Twenty-first century technology is addressing many of the questions posed by 20th-century biology. Although the new approaches, especially those involving genomic data and bioinformatic tools, were first applied to model organisms, they are now stretching across the tree of life. Here, we review some recent revelations in the ferns. We first examine how DNA sequence data have contributed to our understanding of fern phylogeny. We then address evolution of the fern plastid genome, including reports of high levels of RNA editing. Recent studies are also shedding light on the evolution of fern nuclear genomes. Initial analyses of genomic data suggest that despite their very high chromosome numbers homosporous ferns may have experienced relatively few rounds of genome duplication. Genomic data are enabling researchers to examine speciation rates and the mechanisms underlying the formation of new fern species. We also describe genetic tools that have been used to study gene function and development in ferns. Recent findings in fern biology are providing insights that are not only pertinent to this major component of the land flora but can also help to provide an improved evolutionary context for research on flowering plants.

The freshwater macroalga Aegagropila linnaei can occur attached or unattached, but is best known for its free-floating spherical growth form (“lake balls,” “Cladophora balls,” or “marimo””). The worldwide distribution of this species was reconstructed using more than 1200 specimens from 28 herbaria, an extensive literature survey, and field observations. Aegagropila linnaei was found in 283 locations, with the majority located in central and northern Europe. Few records of A. linnaei exist from North America, but it is relatively widespread in Japan. The preferred habitat is inferred to be oligomesotrophic lakes with moderate to high calcium levels. In more than 50% of the known locations, A. linnaei has not been found in the last 30 years, and this decline is assumed to be correlated with changes in trophic conditions in those lakes. The unattached growth forms show a stronger decline than attached populations as a result of the habitat types in which they can occur.

The global decline in biodiversity as a result of urbanization remains poorly understood. Whereas habitat destruction accounts for losses at the species level, it may not explain diversity loss at the community level, because urban centers also attract synanthropic species that do not necessarily exist in wildlands. Here we suggest an alternative framework for understanding this phenomenon: the competitive exclusion of native, non-synanthropic species by invasive species. We use data from two urban centers (Phoenix and Baltimore) and two taxa (birds and spiders) to link diversity loss with reduced community evenness among species in urban communities. This reduction in evenness may be caused by a minority of invasive species dominating the majority of the resources, consequently excluding nonsynanthropic species that could otherwise adapt to urban conditions. We use foraging efficiency as a mechanism to explain the loss of diversity. Thus, to understand the effects of habitat conversion on biodiversity, and to sustain species-rich communities, future research should give more attention to interspecific interactions in urban settings.

Process-based restoration aims to reestablish normative rates and magnitudes of physical, chemical, and biological processes that sustain river and floodplain ecosystems. Ecosystem conditions at any site are governed by hierarchical regional, watershed, and reach-scale processes controlling hydrologic and sediment regimes; floodplain and aquatic habitat dynamics; and riparian and aquatic biota. We outline and illustrate four process-based principles that ensure river restoration will be guided toward sustainable actions: (1) restoration actions should address the root causes of degradation, (2) actions must be consistent with the physical and biological potential of the site, (3) actions should be at a scale commensurate with environmental problems, and (4) actions should have clearly articulated expected outcomes for ecosystem dynamics. Applying these principles will help avoid common pitfalls in river restoration, such as creating habitat types that are outside of a site's natural potential, attempting to build static habitats in dynamic environments, or constructing habitat features that are ultimately overwhelmed by unconsidered system drivers.

Releases of greenhouse gases (GHG) from indirect land-use change triggered by crop-based biofuels have taken center stage in the debate over the role of biofuels in climate policy and energy security. This article analyzes these releases for maize ethanol produced in the United States. Factoring market-mediated responses and by-product use into our analysis reduces cropland conversion by 72% from the land used for the ethanol feedstock. Consequently, the associated GHG release estimated in our framework is 800 grams of carbon dioxide per megajoule (MJ); 27 grams per MJ per year, over 30 years of ethanol production, or roughly a quarter of the only other published estimate of releases attributable to changes in indirect land use. Nonetheless, 800 grams are enough to cancel out the benefits that corn ethanol has on global warming, thereby limiting its potential contribution in the context of California's Low Carbon Fuel Standard.

To explore the potential evolutionary relevance of heritable epigenetic variation, the National Evolutionary Synthesis Center recently hosted a catalysis meeting that brought together molecular epigeneticists, experimental evolutionary ecologists, and theoretical population and quantitative geneticists working across a wide variety of systems. The group discussed the methods available to investigate epigenetic variation and epigenetic inheritance, and how to evaluate their importance for phenotypic evolution. We found that understanding the relevance of epigenetic effects in phenotypic evolution will require clearly delineating epigenetics within existing terminology and expanding research efforts into ecologically relevant circumstances across model and nonmodel organisms. In addition, a critical component of understanding epigenetics will be the development of new and current statistical approaches and expansion of quantitative and population genetic theory. Although the importance of heritable epigenetic effects on evolution is still under discussion, investigating them in the context of a multidisciplinary approach could transform the field.