discrimination, the differential treatment of conspecifics based on kinship, occurs across the tree of life, from animals to plants to fungi to bacteria. When kin and nonkin interact, the ability to identify kin enables individuals to increase their inclusive fitness by helping kin, harming nonkin, and avoiding inbreeding. For a given species, the strength of selection for kin discrimination mechanisms is influenced by demographic, ecological, and life-history processes that collectively determine the scope for discrimination and the payoffs from kin-biased behavior. In this review, we explore how these processes drive variation in kin discrimination across taxa, highlighting contributions of recent empirical, comparative, and theoretical work to our understanding of when, how, and why kin discrimination evolves.

The idea that species interactions are more ecologically and evolutionarily important toward lower latitudes underpins seminal theories in ecology and evolution. Recent global studies have found the predicted latitudinal gradients in interactions, particularly predation. However, latitudinal patterns alone do not reveal why interactions vary geographically and so do not provide strong predictions in space (e.g., for specific ecosystems) or time (e.g., forecasting responses to global change). Here, I review theory to identify a clearer, mechanistic, and testable framework for predicting geographic variation in the importance of species interactions. I review competing metrics of importance, proximate mechanisms that can increase interaction importance, and environmental gradients that could generate predictable geographic patterns (climate extremes and stability, warmer temperatures, productivity, and biodiversity). Strong empirical tests are accumulating thanks to the rise of global experiments and datasets; renewed focus on testing why interactions vary spatially will help move the field from identifying latitudinal patterns to understanding broader mechanisms.

Forbs are important contributors to species diversity and ecosystem functions in low-latitude grasslands, where they support diverse herbivore communities and millions of people. Native forb assemblages tolerate disturbances and physiological stressors (fire, herbivory, drought, and frost) that together have shaped their exceptional functional diversity. Yet, compared to trees and grasses, forbs have received much less attention in grassland studies until recently. Here, we review forb-centric literature to illustrate that land conversion and responsible management of fire and herbivory are crucial to maintaining forb diversity. Management practices promoting forb diversity offer (a) high-quality food items and medicinal resources that support rural livelihoods and animal diversity (from wild ungulates and livestock to fossorial rodents and insects), including their adaptive foraging patterns, and (b) carbon and nutrient inputs that regulate belowground processes. Improved understanding of the above- and belowground regeneration strategies of forbs is critical for restoration and conservation to secure their services in future old-growth tropical and subtropical grasslands.

As the Anthropocene proceeds, the matrix in which remaining habitats are embedded is an increasingly dominant component of altered landscapes. The matrix appears to have diverse and far-reaching effects, yet our understanding of the causes and consequences of these effects remains limited. We first synthesize the broad range of perspectives on the matrix, provide a generalized framing that captures these perspectives, and propose hypotheses for how and why the matrix matters for ecological and evolutionary processes. We then summarize evidence for these hypotheses from experiments in which the matrix was manipulated. Nearly all experiments revealed matrix effects, including changes in local spillover, individual movement and dispersal, and use of resources in the matrix. Finally, we discuss how the matrix has been, and should be, incorporated into conservation and management and suggest future issues to advance research on and applications of the matrix in ecology, evolution, and conservation.

Despite two centuries of research, the mechanisms underlying the formation of species’ elevational range limits remain poorly understood. The climatic variability hypothesis highlights the role of climatic conditions in shaping species’ thermal tolerance and distribution ranges, while the species interactions–abiotic stress hypothesis underscores the relative importance of biotic factors and abiotic stress along environmental gradients. We emphasize Darwin's perspective on the ubiquity of interspecific competition across climatic gradients and the importance of understanding how climate modulates biotic interactions to shape species distributions. Niche theory provides a comprehensive framework, combined with empirical research, to explore how environmental gradients influence species traits, leading to context-dependent species interactions that constrain distributions. In particular, the application of the concept of environmentally weighted performance can further elucidate these complex ecological mechanisms. Future research should integrate multiple approaches, including field and laboratory manipulative experiments, theoretical modeling, and interdisciplinary collaboration, to improve our understanding of species distributions in mountain regions and to inform biodiversity conservation strategies in the face of rapid environmental change.