Annual Review of Ecology, Evolution, and Systematics - Volume 45, 2014

We are witnessing a global, but unplanned, evolutionary experiment with the biodiversity of the planet. Anthropogenic disturbances such as habitat degradation and climate change result in evolutionary mismatch between the environments to which species are adapted and those in which they now exist. The impacts of unmanaged evolution are pervasive, but approaches to address them have received little attention. We review the evolutionary challenges of managing populations in the Anthropocene and introduce the concept of prescriptive evolution, which considers how evolutionary processes may be leveraged to proactively promote wise management. We advocate the planned management of evolutionary processes and explore the advantages of evolutionary interventions to preserve and sustain biodiversity. We show how an evolutionary perspective to conserving biodiversity is fundamental to effective management. Finally, we advocate building frameworks for decision-making, monitoring, and implementation at the boundary between management and evolutionary science to enhance conservation outcomes.

Originating most likely in the early Cretaceous, ants have diversified to become the world's most successful eusocial insects, occupying most terrestrial ecosystems and acquiring a global ecological footprint. Recent advances in our understanding of ant evolutionary history have been propelled by the use of molecular phylogenetic methods, in conjunction with a rich (and still growing) fossil record. Most extant ants belong to the formicoid clade, which contains ∼90% of described species and has produced the most socially advanced and dominant forms. The remaining ants are old lineages of predominantly cryptobiotic species whose relationships to one another and to the formicoids remain unclear. Rooting the ant tree is challenging because of (a) a long branch separating ants from their nearest outgroup, and (b) heterogeneity in evolutionary rates and base composition among ant lineages. These factors will need to be given careful consideration in future phylogenomic studies of ants.

A regional species pool comprises all species available to colonize a focal site. The roots of the concept are imbedded in island biogeography theory, supply-side ecology, and early propagule addition experiments. The pool concept allows ecologists to examine large-scale effects—including geographic area, evolutionary age, and immigration and diversification—on the diversity, composition, and phylogenetic structure of local communities. Both theory and evidence show that pool influences are greatest when local communities are not strongly and predictably structured by species interactions (e.g., under frequent disturbance or if many species are rare). Practical and conceptual issues to consider when delineating species pools include choosing an appropriate spatial scale, whether to account for environmental filtering, whether to include the species within a fixed geographic area versus those whose geographic ranges overlap with a site, or whether to use databases or geographic data sources. Each issue is discussed in the context of 63 studies using the species pool approach. We conclude that the species pool concept has contributed greatly to our understanding of community dynamics by bridging the gap between large and small spatial scales. Future studies must compare pool characteristics with community structure across multiple regions for a more complete understanding of community assembly.

Invasive species, often recognized as ecosystem engineers, can dramatically alter geomorphic processes and landforms. Our review shows that the biogeomorphic impacts of invasive species are common, but variable in magnitude or severity, ranging from simple acceleration or deceleration of preexisting geomorphic processes to landscape metamorphosis. Primary effects of invasive flora are bioconstruction and bioprotection, whereas primary effects of invasive fauna are bioturbation, bioerosion, and bioconstruction. Land-water interfaces seem particularly vulnerable to biogeomorphic impacts of invasive species. Although not different from biogeomorphic impacts in general, invasive species are far more likely to lead to major geomorphic changes or landscape metamorphosis, which can have long-lasting impacts. In addition, invasive species can alter selection pressures in both macroevolution and microevolution by changing geomorphic processes. However, the differing timescales of biological invasions, landscape evolution, and biological evolution complicate assessment of the evolutionary impacts of invasive organisms.

Mutualisms structure ecosystems and mediate their functioning. They also enhance invasions of many alien species. Invasions disrupt native mutualisms, often leading to population declines, reduced biodiversity, and altered ecosystem functioning. Focusing on three main types of mutualisms (pollination, seed dispersal, and plant-microbial symbioses) and drawing on examples from different ecosystems and from species- and community-level studies, we review the key mechanisms whereby such positive interactions mediate invasions and are in turn influenced by invasions. High interaction generalization is “the norm” in most systems, allowing alien species to infiltrate recipient communities. We identify traits that influence invasiveness (e.g., selfing capacity in plants, animal behavioral traits) or invasibility (e.g., partner choice in mycorrhizas/rhizobia) through mutualistic interactions. Mutualistic disruptions due to invasions are pervasive, and subsequent cascading effects are also widespread. Ecological networks provide a useful framework for predicting tipping points for community collapse in response to invasions and other synergistic drivers of global change.

The domestication of plants and animals over the past 11,500 years has had a significant effect not just on the domesticated taxa but also on human evolution and on the biosphere as a whole. Decades of research into the geographical and chronological origins of domestic animals have led to a general understanding of the pattern and process of domestication, though a number of significant questions remain unresolved. Here, building upon recent theoretical advances regarding the different pathways animals followed to become domesticated, we present a large-scale synthesis that addresses the global pattern of animal domestication alongside a discussion of the differential evolutionary processes that have shaped domestic animal populations. More specifically, we present a framework for understanding how unconscious selection characterized the earliest steps of animal domestication and the role of introgression and the importance of relaxed and positive selection in shaping modern domestic phenotypes and genomes.

Coffee agroecosystems have become iconic in the study of how agriculture can contribute to the conservation of biodiversity and how biodiversity can deliver ecosystem services to agriculture. However, coffee farms are also excellent model systems for ecological research. Throughout the tropics coffee farms are cultivated using varying numbers and diversity of shade trees, representing a gradient of diversity and complexity, ranging from forest-like “shade coffee” to intensified shadeless “sun coffee.” Here we synthesize ecological research in the coffee agroecosystem focusing on four topics that have received considerable recent attention: (a) trophic interactions (especially vertebrates and ants as predators), (b) trait-mediated indirect interactions, (c) competition and community assembly (mainly birds and ants), and (d) spatial constraints on interactions.

The evolution of female ornamentation has been subject to considerable debate. Although originally thought to be by-products of selection on males, recent studies have emphasized the adaptive nature of female ornaments. Here, I review current knowledge on the genetic architecture of ornamental traits and how their expression is (or is not) restricted to one sex. Ornament development typically involves deeply conserved developmental genes. Their expression is modified by pre-existing sexually dimorphic signals, such as hormones in vertebrates or doublesex gene products in insects. Changes in dosage and binding affinities in these systems apparently allow frequent switches between sexually dimorphic and monomorphic ornament expression. However, early-developing ornaments may be difficult to modulate, as this would result in severe pleiotropic effects. Comparative studies on the molecular structure of the sex-specific modulating signals and their receptors should provide detailed insight into the mechanisms underlying the loss and gain of female ornaments.

The accumulation of data on the genomic bases of adaptation has triggered renewed interest in theoretical models of adaptation. Among these models, Fisher's geometric model (FGM) has received a lot of attention over the past two decades. FGM is based on a continuous multidimensional phenotypic landscape, but it is mostly used for the emerging properties of individual mutation effects. Despite its apparent simplicity and 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 then discuss how to estimate the different parameters of the model and outline some future directions to connect FGM and the molecular determinants of adaptation.

Understanding what aspects of evolution are predictable, and repeatable, is a central goal of biology. Studying phenotypic convergence (the independent evolution of similar traits in different organisms) provides an opportunity to address evolutionary predictability at different hierarchical levels. Here we focus on recent advances in understanding the molecular basis of convergence. Understanding when, and why, similar molecular solutions are used repeatedly provides insight into the constraints that shape biological diversity. We first distinguish between convergence as a phenotypic pattern and parallelism as a shared molecular basis for convergence. We then address the overarching question: What factors influence when parallel molecular mechanisms will underlie phenotypic convergence? We present four core determinants of convergence (natural selection, phylogenetic history, population demography, and genetic constraints) and explore specific factors that influence the probability of molecular parallelism. Finally, we address frontiers for future study, including integration across different systems, subfields, and hierarchical levels.

The interactions between avian obligate interspecific brood parasites and their hosts provide tractable systems for studying coevolutionary processes in nature. This review highlights recent advances in understanding coevolution in these systems. First, we discuss the evolution and phylogenetic history of avian brood parasitism. Next, we examine coevolved adaptations and counteradaptations in brood parasites and hosts at all stages of the host nesting cycle: those that precede laying of the parasitic egg and those at the egg, chick, and fledgling stages. We then consider the factors that affect the evolution of offense and defense portfolios (the suites of adaptations and counteradaptations across the nesting cycle), and the outcomes of coevolutionary interactions between brood parasites and hosts. Ongoing efforts to document the diversity of host defenses and parasite offenses will facilitate understanding of coevolutionary processes and the ecological and evolutionary consequences of species interactions in the natural world.

Ecological restoration has grown rapidly and now encompasses not only classic ecological theory but also utilitarian concerns, such as preparedness for climate change and provisioning of ecosystem services. Three dominant perspectives compete to influence the science and practice of river restoration. A strong focus on channel morphology has led to approaches that involve major Earth-moving activities, such as channel reconfiguration with the unmet assumption that ecological recovery will follow. Functional perspectives of river restoration aim to regain the full suite of biogeochemical, ecological, and hydrogeomorphic processes that make up a healthy river, and though there is well-accepted theory to support this, research on methods to implement and assess functional restoration projects is in its infancy. A plethora of new studies worldwide provide data on why and how rivers are being restored as well as the project outcomes. Measurable improvements postrestoration vary by restoration method and measure of outcome.

The Earth is warming, especially in polar areas in which winter temperatures and precipitation are expected to increase. Despite a growing research focus on winter climatic change, the impacts on Arctic terrestrial ecosystems remain poorly understood. Snow acts as an insulator, and depth changes affect the enhancement of thermally dependent reactions, such as microbial activity, affecting soil nutrient composition, respiration, and winter gas efflux. Snow depth and spring temperatures influence snowmelt timing, determining the start of plant growth and forage availability. Delays in winter onset affect tundra carbon balance, faunal hibernation, and migration but are unlikely to lengthen the plant growing season. Mild periods in winter followed by a return to freezing have negative consequences for plants and invertebrates, and the resultant ice layers act as barriers to foraging, triggering starvation of herbivores and their predators. In summary, knock-on effects between seasons and trophic levels have important consequences for biological activity, diversity, and ecosystem function.

Hill numbers or the effective number of species are increasingly used to quantify species diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity, which incorporates species evolutionary history, as well as to functional diversity, which considers the differences among species traits. We review these extensions and integrate them into a framework of attribute diversity (the effective number of entities or total attribute value) based on Hill numbers of taxonomic entities (species), phylogenetic entities (branches of unit-length), or functional entities (species-pairs with unit-distance between species). This framework unifies ecologists' measures of species diversity, phylogenetic diversity, and distance-based functional diversity. It also provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of the classic Jaccard, Sørensen, Horn, and Morisita-Horn indexes. A real example shows how this framework extracts ecological meaning from complex data.

Questions of whether trophic cascades occur in Isle Royale National Park (IRNP) or Yellowstone National Park's northern range (NR) cannot lead to simple, precise, or definitive answers. Such answers are limited especially by multicausality in the NR and by complex temporal variation in IRNP. Spatial heterogeneity, contingency, and nonequilibrium dynamics also work against simple answers in IRNP and NR. The existence of a trophic cascade in IRNP and NR also depends greatly on how it is defined. For example, some conceive of trophic cascades as entailing essentially any indirect effect of predation. This may be fine, but the primary intellectual value of such a conception may be to assess an important view in community ecology that most species are connected to most other species in a food web through a network of complicated, albeit weak, indirect effects. These circumstances that work against simple answers likely apply to many ecosystems. Despite the challenges of assessing the existence of trophic cascades in IRNP and NR, such assessments result in considerable insights about a more fundamental question: What causes population abundance to fluctuate?

Recent biogeographic and evolutionary studies have led to improved understanding of the origins of exceptionally high plant diversity in the California Floristic Province (CA-FP). Spatial analyses of Californian plant diversity and endemism reinforce the importance of geographically isolated areas of high topographic and edaphic complexity as floristic hot spots, in which the relative influence of factors promoting evolutionary divergence and buffering of lineages against extinction has gained increased attention. Molecular phylogenetic studies spanning the flora indicate that immediate sources of CA-FP lineages bearing endemic species diversity have been mostly within North America—especially within the west and southwest—even for groups of north temperate affinity, and that most diversification of extant lineages in the CA-FP has occurred since the mid-Miocene, with the transition toward summer-drying. Process-focused studies continue to implicate environmental heterogeneity at local or broad geographic scales in evolutionary divergence within the CA-FP, often associated with reproductive or life-history shifts or sometimes hybridization.

In recent years, scientists have made remarkable progress reconstructing the animal phylogeny. There is broad agreement regarding many deep animal relationships, including the monophyly of animals, Bilateria, Protostomia, Ecdysozoa, and Spiralia. This stability now allows researchers to articulate the diminishing number of remaining questions in terms of well-defined alternative hypotheses. These remaining questions include relationships at the base of the animal tree, the position of Xenacoelomorpha, and the internal relationships of Spiralia. Recent progress in the field of animal phylogeny has important implications for our understanding of the evolution of development, morphology, genomes, and other characters. A remarkable pattern emerges—there is far more homoplasy for all these characters than had previously been anticipated, even among many complex characters such as segmentation and nervous systems. The fossil record dates most deep branches of the animal tree to an evolutionary radiation in the early Cambrian with roots in the Late Neoproterozoic.

Ecological processes in arid lands are often described by the pulse-reserve paradigm, in which rain events drive biological activity until moisture is depleted, leaving a reserve. This paradigm is frequently applied to processes stimulated by one or a few precipitation events within a growing season. Here we expand the original framework in time and space and include other pulses that interact with rainfall. This new hierarchical pulse-dynamics framework integrates space and time through pulse-driven exchanges, interactions, transitions, and transfers that occur across individual to multiple pulses extending from micro to watershed scales. Climate change will likely alter the size, frequency, and intensity of precipitation pulses in the future, and arid-land ecosystems are known to be highly sensitive to climate variability. Thus, a more comprehensive understanding of arid-land pulse dynamics is needed to determine how these ecosystems will respond to, and be shaped by, increased climate variability.

Empirical studies reveal aging occurs in wild populations. Consideration of the ecological and evolutionary consequences of these findings is critical for many areas of research, including life-history evolution, sexual selection, behavior, and applied ecology. Variation in the patterns of age-dependent declines of phenotypic traits has been found both within and among individuals, and this raises future questions aimed at understanding what determines these trajectories across traits and across the tree of life. The presence of older, aging, individuals in populations can have transgenerational effects on offspring and can influence how individuals interact. In some species older individuals in populations can have positive impacts, influencing knowledge and leadership, postreproductive care, and population cycle stabilization. Aging and long life span also need to be recognized in an applied ecology context including management plans, vector-borne disease transmission, and ecotoxicology.

Geckos possess a superlative climbing adaptation in the form of hierarchical arrays of adhesive nanostructures on the underside of their toes. These structures permit rapid, robust, and reliable adhesion to nearly any substrate during full-speed locomotion. We review the fundamental principles and properties of this system, describe its ecological and evolutionary aspects, and offer our assessment of the field alongside suggestions for future research in this direction.