Annual Review of Ecology, Evolution, and Systematics - Volume 37, 2006

Birth-death models, and their subsets—the pure birth and pure death models—have a long history of use for informing thinking about macroevolutionary patterns. Here we illustrate with examples the wide range of questions they have been used to address, including estimating and comparing rates of diversification of clades, investigating the “shapes” of clades, and some rather surprising uses such as estimating speciation rates from data that are not resolved below the level of the genus. The raw data for inference can be the fossil record or the molecular phylogeny of a clade, and we explore the similarites and differences in the behavior of the birth-death models when applied to these different forms of data.

Bayesian analysis has enjoyed explosive growth in phylogenetics over the past five years. Accompanying this popularity has been increased focus on the meaning of the posterior probability (PP) and the role of the prior in phylogenetic inference. Here we discuss the behavior of the PP in Bayesian and frequentist terms and its relationship to parametric and nonparametric bootstrapping. We also review the use of priors in phylogenetics and the issues surrounding the specification of informative and minimally informative prior distributions.

Sexual reproduction is associated with the evolution of anisogamy and sperm-producing males and egg-laying females. The ensuing competition for mates has led to sexual selection and coevolution of the sexes. Mathematical models are extensively used to test the plausibility of different complicated scenarios for the evolution of sexual traits. Unfortunately, the diversity of models is now itself equally bewildering. Here we clarify some of the current debate by reviewing evolutionary explanations for the relationship between anisogamy, potential reproductive rates, parental care, sex roles, and mate choice. We review the benefits females might gain by mating with certain males rather than others. We also consider other forms of selection that can make females mate nonrandomly. One way empiricists can contribute to resolving theoretical disputes is to quantify the cost of expressing mating biases in the appropriate life-history currency.

The selective mechanisms for maintaining polymorphism in natural populations has been the subject of theory, experiments, and review over the past half century. Advances in molecular genetic techniques have provided new insight into many examples of balancing selection. In addition, new theoretical developments demonstrate how diversifying selection over environments may maintain polymorphism. Tests for balancing selection in the current generation, the recent past, and the distant past provide a comprehensive approach for evaluating selective impacts. In particular, sequenced-based tests provide new ways to evaluate the long-term impact of selection on particular genes and the overall genome in natural populations. Overall, there appear to be many loci exhibiting the signal of adaptive directional selection from genomic scans, but the present evidence suggests that the proportion of loci where polymorphism is maintained by environmental heterogeneity is low. However, as more molecular genetic details become available, more examples of polymorphism maintained by selection in heterogeneous environments may be found.

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 introductions of these species (e.g., for biological control or aquaculture).

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.

To maintain sexual reproduction, recombination of good genes through selective mate choice must achieve a twofold genetic benefit in each generation. “Fragrant” immune genes of the major histocompatibility complex (MHC) allow the choosy sex to complement her own set of alleles with a more or less diverse set of male alleles to reach an optimal number of different MHC alleles for the offspring. The optimal complement from the partner should include those MHC alleles that provide resistance against the current parasites, which could be revealed by the expression of costly secondary sexual characters. This maximizes resistance to ever-changing infectious diseases. Because the advantage of sex must be produced through recombination, assortative mating should combine currently advantageous MHC alleles. Preferring just MHC dissimilar mates is only a best-of-bad-job rule. MHC ligand peptides may be the natural “perfume” that reveals a potential partner's MHC genetics probably in all vertebrates. Perfumes may mimick MHC related signals.

Trees do not form a natural group but share attributes such as great size, longevity, and high reproductive output that affect their mode and tempo of evolution. In particular, trees are unique in that they maintain high levels of diversity while accumulating new mutations only slowly. They are also capable of rapid local adaptation and can evolve quickly from nontree ancestors, but most existing tree lineages typically experience low speciation and extinction rates. We discuss why the tree growth habit should lead to these seemingly paradoxical features.

Between fifty and ten thousand years ago, most large mammals became extinct everywhere except Africa. Slow-breeding animals also were hard hit, regardless of size. This unusual extinction of large and slow-breeding animals provides some of the strongest support for a human contribution to their extinction and is consistent with various human hunting models, but it is difficult to explain by models relying solely on environmental change. It is an oversimplification, however, to say that a wave of hunting-induced extinctions swept continents immediately after first human contact. Results from recent studies suggest that humans precipitated extinction in many parts of the globe through combined direct (hunting) and perhaps indirect (competition, habitat alteration) impacts, but that the timing and geography of extinction might have been different and the worldwide magnitude less, had not climatic change coincided with human impacts in many places.

Despite progress in the past decade, researchers struggle to evaluate the hypothesis that environmental conditions compromise immunity and facilitate new disease outbreaks. In this chapter, we review known immunological mechanisms for selected phyla and find that there are critical response pathways common to all invertebrates. These include the prophenoloxidase pathway, wandering phagocytic cells, cytotoxic effector responses, and antimicrobial compounds. To demonstrate the links between immunity and the environment, we summarize mechanisms by which immunity is compromised by environmental conditions. New environmental challenges may promote emergent disease both through compromised host immunity and introduction of new pathogens. Such challenges include changing climate, polluted environment, anthropogenically facilitated pathogen invasion, and an increase in aquaculture. The consequences of these environmental issues already manifest themselves as increased mortality on coral reefs, pathogen range expansion, and transmission of disease from aquaculture to natural populations, as we summarize in a final section on recent marine epizootics.

The role of epistasis in evolution has long been contentious. Resolving the issue requires empirical measurements that are statistically adequate and evolutionarily relevant. We review experimental methods for measuring epistasis, some that are commonly used but weak and others that are less frequently used but stronger. We review statistical genetic methods based on analyses of variances and means as well as molecular genetic methods for detecting gene interactions. We also highlight relevant empirical studies that illustrate the implementation of particular methods. In spite of the inherent weaknesses of most methods, epistasis is surprisingly common. We conclude with a discussion of how technologies for investigating genome-wide epistasis are bridging the gap between physiological and statistical epistasis for model organisms.

Corridors are commonly used to connect fragments of wildlife habitat, yet the identification of conservation corridors typically neglects processes of habitat selection and movement for target organisms. Instead, corridor designs often are based on binary patterns of habitat suitability. New technologies and analytical tools make it possible to better integrate landscape patterns with behavioral processes. We show how resource selection functions can be used to describe habitat suitability with continuous and multivariable metrics and review methods by which animal movement can be quantified, analyzed, and modeled. We then show how the processes of habitat selection and movement can be integrated with landscape features using least-cost paths, graph theory, and step selection functions. These tools offer new ways to design, implement, and study corridors as landscape linkages more objectively and holistically.

Seaweed population biology has received far less attention than trophic dynamics, yet is critically important in establishing and maintaining algal communities. Complex life histories of habitat-forming kelps and fucoids, including spores, gametophytes, gametes, and microscopic and macroscopic benthic stages, must be considered within the context of their highly dynamic nearshore environments. We evaluate differences within and between kelps and fucoids in life histories as they affect population biology; dispersal and potential limitations in population establishment; macroscopic stages and variations in survival and longevity affecting stand structure; and microscopic stage responses to disturbance and variation in the physical environment. We suggest that the commonly made comparisons of seaweeds with terrestrial seed plants are misleading because of large differences in morphology, environments, and the ephemeral nature of propagule banks in the sea. We conclude that progress in understanding algal populations depends on better knowledge of microscopic stages and on feedback through density-dependent reproductive processes, dispersal, and settlement.

Long-term monitoring shows that the poleward range edges of intertidal biota have shifted by as much as 50 km per decade, faster than most recorded shifts of terrestrial species. Although most studies have concentrated on species-range edges, recent work emphasizes how modifying factors such as regional differences in the timing of low tide can overwhelm large-scale climatic gradients, leading to a mosaic of environmental stress. We discuss how changes in the mean and variability in climatic regimes, as modified by local and regional factors, can lead to complex patterns of species distribution rather than simple range shifts. We describe how ecological forecasting may be used to generate explicit hypotheses regarding the likely impacts of different climatic change scenarios on the distribution of intertidal species and how related hindcasting methods can be used to evaluate changes that have already been detected. These hypotheses can then be tested over a hierarchy of temporal and spatial scales using coupled field and laboratory-based approaches.

Madagascar is one of the world's hottest biodiversity hot spots due to its diverse, endemic, and highly threatened biota. This biota shows a distinct signature of evolution in isolation, both in the high levels of diversity within lineages and in the imbalance of lineages that are represented. For example, chameleon diversity is the highest of any place on Earth, yet there are no salamanders. These biotic enigmas have inspired centuries of speculation relating to the mechanisms by which Madagascar's biota came to reside there. The two most probable causal factors are Gondwanan vicariance and/or Cenozoic dispersal. By reviewing a comprehensive sample of phylogenetic studies of Malagasy biota, we find that the predominant pattern is one of sister group relationships to African taxa. For those studies that include divergence time analysis, we find an overwhelming indication of Cenozoic origins for most Malagasy clades. We conclude that most of the present-day biota of Madagascar is comprised of the descendents of Cenozoic dispersers, predominantly with African origins.

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 small threatened populations have a decreased potential for adaptation.

The interface between living plant roots and soils (the rhizosphere) is a central commodities exchange, where organic carbon flux from roots fuels decomposers that, in turn, can make nutrients available to roots. This ongoing exchange operates in the path of vast, transpiration-driven water flow. How the spatio-temporal patterning in resource availability around plant roots affects rhizosphere community composition, activity, and nutrient cycling remains unknown. This review considers how molecular approaches contribute to the exploration of rhizosphere resource exchange, highlighting several recently developed methods linking microbial identity with substrate uptake and gene expression. In particular, strengths and weaknesses of genetically engineered bioreporters are discussed, because currently they alone provide in situ spatio-temporal information at scales of rhizosphere organisms. The soil spatial context is an emerging frontier in ecological soils research. We conclude with parallels linking empirical investigation in the rhizosphere with the quest for understanding general rhizosphere function in Earth's diverse ecosystems.

The importance of hybridization in the evolution of plant species is widely accepted, but its contributions to animal species evolution remain less recognized. Here we review evidence that hybridization has contributed to the evolution of reef corals, a group underpinning the coral reef ecosystem. Increasingly threatened by human and climate-related impacts, there is need to understand the evolutionary processes that have given rise to their diversity and contribute to their resilience. Reticulate evolutionary pathways among the ecologically prominent, mass-spawning genus Acropora suggest that hybridization, although rare on ecological timescales, has been instrumental in their diversification on evolutionary timescales. Evidence that coral hybrids colonize marginal habitats distinct from those of parental species' and that hybridization may be more frequent at peripheral boundaries of species' ranges supports a role for hybridization in range expansion and adaptation to changing environments. We conclude that outcomes of hybridization are significant for the future resilience of reef corals and warrant inclusion in conservation strategies.

Bioinformatics, the application of computational tools to the management and analysis of biological data, has stimulated rapid research advances in genomics through the development of data archives such as GenBank, and similar progress is just beginning within ecology. One reason for the belated adoption of informatics approaches in ecology is the breadth of ecologically pertinent data (from genes to the biosphere) and its highly heterogeneous nature. The variety of formats, logical structures, and sampling methods in ecology create significant challenges. Cultural barriers further impede progress, especially for the creation and adoption of data standards. Here we describe informatics frameworks for ecology, from subject-specific data warehouses, to generic data collections that use detailed metadata descriptions and formal ontologies to catalog and cross-reference information. Combining these approaches with automated data integration techniques and scientific workflow systems will maximize the value of data and open new frontiers for research in ecology.

DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here we review how these studies have used advances in knowledge of molecular evolutionary processes to create more realistic models of evolution, evaluate the information content of data, test phylogenetic hypotheses, attach time to phylogenies, and understand the relative usefulness of mitochondrial and nuclear genes. We also provide a new compilation of conserved polymerase chain reaction (PCR) primers for mitochondrial genes that complements our earlier compilation.