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Background  Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh ( Ammodramus caudacutus ) and Nelson’s ( A. nelsoni ) sparrows ( n  = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits.    Results  Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward  A. caudacutus , which may be driven by differences in mating strategy or differences in population density between the two species.    Conclusions  Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.

Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone