Conspecifics inhabiting divergent environments frequently differ in morphology, physiology and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate and swimming performance in three-spined sticklebacks (Gasterosteus aculeatus L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the ‘typical’ low-plated morph, and a unique ‘small-plated’ morph. We test the hypothesis that similar to plate loss in other freshwater populations, reduction in lateral plate size also evolved in response to selection. Additionally, we test how morphology, physiology, and performance have evolved in concert as a response to differences in selection between marine and freshwater environments. We raised pure-bred second generation fish originating from three populations and quantified their lateral plate coverage, burst- and critical swimming speeds, as well as standard and active metabolic rates. Using a multivariate QST-FST framework, we detected signals of directional selection on metabolic physiology and lateral plate coverage, notably demonstrating that selection is responsible for the reduction of lateral plate coverage in a small-plated stickleback population. We also uncovered signals of multivariate selection amongst all bivariate trait combinations except the two metrics of swimming performance. Divergence between the freshwater and marine populations exceeded neutral expectation in morphology and in most physiological and performance traits, indicating that adaptation to freshwater habitats has occurred, but through different combinations of traits in different populations. These results highlight both the complex interplay between morphology, physiology and performance in local adaptation, and a framework for their investigation.

Adaptation to novel environments can be based either on standing genetic variation or variation attributable to new mutations. When standing genetic variation for a functional adaptation is lacking, and variation due to new mutations is not yet available, adaptation is possible only through alternative functional solutions. Reduction in the number of bony lateral plates as an adaptation to freshwater colonization by marine threespine sticklebacks (Gasterosteus aculeatus) has occurred in numerous independent cases through allelic substitution in the ectodysplasin-a (Eda) gene. Studying the phenotypic and genetic variation in plate number and size in five marine and six freshwater threespine stickleback populations, we found that when variation in Eda was limiting (i.e. alleles associated with the low-plate morph were missing or in extremely low frequency), plate number reduction did not take place in freshwater populations, but reduced lateral plate coverage was achieved by a reduction in the size of lateral plates. Our results suggest that this phenotypically and genetically discrete “small-plated” threespine stickleback – which is the dominant form in three northern European freshwater populations – may be functionally equivalent to the low-plated morph and hence, serve as an example of convergent evolution towards functional similarity in the face of genetic constraints.