Evolutionary developmental biology (EDB) seeks to integrate data from comparative embryology and developmental genetics with morphological evolution and population genetics, and to determine how changes in genes are expressed as changes in phenotypes. Understanding the molecular mechanisms by which genes, together with environment, produce phenotypes helps us understand how phenotypes evolve. Mutational changes in the genes that produce a developmental pathway may cause advantageous alterations of the phenotype, so both the phenotype and its underlying genetic network evolve. The mechanistic proximal causes of phenotypes complement the ultimate causes of allele frequency change, such as natural selection, in understanding the evolution of form.
Many differences among species are due to heterochronic and allometric changes in the relative developmental rates of different body parts or in the rates or durations of different life history stages. Some characteristics have evolved by heterotopy, expression at a novel location on the body. The modularity of morphogenesis in different body parts and in different developmental stages facilitates such changes.
The vast diversity of multicellular eukaryotes is largely due to diverse uses of a toolkit of genes and developmental pathways that are conserved across wide phyletic ranges.
Developmental pathways include signaling proteins, transcription factors, cis-regulatory elements and structural genes. Evolutionary change in the regulatory connections among signaling pathways and transcription factors, and between transcription factors and their targets, is believed to underlie much of the phenotypic diversity seen in nature. Morphological variation within and among species may be caused by changes in either regulatory or protein-coding sequences, although regulatory changes may play a larger role.
A gene may have many cis-regulatory elements (enhancers) that bind different transcription factor proteins and can be expressed in diverse tissues or at different times in development. Some cis-regulatory elements have originated from transposable elements, but most of them have evolved by mutation in their sequence. Changes in their interactions with transcription factor genes can alter the time and place of their activity. Evolution of the coding sequence of a transcription factor can change its developmental function.
During evolution, genes and developmental pathways have often been co-opted, or recruited, for new functions, a process that is probably responsible for the evolution of many novel morphological traits. This process results from evolutionary changes in functional connections between transcription factors and cis-regulatory elements.
Modularity among body parts is achieved by patterning mechanisms whose regulation is often specific to certain structures, segments, and life history stages. Modularity helps different parts of the body develop divergent morphologies (e.g., differences among segments). Pleiotropic effects of genes that affect functionally interacting characteristics may evolve, resulting in the evolution of functional modules (phenotypic integration).
Genetic and developmental constraints can make some imaginable evolutionary changes unlikely to occur.
Based on changes in the expression of certain genes and developmental pathways in response to environmental signals, a single genotype may be expressed as an array of different phenotypes, the genotype’s norm of reaction. Reaction norms are genetically variable, and so can evolve by natural selection. Especially if the environment varies, phenotypic plasticity may evolve. Conversely, selection for a constant phenotype can result in canalization. Genetic assimilation is the genetic fixation of one of the states of a phenotypically plastic character. It is not known how important genetic assimilation is in evolution; nor is it known if adaptation may occur first by a nongenetic phenotypic change that later becomes genetically fixed by natural selection.