Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent's most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range‐wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt‐marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced‐representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range‐wide persistence of similarly highly variable species.

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We describe hook trauma to the roof of the mouth in Dolphinfish Coryphaena hippurus and compare computed tomography (CT) scanning to gross necropsy (GN) as a technique for diagnosing hooking injury in fish. Forty‐two Dolphinfish carcasses spanning a range of hook injuries were collected and CT scanned, and 33 of those carcasses were evaluated using GN. Specimens were hooked either in the roof of the mouth, the eye via the roof or upper jaw, or the jaw (control group). In 75% of roof‐hooked individuals, GN revealed nondisplaced to comminuted fractures of the bones of the suspensorium, hematomas in and laceration of the extraocular muscles, and/or damage to the optic nerve. These injuries have the potential to compromise vision and therefore decrease postrelease survival rates of obligate sight‐feeding species such as the Dolphinfish. We evaluated the effectiveness of CT scanning to diagnose injury and found that CT could efficiently and accurately identify fractures and some soft‐tissue damage, but some injuries found in GN (e.g., optic nerve damage) were not observed on CT scans. Based on our findings, it is likely that mortality is greater in Dolphinfish when hooked in the roof of the mouth than when hooked in the jaw. This study demonstrates a novel technique that was effective at diagnosing hooking injuries associated with the roof of the mouth.