Evolution of adaptation requires both generation of novel phenotypic variation and retention of a locally beneficial subset of this variation. Such retention can be facilitated by genetic assimilation, the accumulation of genetic and molecular mechanisms that stabilize induced phenotypes and assume progressively greater control over their reliable production. A particularly strong inference into genetic assimilation as an evolutionary process requires a system where it is possible to directly evaluate the extent to which an induced phenotype is progressively incorporated into preexisting developmental pathways. Evolution of diet-dependent pigmentation in birds-where external carotenoids are coopted into internal metabolism to a variable degree before being integrated with a feather's developmental processes-provides such an opportunity. Here we combine a metabolic network view of carotenoid evolution with detailed empirical study of feather modifications to show that the effect of physical properties of carotenoids on feather structure depends on their metabolic modification, their environmental recurrence, and biochemical redundancy, as predicted by the genetic assimilation hypothesis. Metabolized carotenoids caused less stochastic variation in feather structure and were more closely integrated with feather growth than were dietary carotenoids of the same molecular weight. These patterns were driven by the recurrence of organism-carotenoid associations: commonly used dietary carotenoids and biochemically redundant derived carotenoids caused less stochastic variation in feather structure than did rarely used or biochemically unique compounds. We discuss implications of genetic assimilation processes for the evolutionary diversification of diet-dependent animal coloration.

The Extended Evolutionary Synthesis (EES) is currently emerging as a theoretical alternative to the Modern Synthesis (MS) in which to frame evolutionary observations and interpretations. These alternative frameworks differ fundamentally in their understanding of the relative roles of the genotype, phenotype, development and environment in evolutionary processes and patterns. While the MS represents a gene-centred view of evolution, the EES instead emphasizes the interactions between organism, development and environment. This novel theoretical framework has generated a number of evolutionary predictions that are mutually incompatible with the equivalent of the MS. While research and empirical testing has begun on a number of these in a neontological context, the field of palaeontology has yet to contribute meaningfully to this endeavour. One of the reasons for this is a lack of methodological approaches capable of investigating relevant evolutionary patterns in the fossil record. In this thesis morphometric methods capable of providing relevant data are developed and employed in the analysis of Cambrian fossils. Results of these analyses provide empirical support for the process of evolution through phenotypic plasticity and genetic assimilation hypothesized by the EES. Furthermore, theoretical revision to the species concept in a palaeontological context is suggested. Finally, predictions of the EES specific to the fossil record are made explicit and promising directions of future research are outlined.