Annual Review of Ecology, Evolution, and Systematics - Volume 46, 2015

The order and timing of species immigration during community assembly can affect species abundances at multiple spatial scales. Known as priority effects, these effects cause historical contingency in the structure and function of communities, resulting in alternative stable states, alternative transient states, or compositional cycles. The mechanisms of priority effects fall into two categories, niche preemption and niche modification, and the conditions for historical contingency by priority effects can be organized into two groups, those regarding regional species pool properties and those regarding local population dynamics. Specifically, two requirements must be satisfied for historical contingency to occur: The regional pool contains species that can together cause priority effects, and local dynamics are rapid enough for early-arriving species to preempt or modify niches before other species arrive. Organizing current knowledge this way reveals an outstanding key question: How are regional species pools that yield priority effects generated and maintained?

Theories of how species evolve in changing environments mostly consider single species in isolation or pairs of interacting species. Yet all organisms live in diverse communities containing many hundreds of species. This review discusses how species interactions influence the evolution of constituent species across whole communities. When species interactions are weak or inconsistent, evolutionary dynamics should be predictable by factors identified by single-species theory. Stronger species interactions, however, can alter evolutionary outcomes and either dampen or promote evolution of constituent species depending on the number of species and the distribution of interaction strengths across the interaction network. Genetic interactions, such as horizontal gene transfer, might also affect evolutionary outcomes. These evolutionary mechanisms in turn affect whole-community properties, such as the level of ecosystem functioning. Successful management of both ecosystems and focal species requires new understanding of evolutionary interactions across whole communities.

Here we review the population, community, and evolutionary consequences of marine reserves. Responses at each level depend on the tendency of fisheries to target larger body sizes and the tendency for greater reserve protection with less movement within and across populations. The primary population response to reserves is survival to greater ages and sizes plus increases in the population size for harvested species, with greater response to reserves that are large relative to species' movement rates. The primary community response to reserves is an increase in total biomass and diversity, with the potential for trophic cascades and altered spatial patterning of metacommunities. The primary evolutionary response to reserves is increased genetic diversity, with the theoretical potential for protection against fisheries-induced evolution and selection for reduced movement. The potential for the combined outcome of these responses to buffer marine populations and communities against temporal environmental heterogeneity has preliminary theoretical and empirical support.

Alien herpetofauna have a broad diversity of ecological and evolutionary impacts, involving seven mechanisms. Ecological impacts usually result from trophic disruptions and may be direct or indirect and top-down or bottom-up; they may vary in scale from single species to communities. A single species may impose impacts involving most or all of these categories. Evolutionary impacts most often result from hybridization and introgression but may include diverse changes in native fauna induced by selection. Impact magnitudes observed to date largely range from moderate to major, but massive impacts (including species extinction) are known for a handful of invasive species. Research remains skewed toward a small sample of all invaders, and major research gaps remain in understanding community-level impacts, the risk posed by competition, determinants of predation impact, the relevance of genetic diversity to impacts, and how to predict impacts.

Understanding and reversing the widespread population declines of birds require estimating the magnitude of all mortality sources. Numerous anthropogenic mortality sources directly kill birds. Cause-specific annual mortality in the United States varies from billions (cat predation) to hundreds of millions (building and automobile collisions), tens of millions (power line collisions), millions (power line electrocutions, communication tower collisions), and hundreds of thousands (wind turbine collisions). However, great uncertainty exists about the independent and cumulative impacts of this mortality on avian populations. To facilitate this understanding, additional research is needed to estimate mortality for individual bird species and affected populations, to sample mortality throughout the annual cycle to inform full life-cycle population models, and to develop models that clarify the degree to which multiple mortality sources are additive or compensatory. We review sources of direct anthropogenic mortality in relation to the fundamental ecological objective of disentangling how mortality sources affect animal populations.

Mobilization of DNA by horizontal gene transfer (HGT) is an important process in the evolution of many organisms because it allows the recipient lineage to rapidly acquire metabolic innovations and adapt to new ecological niches. However, the significance of HGT in specific ecosystems remains poorly understood. In this review, we present major findings that illustrate how HGT affects managed ecosystems, such as farmlands, orchards, pastures, and managed grasslands. First, acquisition of functions via HGT can lead to the emergence of novel or more virulent pathogens and parasites of crops by allowing them to circumvent host defenses and currently used pest management approaches. Second, HGT of antibiotic resistance genes from the application of wastewater effluent for irrigation or manure as fertilizer can facilitate the emergence of highly resistant microbial lineages. Lastly, HGT can enhance the functional diversity of microbial communities and potentially influence biogeochemical processes. Characterization of lineages possessing horizontally acquired genetic material and their ecology will aid in enhancing the productivity and sustainability of managed ecosystems. We conclude with recommendations for key research directions that will advance our understanding of the causes and consequences of HGT in managed ecosystems.

Ecological resilience is the ability of a system to persist in the face of perturbations. Although resilience has been a highly influential concept, its interpretation has remained largely qualitative. Here we describe an emerging family of methods for quantifying resilience on the basis of observations. A first set of methods is based on the phenomenon of critical slowing down, which implies that recovery upon small perturbations becomes slower as a system approaches a tipping point. Such slowing down can be measured experimentally but may also be indirectly inferred from changes in natural fluctuations and spatial patterns. A second group of methods aims to characterize the resilience of alternative states in probabilistic terms based on large numbers of observations as in long time series or satellite images. These generic approaches to measuring resilience complement the system-specific knowledge needed to infer the effects of environmental change on the resilience of complex systems.

Although competition is recognized as a core ecological process, its prevalence and importance in coral reef fish communities have been debated. Here we compile and synthesize the results of 173 experimental tests of competition from 72 publications. We show that evidence for competition is pervasive both within and between species, with 72% of intraspecific tests and 56% of interspecific tests demonstrating a demographically significant consequence of competition (e.g., a decrease in recruitment, survival, growth, or fecundity). We highlight several factors that can interact with the effects of competition and make it more difficult to detect in field experiments. In light of this evidence, we discuss the role of competition in shaping coral reef fish communities and competition's status as one of several processes that contribute to species coexistence. Finally, we consider some of the complex ways that climate change may influence competition, and we provide suggestions for future research.

Coevolution is among the most important evolutionary processes that generate biological diversity. Plant–pollinator interactions play a prominent role in the evolution of reproductive traits in flowering plants. Likewise, plant–herbivore interactions select for myriad defenses that protect plants from damage. These mutualistic and antagonistic interactions, respectively, have traditionally been considered in isolation from one another. Here, we consider whether reproductive traits and antiherbivore defenses are interdependent as a result of pollinator- and herbivore-mediated selection. The evolution of floral traits, self-fertilization, and separate sexes frequently affects the expression and evolution of plant defenses. In turn, the evolution of defense can affect allocation to reproductive traits, and herbivores often impose strong selection directly on floral traits. Theory and empirical evidence suggest that herbivores can influence the evolution of selfing from outcrossing and potentially the evolution of separate sexes from combined sexes. We identify several areas in which future research is needed to increase our understanding of the evolutionary interplay between reproduction and defense in plants.

Living animals display a variety of morphological, physiological, and biochemical characters that enable them to live in low-oxygen environments. These features and the organisms that have evolved them are distributed in a regular pattern across dioxygen (O2) gradients associated with modern oxygen minimum zones. This distribution provides a template for interpreting the stratigraphic covariance between inferred Ediacaran-Cambrian oxygenation and early animal diversification. Although Cambrian oxygen must have reached 10–20% of modern levels, sufficient to support the animal diversity recorded by fossils, it may not have been much higher than this. Today's levels may have been approached only later in the Paleozoic Era. Nonetheless, Ediacaran-Cambrian oxygenation may have pushed surface environments across the low, but critical, physiological thresholds required for large, active animals, especially carnivores. Continued focus on the quantification of the partial pressure of oxygen (pO2) in the Proterozoic will provide the definitive tests of oxygen-based coevolutionary hypotheses.

Learning how complex traits like eyes originate is fundamental for understanding evolution. In this review, we first sketch historical perspectives on trait origins and argue that new technologies afford key new insights. Next, we articulate four open questions about trait origins. To address them, we define a research program to break complex traits into component parts and to study the individual evolutionary histories of those parts. By doing so, we can learn when the parts came together and perhaps understand why they stayed together. We apply this approach to five structural innovations critical for complex eyes and review the history of the parts of each of those innovations. Eyes evolved within animals by tinkering: creating new functional associations between genes that usually originated far earlier. Multiple genes used in eyes today had ancestral roles in stress responses. We hypothesize that photo-oxidative stress had a role in eye origins by increasing the chance that those genes were expressed together in places on animals where light was abundant.

Around the world the development and growth of cities and towns are having a significant impact on local and global biodiversity. There is growing interest in the adaptation of nonhuman organisms to urban environments, and we distinguish between the concepts of adaptation and adaptedness. Most of these studies have focused on animals, especially birds. Commonly recorded responses to urban environments include regulatory and acclimatory responses involving changes in behavior, communication, and physiology. Developmental responses tend to be morphological in nature but can also involve cultural learning. There is growing evidence of microevolutionary changes associated with adaptive responses to urban environments. This review also highlights the urgent need to refine the terminology currently used to describe the adaptation of organisms to urban environments in order to improve scientific understanding and more effectively identify and communicate the actions required to create biodiversity- and adaptation-friendly cities and towns for the future.

Coral reefs are considered one of the ecosystems most vulnerable to ongoing global climate change. However, geographic and taxonomic responses to climate change are highly variable, and fundamental aspects of key research approaches remain unresolved, leaving substantial uncertainty in our ability to predict the future of coral reefs. I review the ecological and evolutionary response of coral reefs to climate change in a broad temporal context, primarily focusing on tropical reef corals. I show critical gaps in our understanding that impede accurate prediction of future responses. These gaps include the response of past reefs to global change, the interpretation of coral response to thermal stress and ocean acidification, how corals and other reef organisms might respond evolutionarily, and our approach to evaluating response to climate in the context of multiple stressors. Reducing uncertainty by filling these gaps and by incorporating variation in geographic and taxonomic response will substantially improve our ability to model coral reef futures and manage coral reefs.

We present strong evidence that pathogens play a critical role in structuring plant communities and maintaining plant diversity. Pathogens mediate plant species coexistence through trade-offs between competitive ability and resistance to pathogens and through pathogen specialization. Experimental tests of individual plant–pathogen interactions, tests of feedback through host-specific changes in soil communities, and field patterns and field experimentation consistently identify pathogens as important to plant species coexistence. These direct tests are supported by observations of the role of pathogens in generating the productivity gains from manipulations of plant diversity and by evidence that escape from native pathogens contributes to success of introduced plant species. Further work is necessary to test the role of pathogen dynamics in large-scale patterns of plant diversity and range limits, the robustness of coexistence to coevolutionary dynamics, the contribution of different pathogens, and the role of pathogens in plant succession.

At the heart of the analyses of landscape genetics are isolation models seeking to explain either interindividual or interpopulation connectivity. These models use spatial, ecological, and topographic predictor variables measured between sites in an attempt to explain observed genetic variation. During the past decade, these models have adopted an increasingly sophisticated set of techniques to quantify intervening physical and ecological spaces, although they are restrained by rather mundane approaches to characterizing the genetic components of connectivity. Population Graphs are one approach to improving the quantification of genetic covariance used in models of landscape genetics. I explain the construction of the Population Graph framework, explain its strengths and weaknesses, and provide examples of how it has been used during the past decade within the contexts of landscape and population genetics.

There is an urgent need to understand species and community responses to climatic and ecological changes to predict biodiversity patterns given anticipated global change. The current distribution of species and the environment provide a limited perspective to study and predict ecological responses; therefore, biodiversity responses to past environmental changes must be examined. The rapid development of ecological niche models (ENMs) and their use in reconstructing past species distributions has facilitated inclusion of past observations into predictive models. Paleodata offer an opportunity to test the predictive ability of ENMs and their underlying assumptions. However, paleodata remain underutilized despite the rapidly growing field of paleoinformatics. New modeling methods that incorporate species associations, coupled with paleodata, provide more robust approaches to studying species and community responses, especially given the predicted emergence of no-analog climates and communities in the future.

Recent studies have generated an explosion of phylogenetic and biogeographic data and have provided new tools to investigate the processes driving large-scale gradients in species diversity. Fossils and phylogenetic studies of plants and animals demonstrate that tropical regions are the source for almost all groups of organisms, and these groups are composed of a mixture of ancient and recently derived lineages. These findings are consistent with the hypothesis that the large extent of tropical environments during the past 10–50 million years, together with greater climatic stability, has promoted speciation and reduced extinction rates. Energy availability appears to only indirectly contribute to global patterns of species diversity, especially considering how some marine diversity gradients can be completely decoupled from temperature and productivity gradients. Instead, climate stability and time–integrated area together determine the baselines of both terrestrial and marine global diversity patterns. Biotic interactions likely augment diversification and coexistence in the tropics.

The flora of southern Africa is, for its latitude and area, very species-rich. Although the hyperdiverse Cape flora contributes almost half of this richness, three other radiations (desert, grassland, and woodland) contribute significantly to the botanical wealth of southern Africa. Each radiation occurs in a different ecological setting and has a different diversification history. Such parallel radiations can develop in suitably complex environments, given gradual change through time and no region-wide catastrophes. These four radiations cross-seeded each other, with clades spawning subclades in other radiations, thus linking all four into one complex radiation. This led to an increase in the number of diversifying clades in each radiation. Such complex radiations accumulate diversifying lineages over a long time, spawn daughter radiations on other continents, and become powerhouses of global-biodiversity generation. We suggest that several of the most species-rich regions may harbor such complex radiations.

Evolutionary constraint due to pleiotropy refers to a situation in which mutations in genes shared among traits generate trait covariance; therefore, traits that are not directly exposed to selective challenge show a correlated response. When such a correlated response is deleterious, it may constrain the trait from evolving. Here, we argue that the idea of absolute constraints draws from the perception that gene effects are inherent to alleles and thus invariant across genetic and environmental backgrounds. However, evidence from studies involving genetic effects on multiple traits, observed across different genetic backgrounds and environments, supports the notion that genes' effects on traits change. Consequently, pleiotropy also varies across backgrounds. We argue for a stronger emphasis on interaction effects when describing a trait's genetic basis and its evolutionary potential. By discussing different cases of trait individuation, we demonstrate how this approach can lead to new insights.

Using basic ecological concepts, we introduce sperm ecology as a framework to study sperm cells. First, we describe environmental effects on sperm and conclude that evolutionary and ecological research should not neglect the overwhelming evidence presented here (both in external and internal fertilizers and in terrestrial and aquatic habitats) that sperm function is altered by many environments, including the male environment. Second, we determine that the evidence for sperm phenotypic plasticity is overwhelming. Third, we find that genotype-by-environment interaction effects on sperm function exist, but their general adaptive significance (e.g., local adaptation) awaits further research. It remains unresolved whether sperm diversification occurs by natural selection acting on sperm function or by selection on male and female microenvironments that enable optimal plastic performance of sperm (sperm niches). Environmental effects reduce fitness predictability under sperm competition, predict species distributions under global change, explain adaptive behavior, and highlight the role of natural selection in behavioral ecology and reproductive medicine.