Annual Review of Ecology Evolution and Systematics

Published by Annual Reviews
Online ISSN: 1545-2069
Print ISSN: 1543-592X
Publications
Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci.
 
There is a growing appreciation that chromosome inversions affect rates of adaptation, speciation, and the evolution of sex chromosomes. Comparative genomic studies have identified many new paracentric inversion polymorphisms. Population models suggest that inversions can spread by reducing recombination between alleles that independently increase fitness, without epistasis or coadaptation. Areas of linkage disequilibrium extend across large inversions but may be interspersed by areas with little disequilibrium. Genes located within inversions are associated with a variety of traits including those involved in climatic adaptation. Inversion polymorphisms may contribute to speciation by generating underdominance owing to inviable gametes, but an alternative view gaining support is that inversions facilitate speciation by reducing recombination, protecting genomic regions from introgression. Likewise, inversions may facilitate the evolution of sex chromosomes by reducing recombination between sex determining alleles and alleles with sex-specific effects. However, few genes within inversions responsible for fitness effects or speciation have been identified.
 
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if positive selection operates on many loci simultaneously, as has recently been suggested for many species including animals such as flies, a different approach is necessary. In this review, I discuss recent progress in characterizing and understanding evolution in rapidly adapting populations where random associations of mutations with genetic backgrounds of different fitness, i.e., genetic draft, dominate over genetic drift. As a result, neutral genetic diversity depends weakly on population size, but strongly on the rate of adaptation or more generally the variance in fitness. Coalescent processes with multiple mergers, rather than Kingman's coalescent, are appropriate genealogical models for rapidly adapting populations with important implications for population genetic inference.
 
Increased mortality from fishing is expected to favor faster life histories, realized through earlier maturation, increased reproductive investment, and reduced postmaturation growth. There is also direct and indirect selection on behavioral traits. Molecular genetic methods have so far contributed minimally to understanding such fisheries-induced evolution (FIE), but a large body of literature studying evolution using phenotypic methods has suggested that FIE in life-history traits, in particular maturation traits, is commonplace in exploited fish populations. Although no phenotypic study in the wild can individually provide conclusive evidence for FIE, the observed common pattern suggests a common explanation, strengthening the case for FIE. This interpretation is supported by theoretical and experimental studies. Evidence for FIE of behavioral traits is limited from the wild, but strong from experimental studies. We suggest that such evolution is also common, but has so far been overlooked.
 
Sexual selection has a reputation as a major cause of speciation, one of the most potent forces driving reproductive isolation. This reputation arises from observations that species differ most in traits involved with mating success and from successful models of sexual selection–driven speciation. But how well proven is the case? Models confirm that the process can occur, but is strongest in conjunction with ecological or niche specialization. Some models also show that strong sexual selection can act against speciation. Studies using the comparative method are equivocal and often inconclusive, but some phylogeographic studies are more convincing. Experimental evolution and genetic or genomic analyses are in their infancy, but look particularly promising for resolving the importance of sexual selection. The case for sexual selection is not as strongly supported as, for example, allopatric speciation. Sexual selection probably contributes most effectively alongside ecological selection or selection...
 
Diagram showing the orientation, distribution, and size, in nucleotides (expressed as kilobases—kb), of the seven rRNA operons in E. coli (modified from Liao 2000).
Diagram showing the basic structure of the genes encoding for eukaryotic rRNA (the rDNA). A single tandem repeat (plus a portion of an adjoining repeat) is shown. The intergenic spacer (IGS) region is highlighted to show the location of variable numbers of subrepeats (which often contain enhancers or promoters) that greatly influence IGS length heterogeneity (modified from Sterner & Elser 2002).
▪ Abstract The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
 
Phototrophy
Cyanobacterial symbioses with eukaryotes are ancient associations that are widely distributed in aquatic and terrestrial environments. Cyanobacteria are a significant driving force in the evolution of their hosts, providing a range of services including photosynthesis, nitrogen fixation, UV protection, and defensive toxins. Although widespread, cyanobacteria occur in a limited range of hosts. Terrestrial symbioses are typically restricted to lichens and early evolved plants, and aquatic symbioses to sessile or slow-moving organisms. This review examines the underlying evolutionary processes that may have lead to these patterns. It also examines the facts that the degree of integration between symbiont and host, and the mode of transmission of the symbiont, do not appear to be an indication of how old the symbiosis is or how important it is to host well-being. Biparental transmission of symbionts may prolong the survival of gametes that persist in the environment, increasing chances of fertilization.
 
▪ Abstract The reconstruction of evolutionary trees from mitochondrial DNA (mtDNA) data is a common tool with which to infer the relationships of living organisms. The wide use of mtDNA stems from the ease of getting new sequence data for a set of orthologus genes and from the availability of many existing mtDNA sequences for a wide array of species. In this review we argue that developing a fuller understanding of the biology of mitochondria is essential for the rigorous application of mtDNA to inferences about the evolutionary history of species or populations. Though much progress has been made in understanding the parameters that shape the evolution of mitochondria and mtDNA, many questions still remain, and a better understanding of the role this organelle plays in regulating organismal fitness is becoming increasingly critical for accurate phylogeny reconstruction. In population biology, the limited information content of one nonrecombining genetic marker can compromise evolutionary inference, and t...
 
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.
 
Changes in climate, land use, fire incidence, and ecological connections all may contribute to current species' range shifts. Species shift range individually, and not all species shift range at the same time and rate. This variation causes community reorganization in both the old and new ranges. In terrestrial ecosystems, range shifts alter aboveground-belowground interactions, influencing species abundance, community composition, ecosystem processes and services, and feedbacks within communities and ecosystems. Thus, range shifts may result in no-analog communities where foundation species and community genetics play unprecedented roles, possibly leading to novel ecosystems. Long-distance dispersal can enhance the disruption of aboveground-belowground interactions of plants, herbivores, pathogens, symbiotic mutualists, and decomposer organisms. These effects are most likely stronger for latitudinal than for altitudinal range shifts. Disrupted aboveground-belowground interactions may have influenced hist...
 
Many multicellular eukaryotes have reasonably high per-generation mutation rates. Consequently, most populations harbor an abundance of segregating deleterious alleles. These alleles, most of which are of small effect individually, collectively can reduce substantially the fitness of individuals relative to what it would be otherwise; this is mutation load. Mutation load can be lessened by any factor that causes more mutations to be removed per selective death, such as inbreeding, synergistic epistasis, population structure, or harsh environments. The ecological effects of load are not clear-cut because some conditions (such as selection early in life, sexual selection, reproductive compensation, and intraspecific competition) reduce the effects of load on population size and persistence, but other conditions (such as interspecific competition and load on resource use efficiency) can cause small amounts of load to have strong effects on the population, even extinction. We suggest a series of studies to im...
 
The number of listed taxa through time, segregated by taxonomic group. Presidential administrations are identified by the gray and white shaded bars. Data are based on the U.S. Fish and Wildlife Service Threatened and Endangered Species System (TESS) database (U.S.F.W.S. 2008c).  
The distribution of listed plant species by FWS region along with a listing index 1 and critical habitat relative to the distribution of listed plants 
The allocation of endangered species expenditures as described by three curves of the cumulative percent of species ranked from those receiving the fewest recovery dollars to highest plotted against the cumulative fraction of those expenditures. These expenditures include all state and federal expenditures (bold blue line), U.S. Fish and Wildlife Service (FWS) expenditures (dashed line), and U.S. FWS expenditures on plant taxa (dotted green line). Data are from fiscal year 2004 as reported by the FWS (U.S.F.W.S. 2006b). In addition, two curves represent recovery plan statements of per annum financial need. One curve represents all types of taxa and is based on summaries from 87 species described in recovery plans published between 2005–2007. Plant recovery costs are estimated from a random selection of 35 recovery plans approved since 1992.  
Arguably the most notable success of the Endangered Species Act (ESA) is that listed species improve in status through time. More species are downlisted than the converse; more species transition from stable to improving status than the converse. Although some listed species have gone extinct, this number is smaller than expected. Given modest recovery funding, the fraction of listed species responding positively is remarkable. Several factors have been linked to improving species status including recovery expenditures, critical habitat listing, and time spent under protection. The inability of government to fully empower the agencies to implement the law has been the most notable failure of the ESA. Listing of species has not matched need, recovery expenditures do not match need or agency-set priorities, and critical habitat determinations have lagged. Alternative protection strategies to listing may be having a positive effect, but are difficult to assess because of sparse data.
 
Populations are locally adapted when populations have the highest relative fitness at their home sites, and lower fitness in other parts of the range. Results from the extensive experimental plantations of populations of forest trees from different parts of the range show that populations can survive and grow in broad areas outside the home site. However, intra- and interspecific competition limit the distribution of genotypes. For populations from large parts of the range, relative fitness, compared with the local population, is often highest at the home site. At the edges of the range, this local adaptation may break down. The extent of local adaptation is determined by the balance between gene flow and selection. Genetic differentiation and strong natural selection occur over a range of tens or hundreds of kilometers, but reliable measurements of gene flow are available only for much shorter distances. Current models of spatially varying selection could be made more realistic by the incorporation of st...
 
▪ Abstract Plant adaptation to serpentine soil has been a topic of study for many decades, yet investigation of the genetic component of this adaptation has only recently begun. We review the defining properties of serpentine soil and the pioneering work leading to three established physiological and evolutionary mechanisms hypothesized to be responsible for serpentine tolerance: tolerance of a low calcium-to-magnesium ratio, avoidance of Mg toxicity, or a high Mg requirement. In addition, we review recent work in serpentine ecology documenting the high proportion of endemic species present, the adaptive morphologies of serpentine-tolerant plants, and the distinctive structure of serpentine communities. Studies of the physiological mechanisms proposed to confer serpentine tolerance have shown that uptake of particular ions and heavy metals varies between serpentine-tolerant and -intolerant species. Recent studies examining the genetic basis of serpentine adaptation have shown serpentine-adaptive quantitat...
 
There is a growing interest in identifying ecological factors that influence adaptive genetic diversity patterns in both model and nonmodel species. The emergence of large genomic and environmental data sets, as well as the increasing sophistication of population genetics methods, provides an opportunity to characterize these patterns in relation to the environment. Landscape genetics has emerged as a flexible analytical framework that connects patterns of adaptive genetic variation to environmental heterogeneity in a spatially explicit context. Recent growth in this field has led to the development of numerous spatial statistical methods, prompting a discussion of the current benefits and limitations of these approaches. Here we provide a review of the design of landscape genetics studies, the different statistical tools, some important case studies, and perspectives on how future advances in this field are likely to shed light on important processes in evolution and ecology.
 
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.
 
Small populations are predicted to have reduced capacity to adapt to environmental change for two reasons. First, population genetic models indicate that genetic variation and potential response to selection should be positively correlated with population size. The empirical support for this prediction is mixed: DNA markers usually reveal low heterozygosity in small populations, whereas quantitative traits show reduced heritability only in the smallest and most inbred populations. Quantitative variation can even increase in bottlenecked populations although this effect seems unlikely to increase the adaptive potential of populations. Second, individuals in small populations have lower fitness owing to environmental stress and genetic problems such as inbreeding, which can substantially increase the extinction probability of populations in changing environments. This second reason has not been included in assessments of critical population size assuring evolvability and makes it likely that many sm...
 
Phylogenetic hypothesis for the major lineages of vertebrates based on morphological, paleontological, and molecular evidence. Disputed relationships are depicted as polytomies. 
The analysis of molecular phylogenetic data has advanced the knowledge of the relationships among the major groups of living vertebrates. Whereas the molecular hypotheses generally agree with traditional morphology-based systematics, they sometimes contradict them.We reviewthe major controversies in vertebrate phylogenetics and the contribution of molecular phylogenetic data to their resolution: (a) the mono-paraphyly of cyclostomes, (b) the relationships among the major groups of rayfinned fish, (c) the identity of the living sistergroup of tetrapods, (d ) the relationships among the living orders of amphibians, (e) the phylogeny of amniotes with particular emphasis on the position of turtles as diapsids, (f ) ordinal relationships among birds, and (g) the radiation of mammals with specific attention to the phylogenetic relationships among the monotremes, marsupial, and placental mammals. We present a discussion of limitations of currently used molecular markers and phylogenetic methods as well as make recommendations for future approaches and sets of marker genes.
 
Researchers are increasingly recognizing that social effects influence the evolution of aging. Kin selection theory provides a framework for analyzing such effects because an individual's longevity and mortality schedule may alter its inclusive fitness via effects on the fitness of relatives. Kin-selected effects on aging have been demonstrated both by models of intergenerational transfers of investment by caregivers and by spatially explicit population models with limited dispersal. They also underlie coevolution between the degree and form of sociality and patterns of aging. In this review I critically examine and synthesize theory and data concerning these processes. I propose a classification, stemming from kin selection theory, of social effects on aging and describe a hypothesis for kin-selected conflict over parental time of death in systems with resource inheritance. I conclude that systematically applying kin selection theory to the analysis of the evolution of aging adds considerably to ...
 
We examine how aging is influenced by various chemical challenges that organisms face and by the molecular mechanisms that have evolved to modulate life span in response to them. For example, environmental information, which is detected and processed through sensory systems, can modulate life span by providing information about the presence and quality of food as well as presence and density of conspecifics and predators. In addition, the diverse forms of molecular damage that result from constant exposure to toxic chemicals that are generated from the environment and from metabolism pose an informatic and energetic challenge for detoxification systems, which are important in ensuring longevity. Finally, systems of innate immunity are vital for recognizing and combating pathogens but are also increasingly seen as of importance in causing the aging process. Integrating ideas of molecular mechanism with context derived from evolutionary considerations will lead to exciting new insights into the evolution of...
 
As an inevitable consequence of increased environmental degradation and anticipated future environmental change, societal demand for ecosystem restoration is rapidly increasing. Here, I evaluate successes and failures in restoration, how science is informing these efforts, and ways to better address decision-making and policy needs. Despite the multitude of restoration projects and wide agreement that evaluation is a key to future progress, comprehensive evaluations are rare. Based on the limited available information, restoration outcomes vary widely. Cases of complete recovery are frequently characterized by the persistence of species and abiotic processes that permit natural regeneration. Incomplete recovery is often attributed to a mixture of local and landscape constraints, including shifts in species distributions and legacies of past land use. Lastly, strong species feedbacks and regional shifts in species pools and climate can result in little to no recovery. More forward-looking paradigms, such a...
 
▪ Abstract Reef corals (and other marine invertebrates and protists) are hosts to a group of exceptionally diverse dinoflagellate symbionts in the genus Symbiodinium. These symbionts are critical components of coral reef ecosystems whose loss during stress-related “bleaching” events can lead to mass mortality of coral hosts and associated collapse of reef ecosystems. Molecular studies have shown these partnerships to be more flexible than previously thought, with different hosts and symbionts showing varying degrees of specificity in their associations. Further studies are beginning to reveal the systematic, ecological, and biogeographic underpinnings of this flexibility. Unusual symbionts normally found only in larval stages, marginal environments, uncommon host taxa, or at latitudinal extremes may prove critical in understanding the long-term resilience of coral reef ecosystems to environmental perturbation. The persistence of bleaching-resistant symbiont types in affected ecosystems, and the possibilit...
 
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 inva...
 
Estimates of the LCA gene complement based on quantitative genomic analysis 
(Continued ) 
Quantitative estimates of the gene complement of the last common ancestor of all extant organisms, that is, the cenancestor, may be hindered by ancient horizontal gene transfer events and polyphyletic gene losses, as well as by biases in genome databases and methodological artifacts. Nevertheless, most reports agree that the last common ancestor resembled extant prokaryotes. A significant number of the highly conserved genes are sequences involved in the synthesis, degradation, and binding of RNA, including transcription and translation. Although the gene complement of the cenancestor includes sequences that may have originated in different epochs, the extraordinary conservation of RNA-related sequences supports the hypothesis that the last common ancestor was an evolutionary outcome of the so-called RNA/protein world. The available evidence suggests that the cenancestor was not a hyperthermophile, but it is currently not possible to assess its ecological niche or its mode of energy acquisition and carbon...
 
Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis and maize enable us to identify genes, gene families, and gene networks that are involved in the regulation of flower initiation, growth and differentiation. These genes can then function as “candidate genes” and their expression, function, and biochemical interactions can be explored in other lineages to determine if they provide a necessary and sufficient toolkit for the development of the flower. Likewise, a view to the fossil record can provide documentation of reproductive innovations occurring within gymnosperms or along the stem lineage leading to angiosperms, elucidating the transitions required for the evolution of the angiosperm flower from an ancestral reproductive strobilus. Here we discuss the origin and subsequent evolution in form of the flower, highlighting recent studies in paleobotany, morphology, evolution, and developmental genetics with the goal of outlining advances in our understanding of...
 
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.
 
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.
 
Much of the information in visual signals is encoded in motion, form, and texture. Current knowledge about the mechanisms underlying visual communication is spread across diverse disciplines. Contemporary perspectives on the physics, psychology, and genetics of visual signal generation and perception can be synthesized into a conceptually integrative approach. Developmental mechanisms of pattern formation suggest that small changes in gene regulation or structure can result in major shifts in signal architecture. Animals in many species have been shown to attend to variation in higher-order stimulus properties. Preferences for these properties can be innately specified or learned, and may also show large shifts or reversals. Perceptual mechanisms, particularly visual attention, associated with spatiotemporal features are likely to be a major force in shaping the design of visual signals.
 
Results of the literature survey
▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...
 
Males in many species invest substantially in structures that are used in combat with rivals over access to females. These weapons can attain extreme proportions and have diversified in form repeatedly. I review empirical literature on the function and evolution of sexually selected weapons to clarify important unanswered questions for future research. Despite their many shapes and sizes, and the multitude of habitats within which they function, animal weapons share many properties: They evolve when males are able to defend spatially restricted critical resources, they are typically the most variable morphological structures of these species, and this variation honestly reflects among-individual differences in body size or quality. What is not clear is how, or why, these weapons diverge in form. The potential for male competition to drive rapid divergence in weapon morphology remains one of the most exciting and understudied topics in sexual selection research today.
 
General patterns in the composition of bacterial communities in various body habitats. Pie charts illustrate percentage of 16S rRNA gene sequences representing the dominant bacterial phyla. Data compiled from Charlson et al. 2010, Costello et al. 2009, Dicksved et al. 2009, Frank et al. 2003, Hayashi et al. 2005, Kim et al. 2009, Pei et al. 2004, Price et al. 2010.
The human body is inhabited by billions of microbial cells and these microbial symbionts play critical roles in human health. Human-associated microbial communities are diverse, and the structure of these communities is variable across body habitats, through time, and between individuals. We can apply concepts developed by plant and animal ecologists to better understand and predict the spatial and temporal patterns in these communities. Due to methodological limitations and the largely unknown natural history of most microbial taxa, this integration of ecology into research on the human microbiome is still in its infancy. However, such integration will yield a deeper understanding of the role of the microbiome in human health and an improved ability to test ecological concepts that are more difficult to test in plant and animal systems.
 
Successful dispersal between populations leaves a genetic wake that can reveal historical and contemporary patterns of connectivity. Genetic studies of differentiation in the sea suggest the role of larval dispersal is often tempered by adult ecology, that changes in differentiation with geographic distance are limited by disequilibrium between drift and migration, and that phylogeographic breaks reflect shared barriers to movement in the present more than common historical divisions. Recurring complications include the presence of cryptic species, selection on markers, and a failure to account for differences in heterozygosity among markers and species. A better understanding of effective population sizes is needed. Studies that infer parentage or kinship and coalescent analyses employing more markers are both likely to spur progress, with analyses based on linkage disequilibrium potentially bridging results from these studies and reconciling patterns that vary at ecological and evolutionary timescales.
 
Biodiversity is not completely known anywhere, so conservation planning is always based on surrogates for which data are available and, hence, assumed effective for the conservation of unknown biodiversity. We review the literature on the effectiveness of surrogates for conservation planning based on complementary representation. We apply a standardized approach based on a Species Accumulation Index of surrogate effectiveness to compare results from 575 tests in 27 studies. Overall, we find positive, but relatively weak, surrogacy power. Cross-taxon surrogates are substantially more effective than surrogates based on environmental data. Within cross-taxon tests, surrogacy was higher for tests within the same realm (terrestrial, marine, freshwater). Surrogacy was higher when extrapolated (rather than field) data were used. Our results suggest that practical conservation planning based on data for well-known taxonomic groups can cautiously proceed under the assumption that it captures species in less well-k...
 
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 rel...
 
■ Abstract Protective ant-plant interactions, important in both temperate and trop- ical communities, are increasingly used to study a wide range of phenomena of general interest. As antiherbivore defenses "worn on the outside," they pose fewer barriers to experimentation than do direct (e.g., chemical) plant defenses. This makes them tractable models to study resource allocation to defense and mechanisms regulating it. As multi-trophic level interactions varying in species specificity and impact on fitness of participants, ant-plant-herbivore associations figure prominently in studies of food-web structure and functioning. As horizontally transmitted mutualisms that are vulnerable to parasites and "cheaters," ant-plant symbioses are studied to probe the evolutionary dynamics of interspecies interactions. These symbioses, products of coevolution between plants and insect societies, offer rich material for studying ant social evolution in novel contexts, in settings where colony limits, resource supply, and nest-site availability are all more easily quantifiable than in the ground-nesting ants hitherto used as models.
 
Manifestations of linearity and the A/P axis in the Echinodermata. Externally, linearity in echinoderms can be obvious even among the earliest echinoderms. (a) The Cambrian fossil Gogia spiralis (Robison 1965; CASG uncataloged, specimen approximately 2 cm long), shows linearity by the sequential arrangement of the mouth, calyx, and stem. Internally, the A/P axis is established via coelomic stacking. Diagrammatically, this is shown in (b) the Cambrian form, Camptostroma, (c) a cystidean larva of an extant crinoid, (d ) an adult extant crinoid, (e) an extant asteroid, ( f ) an extant holothuroid, ( g) and an extant echinoid. Drawings b-g are not to scale, and the mouth is shown facing upward in each case, regardless of natural orientation.
Summary of primary literature describing or using the Extraxial-Axial Theory
The strangeness of echinoderm pentaradiality results from superposition of radial symmetry onto ancestral deuterostome bilaterality. The Extraxial- Axial Theory shows that echinoderms also have an anterior/posterior (A/P) axis developed independently and ontogenetically before radiality. The A/P axis is first established via coelomic stacking in the extraxial region, with ensuing development of the pentamerous hydrocoel in the axial region. This is strongly correlated with a variety of gene expression patterns. The echinoid Hox cluster is disordered into two different sets of genes. During embryogenesis, members of the posterior class demonstrate temporal, spatial, and genetic colinearity within the extraxial region.We suggest that displacement of genes from the more anterior Hox classes toward the 5' end of the chromosome leads to control of the later-developing, radially symmetric axial region. Genetic disorder is therefore another way of using colinearity to build the unique echinoderm symmetry.
 
Ecologists have long grappled with the problem of scaling up from tractable, small-scale observations and experiments to the prediction of large-scale patterns. Although there are multiple approaches to this formidable task, there is a common underpinning in the formulation, testing, and use of mechanistic response functions to describe how phenomena interact across scales. Here, we review the principles of response functions to illustrate how they provide a means to guide research, extrapolate beyond measured data, and simplify our conceptual grasp of reality. We illustrate these principles with examples of mechanistic approaches ranging from explorations of the ecological niche, random walks, and macrophysiology to theories dealing with scale transition, self-organization, and the prediction of extremes.
 
The ideal data set for testing hypotheses about extinction, with all speciations (diamonds), extinctions (crosses), and character states (x axis) recorded. Species’ attributes can be correlated against fates. (b) The information that might more typically be available in the fossil record. (c) The best information obtainable from the phylogeny of extant species. Modified after Purvis et al. (2008).
Relationship between estimated λ−μ (treated as the single parameter in a pure-birth process) and clade age for all crown groups in a phylogeny of 5000 extant species simulated with λ=0.2, μ=0.1. Clades in which λ−μ=0 have two extant species. The red line indicates the correct value of λ−μ. The blue line indicates the lowest regression of λ−μ on clade age, if the two-species clades (which would hardly ever be studied) are included.
Two illustrations of the use of matched pairs to test proposed correlates of extinction. Lines link the two sets of species within each matched pair. (a) Survivors are larger than casualties within genera of Late Neogene Californian scallops (data from Smith & Roy 2006). (b) Primates that decline steeply when habitat is degraded have larger home ranges than do those that decline less (data from Harcourt 1998).
Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.
 
Shifts in phenology and distribution in response to both recent and paleontological climate changes vary markedly in both direction and extent among species. These individualistic shifts are inconsistent with common forecasting techniques based on environmental rather than biological niches. What biological details could enhance forecasts? Organismal characteristics such as thermal and hydric limits, seasonal timing and duration of the life cycle, ecological breadth and dispersal capacity, and fitness and evolutionary potential are expected to influence climate change impacts. We review statistical and mechanistic approaches for incorporating traits in predictive models as well as the potential to use phylogeny as a proxy for traits. Traits generally account for a significant but modest fraction of the variation in phenological and range shifts. Further assembly of phenotypic and phylogenetic data coupled with the development of mechanistic approaches is essential to improved forecasts of the ecological c...
 
▪ Abstract Mutualisms occur when interactions between species produce reciprocal benefits. However, the outcome of these interactions frequently shifts from positive, to neutral, to negative, depending on the environmental and community context, and indirect effects commonly produce unexpected mutualisms that have community-wide consequences. The dynamic, and context dependent, nature of mutualisms can transform consumers, competitors, and parasites into mutualists, even while they consume, compete with, or parasitize their partner species. These dynamic, and often diffuse, mutualisms strongly affect community organization and ecosystem processes, but the historic focus on pairwise interactions decoupled from their more complex community context has obscured their importance. In aquatic systems, mutualisms commonly support ecosystem-defining foundation species, underlie energy and nutrient dynamics within and between ecosystems, and provide mechanisms by which species can rapidly adjust to ecological vari...
 
Individual-based simulations illustrating the effects of epistasis on the response to selection from standing genetic variation. Panel (a) shows the mean phenotype and (b) shows the additive genetic variance as averages over 100 populations subject to linear directional selection. Bars in (a) indicate one standard deviation over the ensemble. Four different genetic architectures are shown: pure additive, positive directional epistasis, negative directional epistasis, and nondirectional epistasis. Each simulated population consists of 1000 individuals, and there are 20 segregating loci connected with normally distributed epistasis with mean epistatic effects being 1, 0, or-1 depending on treatment. Modified from Carter et al. (2005).
Genetic architecture, the structure of the mapping from genotype to phenotype, determines the variational properties of the phenotype and is instrumental in understanding its evolutionary potential. Throughout most of the history of evolutionary biology, genetic architecture has been treated as a given set of parameters and not as a set of dynamic variables. The past decade has seen renewed interest in incorporating the genotype-phenotype map as a dynamical part of population genetics. This has been aided by several conceptual advances. I review these developments with emphasis on recent theoretical work on the evolution of genetic architecture and evolvability.
 
Arthropod generalist predators (AGP) are widespread and abundant in both aquatic and terrestrial ecosystems. They feed upon herbivores, detritivores, and predators, and also on plant material and detritus. In turn, AGP serve as prey for larger predators. Several prominent AGP have become invasive when moved by humans beyond their native range. With complex trophic roles, AGP have diverse effects on other species in their introduced ranges. The invaders displace similar native species, primarily through competition, intraguild predation, transmission of disease, and escape from predation and/or parasites. Invasive AGP often reach higher densities and/or biomass than the native predators they replace, sometimes strengthening herbivore regulation when invasive AGP feed on key herbivores, but sometimes weakening herbivore suppression when they eat key predators. The complexity and unpredictability of ecological effects of invasive AGP underscores the high risk of adverse consequences of intentional in...
 
Food webs are overlaid with infochemical webs that mediate direct and indirect interactions. The infochemicals may result in shifts in trait values, which affect the strength of species interactions. As a consequence, population dynamics and evolutionary changes can be affected. Chemical information can mediate the interactions between animals and their resources, competitors and enemies. Of all chemical information gathered by animals, cues about predation risk are of special significance because predation risk usually has important and immediate consequences on fitness. In this paper we selectively review the role of chemical information in enemy avoidance by arthropods. Arthropods not only constitute important components of food webs, being the largest group in numbers and species diversity; they also make excellent models for ecological studies. We discuss the evidence, the key mechanisms, and the trade-offs involved in chemical detection of enemies by potential arthropod prey. Further, we address the variation in prey responses and the evidence for learning in avoiding enemies by arthropods. Finally, we identify and prioritize major questions to be tackled by future studies.
 
▪ Abstract The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.
 
Comparison of the spans of temporal resolution that characterize ecological and paleontological data. Individual fossil assemblages may encapsulate varying degrees of time (i.e., time-averaging), depending on the circumstances of death and burial (taphonomy) and collection method, whereas samples of extant communities generally represent single or repeated censuses over days to decades. In paleontology, long-term floral or faunal records developed from multiple fossil assemblages are the basis for the analysis of paleocommunity stasis or change though time ( upper gray bar ). In ecology, with the exception of speciation, processes that can be observed or inferred in recent ecosystems ( lower gray bar ) occur over much shorter time intervals than can be resolved by paleontological data. 
Studies of plant and animal assemblages from both the terrestrial and the marine fossil records reveal persistence for extensive periods of geological time, sometimes millions of years. Persistence does not require lack of change or the absence of variation from one occurrence of the assemblage to the next in geological time. It does, however, imply that assemblage composition is bounded and that variation occurs within those bounds. The principal cause for these patterns appears to be species-, and perhaps clade-level, environmental fidelity that results in long-term tracking of physical conditions. Other factors that influence persistent recurrence of assemblages are historical, biogeographic effects, the law of large numbers, niche differentiation, and biotic interactions. Much research needs to be done in this area, and greater uniformity is needed in the approaches to studying the problem. However, great potential also exists for enhanced interaction between paleoecology and neoecology in understanding spatiotemporal complexity of ecological dynamics.
 
Although research on the role of competitive interactions during community assembly began decades ago, a recent revival of interest has led to new discoveries and research opportunities. Using contemporary coexistence theory that emphasizes stabilizing niche differences and relative fitness differences, we evaluate three empirical approaches for studying community assembly. We show that experimental manipulations of the abiotic or biotic environment, assessments of trait-phylogeny-environment relationships, and investigations of frequency-dependent population growth all suggest strong influences of stabilizing niche differences and fitness differences on the outcome of plant community assembly. Nonetheless, due to the limitations of these approaches applied in isolation, we still have a poor understanding of which niche axes and which traits determine the outcome of competition and community structure. Combining current approaches represents our best chance of achieving this goal, which is fundamental to ...
 
▪ Abstract Like South Africa's Greater Cape Floristic Region, the Southwest Australian Floristic Region (SWAFR) is species rich, with a Mediterranean climate and old, weathered, nutrient-deficient landscapes. This region has 7380 native vascular plants (species/subspecies): one third described since 1970, 49% endemic, and 2500 of conservation concern. Origins are complex. Molecular phylogenies suggest multiple dispersal events into, out of, and within the SWAFR throughout the Cretaceous and Cenozoic; in many phylogenetically unrelated clades; and from many directions. Either explosive speciation or steady cladogenesis occurred among some woody sclerophyll and herbaceous families from the mid-Tertiary in response to progressive aridity. Genomic coalescence was sometimes involved. Rainforest taxa went extinct by the Pleistocene. Old lineages nevertheless persist as one endemic order (Dasypogonales) and 6–11 endemic families. Such a rich flora on old landscapes that have been exposed to European land-use pra...
 
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...
 
Belowground-feeding herbivores may be very destructive to plants. Roots are known to produce various defense compounds to protect themselves against these herbivores, both with direct and indirect—inducible—defense compounds. Recent literature reviews reveal no overall pattern for root-shoot defense allocation. Optimal defense allocation patterns within roots may be predicted with an ecophysiological model taking into account the value and vulnerability of root classes. Induced responses elicited by root herbivores are likely to result in systemic responses in the shoots. These systemic responses may affect aboveground herbivores and higher trophic levels. This calls into question whether root-to-shoot systemic induction is an adaptive response. Physiological responses conferring tolerance may co-occur with resistance responses, depending on the biotic and abiotic environment of the roots. More detailed analyses of root defenses and the feeding sites of herbivores are needed to gain a better understanding...
 
Marine invertebrate diversity (Bambach 1993) and phytoplankton diversity (as in Figure 3) over the Phanerozoic. Timescales are as in Figure 3. Data are available at http://mychronos.chronos.org/∼miriamkatz/20040721
Geochemical proxy records showing comparisons of phosphorous flux [(Follmi 1995); curve fit (B.S. Cramer, personal com
The evolutionary succession of marine photoautotrophs began with the origin of photosynthesis in the Archean Eon, perhaps as early as 3.8 billion years ago. Since that time, Earth's atmosphere, continents, and oceans have undergone substantial cyclic and secular physical, chemical, and biological changes that selected for different phytoplankton taxa. Early in the history of eukaryotic algae, between 1.6 and 1.2 billion years ago, an evolutionary schism gave rise to "green" (chlorophyll b -containing) and "red" (chlorophyll c -containing) plastid groups. Members of the "green" plastid line were important constituents of Neoproterozoic and Paleozoic oceans, and, ultimately, one green clade colonized land. By the mid-Mesozoic, the green line had become ecologically less important in the oceans. In its place, three groups of chlorophyll c -containing eukaryotes, the dinoflagellates, coccolithophorids, and diatoms, began evolutionary trajectories that have culminated in ecological dominance in the contemporary oceans. Breakup of the supercontinent Pangea, continental shelf flooding, and changes in ocean redox chemistry may all have contributed to this evolutionary transition. At the same time, the evolution of these modem eukaryotic taxa has influenced both the structure of marine food webs and global biogeochemical cycles. Earth and Planetary Sciences Organismic and Evolutionary Biology
 
Top-cited authors
Thomas Elmqvist
  • Stockholm University
C.s. Holling
  • University of Florida
Brian Walker
  • The Commonwealth Scientific and Industrial Research Organisation
Carl Folke
  • Kungliga Vetenskapsakademien
Jean-Pierre Tremblay
  • Laval University