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Chronological records of elemental concentrations in fish otoliths are a widely used tool to infer the environmental conditions experienced by individual fish. To interpret elemental signals within the otolith, it is important to understand how both external and internal factors impact ion uptake, transport and incorporation. In this study, we have combined chronological records from otoliths and archival data storage tags to quantify the influence of internal (sex, size, age, growth) and external (temperature, depth, salinity) conditions on otolith elemental chemistry of cod (Gadus morhua) in natural settings of the Baltic Sea. This study focused on elements primarily under physiological control: Phosphorus (P), magnesium (Mg) and zinc (Zn); and elements under environmental control: Strontium (Sr), barium (Ba) and manganese (Mn). Based on known spatial and temporal patterns in environmental conditions and fish size, growth, and maturity, we posed a series of hypotheses of expected otolith element patterns. Partial effects of internal and external drivers on element concentration were analyzed using a Linear Mixed Model approach with random variables (fish and year). Predicted effects of otolith concentrations of all elements under physiological control (P, Mg, Zn) showed similar trends, with distinct seasonal patterns (lowest concentration in late spring, highest concentrations in winter), and a positive correlation with water temperature, in addition to higher Zn and lower P in spawning individuals. Predicted effects of otolith concentrations of elements expected to be predominantly under environmental control showed the predicted geographic and depth-related trends based on ambient salinity (Ba) and coastal hypoxia (Mn). However, contrary to expectation, Sr was unrelated to salinity. Predicted otolith Ba, Sr and Mn concentrations also exhibited pronounced seasonal patterns that were out of phase with each other but appeared to be partly explained by spawning/feeding migrations. While performing laboratory validation studies for adult fish is typically not possible, these results highlight the importance of assessing local water chemistry and freshwater endmembers in one’s study system before otolith elemental chemistry can be reliably used to reconstruct fish habitat use and environmental histories. 

Otolith chemistry has gained increasing attention as a tool for analyzing various aspects of fish biology, such as stock dynamics, migration patterns, hypoxia and pollution exposure, and connectivity between habitats. While these studies often assume otolith elemental concentrations reflect environmental conditions, physiological processes are increasingly recognized as a modulating and/or controlling factor. In particular, biomineralization—the complex, enzyme-regulated construction of CaCO3 crystals scaffolded by proteins—is believed to play a critical role in governing otolith chemical patterns. This review aims to summarize the knowledge on otolith composition and biophysical drivers of biomineralization, present hypotheses on how biomineralization should affect element incorporation, and test the validity thereof with selected case studies. Tracers of environmental history are assumed to be dominated by elements that substitute for Ca during crystal growth or that occur randomly trapped within the crystal lattice. Strontium (Sr) and barium (Ba) largely comply with the biomineralization-based hypotheses that otolith element patterns reflect environmental concentrations, without additional effects of salinity, but can be influenced by physiological processes, typically exhibiting decreasing incorporation with increasing growth. Conversely, tracers of physiology are assumed to be elements under physiological control and primarily occur protein-bound in the otolith’s organic matrix. Physiological tracers are hypothesized to reflect feeding rate and/or growth, decrease with fish age, and exhibit minimal influence of environmental concentration. The candidate elements phosphorus (P), copper (Cu) and zinc (Zn) confirm these hypotheses. Magnesium (Mg) is believed to be randomly trapped in the crystal structure and hence a candidate for environmental reconstruction, but the response to all examined drivers suggest Mg to be coupled to growth. Manganese (Mn) substitutes for Ca, but is also a co-factor in matrix proteins, and therefore exhibits otolith patterns reflecting both environmental (concentration and salinity) and physiological (ontogeny and growth) histories. A consistent temperature response was not evident across studies for either environmental or physiological tracers, presumably attributable to variable relationships between temperature and fish behavior and physiology (e.g., feeding rate, reproduction). Biomineralization thus has a controlling effect on otolith element concentrations for elements that are linked with somatic growth, but not for elements that substitute for Ca in the crystal lattice. Interpretation of the ecological significance of patterns from field samples therefore needs to consider the impact of the underlying biomineralization processes of the element in question as well as physiological processes regulating the availability of ions for inclusion in the growing crystal lattice. Such understanding will enhance the utility of this technique to address fisheries management questions. 

Abstract Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring. Graphical abstract