Effects of Selection at Linked Sites on Patterns of Genetic Variability

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

A Dual Role for Behavior in Evolution and Shaping Organismal Selective Environments

The hypothesis that evolved behaviors play a determining role in facilitating and impeding the evolution of other traits has been discussed for more than 100 years with little consensus beyond an agreement that the ideas are theoretically plausible in accord with the Modern Synthesis. Many recent reviews of the genomic, epigenetic, and developmental mechanisms underpinning major behavioral transitions show how facultative expression of novel behaviors can lead to the evolution of obligate behaviors and structures that enhance behavioral function. Phylogenetic and genomic studies indicate that behavioral traits are generally evolutionarily more labile than other traits and that they help shape selective environments on the latter traits. Adaptive decision-making to encounter resources and avoid stress sources requires specific sensory inputs, which behaviorally shape selective environments by determining those features of the external world that are biologically relevant. These recent findings support the hypothesis of a dual role for behavior in evolution and are consistent with current evolutionary theory.

Evolvability: A Quantitative-Genetics Perspective

The concept of evolvability emerged in the early 1990s and soon became fashionable as a label for different streams of research in evolutionary biology. In evolutionary quantitative genetics, evolvability is defined as the ability of a population to respond to directional selection. This differs from other fields by treating evolvability as a property of populations rather than organisms or lineages and in being focused on quantification and short-term prediction rather than on macroevolution. While the term evolvability is new to quantitative genetics, many of the associated ideas and research questions have been with the field from its inception as biometry. Recent research on evolvability is more than a relabeling of old questions, however. New operational measures of evolvability have opened possibilities for understanding adaptation to rapid environmental change, assessing genetic constraints, and linking micro- and macroevolution.

Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates

Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing rates over different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

What Have We Learned from the First 500 Avian Genomes?

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Cascading Impacts of Seed Disperser Loss on Plant Communities and Ecosystems

Seed dispersal is key to the persistence and spread of plant populations. Because the majority of plant species rely on animals to disperse their seeds, global change drivers that directly affect animals can cause cascading impacts on plant communities. In this review, we synthesize studies assessing how disperser loss alters plant populations, community patterns, multitrophic interactions, and ecosystem functioning. We argue that the magnitude of risk to plants from disperser loss is shaped by the combination of a plant species’ inherent dependence on seed dispersers and the severity of the hazards faced by their dispersers. Because the factors determining a plant species’ risk of decline due to disperser loss can be related to traits of the plants and dispersers, our framework enables a trait-based understanding of change in plant community composition and ecosystem functioning. We discuss how interactions among plants, among dispersers, and across other trophic levels also mediate plant community responses, and we identify areas for future research to understand and mitigate the consequences of disperser loss on plants globally. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolution of Mimicry Rings as a Window into Community Dynamics

Mimicry rings are communities of mimetic organisms that are excellent models for ecological and evolutionary studies because the community composition, the nature of the species interactions, the phenotypes under selection, and the selective agents are well characterized. Here, we review how regional and ecological filtering, density- and frequency-dependent selection, toxicity of prey, and age of mimicry rings shape their assembly. We synthesize findings from theoretical and empirical studies to generate the following hypotheses: ( a) the degree of unpalatability and age of mimicry rings increase mimicry ring size and ( b) the degree of unpalatability, generalization of the aposematic signal, and availability of alternative prey are positively related to the breadth of the protection umbrella for an aposematic signal and negatively related to the degree of mimetic resemblance. We also provide a phylogenetic framework in which key aspects of mimicry ring diversification may be studied. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Sensory and Cognitive Ecology of Bats

We see stunning morphological diversity across the animal world. Less conspicuous but equally fascinating are the sensory and cognitive adaptations that determine animals’ interactions with their environments and each other. We discuss the development of the fields of sensory and cognitive ecology and the importance of integrating these fields to understand the evolution of adaptive behaviors. Bats, with their extraordinarily high ecological diversity, are ideal animals for this purpose. An explosion in recent research allows for better understanding of the molecular, genetic, neural, and behavioral bases for sensory ecology and cognition in bats. We give examples of studies that illuminate connections between sensory and cognitive features of information filtering, evolutionary trade-offs in sensory and cognitive processing, and multimodal sensing and integration. By investigating the selective pressures underlying information acquisition, processing, and use in bats, we aim to illuminate patterns and processes driving sensory and cognitive evolution. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolution of Thermal Sensitivity in Changing and Variable Climates

Evolutionary adaptation to temperature and climate depends on both the extent to which organisms experience spatial and temporal environmental variation (exposure) and how responsive they are to the environmental variation (sensitivity). Theoretical models and experiments suggesting substantial potential for thermal adaptation have largely omitted realistic environmental variation. Environmental variation can drive fluctuations in selection that slow adaptive evolution. We review how carefully filtering environmental conditions based on how organisms experience their environment and further considering organismal sensitivity can improve predictions of thermal adaptation. We contrast taxa differing in exposure and sensitivity. Plasticity can increase the rate of evolutionary adaptation in taxa exposed to pronounced environmental variation. However, forms of plasticity that severely limit exposure, such as behavioral thermoregulation and phenological shifts, can hinder thermal adaptation. Despite examples of rapid thermal adaptation, experimental studies often reveal evolutionary constraints. Further investigating these constraints and issues of timescale and thermal history are needed to predict evolutionary adaptation and, consequently, population persistence in changing and variable environments. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.