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Connectivity and local adaptation are two contrasting evolutionary forces highly influencing population structure. To evaluate the impact of early-life traits and environmental conditions on genetic structuring and adaptation, we studied two sympatric fish species in the Western Mediterranean Sea:  Symphodus tinca  and  S. ocellatus . We followed an individual-based approach and measured early-life history traits from otolith readings, gathered information on environmental variables and obtained genome-wide markers from genotyping-by-sequencing (GBS). The two species presented contrasting population structure across the same geographic gradient, with high and significant population differentiation in  S. ocellatus , mostly determined by oceanographic fronts, and low differentiation and no front effect in  S. tinca . Despite their different levels of genetic differentiation, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. Most candidate loci were associated to temperature and productivity in  S. ocellatus  and to temperature and turbulence in  S. tinca  suggesting that different drivers may determine genomic diversity and differentiation in each species. Globally, our study highlights that individual-based approach combining genomic, environmental and phenotypic information is key to identify signals of selection and the processes mediating them.

Individual-based population genomics reveal different drivers of adaptation in sympatric fish