Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves

Despite the potential for long-distance gene flow in the sea, there is growing evidence of cryptic genetic diversity in many marine taxa. Understanding the geographic distribution of cryptic lineages, as well as the spatial patterns of admixture among them, can have important implications for conservation planning. Here, we explore patterns of divergence in a coral reef fish, the neon goby Elacatinus lori, across the species' range. First, we use targeted amplicon sequencing to describe the spatial pattern of genetic divergence using two marker types (57 anonymous ddRAD-derived loci and mtDNA cytb). Second, we quantify the degree of admixture and hybridization between two previously-unidentified divergent lineages within Belize. Third, we assess whether the existing group of marine protected areas (MPAs) in Belize protects this cryptic genetic diversity. The results provide strong evidence for two divergent genetic lineages of E. lori within Belize, separated geographically by only 30 km of low-suitability habitat. There is a sharp genetic cline across these 30 km, and evidence of admixture and introgression at the boundary regions of the habitat break. We also show that the broadly-distributed arrangement of MPAs within Belize protects both major lineages as well as subtle structure within-lineages, and therefore may confer protection to co-distributed species that exhibit similar spatial patterns of divergence.