Changes in the timing and level at which genes are expressed are known to play an important role in evolution, but the mechanisms underlying changes in gene expression remain relatively obscure. Until quite recently, evolutionary biologists, like most biologists, tended to study single genes as isolated entities. These studies have added enormously to our understanding of biological evolution. But because gene regulation by its very nature involves interactions between two (or more) genes, researchers have missed a range of evolutionary phenomena that can be observed only at the level of networks of interacting genes. In this article, we consider the change in perspective that genomic technologies—particularly the advent of large-scale platforms for DNA sequencing, genotyping, and measuring gene expression—are bringing to evolutionary biology. We focus specifically on how these technologies can and are being used to increase our understanding of how and why gene expression evolves.

Six conclusions have emerged from recent research that complicate the ability to predict how biodiversity losses may affect ecosystem function: (1) species traits determine ecosystem function, (2) species within functional groups are not always ecological equivalents, (3) biodiversity losses include declines in the abundance of common species, (4) biodiversity losses affect wholefood webs, (5) the effects of biodiversity losses depend on abiotic and biotic context and spatial and temporal scales, and (6) successfully predicting linkages between biodiversity and ecosystem function requires using multiple empirical approaches across scales. Nutrient recycling by freshwater mussel communities illustrates these conclusions. Nutrient excretion rates depend on the expression of mussel species traits, which vary with flow, temperature, and community structure. Nutrient contributions from mussels depend on which mussel species are dominant, but common species of mussels are declining, leading to shifts in species dominance patterns and thus nutrient recycling. These changes are very likely affecting the rest of the benthic food web because mussel excretion stimulates primary, and subsequently secondary, production.

A broad perspective on hydrologic connectivity is necessary w managing stream ecosystems and establishing conservation priorities. Hydrologic connectivity refers to the water-mediated transport of matter, energy, or organisms within or between elements of the hydrologic cycle. The potential negative consequences of enhancing hydrologic connectivity warrant careful consideration in human-modified landscapes that are increasingly characterized by hydrologic alteration, exotic species, high levels of nutrients and toxins, and disturbed sediment regimes. While connectivity is integral to the structure and function of aquatic ecosystems, it can also promote the distribution of undesirable components. Here we provide examples illustrating how reduced hydrologic connectivity can provide greater ecological benefits than enhanced connectivity does in highly developed, human-modified ecosystems; for example, in urban landscapes, “restoration” efforts can sometimes create population sinks for endangered biota. We conclude by emphasizing the importance of adaptive management and balancing trade-offs associated with further alterations of hydrologic connectivity in human-modified landscapes.

Ecological monitoring and management require detailed information over broad spatial scales. Historically, such information was often acquired through manual interpretation of aerial photographs. As traditional methods of analyzing aerial photographs can he time-consuming, subjective, and can require well-trained interpreters (who are currently in short supply), new approaches must be explored for collecting this ecological information. First, we discuss the benefits and challenges of using aerial photographs for ecological management. We then examine the eight fundamental characteristics used in photograph interpretation and discuss their ecological relevance. Third, we investigate the feasibility of digital-analysis methods (often used for analysis of satellite imagery) for providing more objective, consistent, and cost-effective results. We end with several examples of how the unique information from aerial photographs can aid in solutions to emerging challenges in ecological research and management, and how they may be further used with supplementary data sets.

Multifunctional agriculture (MFA) enhances the quality and quantity of benefits provided by agriculture to society, by joint production of both agricultural commodities and a range of ecological services. In developed countries, new agroecosystem designs for MFA are appearing rapidly, but adoptions are limited. We present a heuristic strategy for increasing the adoption of MFA through development of new enterprises that enable farmers to profit from production of both agricultural commodities and ecological services. We propose that such enterprises can arise through feedback between social and biophysical systems operating across a range of scales. Such feedback depends on coordinated innovation among economic actors in a range of interdependent social sectors, supported by new “subsystems” that produce site-specific agroecological knowledge, and by change in the encompassing “supersystem” of public opinion and policy. This strategy can help guide efforts to increase the adoption of MFA.

Assignment of values for natural ecological benefits and anthropocentric ecosystem services in riverine landscapes has been problematic because a firm scientific basis linking these to the river's physical structure has been absent. We highlight some inherent problems in this process and suggest possible solutions on the basis of the hydrogeomorphic classification of rivers. We suggest this link can be useful in fair asset trading (mitigation and offsets), selection of sites for rehabilitation, cost-benefit decisions on incremental steps in restoring ecological functions, and general protection of rivers.