Annual Review of Ecology, Evolution, and Systematics - Volume 27, 1996

Forest canopies contain a major portion of the diversity of organisms on Earth and constitute the bulk of photosynthetically active foliage and biomass in forest ecosystems. For these reasons, canopy research has become integral to the management of forest ecosystems, and to our better understanding of global change. Ecological research in forest canopies is relatively recent and has been primarily descriptive in scope. The development of new methods of canopy access has enabled scientists to conduct more quantified research in tree crowns. Studies of sessile organisms, mobile organisms, and canopy interactions and processes have emerged as subdisciplines of canopy biology, each requiring different methods for collecting data. Canopy biology is beginning to shift from a descriptive autecology of individuals to a more complex ecosystem approach, although some types of field work are still limited by access.

Questions currently addressed in canopy research are extremely diverse but emphasize comparisons with respect to spatial and temporal variation. Spatial scales range from leaves (e.g. quantifying the number of mites on individual phylloplanes) to trees (e.g. measuring photosynthesis between sun and shade leaves), to forest stands (e.g. measuring turbulence above the canopy), and entire landscapes (e.g. comparing mammals between different forest types). Temporal variation is of particular significance in tropical forest canopies, where populations of organisms and their resources have diurnal, seasonal, or even annual periodicity. As the methods for canopy access improve, more rigorous hypotheses-driven field studies remain a future priority of this newly coalesced discipline.

Nonindigenous species can bring about a form of extinction of native flora and fauna by hybridization and introgression either through purposeful introduction by humans or through habitat modification, bringing previously isolated species into contact. These phenomena can be especially problematic for rare species coming into contact with more abundant ones. Increased use of molecular techniques focuses attention on the extent of this underappreciated problem that is not always apparent from morphological observations alone. Some degree of gene flow is a normal, evolutionarily constructive process, and all constellations of genes and genotypes cannot be preserved. However, hybridization with or without introgression may, nevertheless, threaten a rare species' existence.

Resource polymorphism in vertebrates is generally underappreciated as a diversifying force and is probably more common than is currently recognized. Research across diverse taxa suggest they may play important roles in population divergence and speciation. They may involve various kinds of traits, including morphological and behavioral traits and those related to life history. Many of the evolutionary, ecological, and genetic mechanisms producing and maintaining resource polymorphisms are similar among phylogenetically distinct species. Although further studies are needed, the genetic basis may be simple, in some cases under the control of a single locus, with phenotypic plasticity playing a proximate role in some taxa. Divergent selection including either directional, disruptive, or frequency-dependent selection is important in their evolution. Generally, the invasion of “open” niches or underutilized resources requiring unique trophic characters and decreased interspecific competition have promoted the evolution of resource polymorphisms. Further investigations centered on their role in speciation, especially adaptive radiation, are likely to be fruitful.

Official conservation efforts for the northern spotted owl began in the United States in 1975 when it was declared “threatened” in the state of Oregon; efforts continued in a sporadic and unsystematic way through the 1980s. In 1989 the Interagency Scientific Committee (ISC) was established by Congress and charged with the development of a scientifically defensible conservation strategy covering the entire range of the northern spotted owl, which includes parts of the states of Oregon, Washington, and California. The ISC collated all spotted owl research and approached questions concerning the need for a conservation strategy and the efficacy of potential reserve designs as testable hypotheses. Because the hypothesis tests were based on incomplete data and highly stylized population models, uncertainty concerning the conclusions of the ISC remained. Subsequent research focused on answering those uncertainties, and here we revisit the ISC's conclusions, asking which if any of them have been invalidated. The ISC's major conclusions have remained robust: he population of spotted owls is declining due to reductions in old growth habitat. Subsequent trend-analyses confirmed the levels of population decline calculated by the ISC and in addition concluded that the rate of decline was accelerating. The ISC's response to these conclusions was to recommend the establishment of an extensive network of large reserves. Subsequent research and more detailed computer modeling have confirmed the conceptual validity of this conservation plan but suggest that optimistic assumptions led the ISC to propose a minimal reserve structure. Current federal management plans in the Pacific Northwest propose more habitat than the ISC envisioned, providing a greater likelihood of persistence.

The vertebrate fauna of the West Indies (1262 species) exhibits high levels of endemism and has a taxonomic composition characteristic of more isolated oceanic islands. Many groups that are widespread on the mainland are absent in the islands, and some of those present are characterized by large adaptive radiations. The growing fossil record of West Indian vertebrates, including mid-Tertiary amber fossils (considered here to be 20–30 million years old), indicates that this pattern of reduced higher-taxon diversity has persisted for a long period of time. Phylogenetic relationships of nonvolant groups display a strong South American influence, whereas volant groups (birds and bats) and freshwater fish show closer ties with Central and North America. Molecular estimates of divergence times between island taxa and their mainland counterparts indicate a Cenozoic origin (within the last 65 million years) for nearly all groups examined. Together, data from different sources point to an origin by overwater dispersal for a large majority of the vertebrate fauna. The prevailing current direction, from southeast to northwest, and the wide scattering of estimated times of origin suggest that much of the nonvolant fauna arrived by flotsam carried from the mouths of major rivers in northeastern South America. Spatial relationships, especially considering low sea levels during the Pleistocene, appear to better explain the routes of colonization taken by the volant fauna and freshwater fish. Caribbean geologic history does not preclude an origin by late Mesozoic vicariance for several possibly ancient groups, although an early Cenozoic arrival by dispersal also cannot be discounted. An integrative approach to historical biogeography is shown to be more insightful than the current trend in the field, cladistic biogeography, which places prime emphasis only on phylogenetic relationships.

The Exxon Valdez oil spill was the largest in US maritime history. We review post-spill research and set it in its legal context. The Exxon Corporation, obviously responsible for the spill, focused on restoration, whereas the Trustees, a coalition of state and federal entities, focused on damage and its assessment. Despite billions of dollars expended, little new understanding was gained about the recovery dynamics of a high latitude marine ecosystem subject to an anthropogenic pulse perturbation. We discuss a variety of case studies that highlight the limitations to and shortcomings of the research effort. Given that more spills are inevitable, we recommend that future studies address spatial patterns in the intertidal, and focus on the abundances of long-lived species and on organisms that preserve a chronological record of growth. Oil spills, while tragic, represent opportunities to gain insight into the dynamics of marine ecosystems and should not be wasted.

The study of natural plant populations has provided some of the strongest and most convincing cases of the operation of natural selection currently known, partly because of amenability to reciprocal transplant experiments, common garden work, and long-term in situ manipulation. Genetic differentiation among plant populations over small scales (a few cm to a few hundred cm) has been documented and is reviewed here, in herbaceous annuals and perennials, woody perennials, aquatics, terrestrials, narrow endemics, and widely distributed species. Character differentiation has been documented for most important features of plant structure and function. Examples are known for seed characters, leaf traits, phenology, physiological and biochemical activities, heavy metal tolerance, herbicide resistance, parasite resistance, competitive ability, organellar characters, breeding systems, and life history. Among the forces that have shaped these patterns of differentiation are toxic soils, fertilizers, mowing and grazing, soil moisture, temperature, light intensity, pollinating vectors, parasitism, gene flow, and natural dynamics. The breadth and depth of the evidence reviewed here strongly support the idea that natural selection is the principal force shaping genetic architecture in natural plant populations; that view needs to be more widely appreciated than it is at present.

The proper relationship between systematics practice and our understanding of evolution has been long debated. Systematists seek to avoid assumptions about evolutionary process in their methods, yet a growing body of evidence indicates that patterns in rates of evolution can be used to reduce effects of homoplasy. We review variable evolutionary rates for molecular characters in the context of constraints on mutation and fixation. Some constraints, like the genetic code for protein-coding genes, are consistent in the direction of their effects, whereas others, like population size and cladogenesis frequency, are historically variable within and among lineages.

We review methods for assessing rate variability, and we estimate comparative absolute rates of change for five sets of mitochondrial DNAs in 12 vertebrates for application in phylogenetic analyses. Unequal weights for subsets of mitochondrial DNAs improved congruence with the most highly corroborated tree in many but not all cases. The largest data set (12,120 bases) yielded the same tree under all four weighting alternatives. This is consistent with the notion, echoing the law of large numbers, that as data sets increase in size, homoplasy will tend to cancel itself out. Even if this notion has validity, however, evolutionary biology will remain vital in systematics if we want to: match sets of taxa with characters likely to be historically informative (when data sets are not sufficiently large); avoid comparing characters with different histories due to reticulations, horizontal transfer, or lineage sorting; avoid assuming random distribution of homoplasy; be alerted to the possibility of long-branch attraction problems; and understand the cause of the hierarchy of taxa in nature as inheritance of genetic material and descent with modification.

In this review, we discuss the ecological and evolutionary consequences of plant-herbivore interactions in tropical forests. We note first that herbivory rates are higher in tropical forests than in temperate ones and that, in contrast to leaves in temperate forests, most of the damage to tropical leaves occurs when they are young and expanding. Leaves in dry tropical forests also suffer higher rates of damage than in wet forests, and damage is greater in the understory than in the canopy. Insect herbivores, which typically have a narrow host range in the tropics, cause most of the damage to leaves and have selected for a wide variety of chemical, developmental, and phenological defenses in plants. Pathogens are less studied but cause considerable damage and, along with insect herbivores, may contribute to the maintenance of tree diversity. Folivorous mammals do less damage than insects or pathogens but have evolved to cope with the high levels of plant defenses. Leaves in tropical forests are defended by having low nutritional quality, greater toughness, and a wide variety of secondary metabolites, many of which are more common in tropical than temperate forests. Tannins, toughness, and low nutritional quality lengthen insect developmental times, making them more vulnerable to predators and parasitoids. The widespread occurrence of these defenses suggests that natural enemies are key participants in plant defenses and may have influenced the evolution of these traits. To escape damage, leaves may expand rapidly, be flushed synchronously, or be produced during the dry season when herbivores are rare. One strategy virtually limited to tropical forests is for plants to flush leaves but delay “greening” them until the leaves are mature. Many of these defensive traits are correlated within species, due to physiological constraints and tradeoffs. In general, shade-tolerant species invest more in defenses than do gap-requiring ones, and species with long-lived leaves are better defended than those with short-lived leaves.

Lentic freshwater habitats in temperate regions exist along a gradient from small ephemeral ponds to large permanent lakes. This environmental continuum is a useful axis for understanding how attributes of individuals ultimately generate structure at the level of the community. Community structure across the gradient is determined by both (a) physical factors, such as pond drying and winter anoxia, that limit the potential breadth of species distributions, and (b) biotic effects mediated by ecological interactions, principally predation, that determine the realized success of species. Fitness tradeoffs associated with a few critical traits of individuals often form the basis for species turnover along the gradient. Among species that inhabit temporary ponds, distributions are often constrained because traits that enhance developmental rate and competitive ability also increase susceptibility to predators. In permanent ponds, changes in the composition of major predators over the gradient limit distributions of prey species because traits that reduce mortality risk in one region of the gradient cause increased risk in other regions of the gradient. Integrated across the gradient, these patterns in species success generate distinct patterns in community structure. Additionally, spatial heterogeneity among habitats along the gradient and the fitness tradeoffs created by this heterogeneity may hold important evolutionary implications for habitat specialization and lineage diversification in aquatic taxa.

Natural freeze-tolerance supports the winter survival of many animals including numerous terrestrial insects, many intertidal marine invertebrates, and selected species of terrestrially hibernating amphibians and reptiles. Freeze-tolerant animals typically endure the conversion of 50% or more of total body water into extracellular ice and employ a suite of adaptations that counter the negative consequences of freezing. Specific adaptations control the sites and rate of ice formation to prevent physical damage by ice. Other adaptations regulate cell-volume change: Colligative cryoprotectants minimize cell shrinkage during extracellular ice formation; other protectants stabilize membrane structure; and a high density of membrane transporter proteins ensure rapid cryoprotectant distribution. Cell survival during freezing is also potentiated by anoxia tolerance, mechanisms of metabolic rate depression, and antioxidant defenses. The net result of these protective mechanisms is the ability to reactivate vital functions after days or weeks of continuous freezing. Magnetic resonance imaging has allowed visual examinations of the mode of ice penetration through the body of freeze-tolerant frogs and turtles, and cryomicroscopy has illustrated the effects of freezing on the cellular and microvasculature structure of tissues. Various metabolic adaptations for freezing survival appear to have evolved out of pre-existing physiological capacities of animals, including desiccation-resistance and anoxia-tolerance.

We review deterministic and stochastic demographic models as well as classical population genetic models that have been applied to tropical rain forest tree species. We discuss their implications for conservation. The main conclusions of deterministic demographic models are the key importance of species' longevity in determining susceptibility of population growth rate to harvesting of individuals at different life-stages, the critical effect of patch dynamics, and the importance of density-dependent mechanisms at least for abundant species. Population viability analysis to predict extinction times of tropical rain forest tree species has only been performed for four tropical rain forest tree species using the simplest Lefkovitch matrix linear model. Results obtained are in accordance with results of simple stochastic models for nonstructured populations that have been solved analytically. Population genetic models have shown that tropical rain forest trees: (a) possess high levels of genetic diversity, (b) maintain greater proportions of genetic variation within than among populations, (c) are predominantly outcrossed, and (d) have high levels of gene flow. These results suggest that tropical tree species may not be in immediate danger of extinction from genetic factors if actual conditions are maintained. However, the impact of forest fragmentation is expected to be particularly strong for most tropical rain forest tree species due mainly to the high genetic load kept by their present population genetic structures. Recent theoretical demographic-genetic models for simple systems suggest that the fixation of new mildly detrimental mutations may be comparable in importance to environmental stochasticity, implying minimum viable populations as large as a few thousands. It is urgent to develop a model that integrates genetic and demographic factors, that enables evaluations of their relative importance in long-term persistence of tropical rain forest tree species.

The proliferation of molecular data in systematics has opened a Pandora's box of alternate approaches to inferring hierarchical patterns of relationship among taxa. In this review, we examine practical and theoretical reasons for employing some methods and avoiding others. We offer a philosophical overview of the relationship between systematics patterns and evolutionary processes, and we discuss the differential emphasis given to each of these areas by opposing methodological camps. We review the sources and types of incongruence between data partitions from different sources and recommend a specific procedure for contending with incongruence. We then focus on inference of relationships among closely related taxa, with particular emphasis on mtDNA as a source of characters, its advantages and potential pitfalls. We conclude with a review of several widely cited empirical studies and suggest that the gene tree–species tree problem may be less severe than its prevalence in the literature would suggest.

Inherited environmental effects are those components of the phenotype that are derived from either parent, apart from nuclear genes. Inherited environmental effects arise as the product of parental genes and the parental environment, or their interation, and can include contributions that reflect the abiotic, nutritional, and other ecological features of a parental environment. Separating the impact of inherited environmental effects from inherited genetic effects on offspring phenotype variation has been and continues to be a challenge. This complexity is represented in the presentation of a qualitative model that distinguishes the possible paths of nongenetic cross-generational transmission. This model serves as the framework for considering the nature, in published works, of what was actually measured. Empirical evidence of inherited environmental effects arising from these pathways is documented for a diversity of plant and animal taxa. From these results one can conclude that the impact of inherited environmental effects on offspring can be positive or negative depending on the nature of the contribution and the ecological context in which the offspring exists. Finally, there is a description of theoretical and experimental efforts to understand the consequences of parental effects relative to their impact on population dynamics, the expression of adaptive phenotype plasticity, and character evolution.

The majority of marine populations are demographically open; their replenishment is largely or exclusively dependent on a supply of juveniles from the plankton. In spite of much recent research, no consensus has yet been reached regarding the importance of recruitment relative to other demographic processes in determining local population densities. We argue 1. that demographic theory suggests that, except under restrictive and unlikely conditions, recruitment must influence local population density to some extent. Therefore, 2. the question as to whether the size of a particular population is limited by recruitment is misguided. Finally, 3. the effect of recruitment on population size can be difficult to detect but is nonetheless real. A major weakness of most existing studies is a lack of attention to the survival of recruits over appropriate scales of time and space. Acknowledgment of the multifactorial determination of population density should guide the design of future experimental studies of the demography of open populations.

The performance of an organism is the crucial link between its phenotype and its ecological success. When does an organism's morphology affect its performance? Quantitative mechanistic analyses of how function depends on biological form have shown that the relationship between morphology and performance can be nonlinear, context-dependent, and sometimes surprising. In some cases, small changes in morphology or simple changes in size can lead to novel functions, while in other cases changes in form can occur without performance consequences. Furthermore, the effect of a specific change in morphology can depend on the size, shape, stiffness, or habitat of an organism. Likewise, a particular change in posture or behavior can produce opposite effects when performed by bodies with different morphologies. These mechanistic studies not only reveal potential misconceptions that can arise from the descriptive statistical analyses often used in ecological and evolutionary research, but they also show how new functions, and novel consequences of changes in morphology, can arise simply as the result of changes in size or habitat. Such organismal-level mechanistic research can be used in concert with other tools to gain insights about issues in ecology (e.g. foraging, competition, disturbance, keystone species, functional groups) and evolution (e.g. adaptation, interpretation of fossils, and origin of novelty).

Animals may be camouflaged by a coloration that matches their surroundings or by a combination of color and shape. Some species make themselves conspicuous and rely upon bold and bright coloration as a means of warning off their potential predators. Population biologists have accumulated information on the adaptive significance of coloration for a large number of species. To elucidate the mechanisms underpinning such natural selection events, it is necessary to understand the visual systems of interacting organisms.

Molecular genetic analyses on the human opsin genes by Nathans and his colleagues made it possible to characterize the opsin genes of various vertebrates. A striking level of diversity in the opsin gene sequences reflects adaptive responses of various species to different environments. Comparative analyses of opsins reveal that gene duplications and accumulation of mutations have been important in achieving that diversity. The analyses also identify amino acid changes that are potentially important in controlling wavelength absorption by the photosensitive molecules, the visual pigments. These hypotheses can now be rigorously tested using tissue culture cells. Thanks to the molecular characterization of the opsin genes, it is now possible to study the types of opsins associated with certain environmental conditions. Such surveys will provide important first molecular clues to how animals adapt to their environments with respect to their coloration and behavior.

With the discovery of the eukaryote nucleus, all living organisms were neatly divided into prokaryotes, which lacked a nucleus, and eukaryotes, which possessed it. As data derived directly from the genome became available, it was clear that prokaryotes were comprised of two groups, Eubacteria and Archaebacteria. These were subsequently renamed at the new taxonomic level of Domain as Bacteria and Archaea, with the eukaryotes named as the Eucarya Domain. The interrelationships of the three Domains are still subject to discussion and evaluation, as is their monophyly. Further data, drawn from various protein sequences, suggest conflicting schemes, and resolution may not be straightforward. Additionally, Bacteria and Archaea as well as Eucarya are largely based on organisms already in culture. Investigation of the potentially enormous quantity of uncultured organisms in nature is likely to have as broad-ranging implications as the exploration of new protein sequences.

Comparative, quantitative biogeographic studies are revealing empirical patterns of interspecific variation in the sizes, shapes, boundaries, and internal structures of geographic ranges; these patterns promise to contribute to understanding the historical and ecological processes that influence the distributions of species. This review focuses on characteristics of ranges that appear to reflect the influences of environmental limiting factors and dispersal. Among organisms as a whole, range size varies by more than 12 orders of magnitude. Within genera, families, orders, and classes of plants and animals, range size often varies by several orders of magnitude, and this variation is associated with variation in body size, population density, dispersal mode, latitude, elevation, and depth (in marine systems). The shapes of ranges and the dynamic changes in range boundaries reflect the interacting influences of limiting environmental conditions (niche variables) and dispersal/extinction dynamics. These processes also presumably account for most of the internal structure of ranges: the spatial patterns and orders-of-magnitude of variation in the abundance of species among sites within their ranges. The results of this kind of “ecological biogeography”need to be integrated with the results of phylogenetic and paleoenvironmental approaches to “historical biogeography”so we can better understand the processes that have determined the geographic distributions of organisms.