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

Rationale: A liquid chromatography/tandem mass spectrometry (LC/MS/MS) method was validated and utilized to measure and analyze four steroid hormones related to stress and reproduction in individual samples from a novel tissue, Pacific walrus ( Odobenus rosmarus divergens , herein walrus) bone. This method determines steroid hormone concentrations in the remote walrus population over millennia from archaeological (>200 bp ), historical (200–20 bp ), and modern (2014–2016) time periods. Methods: Lipids were extracted from walrus bone collected from these periods using methanol before LC/MS/MS analysis. Isotopically labeled internal standards for each target hormone were added to every sample. Analytical and physiological validations were performed. Additionally, a tissue comparison was done among paired walrus bone, serum, and blubber samples. A rapid resolution liquid chromatography system coupled to a QqQ mass spectrometer was used to analyze all samples after derivatization for progesterone, testosterone, cortisol, and estradiol concentrations. Multiple reaction monitoring was used for MS analysis and data were acquired in positive electrospray ionization mode. Results: Progesterone, testosterone, cortisol, and estradiol were linear along their respective standard calibration curves based on their R ² values (all > 0.99). Accuracy ranged from 93–111% for all hormones. The recovery of extraction, recovery of hormones without matrix effect, was 92–101%. The overall process efficiency of our method for measuring hormones in walrus bone was 93–112%. Progesterone and testosterone concentrations were not affected by reproductive status among adult females and males, respectively. However, estradiol was different among pregnant and non‐pregnant adult females. Overall, steroid hormones reflect a long‐term reservoir in cortical bone. This method was also successfully applied to walrus bone as old as 3585 bp . Conclusions: LC/MS/MS analysis of bone tissue (0.2–0.3 g) provides stress and reproductive data from elusive walruses that were alive thousands of years ago. Based on physiological validations, tissue comparison, and published literature, steroid hormone concentrations measured in walrus cortical bone could represent an accumulated average around a 10–20‐year time span. By investigating how stress and reproductive physiology may have changed over the past ~3000 years based on bone steroid hormone concentrations, this method will help answer how physiologically resilient walruses are to climate change in the Arctic.

Over the last two decades, ocean warming and rapid loss of sea ice have dramatically changed the Pacific Arctic marine environment^1–3. These changes are predicted to increase harmful algal bloom prevalence and toxicity, as rising temperatures and larger open water areas are more favourable for growth of some toxic algal species⁴. It is well known that algal toxins are transferred through food webs during blooms and can have negative impacts on wildlife and human health^5–7. Yet, there are no long-term quantitative reports on algal toxin presence in Arctic food webs to evaluate increasing exposure risks. In the present study, algal toxins were quantified in bowel samples collected from 205 bowhead whales harvested for subsistence purposes over 19 years. These filter-feeding whales served as integrated food web samplers for algal toxin presence in the Beaufort Sea as it relates to changing environmental conditions over two decades. Algal toxin prevalences and concentrations were significantly correlated with ocean heat flux, open water area, wind velocity and atmospheric pressure. These results provide confirmative oceanic, atmospheric and biological evidence for increasing algal toxin concentrations in Arctic food webs due to warming ocean conditions. This approach elucidates breakthrough mechanistic connections between warming oceans and increasing algal toxin exposure risks to Arctic wildlife, which threatens food security for Native Alaskan communities that have been reliant on marine resources for subsistence for 5,000 years (ref. ⁸).

The Pacific walrus (Odobenus rosmarus divergens) is an iconic Arctic marine mammal and an important resource to many Alaska Natives. A decrease in sea ice habitat and unknown population numbers has led to concern of the long-term future health of the walrus population. There is currently no clear understanding of how walrus physiology might be affected by a changing Arctic ecosystem. In this study, steroid hormone concentrations (progesterone, testosterone, cortisol and estradiol) were analysed in walrus bones collected during archaeological [3585–200 calendar years before present (BP)], historical [1880–2006 common era (CE)] and modern (2014–2016 CE) time periods, representing ~ 3651 years, to track changes in reproductive activity and cortisol concentrations (biomarker of stress) over time. Our results show that modern walrus samples have similar cortisol concentrations (median = 43.97 ± standard deviation 904.38 ng/g lipid) to archaeological walruses (38.94 ± 296.17 ng/g lipid, P = 0.75). Cortisol concentrations were weakly correlated with a 15-year average September Chukchi Sea ice cover (P = 0.002, 0.02, r² = 0.09, 0.04, for females and males, respectively), indicating a possible physiological resiliency to sea ice recession in the Arctic. All steroid hormones had significant negative correlations with mean walrus population estimates from 1960 to 2016 (P < 0.001). Progesterone in females and testosterone in males exhibited significant correlations with average September Chukchi Sea ice cover for years 1880–2016 (P < 0.001 for both, r² = 0.34, 0.22, respectively). Modern walruses had significantly lower (P = < 0.001) reproductive hormone concentrations compared with historic walruses during times of rapid population increase, indicative of a population possibly at carrying capacity. This is the first study to apply bone as a tool to monitor long-term changes in hormones that may be associated with changes in walrus population size and sea ice cover.

Fisheries management relies on accurate population models for estimating biomass and setting harvest goals; however, physiological data for estimating reproductive parameters in population models are difficult to acquire. Here, lifetime reproductive (progesterone and estradiol) and stress-related (cortisol) hormones were measured in annually deposited growth increments in female yelloweye rockfish ( Sebastes ruberrimus) opercula ( N = 22 females, sampled ages 1–90 years). Analyses of these profiles (∼1-year resolution) provided estimates of physiological (complete puberty) and functional age of sexual maturity (females spawn and contribute larvae to the population) and spawning frequency, with lifetime trends of reproduction and stress. The descriptive mean age of physiological sexual maturity was 11 ± 1 years (standard error (SE)), whereas functional age of maturity was 17 ± 2 years. The estimate of marginal mean spawning frequency was 45.1% ± 5.1%. Stress data (∼15% of females experienced distress events) suggested that females were potentially resilient or not exposed to chronic stressors. Although preliminary, we provide a novel method to estimate age-specific reproductive parameters for proper age-based population modeling of a human-targeted teleost.