Luna-Ortiz, A.; Barbanti, A.; Pegueroles, C.; Abreu-Grobois, F. A.; Casale, P.; Freggi, D.; Giralt, S.; Labastida-Estrada, E.; Llera-Herrera, R.; Machkour-M'Rabet, S.; Marco, A.; Margaritoulis, D.; Turkozan, O.; Pascual Berniola, M.; Carreras, C.

1. Effective conservation of highly migratory species requires understanding genetic structure across breeding populations and access high-resolution markers capable of assigning individuals from mixed aggregates (e.g. bycatch or new nesting sites) to their natal origins. Genomic approaches provide unprecedented resolution but add methodological challenges; thus, it is essential to first build a genomic baseline from known breeding areas and then evaluate strategies for assigning unknown individuals. 2. To address this, we used 2b-RAD sequencing, a genomic reduction technique useful for degraded DNA, and loggerhead turtles as a case study. This species shows philopatric breeding, while juveniles and adults form mixed aggregations in foraging grounds. 3. Our results highlight the importance of building baselines that include all potential source populations contributing to mixed aggregations. We detected hierarchical genetic differentiation and high resolution and successfully assigned the natal origin of 124 unknown individuals from four Mediterranean foraging grounds. These grounds showed distinct source contributions, and comparisons with previous studies suggest possible temporal shifts in stock composition. 4. We provide a comprehensive genomic baseline for individual assignment of Altanto-Mediterranean loggerhead turtles of unknown natal origin and a general framework for identifying population-specific threats in highly migratory species.