Demography and Connectivity Shape the Genetic Structure of a Brooding Coral Rather Than Local Adaptations Across Seascapes in the Gulf of California

Abstract

Disentangling the contributions of local adaptation and neutral geographic differentiation in shaping spatial genomic variation is central to understanding how populations evolve across heterogeneous environments. In the Gulf of California (GoC), the interaction between pronounced environmental gradients and complex oceanographic circulation creates a challenging scenario for determining whether adaptive divergence or neutral connectivity shapes the genetic structure of stony corals. We used a seascape genomics framework to examine these drivers in Porites panamensis , a brooding coral distributed throughout this semi‐enclosed basin. Using > 2000 SNPs, we genotyped 131 colonies from 19 sites across most of the species' range in the GoC spanning four different seascapes defined by multi‐year physicochemical satellite data. Population genomic analyses revealed four main genetic groups, with partial spatial concordance with the identified seascapes. Genetic connectivity was high along the Baja California peninsula but markedly reduced in Central mainland and peripheral populations. Crucially, partial redundancy analysis showed that neutral population structure accounted for 14.8% of total variance, whereas the pure environmental fraction was negligible. Thus, in P. panamensis , genetic structure across pronounced environmental gradients appears to be driven mainly by patterns of gene flow shaped by habitat availability and oceanographic circulation rather than by divergent selection among seascapes. These results suggest that for species with restricted dispersal, signals of local adaptation may be masked by strong demographic processes at broad spatial scales, highlighting the need to investigate micro‐geographic environmental heterogeneity to fully understand the adaptive potential of stony corals.

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