Annual Review of Ecology, Evolution, and Systematics - Volume 34, 2003

The extent and diversity of sexual dichromatism in birds is thought to be due to the intensity of current sexual selection on the plumage ornamentation of males and females. This view leads to an expectation of concordance between ecological conditions and sexual dichromatism. Yet, because expression of dichromatism is the result of not only current selection, but also historical patterns of development, function, and selection, the concordance between ecology and current sexual dichromatism is not straightforward. Recent studies have revealed a number of trends in the evolution of avian sexual ornamentation that seem contrary to what is expected if current sexual selection is the primary force shaping dichromatism. For example, change in sexual dichromatism is often the result of evolutionary changes in female rather than male ornamentation. Moreover, sexual dichromatism is often an ancestral rather than a derived state; current expression of dichromatism is frequently the result of selection for lesser ornamentation in one sex and not for ornament elaboration. Loss and gain of sexual ornamentation sometimes precedes changes in preference for sexual ornamentation, and sexual ornaments can have high evolutionary lability despite their developmental and functional complexity. These findings emphasize that phylogenetic reconstructions must play a central role in attempts to understand the function and evolution of sexual dichromatism. With a historical perspective, one can test the relative importance of direct selection, indirect selection, and drift in relation to changes of sexual dichromatism. If sexual selection is invoked, the mechanisms of sexual selection can be explored by examining the concordance between the elaboration of ornamentation and the preferences for ornamentation across species and by tracing phylogenetic trajectories of sexual ornaments. Finally, placing physiological, genetic, and developmental mechanisms of sexual ornamentation into such a phylogenetic framework will enable greater inference about the past evolution and current function of sexual dichromatism in birds.

Paleobiogeography has advanced as a discipline owing to the increasing utilization of a phylogenetic approach to the study of biogeographic patterns. Coupled with this, there has been an increasing interdigitation of paleontology with molecular systematics because of the development of techniques to analyze ancient DNA and because of the use of sophisticated methods to utilize molecules to date evolutionary divergence events. One pervasive pattern emerging from several paleontological and molecular analyses of paleobiogeographic patterns is the recognition that repeated episodes of range expansion or geo-dispersal occur congruently in several different lineages, just as congruent patterns of vicariance also occur in independent lineages. The development of new analytical methods based on a modified version of Brooks Parsimony Analysis makes it possible to analyze both geo-dispersal and vicariance in a phylogenetic context, suggesting that biogeography as a discipline should focus on the analysis of a variety of congruent phenomena, not just vicariance. The important role that extinction plays in influencing apparent biogeographic patterns among modern and fossil groups suggests that this is another area ripe for new methodological developments.

A growing number of species have been transported and introduced by humans to new locations and have established self-sustaining wild populations beyond their natural range limits. Many of these species go on to have significant environmental or economic impacts. However, not all species transported and introduced to new locations succeed in establishing wild populations, and of the established species only some become widespread and abundant. What factors underlie this variation in invasion success? Here, we review progress that has been made in identifying factors underpinning invasion success from studies of bird introductions. We review what is known about the introduction, establishment, and spread of introduced bird species, focusing on comparative studies that use historical records to test hypotheses about what factors determine success at different stages in the invasion process. We close with suggestions for future research.

Variation within a species may be structured both geographically and by genetic background. We review the effects of such structuring on neutral variants, using a framework based on the coalescent process. Short-term effects of sex differences and age structure can be averaged out using fast timescale approximations, allowing a simple general treatment of effective population size and migration. We consider the effects of geographic structure on variation within and between local populations, first in general terms, and then for specific migration models. We discuss the close parallels between geographic structure and stable types of genetic structure caused by selection, including balancing selection and background selection. The effects of departures from stability, such as selective sweeps and population bottlenecks, are also described. Methods for distinguishing population history from the effects of ongoing gene flow are discussed. We relate the theoretical results to observed patterns of variation in natural populations.

Ecological and fisheries approaches to population modeling share many common tools and issues, yet they have developed quite independently over the past decades. The Sustainable Fisheries Act has pushed fisheries modeling into forecasting for management decision-making, which is an area where ecological modeling appears to be headed. We summarize how marine fisheries are managed in the United States, and how data and models are used to make the required forecasts. The recent management deliberations of red grouper in the Gulf of Mexico provide a case study of the sensitive relationship among data, models, and management decisions. We use the U.S. marine fisheries experience and the case study to discuss six lessons that ecologists should consider as they proceed toward forecasting for management. The need for forecasting is accelerating both in ecology and fisheries, while the margin for mistakes is getting smaller.

Animal species have evolved different diel activity rhythms that are of adaptive value. Theory suggests that diel temporal partitioning may facilitate coexistence between competitors and between predators and prey. However, relatively few studies demonstrate a temporal shift that is predation- or competition-induced. Recorded shifts are usually within the preferred activity phase of animal species (day or night), although there are some inversions to the opposite phase cycle. Temporal partitioning is not perceived as a common mechanism of coexistence. This rarity has been variously ascribed to theoretical considerations and to the rigidity of time-keeping mechanisms, as well as to other physiological and anatomical traits that may constrain activity patterns. Our decade-long study of spiny mice of rocky deserts demonstrates that, while different factors select for activity patterns, endogenous rhythmicity may be an evolutionary constraint.

In the search to identify factors that make some plant species troublesome invaders, many studies have compared various measures of native and alien invasive plant performance. These comparative studies provide insights into the more general question “Do alien invasive plants usually outperform co-occurring native species, and to what degree does the answer depend on growing conditions?” Based on 79 independent native-invasive plant comparisons, the alien invaders were not statistically more likely to have higher growth rates, competitive ability, or fecundity. Rather, the relative performance of invaders and co-occurring natives often depended on growing conditions. In 94% of 55 comparisons involving more than one growing condition, the native's performance was equal or superior to that of the invader, at least for some key performance measures in some growing conditions. Most commonly, these conditions involved reduced resources (nutrients, light, water) and/or specific disturbance regimes. Independently of growing conditions, invaders were more likely to have higher leaf area and lower tissue construction costs (advantageous under high light and nutrient conditions) and greater phenotypic plasticity (particularly advantageous in disturbed environments where conditions are in frequent flux). There appear to be few “super invaders” that have universal performance advantages over co-occurring natives; rather, increased resource availability and altered disturbance regimes associated with human activities often differentially increase the performance of invaders over that of natives.

Isozyme variation in 247 plant species is summarized as 57 generic-level comparisons of rare and common species. All species-level measures of variation (Ps, As, APs, Hes) and mean population-level measures (Pp, Ap, APp, Hep, and Ho) show reductions significant at the p < 0.001 level, but FIS and FST did not differ significantly, reflecting the similarity of breeding system in congeneric species and disparate ranges often sampled for rare and common species. The reduction in gene flow (Nm) among populations of rare species was significant when estimated from FST, but not when estimated from private alleles. Species monomorphic for isozymes are predominantly endemic and self-fertile. Although census populations of virtually all rare species are higher than levels at which theory would predict genetic erosion, and higher than levels protected by the U.S. Endangered Species Act (ESA), rare plants evidently have more significant reductions in genetic variation and gene flow than have been recognized previously.

Baculoviruses occur widely among Lepidoptera, and in some species of forest and agricultural insects, they cause epizootics in outbreak populations. Here we review recent developments in baculovirus ecology and evolution, in particular focusing on emerging areas of interest and studies relating to field populations. The expanding application of molecular techniques has started to reveal the structure of baculovirus populations and has highlighted how variable these pathogens are both genotypically and phenotypically at all levels from within individual hosts to among host populations. In addition, the detailed molecular knowledge available for baculoviruses has allowed the interpretation of gene functions across physiological and population levels in a way rarely possible in parasite-host systems and showed the diverse mechanisms that these viruses use to exploit their hosts. Analysis of the dynamic interactions between insects and baculoviruses, and their compatibility for laboratory and field experiments, has formed a basis for studies that have made a significant contribution to unraveling disease interactions in insect populations. In particular, manipulative studies on baculoviruses have been instrumental in developing an understanding of disease transmission dynamics. The results so far indicate that baculoviruses have the potential to be an excellent model for investigations of changes in virulence and resistance in fluctuating and stable host populations.

The latitudinal gradient of decreasing richness from tropical to extratropical areas is ecology's longest recognized pattern. Nonetheless, notable exceptions to the general pattern exist, and it is well recognized that patterns may be dependent on characteristics of spatial scale and taxonomic hierarchy. We conducted an extensive survey of the literature and provide a synthetic assessment of the degree to which variation in patterns (positive linear, negative linear, modal, or nonsignificant) is a consequence of characteristics of scale (extent or focus) or taxon. In addition, we considered latitudinal gradients with respect to generic and familial richness, as well as species evenness and diversity. We provide a classification of the over 30 hypotheses advanced to account for the latitudinal gradient, and we discuss seven hypotheses with most promise for advancing ecological, biogeographic, and evolutionary understanding. We conclude with a forward-looking synthesis and list of fertile areas for future research.

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 review the 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 ray-finned 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.

To assess the frequency and importance of reinforcement in nature we must begin by looking for its signature in the most likely places. Theoretical studies can pinpoint conditions that favor and inhibit reinforcement, and empirical studies can identify both how often these conditions occur and whether reinforcement results. We examine how well these tools have addressed these questions by searching for gaps and mismatches in theoretical and empirical studies of reinforcement. We concentrate on five areas: (a) a broad assessment of selection against interspecific mating, (b) the mode and genetic basis of nonrandom mating, (c) the geography of speciation, (d) divergent selection on mating cues, (e) and the genetics of reproductive isolation. We conclude that reinforcement has probably not been looked for where it is most likely to occur. We pinpoint however, many further areas of study that may ultimately provide a strong assessment of the importance of reinforcement in speciation.

“The grossest blunder in sexual preference, which we can conceive of an animal making, would be to mate with a species different from its own and with which the hybrids are either infertile or, through the mixture of instincts and other attributes appropriate to different courses of life, at so serious a disadvantage as to leave no descendants.”

          —Fisher, 1930 pp. 130

Extra-pair paternity (EPP) is extremely variable among species of birds, both in its frequency and in the behavioral events that produce it. A flood of field studies and comparative analyses has stimulated an array of novel ideas, but the results are limited in several ways. The prevailing view is that EPP is largely the product of a female strategy. We evaluate what is known about the behavioral events leading to EPP and find the justification for this view to be weak. Conflict theory (derived from selection theory) predicts that adaptations in all the players involved will influence the outcome of mating interactions, producing complex and often highly variable patterns of behavior and levels of EPP. Data support some of these predictions, but alternative hypotheses abound. Tests of predictions from conflict theory will require better information on how males and females encounter one another, behave once they have met, and influence fertilization once insemination has occurred.

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 increased attention to sampling and the interpretation of paraphyletic and polyphyletic gene trees in studies of closely related taxa by systematists and population geneticists alike and thus for a new tradition of “congeneric phylogeography.”

Protective ant-plant interactions, important in both temperate and tropical 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.

Plant species differ in how they influence many aspects of ecosystem structure and function, including soil characteristics, geomorphology, biogeochemistry, regional climate, and the activity and distribution of other organisms. Attempts to generalize plant species effects on ecosystems have focused on single traits or suites of traits that strongly covary (functional groups). However, plant effects on any ecosystem process are mediated by multiple traits, and many of these traits vary independently from one another. Thus, most species have unique combinations of traits that influence ecosystems, and there is no single trait or functional-group classification that can capture the effects of these multiple traits, or can predict the multiple functions performed by different plant species.

We present a new theoretical framework, the functional matrix, which builds upon the functional group and single trait approaches to account for the ecosystem effects of multiple traits that vary independently among species. The functional matrix describes the relationship between ecosystem processes and multiple traits, treating traits as continuous variables, and determining if the effects of these multiple traits are additive or interactive. The power of this approach is that the ecosystem effects of multiple traits are the underlying mechanisms determining species effects, how the effects of an individual species change across seasons and under varying environmental conditions, the nonadditive effects of plant species mixtures, and the effects of species diversity.

The literature on effects of habitat fragmentation on biodiversity is huge. It is also very diverse, with different authors measuring fragmentation in different ways and, as a consequence, drawing different conclusions regarding both the magnitude and direction of its effects. Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat. Results of empirical studies of habitat fragmentation are often difficult to interpret because (a) many researchers measure fragmentation at the patch scale, not the landscape scale and (b) most researchers measure fragmentation in ways that do not distinguish between habitat loss and habitat fragmentation per se, i.e., the breaking apart of habitat after controlling for habitat loss. Empirical studies to date suggest that habitat loss has large, consistently negative effects on biodiversity. Habitat fragmentation per se has much weaker effects on biodiversity that are at least as likely to be positive as negative. Therefore, to correctly interpret the influence of habitat fragmentation on biodiversity, the effects of these two components of fragmentation must be measured independently. More studies of the independent effects of habitat loss and fragmentation per se are needed to determine the factors that lead to positive versus negative effects of fragmentation per se. I suggest that the term “fragmentation” should be reserved for the breaking apart of habitat, independent of habitat loss.

Mammals are exposed to a diverse array of parasites and infectious diseases, many of which affect host survival and reproduction. Species that live in dense populations, large social groups, or with promiscuous mating systems may be especially vulnerable to infectious diseases owing to the close proximity and higher contact rates among individuals. We review the effects of host density and social contacts on parasite spread and the importance of promiscuity and mating structure for the spread and evolution of sexually transmitted diseases. Host social organization and mating system should influence not only parasite diversity and prevalence but may also determine the fitness advantages of different transmission strategies to parasites. Because host behavior and immune defenses may have evolved to reduce the spread and pathogenicity of infectious diseases, we also consider selective pressures that parasites may exert on host social and mating behavior and the evolutionary responses of hosts at both the immunological and behavioral levels. In examining these issues, we relate modeling results to observations from wild populations, highlighting the similarities and differences among theoretical and empirical approaches. Finally, the epidemiological consequences of host sociality are very relevant to the practical issues of conserving mammalian biodiversity and understanding the interactions between extinction risk and infectious diseases.

Because it lays the template from which communities develop, the pattern of dispersed seed is commonly believed to influence community structure. To test the validity of this notion, we evaluated theoretical and empirical work linking dispersal kernels to the relative abundance, distribution, dispersion, and coexistence of species. We found considerable theoretical evidence that seed dispersal affects species coexistence by slowing down exclusion through local dispersal and a competition-dispersal trade-off, yet empirical support was scant. Instead, most empirical investigations examined how dispersal affects species distribution and dispersion, subjects with little theory. This work also relied heavily on dispersal proxies and correlational analyses of community patterns, methods unable to exclude alternative hypotheses. Owing to the overall dichotomy between theory and empirical results, we argue that the importance of dispersal cannot be taken for granted. We conclude by advocating experiments that manipulate the seed dispersal pattern, and models that incorporate empirically documented dispersal kernels.