Linking otolith microchemistry and dendritic isoscapes to map heterogeneous production of fish across river basins

Integrating machine learning with otolith isoscapes: Reconstructing connectivity of a marine fish over four decades

Stable isotopes are an important tool to uncover animal migration. Geographic natal assignments often require categorizing the spatial domain through a nominal approach, which can introduce bias given the continuous nature of these tracers. Stable isotopes predicted over a spatial gradient (i.e., isoscapes) allow a probabilistic and continuous assignment of origin across space, although applications to marine organisms remain limited. We present a new framework that integrates nominal and continuous assignment approaches by (1) developing a machine-learning multi-model ensemble classifier using Bayesian model averaging (nominal); and (2) integrating nominal predictions with continuous isoscapes to estimate the probability of origin across the spatial domain (continuous). We applied this integrated framework to predict the geographic origin of the Northwest Atlantic mackerel (Scomber scombrus), a migratory pelagic fish comprised of northern and southern components that have distinct spawning sites off Canada (northern contingent) and the US (southern contingent), and seasonally overlap in the US fished regions. The nominal approach based on otolith carbon and oxygen stable isotopes (δ13C/δ18O) yielded high contingent classification accuracy (84.9%). Contingent assignment of unknown-origin samples revealed prevalent, yet highly varied contingent mixing levels (12.5-83.7%) within the US waters over four decades (1975-2019). Nominal predictions were integrated into mackerel-specific otolith oxygen isoscapes developed independently for Canadian and US waters. The combined approach identified geographic nursery hotspots in known spawning sites, but also detected geographic shifts over multi-decadal time scales. This framework can be applied to other marine species to understand migration and connectivity at a high spatial resolution, relevant to management of unit stocks in fisheries and other conservation assessments.

Silver Linings at the Dawn of a “Golden Age”

Nearly four decades after the first applications of strontium isotope analyses in archaeology and paleoecology research, it could be said that we are entering a “Golden Age”. Here, we reflect on major past developments and current strengths in strontium isotope research, as well as speculate on future directions. We review (1) the currently limited number of (but much needed) controlled feeding experiments, (2) recent advances in isoscape mapping and spatial assignment, and (3) the strength of multi-proxy approaches (including both the integration of strontium isotopes with other isotope systems and complementary techniques such as ancient DNA analyses). We also explore the integration of strontium isotope research with other types of paleoecological or archaeology data, as well as with evidence and interpretative frameworks from other fields (such as conservation ecology, conservation paleobiology or history). This blending is critical as we seek to advance the field beyond simply distinguishing local or relatively sedentary individuals from those that were non-local or highly mobile. We finish with a call for future research centered on balancing methodological developments and novel applications with critical self-reflection, deeper theoretical considerations and cross-disciplinarity.

Shifting habitat mosaics and fish production across river basins

Watersheds are complex mosaics of habitats whose conditions vary across space and time as landscape features filter overriding climate forcing, yet the extent to which the reliability of ecosystem services depends on these dynamics remains unknown. We quantified how shifting habitat mosaics are expressed across a range of spatial scales within a large, free-flowing river, and how they stabilize the production of Pacific salmon that support valuable fisheries. The strontium isotope records of ear stones (otoliths) show that the relative productivity of locations across the river network, as both natal- and juvenile-rearing habitat, varies widely among years and that this variability is expressed across a broad range of spatial scales, ultimately stabilizing the interannual production of fish at the scale of the entire basin.

Complex life histories discovered in a critically endangered fish

Effective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California’s endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized “hot-spots” of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.

A bioavailable strontium isoscape for Western Europe: A machine learning approach

Strontium isotope ratios (⁸⁷Sr/⁸⁶Sr) are gaining considerable interest as a geolocation tool and are now widely applied in archaeology, ecology, and forensic research. However, their application for provenance requires the development of baseline models predicting surficial ⁸⁷Sr/⁸⁶Sr variations (“isoscapes”). A variety of empirically-based and process-based models have been proposed to build terrestrial ⁸⁷Sr/⁸⁶Sr isoscapes but, in their current forms, those models are not mature enough to be integrated with continuous-probability surface models used in geographic assignment. In this study, we aim to overcome those limitations and to predict ⁸⁷Sr/⁸⁶Sr variations across Western Europe by combining process-based models and a series of remote-sensing geospatial products into a regression framework. We find that random forest regression significantly outperforms other commonly used regression and interpolation methods, and efficiently predicts the multi-scale patterning of ⁸⁷Sr/⁸⁶Sr variations by accounting for geological, geomorphological and atmospheric controls. Random forest regression also provides an easily interpretable and flexible framework to integrate different types of environmental auxiliary variables required to model the multi-scale patterning of ⁸⁷Sr/⁸⁶Sr variability. The method is transferable to different scales and resolutions and can be applied to the large collection of geospatial data available at local and global levels. The isoscape generated in this study provides the most accurate ⁸⁷Sr/⁸⁶Sr predictions in bioavailable strontium for Western Europe (R² = 0.58 and RMSE = 0.0023) to date, as well as a conservative estimate of spatial uncertainty by applying quantile regression forest. We anticipate that the method presented in this study combined with the growing numbers of bioavailable ⁸⁷Sr/⁸⁶Sr data and satellite geospatial products will extend the applicability of the ⁸⁷Sr/⁸⁶Sr geo-profiling tool in provenance applications.