Conservation and management implications of genetic and geometric scale variation in the ancient fish giant featherback ( Chitala lopis )

Giant featherback ( Chitala lopis ) is an ancient species of freshwater fish considered globally extinct until extant populations were re‐discovered in the Sundaland region of Indonesia in 2022. To improve management of the remaining populations, this study used genomic DNA and landmark‐based geometric morphometric analyses of fish scales to evaluate whether these approaches can discriminate among phylogenetic clades, sexes and broad habitat ecotypes inhabited by extant C. lopis populations. DNA analyses of 39 specimens from eight rivers provided the first evidence of two phylogenetic clades: (i) those from Central and South Borneo and (ii) those from West Borneo, Riau, South Sumatra and Jambi. Scale morphology was characterised across eight body areas using scale dimensions (relative height and width to standard length and height‐to‐width ratio), centroid size and Procrustes shape coordinates, with repeated‐measures structure accounted for using linear mixed models and Procrustes ANOVA with a randomised residual permutation procedure (RRPP). Scale dimensions and centroid size varied significantly among body areas (all p < 0.001), with lateral and dorsal regions bearing the largest scales and the pectoral region the smallest. Clade membership had a small but significant effect on relative scale height (H/SL; β = −0.44, p = 0.024), with Clade 2 individuals consistently showing lower values than Clade 1, though scale geometry overall showed limited promise as a rapid non‐destructive stock discriminator. Both clade and sex had small but significant effects on Procrustes scale shape ( R 2 = 0.015 and 0.013, respectively; both p = 0.001), while phenotypic trajectory analysis revealed that males exhibited a significantly greater amplitude of scale shape change across body positions than females (trajectory magnitude: M = 0.289, F = 0.207; p = 0.034), despite both sexes following parallel shape trajectories along the body axis. These results provide a novel morphometric baseline for C. lopis and highlight the importance of body‐position‐specific and multivariate approaches when characterising scale morphology in endangered freshwater fishes.