Human disturbances to ecosystems have created challenges to populations worldwide, forcing them to respond phenotypically in ways that increase their fitness under current conditions. One approach to examining population responses to disturbance in species with complex life histories is to study species that exhibit spatial patterns in their phenotypic response across populations or demes. In this study, we investigate a threatened population of fall chinook salmon (Oncorhynchus tshawytscha) in the Snake River of Idaho, in which a significant fraction of the juvenile population have been shown to exhibit a yearling out-migration strategy which had not previously been thought to exist. It has been suggested that dam-related environmental changes may have altered the selective pressures experienced by out-migrating fall chinook, driving evolution of a later and more selectively advantageous migration strategy. Using isotopic analysis of otoliths from returning adult spawners, we reconstructed the locations of individual fish at three major juvenile life stages to determine if the representation of the yearling life history was geographically structured within the population. We reconstructed juvenile locations for natal, rearing and overwintering life stages in each of the major spawning areas in the basin. Our results indicate that the yearling life-history strategy is predominantly represented within one of the main spawning regions, the Clearwater River, rather than being distributed throughout the basin. Previous studies have shown the Clearwater River to have cooler temperatures, later hatch dates, and later outmigration of juveniles, indicating a link between environment and expression of the yearling life history. Our data suggest that this new yearling life history may be disproportionally represented in returning adult spawners, indicating selection for this life history within the population.

Animal migrations provide important ecological functions and can allow for increased biodiversity through habitat and niche diversification. However, aquatic migrations in general, and those of the world’s largest fish in particular, are imperiled worldwide and are often poorly understood. Several species of large Amazonian catfish carry out some of the longest freshwater fish migrations in the world, travelling from the Amazon River estuary to the Andes foothills. These species are important apex predators in the main stem rivers of the Amazon Basin and make up the region’s largest fishery. They are also the only species to utilize the entire Amazon Basin to complete their life cycle. Studies indicate both that the fisheries may be declining due to overfishing, and that the proposed and completed dams in their upstream range threaten spawning migrations. Despite this, surprisingly little is known about the details of these species’ migrations, or their life history. Otolith microchemistry has been an effective method for quantifying and reconstructing fish migrations worldwide across multiple spatial scales and may provide a powerful tool to understand the movements of Amazonian migratory catfish. Our objective was to describe the migratory behaviors of the three most populous and commercially important migratory catfish species, Dourada (Brachyplatystoma rousseauxii), Piramutaba (Brachyplatystoma vaillantii), and Piraíba (Brachyplatystoma filamentosum). We collected fish from the mouth of the Amazon River and the Central Amazon and used strontium isotope signatures (87Sr/86Sr) recorded in their otoliths to determine the location of early rearing and subsequent. Fish location was determined through discriminant function classification, using water chemistry data from the literature as a training set. Where water chemistry data was unavailable, we successfully in predicted 87Sr/86Sr isotope values using a regression-based approach that related the geology of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region.

Connecting maternal migratory behavior with the behavior and ecology of their progeny can reveal important details in the ecology of a population. One method for linking maternal migration to early juvenile life history is through maternal chemistry recorded in otoliths. Despite the wide use of maternal signatures to infer anadromy, the duration and dynamics of maternal otolith signatures are not well understood. Shifts in the elemental ratios and strontium isotope (87Sr/86Sr) chemistry in otoliths from juvenile Chinook salmon (Oncorhynchus tshawytscha) correlate with the timing of hatch and emergence, respectively, indicating a chemical marker of these ontological stages. Additionally, analysis of maternal signatures show that maternally derived 87Sr/86Sr may be influenced by equilibration of the mother to fresh water, and in some cases the 87Sr/86Sr signatures of the eggs can shift substantially after being laid. These results provide guidance in separating maternal and juvenile signatures as researchers increasingly target early juvenile otolith chemistry. These results also caution against the use of 87Sr/86Sr alone as a marker of anadromy in populations with major inland migrations.

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The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/018671 doi: bioRxiv preprint first posted online May. 7, 2015; in the main stem rivers of the Amazon Basin and make up the regions largest fishery.

Chronological data from hard structures has been instrumental in reconstructing information about the past across numerous disciplines. Isotopic and trace elemental chronologies from the depositional layers of speleothems, corals, bivalve shells, fish otoliths and other structures are routinely used to reconstruct climate, growth, temperature, geological, archeological and migratory histories. Advances in instrumentation have revolutionized the use of these structures and publications detailing new chemical and isotopic methods in sclerochronology and speleothem chronology have steadily increased in number. This is particularly true of fish, in which detailed origin, life-history, and migration history can be reconstructed from their otoliths. Specifically, improvements in laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have allowed increases temporal resolution, precision, and sample throughput. Many studies now combine multiple chemical and isotopic tracers, taking advantage of multivariate statistical methods and multiple tracep-element and isotope systems to glean further information from individual samples. This paper describes a novel laser ablation split-stream (LASS) method which allows simultaneous collection of 87 Sr/ 86 Sr and traceelemental data from chronological carbonate samples. The study tests the accuracy and precision of multiple laser spot sizes on a marine shell standard and fish otoliths using LASS and traditional single stream methods and compared to prior otolith data on the same samples. Our results indicate that LASS techniques can be used to provide accurate and precise data at useful laser spot sizes for otolith studies, while providing time and integration-matched data reduction using newly developed features for the Iolite data reduction platform.

The migration of Pacific salmon is an important part of functioning freshwater ecosystems, but as populations have decreased and ecological conditions have changed, so have migration patterns. Understanding how the environment, and human impacts, change salmon migration behavior requires observing migration at small temporal and spatial scales across large geographic areas. Studying these detailed fish movements is particularly important for one threatened population of Chinook salmon in the Snake River of Idaho whose juvenile behavior may be rapidly evolving in response to dams and anthropogenic impacts. However, exploring movement data sets of large numbers of salmon can present challenges due to the difficulty of visualizing the multivariate, time-series datasets. Previous research indicates that sonification, representing data using sound, has the potential to enhance exploration of multivariate, time-series datasets. We developed sonifications of individual fish movements using a large dataset of salmon otolith microchemistry from Snake River Fall Chinook salmon. Otoliths, a balance and hearing organ in fish, provide a detailed chemical record of fish movements recorded in the tree-like rings they deposit each day the fish is alive. This data represents a scalable, multivariate dataset of salmon movement ideal for sonification. We tested independent listener responses to validate the effectiveness of the sonification tool and mapping methods. The sonifications were presented in a survey to untrained listeners to identify salmon movements with increasingly more fish, with and without visualizations. Our results showed that untrained listeners were most sensitive to transitions mapped to pitch and timbre. Accuracy results were non-intuitive; in aggregate, respondents clearly identified important transitions, but individual accuracy was low. This aggregate effect has potential implications for the use of sonification in the context of crowd-sourced data exploration. The addition of more fish, and visuals, to the sonification increased response time in identifying transitions.

An animal's performance during its early life stage can greatly influence its survival to adulthood. Therefore, understanding aspects of early life history can be informative, particularly when designing management plans to rebuild a population. For a threatened population of fall Chinook salmon (Oncorhynchus tshawytscha) in the Snake River of Idaho, we reconstructed the early life history for 124 returning wild and hatchery adults using information recorded in their otoliths. Of our sampled wild adults (n = 61), 43% and 49% reared within the Snake River and Clearwater/Salmon rivers. We also found that only 21% of our sampled wild adults exhibited the historically common subyearling out‐migration strategy, in which juveniles exit freshwater shortly after hatching, while the remaining wild adults exhibited the yearling out‐migration strategy (i.e., individuals delay their freshwater exit). As expected, yearlings had, on average, a significantly larger body size than subyearlings at ocean entry. However, 35% of wild yearlings overlapped in size with wild subyearlings suggesting that spending more time in freshwater might not necessarily result in a larger body size. Lastly, we observed that variability in fork length at Snake River egress and ocean entry were best explained by migration strategy and where it reared, followed by hatch year and sex. Results from this study highlight the utility of adult otoliths in providing details about early life history, an understanding of which is critical to the conservation of Snake River fall Chinook salmon.