Like many native endemic desert freshwater fish species, the June Sucker (Chasmistes liorus) is currently listed as endangered. Managers have increasingly turned to habitat restoration as a key component to recovery plans. For endangered species, one of the primary outcomes of habitat restoration is that it should result in successful reproduction and recruitment of individuals into the adult population. Confirmation of natural recruitment as a function of habitat restoration can only be achieved by establishing natal origins. Recent research has proven the validity of otolith microchemistry, a technique that analyzes small quantities of elements, to trace potamodromous fish to their natal tributaries. Previous studies have documented that localized habitats in terms of microchemistry are reflected in otolith composition, thereby potentially making this a valuable way of determining fish origins. The primary goal of this study is to use otolith microchemistry to establish natal origins of June Sucker, ultimately in order to evaluate whether tributary habitat restoration results in natural recruitment. To accomplish this I first determined if the water chemistry among the three main spawning tributaries differed from one another. Second, I determined if the otolith chemistry reflected the otolith chemistry. Lastly, I developed a statistical model capable of classifying fish to their respective tributary based the element:calcium ratios in the otolith microchemistry. Water chemistry differed significantly among all three spawning tributaries, and I observed a strong and significant relationship between otolith chemistry and water chemistry. The classification models based on otolith element:Ca signatures were capable of accurately classifying individual fish to their natal tributary (classification tree 89% accuracy; random forest model 91% accuracy), increasing the ability to determine if the fish’s origin is wild vs. hatchery. The data obtained from this study will advance the current understanding of the June sucker recruitment dynamics and result in a fundamental improvement in our ability to determine where natural recruitment into the adult spawning population is occurring. In addition, this knowledge may help evaluate factors limiting recruitment in Utah Lake tributaries, identify future restoration localities, and assist effectiveness monitoring of spawning habitat restoration efforts.

Le saumon Atlantique fait partie du patrimoine écologique et économique du bassin de l’Adour. Dans le cadre de la gestion actuelle du saumon dans ce bassin, l’origine natale des géniteurs, le taux de retour des individus d’origine piscicole, le taux de homing sur chaque sous-bassin ou encore le soutient par des géniteurs extérieurs au bassin de l’Adour sont des thématiques qui restent sans réponses. Ce projet propose donc de tester le potentiel de la géochimie des otolithes sur le saumon Atlantique du bassin de l’Adour. Nos travaux démontrent que la variation géographique de la composition chimique de l’eau dans 12 rivières colonisées par le saumon, associée à un enregistrement dans l’otolithe proportionnel à la signature géochimique du milieu de vie, permettent de discriminer l’origine géographique des individus. La combinaison des signatures élémentaires (Sr:Ca et Ba:Ca) et surtout l’isotopie du Sr (temporellement plus stable et sans fractionnement biologique) dans les otolithes améliore la précision du classement à l’échelle de la rivière de développement. En se basant sur la transmission de signatures géochimiques (élémentaires et isotopiques) transgénérationelles entre la femelle reproductrice et les otolithes des embryons produits par cette dernière, nous avons discriminé avec succès les individus nés en rivière de ceux nés en pisciculture. Le classement des géniteurs (180 individus) selon leur rivière natale a confirmé que le sous bassin du gave d’Oloron, et plus particulièrement le gave d’Ossau, reste le lieu qui produit le plus de saumon de retour. De façon non négligeable, le gave de Pau contribue lui aussi au renouvellement de la population (10 d’origine piscicole et 6 d’origine naturelle). 18 saumons sur 180 sont issus de l’alevinage (soit 10%); la majorité s’étant développée dans le sous-bassin du gave de Pau. Par ailleurs, nous avons mis à jour l’existence de périodes au cours de la vie des juvéniles (changements de milieu: sac vitellin—milieu extérieur et pisciculture—rivière) durant lesquelles l’enregistrement du Ba dans l’otolithe n’est pas en relation avec la chimie de l’eau. L’originalité de notre approche est d’avoir étudié l’influence des facteurs endogènes et environnementaux chez des poissons ayant vécu dans le milieu naturel ou ayant séjourné en milieu naturel contrôlé. Nos travaux mettent l’accent sur la complexité de l’intégration du rapport Ba:Ca dans l’otolithe et démontrent l’utilité des éléments traces et des isotopes du Sr comme « tag naturel » pour distinguer l’origine natale du saumon Atlantique. / The Adour basin holds one of the largest populations of Atlantic salmon in southern Europe exploited by commercial and sport fisheries. Determining the relative contributions of individual rivers and hatcheries to the Adour basin populations becomes crucial to understand key sources that contribute the most to its persistence. We successfully used Sr:Ca, Ba:Ca and 87Sr:86Sr ratios as natural tags for determining the natal origins of adults from 12 tributaries. Success in discriminating between fish from different sites was greatest using Sr isotopes since the latter remained relatively constant across years at a given location. Geochemical signatures from core regions of the otolith were also used to identify fish from hatchery or naturally spawned sources. The predominance of adults spawned in the Ossau River among returning adults corresponded with long-term juvenile production trends in the Ossau River. Despite the limited upstream accessibility of the Pau River, our study demonstrated that Atlantic salmon recruits can successfully leave this river to join the adult population in the Adour basin. We observed relatively clear separation between hatchery and wild juveniles using both Sr:Cacore (wild > 2.5 and hatchery < 0.80) and 87Sr:86Srcore (wild < 0.710 and hatchery > 0.710). The return of hatchery reared fish as adult spawners represented 10% of the total sampled fish we analyzed. Almost all adults, previously identified as belonging to the Ouzom River, were hatchery produced. Adults originated from the Pau River were either wild or hatchery reared fish. We also conducted field controlled experiments that characterized the elemental uptake process in juvenile Atlantic salmon otoliths during freshwater residency. Physiological effects influenced Ba deposition. Ba:Ca otolith profiles from hatchery-reared and field collected fish were characterised by a peak at yolk absorption mark. Hatchery-reared fish stocked in a river also displayed a peak of Ba:Ca following transfer which was not related to the water chemistry. Our experiment revealed a 20-day lag time between initial Ba:Cawater changes and Ba:Caotolith saturation. Results suggested that such effects should be considered during any attempts to determine rivers of origin of Atlantic salmon based on otolith elemental composition or reconstruct the movement of individual fish among and within streams.