Reproductive isolation and differential introgression shape the genomic landscape of the red alga Amansia glomerata in the Hawaiian Archipelago.

Reproductive isolation; Genomic divergence; Introgression; Seaweed, Hawai'i. Speciation in marine environments is inherently complex, and the mechanisms underlying the evolution of reproductive isolation remain a fundamental yet understudied challenge in macroalgae. This study investigates two lineages of the marine red alga Amansia glomerata around O'ahu, Hawai'i, to test the hypothesis that lineage boundaries are maintained by strong reproductive barriers. Using genomic sequencing (ddRAD), fine-scale spatial transects, and demographic modeling, we characterized lineage spatial structure and genomic divergence. Our results revealed that lineages form extensive sympatric populations and remain strongly differentiated across the genome, even when co-occurring at fine spatial scales. Demographic analyses supported a scenario of allopatric divergence followed by secondary contact, likely driven by Pleistocene sea-level fluctuations within the Hawaiian Archipelago. The absence of backcrosses and second-generation hybrids, combined with numerous loci acting as barriers to gene flow, is consistent with a lack of contemporary admixture. Nevertheless, genomic footprints of introgression were detected, and their spatial configuration around O'ahu may indicate past, geographically restricted episodes of asymmetric gene flow during secondary contact. While our findings highlight allopatric divergence as a major driver of speciation in this system, the potential role of ecological differentiation remains to be explored. Overall, this study offers additional genomic perspectives on algal speciation and underscores the potential of Hawaiian seaweeds to yield new insights into this process.