It is not generally understood that prior to publication of Darwin's theory of evolution by natural selection many biologists were already evolutionists, i.e., they believed that new species arose from the divergence of earlier species but did not have much of an idea about why this occurred.   They had already begun trying to deduce the chronological sequence of divergences and relationships of species (phylogeny) for both extant species and extinct species identified from fossils.

     Comparison of embryology of various species was also applied to this task.  At the time, there was no microscopic photography, so depictions of embryonic stages were through drawings.  It was noted that all vertebrates at some period in development looked more similar than at earlier or later stages. It was usually considered to be during the pharyngula stage of development.

     Vertebrate embryos at the pharyngula stage look somewhat fish-like, minus the fins and tail.  Since fish evolved earlier than other vertebrates, this led to the idea more recent species they must successively pass through the development stages of their ancestors before developing structures unique to their species.  This was called recapitulation.

     Ernst Haeckel published drawings of several vertebrate embryos at various stages and advocated a very strong form of recapitulation.  He claimed that more advanced species during development pass through stages representative of the adult forms of more primitive species.  For example, he claimed that grooves in the neck region observed in all mammalian embryos (pharyngeal arches) represented gill structures as in fish.  This contrasted with the earlier view favored by Karl Ernest von Baer, the founder of comparative embryology, that structures specific to a closely related group of species only form after structures shared by a larger grouping.

      Haeckel’s views had considerable influence for a time.  However, both the accuracy of his drawings and his interpretation of their meaning were questioned, and the modern interpretation is closer to that of von Baer.  However, I think that what might be called weak recapitulation could be said to be an important feature in vertebrate development, but in regard specific organs and not the whole embryo.

     It appears that oftentimes an early part of a developmental pathway that was used in ancestors in forming a specific feature has been used in the initial steps forming new features.  In mammals, the structures forming the pharyngeal arches have been utilized as precursors of the jawbone and two bones of the inner ear.

     An analogy can be made to the decision on how to modernize a house.    One approach is “gut everything down to the studs.”  However, this makes the house unlivable for a long time.  For living things, new features can only evolve in small steps, rather than with sudden large changes in essential features.  In constructing houses, supporting systems, such as wiring, piping, and ductwork, are installed before the operating equipment.  Modernization often takes the form of installing modern operating equipment, such as a new water heating system, without tearing out the existing piping.  Oftentimes, the old heater can be utilized while the new one is installed, with a quick switch without interruption.  In mammalian hearts, a fish-like tube heart can initially accomplish the circulatory requirements of the fetus before undergoing modifications to become the four-chambered organ necessary to support post-natal life.

     Sometimes new features have evolved by subtraction from existing features.   In mammals, initially five digits form at the end of each limb.  In some species, some of these digits then regress.  For example, in the horse four digits regress, with the nail on the one remaining digit becoming the hoof.  In house remodeling, this is analogous to removing part of a wall to produce new doorway.

     In the late 20th century, ideas were developed about why vertebrate embryos were similar during the pharyngula stage.  Sander (83) introduced the term “phylotypic stage” and pointed out that certain features of the embryos characteristic of different animal phyla are present in the embryo before other features characterizing their subgroups.  For example, the characters shared by all vertebrates are the notochord, a hollow neural tube (the spinal tube), a post-anal tail, and pharyngeal arches.  Raff (96) argued that the conservation of the basic body plan in vertebrates that resulted in the phylotypic stage resulted from the interaction of different developmental modules in different parts of the developing embryo.  Mutations or other disturbances in one module would interact with other modules producing many (pleiotropic) effects, of which some may be deleterious, that would select against any change in the basic body plan, thus explaining the conservation of the phylotypic stage.  Later development of individual organs and novel structures would occur with less interaction with other modules, thus allowing favorable mutations to survive.