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This chapter outlines three basic ways in which humans can alter evolution on adaptive landscapes: through changes in topography, changes in dimensionality, and phenotypic excursions. Changes in topography involve the numbers, positions, gradients, and elevations of surface features on the landscape, such as peaks and valleys. Changes in dimensionality involve the number of at least partially independent traits under selection. Excursions typically involve more or less abrupt changes in the phenotypic position of populations on existing adaptive landscapes, such as through plasticity, hybridization, or genetic manipulation. These different types of change can generate predictions for changes in selection and alterations in evolution — assuming the population can persist through the disturbance. Invasive species can have all of these classes of effects, either for the invasive species or for native species. Climate change will most obviously involve a shift in peak position, such as breeding times under warmer temperatures. Hunting/harvesting will also often involve a shift in peak position, particularly toward smaller and slower growing individuals, and might also decrease phenotypic variance. Habitat loss and fragmentation will influence numbers and positions of adaptive peaks, and can also influence excursions by altering patterns of gene flow in meta-populations. Finally, a decrease in habitat quality can decrease the heights of fitness peaks and cause adaptive landscapes to become smoother. It can also change dimensionality, such as through the introduction of a new contaminant. In conclusion, viewing human-induced environmental change in the framework of changes to adaptive landscapes offers new insights and new perspectives for research.

Ecology and evolution go hand in hand. However, since evolution occurs over relatively long time scales, ecologists had long thought it unlikely that evolutionary events could affect population dynamics or species interactions in ecological time. This view is changing. Today, there are multiple areas of research examining how evolutionary processes feedback directly on ecology. For example, eco-evolutionary dynamics focus on the cyclical interaction between ecology and adaptive evolution, such that changes in ecological interactions drive selection on organismal traits that, in turn, alter the outcome of ecological interactions. Striking examples of eco-evolutionary feedbacks are found in predator–prey interactions of laboratory populations. However, less is known about eco-evolutionary feedbacks in nature. Evolutionary rescue describes a process whereby rapid adaptation may prevent extinction in a changing environment. Other topics covered in this chapter are community phylogenetics and the evolution of regional species pools.

Centromeres and the kinetochore proteins that bind them are required for chromosome segregation during eukaryotic cell division. Despite this conserved function, both centromeric DNA and kinetochore proteins evolve rapidly. This chapter hypothesizes that this paradox can be explained by an on-going conflict between selfish centromeric DNA elements and the DNA binding proteins of the kinetochore. In this model, centromeres are able to gain an evolutionary advantage by promoting their own transmission during asymmetric female meiosis. Deleterious consequences of this selfish behaviour in turn select for variant kinetochore proteins that can suppress centromeric imbalances. This conflict, termed ‘Centromere Drive’, provides an explanation for observed differences in evolutionary rates between components of the kinetochore, and makes predictions about which taxa might experience accelerated centromeric evolution.

Interspecific comparisons of gene expression patterns have shown that much variability exists in the rates of divergence among loci. Furthermore, divergence rates within loci vary depending on the tissue(s) and developmental stage(s) being compared. Several broad patterns explaining these rate differences have emerged and, in general, it appears that genes with tissue-specific patterns of expression (especially in tissues under frequent directional selection), and/or biased expression during late developmental stages, are more likely to be involved in rapid evolution. Novel techniques are now allowing us to identify those instances of rapid evolution that are adaptive, as well as probe under-explored aspects of transcriptome divergence — such as alternative splicing and the contribution of non-coding RNAs — and are beginning to unravel the underlying complexity of the transcriptome and how it may be an agent of rapid phenotypic evolution at the organismal level.

The opportunity for arms-race evolution between host and pathogens is one reason why genes involved in immune functions are often rapidly evolving. Innate immune systems lack the degree of pathogen specificity that makes such arms races easy to initiate, but nevertheless they too harbour rapidly evolving genes. While core signalling genes retain one-to-one orthology, both recognition and antimicrobial peptide genes display rapid changes in copy number. With respect to turnover of amino acids in the proteins themselves, receptors that are involved in phagocytosis evolve the fastest, with signalling proteins also evolving rapidly as a consequence of microbial attack. Antimicrobial peptides have a comparatively slow rate of amino acid replacement. Finally, several proteins involved in viral and transposon defence are exceptionally rapid in their evolutionary rates, possibly as a consequence of an arms race process whose rate is driven by the high mutation rate of viruses.

In a rapidly changing world, understanding how organisms and populations respond to new or changing environments is of importance for addressing challenges related to conservation of biodiversity, ecosystem function, and human health. Contemporary colonization events provide a rare opportunity to study developmental and evolutionary responses to novel environments in ‘real time.’ In this chapter, we provide a comprehensive review of nearly two decades of research examining a unique Junco colonization event in S. California, in which a typically montane-breeding subspecies (J.hyemalis thurberi) recently (c. 1983) established a small population in an urban and coastal environment. First, we discuss the unique natural history of this study system. Second, we summarize observed phenotypic changes in behavior, morphology, and physiology that have been documented to date, including evidence for both [developmental] plasticity and rapid [genetic] evolution, inferred from field and common garden studies. Third, we discuss the relevance of these studies in the wider context of efforts to link integrative and evolutionary biology by studying hormones and hormone-mediated traits. We conclude by exploring the promise of ongoing and future work in this system, including a scope for adding replicate population comparisons from other Junco colonizations of urban habitats and offshore islands.

The spreading dynamics of invasive species in their novel range is often faster and has greater variability than would be predicted from diffusion-based models, which leads to an underestimation of rates of spread and often to delayed intervention which reduces the efficient of management. Diverse mechanisms that underpin such boosted range expansion and invasion performance are related to either altered biotic interactions with other species (e.g. enemy release) or readjustment of the invader’s life-history strategies, especially due to augmented dispersal and rapid adaptation at the advancing range margin. This chapter deals with boosted range expansion due to the readjustment of life-history strategies. Key mechanisms include long-distance dispersal, human-mediated translocation, the rapid evolution of dispersal and life-history traits, and spatial sorting. An integrated framework based on joint mechanisms of fat-tailed dispersal and spatial selection at the advancing edge is presented to explain boosted range expansion.