Annual Review of Ecology, Evolution, and Systematics - Volume 42, 2011

Animals pollinate 87% of the world's flowering plant species. Therefore, how pollinators respond to human-induced land-use change has important implications for plants and the species that depend on them. Here, we synthesize the published literature on how land-use change affects the main groups of pollinators: bees, butterflies, flies, birds, and bats. Responses to land-use change are predominantly negative but are highly variable within and across taxa. The directionality of pollinator response varies according to study design, with comparisons across gradients in surrounding landscape cover finding largely negative responses and comparisons across local land-use types finding largely positive responses. Furthermore, among the studies using landscape designs, most were performed in systems where land-use change is extreme, and such studies find stronger negative effects than those performed in more moderate systems. Across multiple taxa, dietary specialists show greater sensitivity to land use than do generalists. There is a need for studies of pollinator species composition and relative abundance, rather than simply species richness and aggregate abundance, to identify the species that are lost and gained with increasing land-use change.

Plants are rife with bacteria and fungi that colonize roots and shoots both externally and internally. By providing novel nutritional and defense pathways and influencing plant biochemical pathways, microbes can fundamentally alter plant phenotypes. Here we review the widespread nature of microbially mediated plant functional traits. We highlight that there is likely fitness conflict between hosts and symbionts and that fitness outcomes can depend on partner genotypes and ecological factors. Microbes may influence ecosystems through their effects on the functional trait values and population dynamics of their plant hosts. These effects may feed back on symbiont evolution by altering transmission rates of symbionts and scale up to ecosystem processes and services. We end by proposing new avenues of research in this emerging field.

We review the fossil and genetic evidence that relate to evolution in the genus Homo. We focus on the origin of Homo and on the evidence for taxonomic diversity at the beginning of the evolutionary history of Homo and in the last 200,000 years. We set out the arguments for recognizing a second early Homo taxon, Homo rudolfensis, and the arguments for and against including Homo habilis sensu stricto and Homo rudolfensis within Homo. We end by reviewing recent genomic evolution within Homo. The challenge of the upcoming decades is to meld innovations in molecular genetic methods and technology with evidence from the fossil record to generate hypotheses about the developmental bases of the phenotypic and behavioral developments we see within the genus Homo.

After almost 50 years of scrutiny, the ideas that Ehrlich and Raven presented in their classical paper on the coevolution between butterflies and plants are still very much alive. Much of this interest has involved the potential for codiversification, both in how the interaction itself diversifies and how the interaction affects modes and rates of speciation. Despite high levels of conservatism and specialization, diversification of the interaction appears to be mainly a consequence of host shifts, but this somewhat paradoxical conclusion can be understood by an appreciation of the ecological as well as genetic mechanisms behind host shifts. There are several ways that the interaction can influence speciation, with or without host-plant-based divergent selection on reproductive barriers. One current debate is over the relative importance of radiations following shifts to new adaptive zones and elevated rates of speciation in groups with plastic and diverse host use.

Division of labor is a complex phenomenon observed throughout nature. Theoretical studies have focused either on its emergence through self-organization mechanisms or on its adaptive consequences. We suggest that the interaction of self-organization, which undoubtedly characterizes division of labor in social insects, and evolution should be further explored. We review the factors empirically shown to influence task choice. In light of these factors, we review the most important self-organization and evolutionary models for division of labor and outline their advantages and limitations. We describe ways to unify evolution and self-organization in the theoretical study of division of labor and recent results in this area. Finally, we discuss some benchmarks and primary challenges of this approach.

The closely related and morphologically indistinguishable mosquito species in the Afrotropical Anopheles gambiae complex differ dramatically in their contribution to malaria transmission, ranging from major vectors through minor or locally important vectors and nonvectors. Radiation of the A. gambiae complex and ongoing diversification within its nominal species appears to be a product of recent and rapid adaptation to environmental heterogeneities, notably those of anthropogenic origin. Polytene chromosome and genomic analyses suggest that paracentric chromosomal inversions and possibly other low-recombination regions have played instrumental roles in this process by facilitating ecotypic differentiation both within and across semipermeable species boundaries. Forthcoming complete genome sequences from several members of the A. gambiae complex will provide powerful tools to accelerate ongoing investigation of how genetic diversification of populations and species has shaped behavioral and physiological traits, such as vector competence, that bear on vectorial importance.

North American and European grasslands consist of relatively young communities that have evolved under human influences. These communities are uniformly sensitive to top-down controls and exhibit rapid changes in plant composition when the intensity and frequency of these controls are altered. These changes are intensifying due to the suite of global change factors, including the continued presence and introduction of new plant species. Establishment of nonnative plant species into grasslands requires resource opportunities generated by natural and human-induced disturbances and by niche differences of the new species. Persistence and spatial expansion require that the traits of the introduced species be compatible with a new regime of competitors, predators, pathogens, and symbionts. Plant traits of the invaders may then further facilitate the invasion process by preempting resources or by restructuring the soil microbial community and trophic food web in ways that directly or indirectly benefit the invading species.

We evaluate the extent to which physiological tolerances and capacities can be considered as factors that impact the geographic range of animals. We also discuss the importance of understanding how environmental variability interacts with physiological function, concluding with a consideration of how our understanding of physiology in a macroecological context may contribute to our ability to predict the effects of climate change. The extent to which advances have occurred in predicting geographic range through constructing and testing hypotheses involving tolerances, physiological capacities, and plasticity (namely pervasive plasticity, climatic variability, and the Brattstrom hypothesis) is evaluated. Finally, we attempt to integrate our understanding of the interaction between physiology and distribution within current global warming scenarios. We suggest that it may be necessary to evaluate patterns of physiological diversity as a function of different ecological regions oriented to produce mechanistic explanations regarding the likely new (or lack of) physiological responses of animals to altered climatic conditions along geographic ranges.

Free-air CO2 enrichment (FACE) experiments have provided novel insights into the ecological mechanisms controlling the cycling and storage of carbon in terrestrial ecosystems and contribute to our ability to project how ecosystems respond to increasing CO2 in the Earth's atmosphere. Important lessons emerge by evaluating a set of hypotheses that initially guided the design and longevity of forested FACE experiments. Net primary productivity is increased by elevated CO2, but the response can diminish over time. Carbon accumulation is driven by the distribution of carbon among plant and soil components with differing turnover rates and by interactions between the carbon and nitrogen cycles. Plant community structure may change, but elevated CO2 has only minor effects on microbial community structure. FACE results provide a strong foundation for next-generation experiments in unexplored ecosystems and inform coupled climate-biogeochemical models of the ecological mechanisms controlling ecosystem response to the rising atmospheric CO2 concentration.

The extraordinary species richness and endemism of the Indo-Australian Archipelago (IAA) exists in one of the most geologically dynamic regions of the planet. The provenance of its biota has been debated, particularly in the area known as Wallacea. Application of molecular genetic approaches and a better understanding of the region's complex geology have stimulated much recent biogeographic work in the IAA. We review molecular phylogenetic and phylogeographic studies in light of current geological evidence. Present distribution patterns of species have been shaped largely by pre-Pleistocene dispersal and vicariance events, whereas more recent changes in the connectivity of islands within the Archipelago have influenced the partitioning of intraspecific variation. Many genetic studies have uncovered cryptic species with restricted distributions. We discuss the conservation significance of the region and highlight the need for cross-taxon comparative studies using newly developed analytical approaches well suited to the challenges of historical inference in this region.

Squamate reptiles (lizards and snakes) are a diverse clade in which there appear to have been multiple origins of many remarkable traits, including (a) parthenogenetic reproduction, (b) viviparity, (c) snake-like, limb-reduced body form, (d) herbivory, and (e) venom. These repeated transitions make squamates an outstanding/excellent system for addressing many fundamental questions in evolutionary biology. For example, they are the only vertebrate group with true parthenogenesis (with at least 40 separate origins), they have more origins of viviparity than any other group of vertebrates, and they have undergone dramatic changes in body form (lizard-like to snake-like) dozens of times. New molecular phylogenies for squamates have overturned many traditional hypotheses and taxonomies based on morphology and are now revealing exciting new insights into the evolution of many of these traits at both higher and lower taxonomic levels. In this review, we summarize many of these new insights and outline important areas for future research.

Early studies of protein evolution established that evolutionary rates vary among sites, genes, and lineages. Here, we review rate variation within each of these three components, with an emphasis on plant nuclear genes. Evolutionary rates vary among nucleotide sites as a consequence of selection and mutational biases. Mutation varies among sites as a function of the base, its neighboring bases, and its proximity to insertion-deletion polymorphisms. Nonsynonymous rate variation among genes correlates most strongly with gene expression, perhaps owing to selection for translational robustness. Among lineages, perennial plants evolve more slowly than annuals, but the mechanism driving this effect remains unclear. There are also interactions among these three main components; we discuss the patterns of interaction and their significance for understanding the evolutionary forces that shape nucleotide substitution rates in plants. Finally, we highlight gaps in our knowledge and future opportunities to answer fundamental questions in plant molecular evolution.

This review focuses on biotic responses during intervals of time in the fossil record when the magnitude and rate of climate change exceeded or were comparable with those predicted to occur in the next century (Solomon et al. 2007). These include biotic responses during: (a) the Paleo-Eocene Thermal Maximum and early Eocene Climatic Optimum, (b) the mid-Pliocene warm interval, (c) the Eemian, and (d) the most recent glacial-interglacial transition into the Holocene. We argue that although the mechanisms responsible for these past changes in climate were different (i.e., natural processes rather than anthropogenic), the rate and magnitude of climate change were often similar to those predicted for the next century and therefore highly relevant to understanding future biotic responses. In all intervals we examine the fossil evidence for the three most commonly predicted future biotic scenarios, namely, extirpation, migration (in the form of a permanent range shift), or adaptation. Focusing predominantly on the terrestrial plant fossil record, we find little evidence for extirpation during warmer intervals; rather, range shifts, community turnover, adaptation, and sometimes an increase in diversity are observed.

Foraging for resources influences ecological interactions among individuals and species, regardless of taxonomic affiliation. Here we review studies of nutrient foraging in plants, with an emphasis on how nutritious and non-nutritious cues in the soil alter behavioral decisions and patterns of root placement. Three patterns emerge: (a) Plants alter root placement in response to many diverse cues; (b) species respond differently to these cues; and (c) there are nonadditive responses to multiple cues, indicating that plants exhibit complex multidimensional root foraging strategies. We suggest that this complexity calls for novel approaches to understanding nutrient foraging by plants. Resource selection functions are commonly used by animal behaviorists and may be useful to describe plant foraging strategies. Understanding such approaches may allow researchers to link individual behavior to population and community dynamics.

Populations left behind during climate-driven range shifts can persist in enclaves of benign environmental conditions within an inhospitable regional climate. Such climate relicts exist in numerous plant and animal species worldwide, yet our knowledge of them is fragmented and lacks a general framework. Here we synthesize the empirical evidence considering (a) relict habitats, (b) abiotic and biotic constraints on population dynamics, (c) mechanisms promoting population persistence, and (d) uncertainties concerning their future prospects. We identify three major types of climate relicts: (a) those constrained primarily by climate-driven abiotic factors, (b) those restricted to areas that are inaccessible to antagonistic species for climatic reasons, and (c) those requiring a host or mutualistic species that is itself limited by climate. Understanding the formation and functioning of climate relicts is essential for their conservation and for our understanding of the response of species and populations to climate change.

Understanding the forces that allow multiple species to coexist remains a central focus of community ecology. Building evidence that evolutionary changes frequently occur on timescales relevant for ecological dynamics suggests that a complete understanding of the maintenance of diversity is likely to require incorporation of evolutionary dynamics. Coexistence mechanisms can be classified into two groups on the basis of whether they reduce inherent differences in species performance (equalizing effects) or buffer against extinction by providing advantages to rare species (stabilizing effects). Theoretical and empirical evidence suggests that rapid evolution can increase equalizing and/or stabilizing effects in several ways. Directional evolutionary changes can result in new ecological conditions that are more equal or stable than the initial state. Additionally, coevolution between competitors or consumers can lead to cyclic dynamics that provide novel evolutionary equalizing or stabilizing effects.

Complex structures with significant biological function can arise multiple times in evolution by common gene patterning and developmental pathways. The mammalian middle ear, with its significant hearing function, is such a complex structure and a key evolutionary innovation. Newly discovered fossils have now shown that the detachment of the ear from the jaw, an important transformation of the middle ear in early mammals, has major homoplasies; the morphogenesis of these homoplasies is also illuminated by new genetic studies of ear development in extant mammals. By extrapolating the developmental morphogenesis of genetic studies into the early mammal fossil record, evolution of the middle ear in early mammals provides an integrated case study of how development has impacted, mechanistically, the transformation of a major structural complex in evolution.

Spatial management, including setting aside conservation areas, is central to curbing the global decline of biodiversity, but many threats originate from beyond the boundaries of conservation areas. This is a particular problem in marine systems, which are influenced by many activities on land. In addition, connections between land and sea support many species and ecological processes valued for conservation. Integrated land and sea conservation planning is therefore of utmost importance. We review the literature describing connections between land and sea and how they have been incorporated into conservation planning. Land-sea connections include land-sea processes, the natural flows occurring between realms; cross-system threats, which originate in one realm and affect another; and socioeconomic interactions associated with management decisions to maintain or restore land-sea processes and to prevent or mitigate cross-system threats. We highlight the need to explicitly incorporate land-sea connections in conservation planning and suggest ways of doing this through the use of a novel operational framework for integrated land-sea planning. On the basis of expert surveys and a literature review, we also identify those aspects of conservation planning for which improved integration between land and sea is most needed.

Stable isotope analysis (SIA) has proven to be a useful tool in reconstructing diets, characterizing trophic relationships, elucidating patterns of resource allocation, and constructing food webs. Consequently, the number of studies using SIA in trophic ecology has increased exponentially over the past decade. Several subdisciplines have developed, including isotope mixing models, incorporation dynamics models, lipid-extraction and correction methods, isotopic routing models, and compound-specific isotopic analysis. As with all tools, there are limitations to SIA. Chief among these are multiple sources of variation in isotopic signatures, unequal taxonomic and ecosystem coverage, over-reliance on literature values for key parameters, lack of canonical models, untested or unrealistic assumptions, low predictive power, and a paucity of experimental studies. We anticipate progress in SIA resulting from standardization of methods and models, calibration of model parameters through experimentation, and continued development of several recent approaches such as isotopic routing models and compound-specific isotopic analysis.

Phylogenetic approaches to biogeography are rapidly becoming more sophisticated. Four types of models are being explored in the literature: (a) diffusion models, (b) island models, (c) hierarchical vicariance models (HVMs), and (d) reticulate models. Diffusion models are used primarily for phylogeographic inference but can also offer insights into geographic discontinuities of significance on longer time scales. For the island models, statistical approaches are now well developed and typically offer more detailed insight than parsimony analysis. In contrast, parsimony may still be the best option for HVM analysis, because existing statistical approaches do not yet accommodate dispersal. The proposed probabilistic models of reticulate scenarios remain poorly understood, even though they may currently do the best job of integrating diversification processes into biogeographic analysis. Statistical approaches are gaining in popularity across the field, in part because of the flexibility of stochastic modeling. This allows investigators to address important related processes, such as ecological interactions and climate change, in biogeographic inference.