Phylogenetic and ecological duality in the otoliths of Sciaenidae

Teleost fishes have evolved taxon-specific otoliths that vary greatly in size and shape and are primarily involved in hearing and balance. This study identifies the main drivers of otolith shape disparity in Sciaenidae, a clade of sound-producing bony fishes, using three-dimensional geometric morphometrics (3DGM). We quantified variation in overall sagittal shape and sulcus configuration, performed cluster analysis, inferred 3D shape-based trees, assessed phylogenetic signal using COI-based molecular trees, and tested associations with ecological and biological factors. Overall sagittal shape formed nine morphogroups, mainly reflecting variation in longitudinal size and outer-face protuberances, features that are often missed in 2D analyses. Shape-based trees did not closely match COI-based tree. The entire sulcus shape formed four morphogroups based on ostium curvature and cauda elongation. Phylogenetic signal was low but significant for overall sagittal shape (λ = 0.0000026, P = 0.0061), but not significant for the entire sulcus (λ = 0.0000015, P = 0.328), suggesting that overall sagittal shape is likely more evolutionarily conserved. A weak but significant association between overall sagittal shape and swim bladder shape (R² = 0.123, P = 0.017) supports the hypothesis that enhanced hearing and acoustic sensitivity contribute to otolith shape diversification in sciaenids. Our results establish 3DGM as a significant advancement in otolith research, offering a robust approach for quantifying shape disparity and understanding the combined effects of phylogeny and ecology across multiple levels of otolith structure. This 3DGM framework can be applied beyond Sciaenidae to reconstruct macroevolutionary history and identify drivers of otolith diversification over geological timescales using fossil otoliths.