MainWhen highly transmissible pathogens are introduced into a naive community of susceptible hosts, these often experience one or a series of epizootic waves1. Over time, barring extinction of the pathogen or the host, epizootic disease dynamics will usually subside into more stable enzootic equilibria. Divergent trajectories and asynchronous rates of recovery can generate contemporary patterns of epizootic and enzootic disease dynamics between persisting host populations2,3. Comparative studies between these populations can offer insights into the role of host immunity in shaping population-level disease outcomes4. Antimicrobial peptides (AMPs) are a crucial and near-ubiquitous component of innate immune defense across the tree of life5 and have been shown to inhibit the growth of bacterial, viral and fungal taxa in vitro6. Innate immune effectors, including AMPs, are traditionally considered a primitive, broad-spectrum antimicrobial barrier for preventing infection7. Despite this long-held perception, there is a growing body of work challenging this oversimplification5,8. While the innate immune system does constitute the first line of defense against novel pathogens, the complexity and specificity of the constituent AMPs has been long overlooked.As anthropogenically spread emerging infectious diseases (EIDs) increasingly impact humans, agriculture and wildlife9, there is a pressing need to understand the interactions between host immunity and these novel pathogens. Here, the amphibian-infecting chytrid fungus, Batrachochytrium dendrobatidis (Bd), is one of the most impactful EIDs known and is a recognized threat to amphibian diversity worldwide10. Chytridiomycosis, the disease caused by Bd, causes acute epidermal disruption, leading to pathophysiological changes associated with high rates of mortality in susceptible species11. The resulting population declines have been monitored over the past forty years and the loss of amphibian taxa, particularly in tropical montane ecosystems, results in the loss of ecosystem function12,13 and the collapse of predator communities through trophic cascades14. Despite these localized catastrophic events, at a global level, the emergence of Bd is associated with heterogeneous patterns of declines of susceptible amphibians at both interspecific11 and intraspecific levels2,3.There is some evidence to suggest that increased host immunity is contributing to the persistence of susceptible host populations11,15. As a pathogen of amphibian skin, Bd must first survive contact with the epidermal mucosal layer before it can infect the host. Variation in the efficacy of these mucosal defenses may explain the observed heterogeneity in population-level responses to a Bd epizootic. The highly diverse mixtures of both host16 and microbial compounds17 present in the mucosal layer have been shown to inhibit the growth of Bd in vitro18 and in vivo15. AMPs, in particular, are thought to be a critical component of an amphibian’s mucosal innate immune defense against pathogens such as Bd. This hypothesis owes much to previous in vitro work showing increased anti-Bd efficacy of mucosal samples from resistant amphibian species and the corresponding in vitro activity of synthetic amphibian AMPs19. However, there has been substantial difficulty in linking these in vitro AMP experiments to population-level studies in the field.In many amphibian species, the metamorphosis from the larval to postmetamorphic stages carries an elevated risk of mortality from chytridiomycosis20. This elevated risk is generated through two simultaneous developmental processes, keratinization of the skin and immune maturation. As a keratinophilic parasite, Bd requires keratinized amphibian skin as a substrate for its survival in vivo21. In fatal chytridiomycosis, the osmoregulatory capacity of the amphibian’s skin breaks down, leading to cardiac asystolic death through electrolyte imbalance11. However, tadpoles do not possess keratinized skin22. Whilst Bd can infect their keratinized mouthparts, this does not develop into chytridiomycosis and is generally not fatal23. During metamorphosis, as keratinization of the skin occurs, the pathogen can spread to the skin, which can then develop into chytridiomycosis. This transition from a Bd-tolerant to a Bd-susceptible life stage coincides with a critical period of immune reorganization24. The immune system of tadpoles is considered immature and less effective in comparison to postmetamorphic animals25. At an organismal level, the development of the constitutive, innate and adaptive immune defenses takes places at discrete stages before, during and after metamorphosis as the requisite organs develop26. At a skin level, the AMP repertoire of tadpoles is considerably different to postmetamorphic life stages25,27, with further changes potentially occurring between recent metamorphs and sexually mature adults28. The inhibitory potential of these limited AMP defenses in larval amphibians has been reported to be significantly lower than those of postmetamorphic animals27. However, there has been no research into the population-level variation of these immune profiles across life stages in nature.The common midwife toad (Alytes obstetricans) is susceptible to Bd but its population-level response to Bd introduction has been highly variable2,29,30,31. This species is particularly susceptible to chytridiomycosis during or shortly after metamorphosis, often leading to seasonal mass mortality events in montane regions31. In the Western Pyrenean Mountain range, all populations of A. obstetricans experienced heavy declines following Bd introduction, yet four of these populations have persisted 19 years later, with three transitioning to stable, enzootic disease dynamics2. At Lac d’Arlet, one population continues to exhibit epizootic dynamics characterized by high Bd infection intensity, seasonal mass mortality events and near extirpation. This observed heterogeneity in disease dynamics is known to be associated with amongst-lake variation in host microbiome2,4; however, an underlying immunological mechanism driving these host–microbe interactions is missing.Here, we aimed to investigate the extent to which the observed disease dynamics were associated with variation in host AMP defenses. The AMP defenses of A. obstetricans include the alyteserin family, which consists of 12 cationic, α-helical cytolytic AMPs that are C-terminally amidated32. However, it remains unknown whether some or all the known alyteserins inhibit Bd or whether they could operate synergistically as is the case in other amphibian AMP systems33,34. If there is variation in anti-Bd efficacy between AMPs, then population-level responses to chytridiomycosis could occur through differences in composition or concentration of their AMP arsenal.Since the description of the alyteserin AMPs in A. obstetricans in 2009, recent advances in mass spectrometry (MS)-based proteomics35,36, when integrated with transcriptomic references, has allowed for the high-throughput characterization of complex peptidomic mixtures. While these methods are typically used in human health research37,38, we were able to apply these analytical techniques to this wild amphibian disease system. In combination with molecular diagnostics, in vitro AMP Bd inhibition assays and confocal microscopy, we leveraged a multidisciplinary approach to investigate whether these differences in contemporary disease dynamics in the Western Pyrenees are associated with (1) the composition and efficacy of host AMP defenses in recently metamorphosed animals; (2) preinvestment in AMPs at the larval stage; and (3) the varied epidemiological outcomes that we observe across this long-term study system.ResultsWe confirm the continuation of epizootic disease dynamics, characterized by high levels of mortality (Fig. 1a) and infection intensity (Fig. 1b), in recently metamorphosed A. obstetricans at Lac d’Arlet. While this population has continued to persist despite many years of heavy chytridiomycosis-driven mortality, the low numbers of postmetamorphic individuals found during surveys (2019: n = 2, 2020: n = 7) relative to the enzootic populations (Ibón de Acherito, Puits d’Arious and Lac de Lhurs) shows that the population has yet to successfully coexist with the introduced pathogen.Fig. 1: Post metamorphic Bd disease dynamics in the Western Pyrenees.Full size imagea, Proportion of deceased postmetamorphic individuals (Ibón de Acherito, n = 7; Lac d’Arlet, n = 17; Lac d’Lhurs, n = 0; Puits d’Arious, n = 3) from total encountered (Ibón de Acherito, N = 47; Lac d’Arlet, N = 26; Lac d’Lhurs, N = 40; Puits d’Arious, N = 43) during field surveys. Significance was determined by Kruskal–Wallis test (χ2(3) = 58.497, P