Annual Review of Ecology, Evolution, and Systematics - Volume 40, 2009

This review suggests that the ecology and patchy global distribution of seasonally dry tropical forest (SDTF) has distinctively structured the evolutionary history and biogeography of woody plant groups that are confined to it. SDTFs have few widespread woody plant species causing high β-diversity between separate areas of forests. These separate areas contain geologically old, monophyletic clades of endemic plant species that often have geographically structured intraspecific genetic variation. These patterns of diversity, endemism, and phylogeny indicate a stable, dispersal-limited SDTF system. SDTF species tend to belong to larger clades confined to this vegetation, exemplifying phylogenetic niche conservatism, and we argue that this is evidence that the SDTF is a metacommunity (biome) for woody plant clades. That phylogenetic, population genetic, biogeographic, and community ecological patterns differ in woody plants from tropical rain forests and savannas suggests a hypothesis that broad ecological settings strongly influence plant diversification in the tropics.

With the sequencing of 12 complete euchromatic Drosophila genomes, the genus Drosophila is a leading model for comparative genomics. In this review, we discuss the novel insights into evolutionary processes afforded by the newly available genomic sequences when placed in the context of the phylogeny. We focus on three levels: insights into whole-genome content, such as changes in genome size and content across the phylogeny; insights into large-scale patterns of divergence and conservation, such as selective constraints on genes and chromosome-level evolution of sex chromosomes; and insights into finer-scale processes in individual lineages and genes, such as lineage-specific evolution in response to ecological context. As the field of comparative genomics is still young, we also discuss current challenges, such as the development of more sophisticated evolutionary models to capture nonequilibrium processes and the improvement of assembly and alignment algorithms to better capture uncertainty in the data.

Although range expansions have occurred recurrently in the history of most species, their genetic consequences have been little investigated. Theoretical studies show that range expansions are quite different from pure demographic expansions and that the extent of recent gene flow conditions expected patterns of molecular diversity within and between populations. Spatially explicit simulation studies have led to unexpected and fascinating results about genetic patterns emerging after a range expansion. For instance, spatial expansions can generate allele frequency gradients, promote the surfing of rare variants into newly occupied territories, induce the structuring of newly colonized areas into distinct sectors of low genetic diversity, or lead to massive introgression of local genes into the genome of an invading species. Interestingly, most of these patterns had been previously attributed to distinct selective processes, showing that taking into account the dynamic nature of a species range can lead to a paradigm shift in our perception of evolutionary processes.

A stoichiometrically explicit approach to food web ecology yields new insight into promotion and degradation of diversity, changes in species composition along environmental gradients, biomass partitioning among trophic levels, and limitation of primary production. These revelations emerge from food web modules that incorporate fundamental constraints imposed by mass balance and a key trait, stoichiometric body composition, into a species’ niche. These niche components involve a species’ requirements from its environment and its own impacts on its environment. More specifically, stoichiometric composition influences minimal nutrient requirements of consumers (perhaps especially grazers); this component becomes pertinent because large imbalances often arise between nutrient:carbon content of consumers relative to prey. Furthermore, these imbalances then modulate the impact of consumers on their own resources through nutrient recycling. Once these niche components become synthesized, their implications in shaping food webs provide powerful mechanisms linking changes in environmental gradients with community structure and ecosystem function.

Global environmental changes may be altering the ecology of tropical forests. Long-term monitoring plots have provided much of the evidence for large-scale, directional changes in tropical forests, but the results have been controversial. Here we review evidence from six complementary approaches to understanding possible changes: plant physiology experiments, long-term monitoring plots, ecosystem flux techniques, atmospheric measurements, Earth observations, and global-scale vegetation models. Evidence from four of these approaches suggests that large-scale, directional changes are occurring in the ecology of tropical forests, with the other two approaches providing inconclusive results. Collectively, the evidence indicates that both gross and net primary productivity has likely increased over recent decades, as have tree growth, recruitment, and mortality rates, and forest biomass. These results suggest a profound reorganization of tropical forest ecosystems. We evaluate the most likely drivers of the suite of changes, and suggest increasing resource availability, potentially from rising atmospheric CO2 concentrations, is the most likely cause.

A limited diversity of character states for reproductive traits and a robust phylogeny make scleractinian corals an ideal model organism with which to explore the evolution of life-history traits. Here, we explore systematic and biogeographical patterns in the reproductive biology of the Scleractinia within the context of a new molecular phylogeny and using reproductive traits from nearly 400 species. Our analyses confirm that coral sexuality is highly conserved, and mode of larval development is relatively plastic. An overabundance of species with autotrophic larvae in the eastern Pacific and Atlantic is most likely the result of increased capacity for long-distance dispersal conferred by vertical transmission of symbiotic zooxanthellae. Spawning records from diverse biogeographical regions indicate that multispecies spawning occurs in all speciose coral assemblages. A new quantitative index of spawning synchrony shows peaks at mid-tropical latitudes in the Indo-Pacific, influenced in part by two spawning seasons in many species on equatorial reefs.

Claims about the role of predator diversity in maintaining ecosystem function and providing ecosystem services such as pest control are controversial, but evaluative tests are beginning to accumulate. Empirical and experimental comparisons of species-rich versus species-poor assemblages of entomophagous arthropods and vertebrates range from strong suppression to facilitative release of herbivorous arthropod prey. Top-down control can be strengthened when natural enemies complement each other, dampened by negative interactions, balanced by both factors, and driven by single influential species. A meta-analytic synthesis shows a significant overall effect of enemy richness increasing top-down control of herbivores, which is consistent in agricultural studies conducted in tropical versus temperate zones, in studies using caged versus open-field designs, but not so in nonagricultural habitats. Synthetic analyses address theory and help set precautionary policy for conserving ecological services broadly, while characterizing uncertainty associated with herbivore response to changes in enemy diversity.

Phylogeography's objective—to understand the processes underlying the spatial and temporal dimensions of genetic variation—underlies both the prominence and extensive methodological transformations that characterize this nascent field. Here I discuss the insights that come from detailed demographic information and how an understanding of phylogeographic history is crucial to addressing a range of evolutionary and ecological questions, from understanding the source of adaptive divergence to the factors structuring ecological communities. I review recent progress in phylogeography, including its expanding role in evolutionary and ecological study and the molecular and methodological advances that now provide unprecedented details about the factors governing population genetic variation and structure. As a field, phylogeography draws together information across disciplines (e.g., from genetics, ecology, systematics, and paleontology), using a diversity of technical and conceptual approaches. This unified eclectic perspective has been key to phylogeography's success and will be key to phylogeography's enduring future.

Observations of the tropical nitrogen (N) cycle over the past half century indicate that intact tropical forests tend to accumulate and recycle large quantities of N relative to temperate forests, as evidenced by plant and soil N to phosphorus (P) ratios, by P limitation of plant growth in some tropical forests, by an abundance of N-fixing plants, and by sustained export of bioavailable N at the ecosystem scale. However, this apparent up-regulation of the ecosystem N cycle introduces a biogeochemical paradox when considered from the perspective of physiology and evolution of individual plants: The putative source for tropical N richness—symbiotic N fixation—should, in theory, be physiologically down-regulated as internal pools of bioavailable N build. We review the evidence for tropical N richness and evaluate several hypotheses that may explain its emergence and maintenance. We propose a leaky nitrostat model that is capable of resolving the paradox at scales of both ecosystems and individual N-fixing organisms.

Although animal pollination is often proposed as a major driver of floral divergence, questions remain about its importance in plant speciation. One issue is whether pollinator specialization, traditionally thought necessary for floral isolation, is prevalent enough to have played a major role in speciation. Furthermore, the ecological and geographic scenarios under which pollinator transitions occur are poorly understood, and the underlying genetic factors are just beginning to be uncovered for a few systems. Nevertheless, macroevolutionary studies consistently show that transitions to animal pollination are accompanied by an increase in diversification rate. Here we consider several models and diverse empirical data on how pollinators could influence speciation. We conclude that floral isolation is rarely, if ever, sufficient to cause speciation on its own, but that it acts synergistically with other isolating mechanisms. A more comprehensive approach is the key to an improved understanding of the role of pollinators in angiosperm speciation.

Darwin thought evolution is slow. Evolution is slow on long time scales, but the fundamental process works on a generation-to-generation scale, not long time scales. Phenotypic variation is geometric normal, with normality reflecting its underlying polygenic source; ln transformation is part of the measurement process. The natural rate unit is the haldane, particularly H0, representing change in standard deviations per generation on a timescale of one generation. When appropriately sampled, rates calculated on longer scales can be projected to a generational timescale. Empirical studies are reviewed concerning: (a) rates of polygenic mutation, (b) rates of response to human versus natural disturbance; and (c) rates of change in a classic study of punctuated equilibrium. Rate studies commonly find phenotypic change on the order of H0 = 0.1 to 0.3 standard deviations per generation. This is fast by any standard. Darwin was wrong on rates, but more right than we knew on natural selection.

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

The factors that influence a plant's ability to invade are not well understood. Many mechanisms are involved and the relative importance of different mechanisms depends on the specific invasion. Here we consider one factor—mycorrhizal symbioses. These symbioses are ubiquitous interactions involving the plants and soil fungi of most terrestrial ecosystems. We develop a conceptual framework for considering mycorrhizal symbioses in plant species invasions. The most critical aspects of this framework are: (a) the mycorrhizal status and (b) the growth response of the invading plant, (c) the ability of the plant to associate with different fungi, (d) the quality of the plant as a host for local fungi and feedback dynamics, (e) the biogeography and dispersal of the fungi, (f) the introduction and spread of the fungi, and (g) the ecological consequences of the creation of novel mycorrhizas. These aspects can critically influence the trajectory of a plant invasion, and this symbiosis deserves more attention in plant invasion biology.