Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Mollusk shells protect the animals that form and inhabit them. They are composites of minerals and organics, with diverse mesostructures, including nacre, prismatic calcite, crossed‐lamellar aragonite, and foliated calcite. Twins, that is, crystals mirror symmetric with respect to their coherent interface, occurring as formation or deformation twins, are observed in all mollusk shell mesostructures but never within calcite prisms. Here, nanotwins and microwins within single calcite prisms are observed in different shells. Using Polarization‐dependent Imaging Contrast (PIC) mapping with 20–60 nm resolution, twins are observed to be 0.2–3 µm thick layers of differently oriented and colored crystals with respect to the main prism crystal. Multiple twins are interspersed with the prism crystal, parallel to one another, and similarly oriented. When comparing images of calcite prisms and twins obtained by PIC mapping and by Electron Back‐Scattered Diffraction (EBSD), the images correspond precisely. All twins are e‐twin types, with 127° angular distance between c‐axes. E‐twins are the most common deformation twins in geologic calcite, as also observed here in Carrara marble. Location of all twins near the outer surface of all shells and e‐twin type both suggest that twins within calcite prisms in mollusk shells result from deformation twinning.