Annual Review of Ecology, Evolution, and Systematics - Volume 33, 2002

The 500 cone snail species (Conus) use complex venoms to capture prey, defend against predators and deter competitors. Most biologically active venom components are small, highly structured peptides, each encoded by a separate gene. Every Conus species has its own distinct repertoire of 100–200 venom peptides, with each peptide presumably having a physiologically relevant target in prey or potential predators/competitors. There is a remarkable interspecific divergence observed in venom peptide genes, which can be rationalized because of biotic interactions that are species specific. The peptide families/subfamilies characteristic of clades of related Conus species are potentially useful clade markers and can be used to indicate common biological mechanisms characterizing that clade. By knowing both the distribution and the physiological function of venom peptides, a type of reverse ecology becomes possible; the peptides in a Conus venom are a molecular readout of the biotic interactions of a species or clade.

The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.

The origin and early evolution of Cetacea (whales, dolphins, and porpoises) is one of the best examples of macroevolution as documented by fossils. Early whales are divided into six families that differ greatly in their habitats, which varied from land to freshwater, coastal waters, and fully marine. Early cetaceans lived in the Eocene (55–37 million years ago), and they show an enormous morphological diversity. Toward the end of the Eocene the modern cetacean body plan originated, and this body plan remained more or less the same in the subsequent evolution. It is possible that some aspects of this body plan are rooted in constraints that are dictated by cetacean embryol ogic development and controlled by genes that affect many organ systems at once. It may be possible to use a study of patterns of correlations among morphological traits to test hypotheses of developmental links among organ systems.

Until recently, most knowledge of the early history of birds and the evolution of their unique specializations was based on just a handful of diverse Mesozoic taxa widely separated in time and restricted to marine environments. Although Archaeopteryx is still the oldest and only Jurassic bird, a wealth of recent discoveries combined with new phylogenetic analyses have documented the divergence of a number of lineages by the beginning of the Cretaceous. These and younger Cretaceous fossils have filled much of the morphological chasm that existed between Archaeopteryx and its living counterparts, providing insights into the evolutionary development of feathers and other important features of the avian flight system. Dramatic new perceptions of the life history, growth and development of early birds have also been made possible by the latest data. Although no primitive birds are known to have survived beyond the end of the Cretaceous, the present fossil record provides no evidence for a sudden disappearance. Likewise, a Mesozoic origin for extant birds remains controversial.

An important aim of plant ecology is to identify leading dimensions of ecological variation among species and to understand the basis for them. Dimensions that can readily be measured would be especially useful, because they might offer a path towards improved worldwide synthesis across the thousands of field experiments and ecophysiological studies that use just a few species each. Four dimensions are reviewed here. The leaf mass per area–leaf lifespan (LMA-LL) dimension expresses slow turnover of plant parts (at high LMA and long LL), long nutrient residence times, and slow response to favorable growth conditions. The seed mass–seed output (SM-SO) dimension is an important predictor of dispersal to establishment opportunities (seed output) and of establishment success in the face of hazards (seed mass). The LMA-LL and SM-SO dimensions are each underpinned by a single, comprehensible tradeoff, and their consequences are fairly well understood. The leaf size–twig size (LS-TS) spectrum has obvious consequences for the texture of canopies, but the costs and benefits of large versus small leaf and twig size are poorly understood. The height dimension has universally been seen as ecologically important and included in ecological strategy schemes. Nevertheless, height includes several tradeoffs and adaptive elements, which ideally should be treated separately. Each of these four dimensions varies at the scales of climate zones and of site types within landscapes. This variation can be interpreted as adaptation to the physical environment. Each dimension also varies widely among coexisting species. Most likely this within-site variation arises because the ecological opportunities for each species depend strongly on which other species are present, in other words, because the set of species at a site is a stable mixture of strategies.

The evolution of proteins involved in reproduction is only now beginning to be studied. A reoccurring observation is the rapid evolution of the molecules mediating reproductive events following the release of gametes. We review the examples where rapid evolution of reproductive proteins has been documented, covering taxa ranging from diatoms to humans. The selective pressures causing this divergence remain unknown, but several hypotheses are presented. The functional consequences of this rapid divergence could be involved in speciation.

Invasions by non-native ants are an ecologically destructive phenomenon affecting both continental and island ecosystems throughout the world. Invasive ants often become highly abundant in their introduced range and can outnumber native ants. These numerical disparities underlie the competitive asymmetry between invasive ants and native ants and result from a complex interplay of behavioral, ecological, and genetic factors. Reductions in the diversity and abundance of native ants resulting from ant invasions give rise to a variety of direct and indirect effects on non-ant taxa. Invasive ants compete with and prey upon a diversity of other organisms, including some vertebrates, and may enter into or disrupt mutualistic interactions with numerous plants and other insects. Experimental studies and research focused on the native range ecology of invasive ants will be especially valuable contributions to this field of study.

The second largest zone of coastal hypoxia (oxygen-depleted waters) in the world is found on the northern Gulf of Mexico continental shelf adjacent to the outflows of the Mississippi and Atchafalaya Rivers. The combination of high freshwater discharge, wind mixing, regional circulation, and summer warming controls the strength of stratification that goes through a well-defined seasonal cycle. The physical structure of the water column and high nutrient loads that enhance primary production lead to an annual formation of the hypoxic water mass that is dominant from spring through late summer. Paleoindicators in dated sediment cores indicate that hypoxic conditions likely began to appear around the turn of the last century and became more severe since the 1950s as the nitrate flux from the Mississippi River to the Gulf of Mexico tripled. Whereas increased nutrients enhance the production of some organisms, others are eliminated from water masses (they either emigrate from the area or die) where the oxygen level falls below 2 mg l⁻¹ or lower for a prolonged period. A hypoxia-stressed benthos is typified by short-lived, smaller surface deposit-feeding polychaetes and the absence of marine invertebrates such as pericaridean crustaceans, bivalves, gastropods, and ophiuroids. The changes in benthic communities, along with the low dissolved oxygen, result in altered sediment structure and sediment biogeochemical cycles. Important fisheries are variably affected by increased or decreased food supplies, mortality, forced migration, reduction in suitable habitat, increased susceptibility to predation, and disruption of life cycles.

Supertree construction is a new, rigorous approach for combining phylogenetic information to produce more inclusive phylogenies. It has been used to provide some of the largest, most complete phylogenies for diverse groups (e.g., mammals, flowering plants, and dinosaurs) at a variety of taxonomic levels. We critically review methods for assembling supertrees, discuss some of their more interesting mathematical properties, and describe the strengths and limitations of the supertree approach. To document the need for supertrees in biology, we identify how supertrees have already been used beyond the systematic information they provide to examine models of evolution, test rates of cladogenesis, detect patterns of trait evolution, and extend phylogenetic information to biodiversity conservation.

Biotic homogenization is the increased similarity of biotas over time caused by the replacement of native species with nonindigenous species, usually as a result of introductions by humans. Homogenization is the outcome of three interacting processes: introductions of nonnative species, extirpation of native species, and habitat alterations that facilitate these two processes. A central aspect of the homogenization process is the ability of species to overcome natural biogeographic barriers either through intentional transport by humans or through colonization routes created by human activities. Habitat homogenization through reservoir construction contributes to biotic homogenization as local riverine faunas are replaced with cosmopolitan lentic species. The homogenization process has generally increased biodiversity in most freshwater faunas, as the establishment of new species has outpaced the extinction of native species. There are important exceptions, however, where the establishment of nonindigenous species has had devastating impacts on endemic species. The homogenization process appears likely to continue, although it could be slowed through reductions in the rate of invasions and extirpations and by rehabilitating aquatic habitats so as to favor native species.

Twenty-five years ago, the centuries-old Pacific Island practice of community-based marine resource management (CBMRM) was in decline, the victim of various impacts of westernization. During the past two decades, however, this decline has reversed in various island countries. Today CBMRM continues to grow, refuting the claim that traditional non-Western attitudes toward nature cannot provide a sound foundation for contemporary natural resource management. Limited entry, marine protected areas, closed areas, closed seasons, and restrictions on damaging or overly efficient fishing methods are some of the methods being used. Factors contributing to the upsurge include a growing perception of scarcity, the restrengthening of traditional village-based authority, and marine tenure by means of legal recognition and government support, better conservation education, and increasingly effective assistance, and advice from regional and national governments and NGOs. Today's CBMRM is thus a form of cooperative management, but one in which the community still makes and acts upon most of the management decisions.

Animals are important in nutrient cycling in freshwater ecosystems. Via excretory processes, animals can supply nutrients (nitrogen and phosphorus) at rates comparable to major nutrient sources, and nutrient cycling by animals can support a substantial proportion of the nutrient demands of primary producers. In addition, animals may exert strong impacts on the species composition of primary producers via effects on nutrient supply rates and ratios. Animals can either recycle nutrients within a habitat, or translocate nutrients across habitats or ecosystems. Nutrient translocation by relatively large animals may be particularly important for stimulating new primary production and for increasing nutrient standing stocks in recipient habitats. Animals also have numerous indirect effects on nutrient fluxes via effects on their prey or by modification of the physical environment. Future studies must quantify how the importance of animal-mediated nutrient cycling varies among taxa and along environmental gradients such as ecosystem size and productivity.

Ozone depletion by anthropogenic gases has increased the atmospheric transmission of solar ultraviolet-B radiation (UV-B, 280–315 nm). Our understanding of the consequencences of enhanced UV-B levels on primary producers has grown dramatically over the past 20 years, but it has been hampered by how realistically experimental UV-B exposures mimic ozone-depletion scenarios. Overcoming these shortcomings will require sophisticated and creative approaches. Biological weighting functions and solar spectral irradiance estimates are critical in evaluating effects and require more attention. Whereas UV screening compounds in terrestrial and aquatic producers commonly increase with UV-B exposure, the implications, while potentially far reaching, are unclear. Photosynthesis is more sensitive to UV-B in phytoplankton than in terrestrial plants, probably owing to less effective screening in phytoplankton. Productivity of terrestrial plants is usually unaffected by enhanced UV-B, although reduced growth has been observed and may increase in magnitude over successive years. Aquatic productivity is often compromised by short-term exposures to enhanced UV-B, and long-term assessments are complicated by the dynamic nature of aquatic systems and by nonlinear responses. Recent work examining UV-B effects on multiple trophic levels suggests that outcomes will be diverse and difficult to predict. Such effects may lead to feedbacks on primary producers.

Examples of androdioecy, the coexistence of males and hermaphrodites, was unknown when the subject was last reviewed about two decades ago. Since then, several examples have been discovered in both plants and animals, and we are now in a position to reappraise theoretical work on the subject. Whereas early ideas were framed largely in terms of the invasion of males into hermaphroditic populations, all of the clearest examples of androdioecy now known appear to have evolved from dioecy. There are strong indications that this has occurred repeatedly as a result of the selection of self-fertile hermaphroditism for reproductive assurance during colonization. Male frequencies in these species are highly variable, self-fertilization in hermaphrodites is delayed, and mating opportunities appear to depend strongly on population density. Results from theoretical work on the evolution and maintenance of androdioecy in single populations and in metapopulations are summarized, and several case studies of androdioecious plants and animals are reviewed.

For many years biologists have debated whether mast seeding (the synchronous intermittent production of large seed crops in perennial plants) results from weather conditions or is an evolved plant reproductive strategy. In this review, we analyze the evidence for the underlying causes of masting. In the absence of selection for higher or lower variability, plants will vary in tandem with the environment (resource matching). Two selective factors often favor the evolution of masting: increased pollination efficiency in wind-pollinated species, and satiation of seed predators. Other factors select against masting, including animal pollination and frugivore dispersal. A survey of 570 masting datasets shows that wind-pollinated species had higher seed production coefficients of variation (CVs) than biotically pollinated ones. Frugivore-dispersed species had low CVs whereas predator-dispersed plants had high CVs, consistent with gaining benefits from predator satiation rather than dispersal. The global pattern of masting shows highest seed crop variability at mid latitudes and in the Southern Hemisphere, which are similar to the patterns in variability of rainfall. We conclude that masting is often an adaptive reproductive trait overlaid on the direct influence of weather.

The direct effects of marine habitat disturbance by commercial fishing have been well documented. However, the potential ramifications to the ecological function of seafloor communities and ecosystems have yet to be considered. Soft-sediment organisms create much of their habitat's structure and also have crucial roles in many population, community, and ecosystem processes. Many of these roles are filled by species that are sensitive to habitat disturbance. Functional extinction refers to the situation in which species become so rare that they do not fulfill the ecosystem roles that have evolved in the system. This loss to the ecosystem occurs when there are restrictions in the size, density, and distribution of organisms that threaten the biodiversity, resilience, or provision of ecosystem services. Once the functionally important components of an ecosystem are missing, it is extremely difficult to identify and understand ecological thresholds. The extent and intensity of human disturbance to oceanic ecosystems is a significant threat to both structural and functional biodiversity and in many cases this has virtually eliminated natural systems that might serve as baselines to evaluate these impacts.

As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.

The use of stable isotope techniques in plant ecological research has grown steadily during the past two decades. This trend will continue as investigators realize that stable isotopes can serve as valuable nonradioactive tracers and nondestructive integrators of how plants today and in the past have interacted with and responded to their abiotic and biotic environments. At the center of nearly all plant ecological research which has made use of stable isotope methods are the notions of interactions and the resources that mediate or influence them. Our review, therefore, highlights recent advances in plant ecology that have embraced these notions, particularly at different spatial and temporal scales. Specifically, we review how isotope measurements associated with the critical plant resources carbon, water, and nitrogen have helped deepen our understanding of plant-resource acquisition, plant interactions with other organisms, and the role of plants in ecosystem studies. Where possible we also introduce how stable isotope information has provided insights into plant ecological research being done in a paleontological context. Progress in our understanding of plants in natural environments has shown that the future of plant ecological research will continue to see some of its greatest advances when stable isotope methods are applied.

Advances in taphonomy and stratigraphy over the past two decades have dramatically improved our understanding of the causes, effects, and remedies of incompleteness in the fossil record for the study of evolution. Taphonomic research has focused on quantifying probabilities of preservation across taxonomic groups, the temporal and spatial resolution of fossil deposits, and secular changes in preservation over the course of the Phanerozoic. Stratigraphic research has elucidated systematic trends in the formation of sedimentary gaps and permanent stratigraphic records, the quantitative consequences of environmental change and variable rock accumulation rates over short and long timescales, and has benefited from greatly improved methods of correlation and absolute age determination. We provide examples of how these advances are transforming paleontologic investigations of the tempo and mode of morphologic change, phylogenetic analysis, and the environmental and temporal analysis of macroevolutionary patterns.

Here we review the biology of early generation neopolyploids and discuss the profound changes that accompany their formation. Newly formed auto- and allopolyploids exhibit considerable meiotic complexity, including multivalent pairing, multisomic inheritance, and the production of unbalanced gametes. The cytogenetic behavior of allopolyploids and autopolyploids differ statistically, but are more similar than commonly believed. The progeny of neopolyploids include a high frequency of aneuploids, pseudoeuploids and homeologue-recombinant genotypes that may contribute to the phenotypic variability observed in early generation polyploids. We find no evidence to support the traditional view that autopolyploids possess lower fertility than allopolyploids, casting doubt on the paradigm that allopolyploids should be more frequent due to their inherent fertility. The fertility of early generation polyploids increases rapidly, owing largely to selection against meiotic configurations that generate unbalanced gametes. Neopolyploids are commonly differentiated from progenitors by a combination of morphological, phenological and life-history characteristics. Further progress toward understanding polyploid evolution will require studies in natural populations that can evaluate the demographic and larger ecological significance of the cytogenetic and phenotypic character of neopolyploids.

Herbivore offense describes traits that allow herbivores to increase their feeding and other uses of host plants when these uses benefit the herbivores. We argue that ecological interactions and coevolution between plants and herbivores cannot be understood without an offense-defense framework. Thus far, plant defense theory and data have far outpaced knowledge of herbivore offense. Offensive tactics include feeding and oviposition choices, enzymatic metabolism of plant compounds, sequestration, morphological adaptations, symbionts, induction of plant galls, and induced plant susceptibility, trenching, and gregarious feeding. We propose that offensive tactics can be categorized usefully depending upon when they are effective and whether they are plastic or fixed traits. The advantages of offensive traits have not been adequately described in terms of herbivore fitness. Similarly, a more complete understanding of the costs and limitations of offensive traits will help put the herbivore back in plant-herbivore interactions and coevolution.

Politicians, scientists, government agencies, and the public are all engaged in recovery planning for Pacific salmon. In order for science to fulfill its potential in the arena of salmon recovery planning, several shortcomings of the science and its application to decision-making must be rectified. The definition of conservation units using genetic and phylogenetic inference needs to be sharpened. Ecological analyses must get beyond casting blame for past declines in salmon numbers and examine mixed strategies of management that consider interactions between hatcheries, harvest, hydropower, and habitat factors as well as background natural stresses and invasive species. Glib acceptance of expert opinion and extrapolated or inferred data should be tempered. To deal with uncertainty, recovery teams should engage in scenario analyses in which a wide variety of assumptions are played out. Finally, there is a pressing need for analyses aimed at determining what circumstances and communication strategies give science an effective voice in decision-making.

Molecular clocks have profoundly influenced modern views on the timing of important events in evolutionary history. We review recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales. On the phylogenetic scale, we address the complexities of DNA sequence evolution as they relate to estimating divergences, focusing on models of nucleotide substitution and problems associated with among-site and among-lineage rate variation. On the population genetic scale, we review advances in the incorporation of ancestral population processes into the estimation of divergence times between recently separated species. Throughout the review we emphasize new statistical methods and the importance of model testing during the process of divergence time estimation.

Variations in Earth's orbit with periods of 10–100 thousand years (kyr) (Milankovitch oscillations) have led to recurrent and rapid climatic shifts throughout Earth's history. These cause changes in the geographical distributions of clades, which we term orbitally forced range dynamics (ORD). The magnitude of ORD varies geographically, e.g., with latitude. Climatic shifts cause extinction, splitting, and merging of gene pools and clades. They select among individuals and clades for traits enhancing the ability to survive in situ and to establish new populations. There is also nonadaptive sorting caused by the large geographical variation in ORD, as only gene pools that are in the right place when climate shifts survive. ORD lead to sorting at many levels of genealogic inclusiveness. Clades that have survived climatic shifts during at least one entire period of the longest significant Milankovitch oscillations (100 kyr), we name β-clades. The products of more recent cladogenesis are α-clades, which are always nested within a β-clade. We conclude that ORD may promote α-clade formation but curb rates of β-clade formation. In areas with little ORD, where gene pools persist without going extinct or merging, clade splits and divergence may accumulate leading to high rates of β-clade formation and β-anagenesis (evolutionary change persisting >100 kyr). High ORD should lead to low numbers of β-clades, β-clades with low levels of spatial genetic divergence, little geographical subdivision and large ranges, organisms with high vagility and low specialization, high proportions of β-clades formed by polyploidization, and little β-anagenesis. We predict global and interregional geographic patterns in these variables caused by differential ORD. Thus, ORD potentially explains a wide array of patterns, suggesting ORD as a fundamental factor in evolution. The vulnerability of biotas to many human activities should vary with the magnitude of ORD.