Morphology-based taxonomic research frequently applies linear morphometrics (LMM) in skulls to quantify species distinctions. The choice of which measurements to collect generally relies on the expertise of the investigators or a set of standard measurements, but this practice may ignore less obvious or common discriminatory characters. In addition, taxonomic analyses often ignore the potential for subgroups of an otherwise cohesive population to differ in shape purely due to size differences (or allometry). Geometric morphometrics (GMM) is more complicated as an acquisition technique, but can offer a more holistic characterization of shape and provides a rigorous toolkit for accounting for allometry. In this study, we used linear discriminant analysis to assess the discriminatory performance of four published LMM protocols and a 3D GMM dataset for three clades of antechinus known to differ subtly in shape. We assessed discrimination of raw data (which are frequently used by taxonomists); data with isometry removed; and data after allometric correction. We found that group discrimination among raw data was high for LMM, possibly inflated relative to GMM when visualised in PCA plots. However, GMM produced better results in group discrimination after the size and allometry treatments. High measurement redundancy in LMM protocols appears to result in relatively high allometry but low discriminatory performance. These findings suggest that taxonomic measurement protocols might benefit from GMM-based pilot studies, because this offers the option of differentiating allometric and non-allometric shape differences between species, which can then inform on the development of the easier-to-apply LMM protocols.

The biogeographical distribution of diversity among populations of threatened mammalian species is generally investigated through population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences – geometric morphometrics – to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along the northern Australian coast. Skull shape is a proxy of feeding, behaviour, and phenotypic differentiation, allowing us to ask if populations can be distinguished and if patterns of variation indicate adaptability to changing environmental conditions. We analysed skull shape in 101 individuals across the four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and latitude/longitude to skull shape variation through Principal Components, Procrustes ANOVA, and variation partitioning analyses. Regardless of land area inhabited, northern quoll populations harbour similar amounts of broadly overlapping skull shape variation. Size predicted skull shape best, coinciding with braincase size variation and differences in the cheekbone shape. Size-adjusted population differences explained less variation with far smaller effect sizes, relating to changes in insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little or nothing. Strikingly, the vast majority of shape variation - 76% - remained unexplained. Our results suggest a uniform within-species scope for shape variation, possibly due to phenotypic plasticity or allometric constraints. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g. specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetics-based conservation studies.