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Summary Do morphogenetic processes cause common patterns of phenotypic covariation, and do those patterns evolve over microevolutionary timescales? Evolution of molar shape variance–covariance (P) matrixes was studied in five populations of the common shrew, Sorex araneus. P matrix evolution was assessed using matrix correlation, matrix disparity, and common principal component analysis (CPCA). Significant changes in covariance structure were found among the populations, but the differences were small. A computer model was used to estimate the theoretical covariance introduced into the phenotype by developmental interactions. Molar developmental processes explained some of the covariance in the shrew samples, especially as measured by matrix correlation, but the proportion was relatively small. Developmental principal components (PCs) were only infrequently associable with common principal components. The results suggest that molar shape P matrixes can evolve quickly in a manner only loosely constrained by development, and that their shared covariance is probably dominated by factors more proximate than development. Rarefaction showed that sample size severely affected P comparisons when n < 15 for matrix correlation and disparity, and when n < 30 for CPCA. Among CPCA evaluation criteria, Akaike Information Criterion performed better than jump-up at n < 30, but worse at n > 30.