Annual Review of Ecology, Evolution, and Systematics

Stable isotope analysis (SIA) has proven to be a useful tool in reconstructing diets, characterizing trophic relationships, elucidating patterns of resource allocation, and constructing food webs. Consequently, the number of studies using SIA in trophic ecology has increased exponentially over the past decade. Several subdisciplines have developed, including isotope mixing models, incorporation dynamics models, lipid-extraction and correction methods, isotopic routing models, and compound-specific isotopic analysis. As with all tools, there are limitations to SIA. Chief among these are multiple sources of variation in isotopic signatures, unequal taxonomic and ecosystem coverage, over-reliance on literature values for key parameters, lack of canonical models, untested or unrealistic assumptions, low predictive power, and a paucity of experimental studies. We anticipate progress in SIA resulting from standardization of methods and models, calibration of model parameters through experimentation, and continued development of several recent approaches such as isotopic routing models and compound-specific isotopic analysis.

We present strong evidence that pathogens play a critical role in structuring plant communities and maintaining plant diversity. Pathogens mediate plant species coexistence through trade-offs between competitive ability and resistance to pathogens and through pathogen specialization. Experimental tests of individual plant–pathogen interactions, tests of feedback through host-specific changes in soil communities, and field patterns and field experimentation consistently identify pathogens as important to plant species coexistence. These direct tests are supported by observations of the role of pathogens in generating the productivity gains from manipulations of plant diversity and by evidence that escape from native pathogens contributes to success of introduced plant species. Further work is necessary to test the role of pathogen dynamics in large-scale patterns of plant diversity and range limits, the robustness of coexistence to coevolutionary dynamics, the contribution of different pathogens, and the role of pathogens in plant succession.

The net primary production of the biosphere is consumed largely by microorganisms, whose metabolism creates the trophic base for detrital foodwebs, drives element cycles, and mediates atmospheric composition. Biogeochemical constraints on microbial catabolism, relative to primary production, create reserves of detrital organic carbon in soils and sediments that exceed the carbon content of the atmosphere and biomass. The production of organic matter is an intracellular process that generates thousands of compounds from a small number of precursors drawn from intermediary metabolism. Osmotrophs generate growth substrates from the products of biosynthesis and diagenesis by enzyme-catalyzed reactions that occur largely outside cells. These enzymes, which we define as ecoenzymes, enter the environment by secretion and lysis. Enzyme expression is regulated by environmental signals, but once released from the cell, ecoenzymatic activity is determined by environmental interactions, represented as a kinetic cascade, that lead to multiphasic kinetics and large spatiotemporal variation. At the ecosystem level, these interactions can be viewed as an energy landscape that directs the availability and flow of resources. Ecoenzymatic activity and microbial metabolism are integrated on the basis of resource demand relative to environmental availability. Macroecological studies show that the most widely measured ecoenzymatic activities have a similar stoichiometry for all microbial communities. Ecoenzymatic stoichiometry connects the elemental stoichiometry of microbial biomass and detrital organic matter to microbial nutrient assimilation and growth. We present a model that combines the kinetics of enzyme activity and community growth under conditions of multiple resource limitation with elements of metabolic and ecological stoichiometry theory. This biogeochemical equilibrium model provides a framework for comparative studies of microbial community metabolism, the principal driver of biogeochemical cycles.

High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data collection by several orders of magnitude. This deluge of data is exerting tremendous pressure on downstream data-analysis methods providing new opportunities for method development. In this review, we present (a) recent advances in laboratory methods for collection of high-throughput phylogenetic data and (b) challenges and constraints for phylogenetic analysis of these data. We compare the merits of multiple laboratory approaches, compare methods of data analysis, and offer recommendations for the most promising protocols and data-analysis workflows currently available for phylogenetics. We also discuss several strategies for increasing accuracy, with an emphasis on locus selection and proper model choice.

The relationship between facilitation and evolutionary ecology is poorly understood. We review five issues elucidating how the phylogenetic relatedness of species provides insight into the role of facilitation in community assembly: (a) Are the facilitative interactions more common between species that differ in a regeneration niche? (b) Are facilitative interactions more common between distantly related species? (c) Do communities governed by facilitation (rather than competition) have higher phylogenetic diversity? (d) As facilitated juvenile plants mature, do they compete with their nurses more often if they are closely related to them? (e) How does the phylogenetic signature in a community reveal ecological processes, such as succession, regeneration dynamics, indirect interactions, and coextinction cascades? The evolutionary history of lineages explains the regeneration niche of species, which ultimately determines the facilitation-competition balance and therefore community assembly and dynamics. We apply this framework to the conservation of biodiversity and propose future research avenues.

▪ Abstract  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.

Các phương pháp tiếp cận dựa trên đặc tính đang ngày càng được sử dụng trong sinh thái học. Cộng đồng tảo, với lịch sử phong phú về các hệ thống mô hình trong sinh thái học cộng đồng, rất lý tưởng để áp dụng và phát triển thêm các khái niệm này. Tại đây, chúng tôi tóm tắt các thành phần thiết yếu của các phương pháp dựa trên đặc tính và duyệt xét việc áp dụng lịch sử cũng như tiềm năng của chúng trong việc tìm hiểu sinh thái cộng đồng tảo. Các trục sinh thái quan trọng liên quan đến tảo bao gồm thu nhận và sử dụng ánh sáng và dinh dưỡng, tương tác với kẻ thù tự nhiên, sự biến đổi hình thái, độ nhạy cảm với nhiệt độ, và các phương thức sinh sản. Các sự đánh đổi giữa các đặc tính này đóng vai trò quan trọng trong việc xác định cấu trúc cộng đồng. Môi trường nước ngọt và biển có thể lựa chọn một chuỗi các đặc tính khác nhau do các đặc tính vật lý và hóa học khác nhau của chúng. Chúng tôi mô tả các kỹ thuật toán học để tích hợp các đặc tính vào các biện pháp tăng trưởng và thể lực và dự đoán cách cấu trúc cộng đồng thay đổi dọc theo các gradient môi trường. Cuối cùng, chúng tôi vạch ra các thách thức và định hướng tương lai cho việc áp dụng các phương pháp dựa trên đặc tính vào sinh thái học tảo.

Bivalve molluscs are abundant in marine and freshwater ecosystems and perform important ecological functions. Bivalves have epifaunal or infaunal lifestyles but are largely filter feeders that couple the water column and benthos. Bivalve ecology is a large field of study, but few comparisons among aquatic ecosystems or lifestyles have been conducted. Bivalves impact nutrient cycling, create and modify habitat, and affect food webs directly (i.e., prey) and indirectly (i.e., movement of nutrients and energy). Materials accumulated in soft tissue and shells are used as environmental monitors. Freshwater mussel and oyster aggregations in rivers and estuaries are hot spots for biodiversity and biogeochemical transformations. Historically, human use includes food, tools, currency, and ornamentation. Bivalves provide direct benefits to modern cultures as food, building materials, and jewelry and provide indirect benefits by stabilizing shorelines and mitigating nutrient pollution. Research on bivalve-mediated ecological processes is diverse, and future synthesis will require collaboration across conventional disciplinary boundaries.

Secondary tropical forests that are in a state of regeneration following clearing for agriculture are now more abundant than primary forests. Yet, despite their large spatial extent and important role in the global carbon (C) cycle, secondary tropical forests are understudied, which challenges our ability to predict how tropical landscapes will respond to future disturbance and global change. We summarize research advances on alterations to C and nutrient dynamics during reforestation and how these are influenced by ecosystem state factors. During forest succession, aboveground biomass stocks and litter fluxes increase in a predictable way, but patterns in soil C dynamics are highly variable. The heterogeneous response of nutrients to reforestation is influenced by multiple factors, including losses incurred during prior land use and management. In contrast to primary tropical forests, where productivity is often limited by rock-derived nutrients, secondary forest growth may be more limited by nutrients from the atmosphere. Future research should identify which nutrients constrain forest regrowth.

▪ Abstract  Mutualisms occur when interactions between species produce reciprocal benefits. However, the outcome of these interactions frequently shifts from positive, to neutral, to negative, depending on the environmental and community context, and indirect effects commonly produce unexpected mutualisms that have community-wide consequences. The dynamic, and context dependent, nature of mutualisms can transform consumers, competitors, and parasites into mutualists, even while they consume, compete with, or parasitize their partner species. These dynamic, and often diffuse, mutualisms strongly affect community organization and ecosystem processes, but the historic focus on pairwise interactions decoupled from their more complex community context has obscured their importance. In aquatic systems, mutualisms commonly support ecosystem-defining foundation species, underlie energy and nutrient dynamics within and between ecosystems, and provide mechanisms by which species can rapidly adjust to ecological variance. Mutualism is as important as competition, predation, and physical disturbance in determining community structure, and its impact needs to be adequately incorporated into community theory.