Annual Review of Ecology, Evolution, and Systematics - Volume 41, 2010

We review the impact of developments from animal breeding on our understanding of evolution and on the methodology used in evolutionary biology. The theory developed for improvement of polygenic traits, in particular the breeders' equation and the effects of finite population size, has had a significant influence. The effectiveness of within population selection is exemplified by the continued rapid genetic change, often with concomitant effects on fitness, produced by breeders. Many of the models and methods for estimation of quantitative genetic parameters, notably the animal model, have been motivated by animal breeding problems. Results from selection programs and quantitative trait loci (QTL) experiments show quantitative traits are often highly polygenic and can be adequately modeled by the infinitesimal model.

Graph theory is a powerful body of mathematical knowledge, based on simple concepts, in which structural units are depicted as nodes with relationships between them depicted as lines. The nodes may have qualitative and quantitative characteristics, and the edges may have properties such as weights and directions. Graph theory provides a flexible conceptual model that can clarify the relationship between structures and processes, including the mechanisms of configuration effects and compositional differences. Graph concepts apply to many ecological and evolutionary phenomena, including interspecific associations, spatial structure, dispersal in landscapes, and relationships within metapopulations and metacommunities. We review applications of graph theory in biology, emphasizing graphs with spatial contexts. We show how spatial graph properties can be used for description and comparison as well as to test specific hypotheses. We suggest that future applications should include explicit spatial elements for landscape studies of ecological, genetic and epidemiological phenomena.

Oviposition-site choice is a major maternal effect by which females can affect the survival and phenotype of their offspring. Across oviparous species, the ultimate reasons for females' selection of oviposition sites often differ. We present six hypotheses that have been used to explain nonrandom oviposition-site choice in insects, fish, amphibians, reptiles, and birds: (a) maximizing embryo survival, (b) maximizing maternal survival, (c) modifying offspring phenotype, (d) proximity to suitable habitat for offspring, (e) maintaining natal philopatry, and (f) indirect oviposition-site choice via mate choice. Because these hypotheses differ in their relevance across oviparous taxa, each hypothesis must be tested to ensure accurate understanding of the ultimate reason behind oviposition-site choice in a particular taxon. By presenting the major hypotheses for oviposition-site choice as they relate to diverse oviparous animals, we nonetheless illustrate particular trends across animal taxa, while highlighting avenues for future research into the ecological and evolutionary drivers of oviposition-site choice.

Exotic species affect the biogeochemical pools and fluxes of materials and energy, thereby altering the fundamental structure and function of their ecosystems. Rapidly accumulating evidence from many species of both animal and plant invaders suggests that invasive species often increase pool sizes, particularly of biomass, and promote accelerated flux rates, but many exceptions can be found. Ecosystem dynamics are altered through a variety of interacting, mutually reinforcing mechanistic pathways, including species' resource acquisition traits; population densities; ability to engineer changes to physical environmental conditions; effects on disturbance, especially fire; regimes; the ability to structure habitat for other species; and their impact on food webs. Local factors of landscape setting, history, and other sources of disturbance constrain ecosystem responses to invasions. New research directions are suggested, including the need for whole-system budgets, the quantification of abundance-impact relationships for particular ecosystem processes, and a better exploration of food web impacts on ecosystem processes.

Sexually selected traits contribute greatly to phenotypic diversity, yet we have historically understood little about their genetic basis and how that basis may affect their evolution. Recent work in developmental and quantitative genetics has provided both mechanistic and statistical descriptions of genotype-phenotype maps for sexually selected traits. These studies expose generally complex genetic architectures; genotype-phenotype maps are polygenic with allelic effects that are pleiotropic and highly context-dependent. At the same time, developments in quantitative genetics have provided new insights into the microevolutionary potential of standing variation and indicate genetic constraints on the contemporary evolution of male sexually selected characters, mate preferences, and also male mating success itself. Understanding the extent to which these constraints are a function of genetic architecture will require a tighter integration of developmental, molecular, and quantitative genetic approaches in a variety of model systems. Emerging genomic technologies offer an unprecedented opportunity to deepen our understanding of sexual selection as an evolutionary process.

Comparative analysis of patterns of species invasion, dispersal, and impact on ecosystems in the Ponto-Caspian seas has been ongoing since 1900. The Black Sea is an important international shipping destination. High shipping intensity has facilitated species invasions into the Black Sea. Many species have successfully established because of Black Sea disturbances. The Black Sea serves as a hub for species that then spread further to the Sea of Azov, the Caspian Sea, the Sea of Marmara, and in some cases the eastern Mediterranean Sea. The Black Sea has thus become the main recipient for non-native species and acts as a donor to the seas of Eurasia. Native biodiversity has declined and invaders now dominate the Ponto-Caspian seas. This process has caused biotic homogenization of the Ponto-Caspian, as the same invaders determine community structure and in some cases ecosystem functioning in the different seas. Among these invaders, gelatinous species have become the main drivers of ecosystem functioning. The invasion rate of new species is accelerating.

Ocean acidification (OA), a consequence of anthropogenic carbon dioxide emissions, poses a serious threat to marine organisms in tropical, open-ocean, coastal, deep-sea, and high-latitude sea ecosystems. The diversity of taxonomic groups that precipitate calcium carbonate from seawater are at particularly high risk. Here we review the rapidly expanding literature concerning the biological and ecological impacts of OA on calcification, using a cross-scale, process-oriented approach. In comparison to calcification, we find that areas such as fertilization, early life-history stages, and interaction with synergistic stressors are understudied. Although understanding the long-term consequences of OA are critical, available studies are largely short-term experiments that do not allow for tests of long-term acclimatization or adaptation. Future research on the phenotypic plasticity of contemporary organisms and interpretations of performance in the context of current environmental heterogeneity of pCO2 will greatly aid in our understanding of how organisms will respond to OA in the future.

Citizen science, the involvement of volunteers in research, has increased the scale of ecological field studies with continent-wide, centralized monitoring efforts and, more rarely, tapping of volunteers to conduct large, coordinated, field experiments. The unique benefit for the field of ecology lies in understanding processes occurring at broad geographic scales and on private lands, which are impossible to sample extensively with traditional field research models. Citizen science produces large, longitudinal data sets, whose potential for error and bias is poorly understood. Because it does not usually aim to uncover mechanisms underlying ecological patterns, citizen science is best viewed as complementary to more localized, hypothesis-driven research. In the process of addressing the impacts of current, global “experiments” altering habitat and climate, large-scale citizen science has led to new, quantitative approaches to emerging questions about the distribution and abundance of organisms across space and time.

Constant final yield is an empirical generalization concerning the total biomass production of plant stands growing at different densities after a period of growth. Total standing biomass initially increases in proportion to density, levels off, and then remains constant as density increases further. We review the empirical basis for and mathematical formulations of this pattern, and we clarify the relationship of constant final yield to density-dependent mortality (self-thinning). There are several mechanisms that can explain the pattern, and it has a clear evolutionary basis. Constant final yield is a key to understanding population- and community-level phenomena. Establishing whether or not a plant community is at or close to constant final yield is important for understanding and predicting its behavior. It represents the maximum biomass for a genotype in an environment after a period of growth and, as such, can serve as a baseline for the measurement of disturbance in plant communities.

Many flowering plants exhibit dual reproductive modes, producing both sexual and asexual offspring. The commonest form of asexual reproduction is clonal growth, in which vegetative modules (ramets) are produced by the parental genotype (genet). In plants, sexual and asexual reproduction usually occur simultaneously, and this can lead to allocation trade-offs and antagonism between reproductive modes. Our review considers the ecological and evolutionary consequences of functional interactions between clonal reproduction and pollination and mating. Clonal reproduction is commonly associated with mass flowering, restricted pollen dispersal, and geitonogamous self-pollination, processes that can result in inbreeding depression and pollen discounting. We review evidence for the correlated evolution of clonality and sexual systems, particularly self-incompatibility, and identify several floral mechanisms that function to reduce mating costs by limiting selfing and pollen discounting. We conclude by discussing the loss of sexuality in clonal plants and consider the genetic and environmental basis of sexual dysfunction.

Since Darwin first proposed that new species could arise without geographic separation, biologists have debated whether or not divergence occurs in the presence of gene exchange. Today we understand that new species can diverge while exchanging genes, depending on the strength of disruptive natural selection and the factors that affect the linkage relationships of genes under disruptive selection. This mode of diversification—divergence with gene flow—includes sympatric speciation, in which gene exchange occurs since onset of divergence, and secondary contact following a period of geographic isolation, as well as all sorts of situations in which gene flow happens intermittently. In recent years, statistical tools have been developed that can reveal the action of gene flow during divergence. Isolation-with-migration (IM) models include parameters for population size, time of population separation, and gene exchange, and they have been used extensively to estimate levels of gene exchange. A survey of studies that have used these models shows that a plurality find little evidence of gene flow; however, many report nonzero gene exchange.

Since the rise of modern humans, changes in demography and land use and frequent contact with wildlife and domesticated animals have created ongoing opportunities for pathogen loss, gain, and evolution in the human population. Early transportation networks and population expansion created a world where many human-specific pathogens are now ubiquitous, yet zoonoses continue to emerge as humans encroach into the last remaining wild areas, increase livestock production, and plug into vast global trade networks. Pathogens are exploiting almost any change in human ecology that provides new opportunities for transmission, the most recent being rampant use of antibiotics resulting in new multidrug-resistant pathogens. Public health advances have benefitted some nations, but others continue to suffer from pathogens long eradicated by developed nations. Generalities of pathogen occurrence aid in disease prediction, but a systemic approach incorporating ecology, biogeography, public health, and conservation biology is ultimately necessary to fully comprehend the changing geographic distributions of human pathogens.

Adaptive radiation is a response to natural selection and ecological opportunity involving diversification of species and associated adaptations. Although evolutionary biologists have long speculated that adaptive radiation is responsible for most of life's diversity, persistent confusion and disagreement over some of its most fundamental questions have prevented it from assuming a central role in explaining the evolution of biological diversity. Today, answers to many of these questions are emerging from a new wave of integrative research that combines phylogenetic trees with a variety of other data and perspectives. In this review, I discuss how modern phylogenetic analyses are central to (a) defining and diagnosing adaptive radiation, (b)identifying the factors underlying the occurrence and scope of adaptive radiation, (c)diagnosing predictable patterns of ecological diversification during adaptive radiation, and (d) reconstructing the history of adaptive radiations.

Not all floral visitors attracted to flowers are pollinators. Instead, some visitors circumvent the floral opening, usually removing nectar without contacting the anthers and/or stigma. Here we review the evolutionary ecology of nectar robbing from both the plant and animal perspective. Effects of robbing on female and male components of plant reproduction range from negative to positive. Their underlying mechanisms are diverse, including direct effects and indirect effects mediated through changes in pollination. We detail how plants may be able to deter robbers through morphological and chemical traits. For the evolutionary ecology of robbing to move beyond a phytocentric perspective, studies must also address the causes of robbing and the consequences for both robbers and pollinators. We use an energetics approach to evaluate these causes and consequences. Finally, we highlight unanswered questions in need of further research.

Germination behavior is one of the earliest phenotypes expressed by plants. This fact has several consequences for the evolution of postgermination traits, ecological niches, and geographic ranges. By determining the conditions that plants experience after they germinate, germination influences phenotypic expression of postgermination traits, natural selection on them, and their genetic basis. The breadth of germination niches may influence the ecological breadth and geographic ranges of species. Because germination is expressed early, it is frequently subjected to natural selection before other traits are expressed. We review evidence for natural selection on and adaptation of germination and discuss how the breadth of the germination niche is associated with the ecological niche and range of plant species. We review evidence for the coevolution of germination and postgermination traits and compare germination to postgermination niches. Finally, we discuss how germination responses to altered environments can influence species distribution and the evolution of postgermination traits after environmental change.

Today's scientists are facing the enormous challenge of predicting how climate change will affect species distributions and species assemblages. To do so, ecologists are widely using phenomenological models of species distributions that mainly rely on the concept of species niche and generally ignore species' demography, species' adaptive potential, and biotic interactions. This review examines the potential role of the emerging synthetic discipline of evolutionary community ecology in improving our understanding of how climate change will alter future distribution of biodiversity. We review theoretical and empirical advances about the role of niche evolution, interspecific interactions, and their interplay in altering species geographic ranges and community assembly. We discuss potential ways to integrate complex feedbacks between ecology and evolution in ecological forecasting. We also point at a number of caveats in our understanding of the eco-evolutionary consequences of climate change and highlight several challenges for future research.

The ecological impact of biofuels is mediated through their effects on land, air, and water. In 2008, about 33.3 million ha were used to produce food-based biofuels and their coproducts. Biofuel production from food crops is expected to increase 170% by 2020. Economic model estimates for land-use change (LUC) associated with food-based biofuels are 67–365 ha 10⁻⁶ l⁻¹, leading to increased greenhouse gas emissions for decades compared to business as usual. Biodiversity is reduced by about 60% in U.S. corn and soybean fields and by about 85% in Southeast Asian oil palm plantations compared to unconverted habitat. Consequently, the largest ecological impact of biofuel production may well come from market-mediated LUC. Mitigating this impact requires targeting biofuel production to degraded and abandoned cropland and rangeland; increasing crop yields and livestock production efficiency; use of wastes, residues, and wildlife-friendly crops; and compensatory offsite mitigation for residual direct and indirect impacts.

In the past 10years a statistical technique, approximate Bayesian computation (ABC), has been developed that can be used to infer parameters and choose between models in the complicated scenarios that are often considered in the environmental sciences. For example, based on gene sequence and microsatellite data, the method has been used to choose between competing models of human demographic history as well as to infer growth rates, times of divergence, and other parameters. The method fits naturally in the Bayesian inferential framework, and a brief overview is given of the key concepts. Three main approaches to ABC have been developed, and these are described and compared. Although the method arose in population genetics, ABC is increasingly used in other fields, including epidemiology, systems biology, ecology, and agent-based modeling, and many of these applications are briefly described.