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Abstract AimAs within‐species genomic data have been shown useful in interpreting broader biogeographic trends, we analysed the mode of population genomic isolation involved in a well‐studied intertidal genomic cline to better understand the mechanisms maintaining it. These results were interpreted in the context of spatial variation in habitat use and availability as well as likely fitness consequences for hybridization between the two lineages. LocationPacific coast of North America. TaxonArthropods (Class Maxillopoda, Order Sessilia, Family Balanidae;Balanus glandula). MethodsGenotype‐by‐sequencing approaches were used to generate single‐nucleotide polymorphism markers across sites sampled between southern Alaska and Southern California. Inference using standard population genomic methods, including analysis of population structure, inbreeding and linkage disequilibrium, was used to identify the steepest transitions across the largest number of loci examined. These data were put in the context of observed population density and habitat availability. ResultsWe show that the majority of markers analysed show strong clinal transitions in a very narrow portion of the California coast. Patterns of linkage disequilibrium among markers, along with prior evidence of variation in reproductive potential by latitude and by mitochondrial lineage, suggest some reproductive isolation among the northern and southern lineages ofB. glandulathat are concordant with the drop in population density and habitat availability in central California. Main ConclusionsA significant clinal transition in genomic diversity is stronger and more localized than previously recognized and exhibits statistical patterns suggesting that the lineages are reproductively and phenotypically distinct in ways that may be ecologically important. As this species has been used to infer process in coastal biogeography, further study of concordant patterns will be important for advancing our understanding of this region. 

Abstract Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species,Asterias rubensandA. forbesi, distributed along rocky European and North American coastlines of the North Atlantic, and use genome‐wide molecular markers to infer the distribution of genomic variation within and between species in this group. Using genomic data and environmental niche modelling, we document hybridization occurring between northern New England and the southern Canadian Maritimes. We investigate the factors that maintain this hybrid zone, as well as the environmental variables that putatively drive selection within and between species. We find that the two species differ in their environmental niche breadth;Asterias forbesidisplays a relatively narrow environmental niche while conversely,A. rubenshas a wider niche breadth. Species distribution models accurately predict hybrids to occur within environmental niche overlap, thereby suggesting environmental selection plays an important role in the maintenance of the hybrid zone. Our results imply that the distribution of genomic variation in North Atlantic sea stars is influenced by the environment, which will be crucial to consider as the climate changes.