Comparative phylogeography (CP) can be defined as the study of the effects of evolutionary history and biogeography on the distribution of genetic variation of codistributed species. CP studies have intensified in recent years, which is a natural progression from an extensive history of intraspecific phylogeography research. On the basis of a thorough review of published studies that specifically deal with CP, our objective in the present review is to provide a comprehensive guide to the discipline that will help those wishing to develop a CP project. We describe the characteristics that shape a CP study and summarize the field's prime theoretical, methodological, and analytical requirements; frequent hypotheses tested; and current achievements and limitations, including a variety of illustrative examples throughout. We finally highlight some new approaches in CP and briefly discuss future directions for the field.

Although research has explained how plant roots mechanically stabilize soils, in this article we explore how root systems create networks of preferential flow and thus influence water pressures in soils to trigger landslides. Root systems may alter subsurface flow: Hydrological mechanisms that promote lower pore-water pressures in soils are beneficial to slope stability, whereas those increasing pore pressure are adverse. Preferential flow of water occurs in the following types of root channels: (a) channels formed by dead or decaying roots, (b) channels formed by decayed roots that are newly occupied by living roots, and (c) channels formed around live roots. The architectural analysis of root systems improves our understanding of how roots grow initially, develop, die, and interconnect. Conceptual examples and case studies are presented to illustrate how root architecture and diverse traits (e.g., diameter, length, orientation, topology, sinuosity, decay rate) affect the creation of root channels and thus affect preferential flow.

Marine species are in constant motion in the ballast water and on the hulls of the ships that ply the world's oceans; ships serve as a major vector for biological invasions. Despite federal and state regulations that require ballast water exchange (BWE), particular trade routes impose geographic and temporal constraints on compliance, limiting whether a ship can conduct BWE at the required distance (≥200 nautical miles) from shore to minimize transfers of coastal organisms. Ships moving across the Americas are largely unable to conduct open-ocean BWE, but instead often conduct exchanges inside coastal waters. Overall, strong differences exist in volumes, geographic sources, and the use of BWE for ballast water discharge among the three major coasts of the contiguous United States. Such patterns suggest important geographic differences in invasion opportunities and also argue for more effective alternative ballast water treatments that can be applied more evenly.

Sponges are now the dominant habitat-forming animals on Caribbean reefs, where the combined effects of climate change, pollution, and disease have decimated reef-building corals. Natural products chemists have been isolating novel secondary metabolites from Caribbean sponges for many decades, but relevant studies of the ecological functions of these compounds have been more recent. Bioassay-guided surveys have revealed sponge chemical defenses against predators, competitors, and pathogens, but many common sponge species lack chemical defenses and appear to have followed a different evolutionary trajectory, investing instead in greater reproduction or growth. The emerging conceptual model predicts that changes in the abundances of fish- and sponge-eating fishes on Caribbean reefs will have a cascading impact on the sponge community, with indirect effects on the broader community of corals and seaweeds. Caribbean sponges provide an important alternative to terrestrial plant and insect communities for testing basic ecological theories about chemical defenses and resource allocation.

Scientific synthesis has transformed ecological research and presents opportunities for advancements across the sciences; to date, however, little is known about the antecedents of success in synthesis. Building on findings from 10 years of detailed research on social interactions in synthesis groups at the National Center for Ecological Analysis and Synthesis, we demonstrated with large-scale quantitative analyses that face-to-face interaction has been vital to success in synthesis groups, boosting the production of peer-reviewed publications. But it has been about more than just meeting; the importance of resident scientists at synthesis centers was also evident, in that including synthesis-center residents in geographically distributed working groups further increased productivity. Moreover, multi-institutional collaboration, normally detrimental to productivity, was positively associated with productivity in this stimulating environment. Finally, participation in synthesis groups significantly increased scientists' collaborative propensity and visibility, positively affecting scientific careers and potentially increasing the capacity of the scientific community to leverage synthesis for enhanced scientific understanding.

The sustainable seafood movement has adopted a variety of certification and ecolabeling systems, as well as seafood-awareness campaigns, to influence industry and help consumers make informed decisions regarding their seafood consumption. However, a review of these programs revealed that the majority are focused on marine and coastal fisheries. Globally, freshwaters and their fish assemblages represent some of the most threatened systems and taxa because of multiple anthropogenic stressors. There is an urgent need to harness the momentum of the sustainable seafood movement for marine systems to benefit all aquatic systems, including freshwater. Moreover, given that freshwater systems are at particular risk in developing countries in which small-scale fisheries dominate, it is essential to expand awareness campaigns, through grassroots initiatives that differ significantly from current awareness campaigns that are global in focus, involve industrialized large-scale fisheries, and assume significant exports of seafood. Addressing the limitations of marine campaigns is a logical first step before launching new programs aimed at inland fisheries. In the long term, failure of the sustainable seafood movement to incorporate freshwater fisheries will lead to public perception that these fisheries are not in peril and may allow unsustainable practices to continue.

More than 18% of tropical rainforests are now covered by totally protected areas. If these were well protected, we could feel reasonably confident that current conservation strategies might succeed in preserving a substantial proportion of tropical biodiversity. However, in most parts of the tropics, poachers enter and leave reserves with impunity. On the basis of reports from the hunting literature, it seems likely that a majority of tropical nature reserves may already be considered empty forests—meaning that all bird and mammal species larger than approximately two kilograms—barring a few hunting-tolerant species—have either been extirpated or exist at densities well below natural levels of abundance. The disruption of ecological functions caused by the loss of symbionts further compromises the capacity of these reserves to conserve biodiversity over the long term. A substantial shift toward improving the management and enforcement of tropical protected-area networks is required.