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Supergenes are tightly linked sets of loci that are inherited together and control complex phenotypes. While classical supergenes—governing traits such as wing patterns in Heliconius butterflies or heterostyly in Primula —have been studied since the Modern Synthesis, we still understand very little about how they evolve and persist in nature. The genetic architecture of supergenes is a critical factor affecting their evolutionary fate, as it can change key parameters such as recombination rate and effective population size, potentially redirecting molecular evolution of the supergene in addition to the surrounding genomic region. To understand supergene evolution, we must link genomic architecture with evolutionary patterns and processes. This is now becoming possible with recent advances in sequencing technology and powerful forward computer simulations. The present theme issue brings together theoretical and empirical papers, as well as opinion and synthesis papers, which showcase the architectural diversity of supergenes and connect this to critical processes in supergene evolution, such as polymorphism maintenance and mutation accumulation. Here, we summarize those insights to highlight new ideas and methods that illuminate the path forward for the study of supergenes in nature. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’. 

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.

 

Sandy beaches are iconic interfaces that functionally link the ocean with the landviathe flow of organic matter from the sea. These cross‐ecosystem fluxes often comprise uprooted seagrass and dislodged macroalgae that can form substantial accumulations of detritus, termed ‘wrack’, on sandy beaches. In addition, the tissue of the carcasses of marine animals that regularly wash up on beaches form a rich food source (‘carrion’) for a diversity of scavenging animals. Here, we provide a global review of how wrack and carrion provide spatial subsidies that shape the structure and functioning of sandy‐beach ecosystems (sandy beaches and adjacent surf zones), which typically have littlein situprimary production. We also examine the spatial scaling of the influence of these processes across the broader land‐ and seascape, and identify key gaps in our knowledge to guide future research directions and priorities. Large quantities of detrital kelp and seagrass can flow into sandy‐beach ecosystems, where microbial decomposers and animals process it. The rates of wrack supply and its retention are influenced by the oceanographic processes that transport it, the geomorphology and landscape context of the recipient beaches, and the condition, life history and morphological characteristics of the macrophyte taxa that are the ultimate source of wrack. When retained in beach ecosystems, wrack often creates hotspots of microbial metabolism, secondary productivity, biodiversity, and nutrient remineralization. Nutrients are produced during wrack breakdown, and these can return to coastal waters in surface flows (swash) and aquifers discharging into the subtidal surf. Beach‐cast kelp often plays a key trophic role, being an abundant and preferred food source for mobile, semi‐aquatic invertebrates that channel imported algal matter to predatory invertebrates, fish, and birds. The role of beach‐cast marine carrion is likely to be underestimated, as it can be consumed rapidly by highly mobile scavengers (e.g. foxes, coyotes, raptors, vultures). These consumers become important vectors in transferring marine productivity inland, thereby linking marine and terrestrial ecosystems. Whilst deposits of organic matter on sandy‐beach ecosystems underpin a range of ecosystem functions and services, they can be at variance with aesthetic perceptions resulting in widespread activities, such as ‘beach cleaning and grooming’. This practice diminishes the energetic base of food webs, intertidal fauna, and biodiversity. Global declines in seagrass beds and kelp forests (linked to global warming) are predicted to cause substantial reductions in the amounts of marine organic matter reaching many beach ecosystems, likely causing flow‐on effects for food webs and biodiversity. Similarly, future sea‐level rise and increased storm frequency are likely to alter profoundly the physical attributes of beaches, which in turn can change the rates at which beaches retain and process the influxes of wrack and animal carcasses. Conservation of the multi‐faceted ecosystem services that sandy beaches provide will increasingly need to encompass a greater societal appreciation and the safeguarding of ecological functions reliant on beach‐cast organic matter on innumerable ocean shores worldwide.