Annual Review of Ecology, Evolution, and Systematics - Volume 46, 2015

Increased mortality from fishing is expected to favor faster life histories, realized through earlier maturation, increased reproductive investment, and reduced postmaturation growth. There is also direct and indirect selection on behavioral traits. Molecular genetic methods have so far contributed minimally to understanding such fisheries-induced evolution (FIE), but a large body of literature studying evolution using phenotypic methods has suggested that FIE in life-history traits, in particular maturation traits, is commonplace in exploited fish populations. Although no phenotypic study in the wild can individually provide conclusive evidence for FIE, the observed common pattern suggests a common explanation, strengthening the case for FIE. This interpretation is supported by theoretical and experimental studies. Evidence for FIE of behavioral traits is limited from the wild, but strong from experimental studies. We suggest that such evolution is also common, but has so far been overlooked.

Dust is produced primarily in desert regions and transported long distances through the atmosphere to the oceans. Upon deposition of dust, its dissolution can provide an important source of a range of nutrients, particularly iron, to microbes living in open ocean surface waters. The dust supply is greatest nearest to deserts, hence in the Northern Hemisphere. The Southern Ocean region is farthest from these dust sources and shows clear evidence that phytoplankton primary production is limited, at least in part, by the rate of supply of iron. Iron is also essential for nitrogen fixation. In regions of high atmospheric iron supply, such as the tropical North Atlantic, stimulation of nitrogen fixation drives the phytoplankton population toward a state in which phosphorus supply rates limit primary production. Atmospheric deposition is also an important source of nitrogen to the low latitude ocean, where it stimulates primary production. In this review we consider the sources, transport, and deposition of atmospheric dust/iron and nitrogen to the oceans and their impacts on plankton systems. In conclusion, we suggest key areas for future research.

Although their diversity greatly exceeds that of plants and animals, microbial organisms have historically received less attention in ecology and evolutionary biology research. This knowledge gap is rapidly closing, owing to recent technological advances and an increasing appreciation for the role microbes play in shaping ecosystems and human health. In this review, we examine when and how the process and patterns of bacterial adaptation might fundamentally differ from those of macrobes, highlight methods used to measure adaptation in natural microbial populations, and discuss the importance of examining bacterial adaptation across multiple scales. We emphasize the need to consider the scales of adaptation as continua, in which the genetic makeup of bacteria blur boundaries between populations, species, and communities and with them concepts of ecological and evolutionary time. Finally, we examine current directions of the field as we move beyond the stamp-collecting phase and toward a better understanding of microbial adaptation in nature.

Ecologists and evolutionary biologists are increasingly using big-data approaches to tackle questions at large spatial, taxonomic, and temporal scales. However, despite recent efforts to gather two centuries of biodiversity inventories into comprehensive databases, many crucial research questions remain unanswered. Here, we update the concept of knowledge shortfalls and review the tradeoffs between generality and uncertainty. We present seven key shortfalls of current biodiversity data. Four previously proposed shortfalls pinpoint knowledge gaps for species taxonomy (Linnean), distribution (Wallacean), abundance (Prestonian), and evolutionary patterns (Darwinian). We also redefine the Hutchinsonian shortfall to apply to the abiotic tolerances of species and propose new shortfalls relating to limited knowledge of species traits (Raunkiæran) and biotic interactions (Eltonian). We conclude with a general framework for the combined impacts and consequences of shortfalls of large-scale biodiversity knowledge for evolutionary and ecological research and consider ways of overcoming the seven shortfalls and dealing with the uncertainty they generate.

Earth's climate has experienced strong changes on timescales ranging from decades to millions of years. As biodiversity has evolved under these circumstances, dependence on these climate dynamics is expected. In this review, we assess the current state of knowledge on paleoclimatic legacies in biodiversity and ecosystem patterns. Paleoclimate has had strong impacts on past biodiversity dynamics, driving range shifts and extinctions as well as diversification. We outline theory for how these dynamics may have left legacies in contemporary patterns and review the empirical evidence. We report ample evidence that Quaternary glacial–interglacial climate change affects current patterns of species distributions and diversity across a broad range of organisms and regions. We also report emerging evidence for paleoclimate effects on current patterns in phylogenetic and functional diversity and ecosystem functioning and for legacies of deeper-time paleoclimate conditions. Finally, we discuss implications for Anthropocene ecology and outline an agenda to improve our understanding of paleoclimate's role in shaping contemporary biodiversity and ecosystems.

Communication is ubiquitous. Developing a framework for the diversity of signals has important consequences for understanding alternative models of sexual selection and the processes contributing to speciation. In this article we review how models of neutral evolution in the perceptual space of signal perceivers provide a first step toward constructing a framework for signal diversity. We discuss how the distinction between additive and multiplicative effects of multimodal signaling represents a second step. We then assess how signal efficiency, reliability, and the aesthetics of perceivers provide distinct mechanisms for signals to be effective, thereby partly explaining signal diversity. Understanding the relative contribution of each of these mechanisms to the effectiveness of mate choice signals unravels the relative importance of alternative models of sexual selection. It can also help to distinguish whether divergence of communication is a driver or a consequence of speciation. Throughout the review we emphasize the importance of verification and learning in repeated interactions for understanding variation in signals.

Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of selfing is characterized by a loss of self-incompatibility, the selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asymmetry. Prevalence of dominant self-compatible mutations is consistent with Haldane's sieve, which acts against recessive adaptive mutations. Time estimates based on genome-wide polymorphisms and self-incompatibility genes generally support the recent origin of selfing.

We review patterns and causes of β-diversity in the deep-sea benthos at different spatial scales and for different body sizes. Changes in species composition occurring with depth are generally gradual, the rate of change being a function of the rate of descent. This gradual change can be interrupted by abrupt environmental shifts, such as oxygen minimum zones, and by major topographic features that alter oceanographic conditions. Changes in species composition with depth can involve both species replacement and species loss, leading to nestedness. Horizontal β-diversity is more moderate than that occurring with depth, except at upper bathyal zones impacted by coastal influences. At very large oceanic scales, both environmental filtering and dispersal limitation influence β-diversity. Although many ecological and evolutionary–historical factors must shape β-diversity in the deep sea, energy availability appears to structure community makeup at all scales examined. We recommend that standardized sampling protocols, statistical methods, and data archiving be used to direct future research.