Developmental Evolution: An Introduction

This textbook is an introduction to the developmental evolution perspective that argues that genomic and regulatory developmental mechanisms are the foundation of all evolutionary change. It is based on the assumptions that (1) the genome is an integrated four dimensional system of regulatory states that causally controls development and evolution; (2) the mechanisms generating phenotypes and phenotypic variation are the first step in all explanations of evolutionary change; and (3) based on this regulatory perspective a causal-mechanistic, developmental and experimental approach to the problem of phenotypic evolution is possible and that this experimental approach includes the possibility of recreating evolutionary transitions through the direct manipulation of underlying genomic regulatory systems (Synthetic Experimental Evolution, SEE).

The logic of developmental evolution
This book is about explanations of phenotypic evolution. Explanations of phenotypic evolution follow a simple logic that represents the evolutionary process within a causal-mechanistic framework that can be captured by the following logical structure: (1) all phenotypes are the product of developmental mechanisms; (2) all phenotypic variation is therefore a consequence of a corresponding variation in the developmental process; (3) understanding these developmental processes provides a causal-mechanistic explanation for the origin of phenotypic variation (Darwin’s first question); (4) the subsequent fate of phenotypic variation can be analyzed within the population-based framework of adaptive dynamics.

Furthermore, based on insights into the structure of genomic regulatory networks (GRNs) a new kind of experimental approach to evolution is emerging, synthetic experimental evolution. This approach studies the phenotypic consequences of targeted changes to GRNs, which in principle allows to re-engineer major phenotypic transformations in evolutionary history. The preconditions for these types of experiments are all within reach: (1) comparative analysis of GRNs of a species that has acquired a novel phenotypic character as well as of related species that represent the ancestral condition; (2) identification and experimental verification of those changes to the structure of the GRN that are causally sufficient to generate the novel phenotype; (3) targeted insertion of these GRN elements into the genome of the species representing the ancestral condition; and (4) testing the prediction that a rewired GRN will generate a phenotype similar to the one that has been acquired during the evolution of the derived lineage. Taken together, these experimental approaches enable the study the developmental basis of evolutionary transformations and investigate how different kinds of phenotypic variation are generated.

As a consequence, developmental evolution is now becoming a causal mechanistic and experimental science that is closely aligned with two transformative paradigms of 21st century biology: systems biology and synthetic biology. The focus on genomic regulatory systems (GRNs) is only a first step in the direction of a more inclusive systems focus within developmental evolution. The consequences of a number of additional regulatory systems—from microRNAs to epigenetic systems—for developmental evolution are also being investigated. However, all these additional layers of regulatory control are being anchored by the regulatory genome, which therefore occupies a privileged position within both developmental and evolutionary processes. Additional connections to systems and synthetic biology are methodological and include a close connection between targeted experimental interventions designed to re-engineer functional control circuits and mathematical and bioinformatic approaches.

This book will be the first that fully develops an introduction to the developmental evolution perspective sketched above. It will emphasize the conceptual changes associated with this emerging transformation of evolutionary theory and proceed along the following structure:

  1. A historical and conceptual outline and analysis of explanations of phenotypic evolution (Part 1)
  2. A detailed account of the logic of developmental evolution (Part 2)
  3. Based on an understanding of the logic of developmental evolution an analysis and explanation of the main phenomena and mechanisms of phenotypic evolution and their associated concepts (Part 3)
  4. An analysis of major events and problems in phenotypic evolution (Part 4)
  5. An integrated perspective of developmental evolution as a mechanistic science and a discussion of the historical and conceptual transformation associated with this new perspective (Part 5)