ological changes (Mishmar et al., 2006; Lane, 2009). Over longer time periods, anatomical mutations can be added, leading toward speciation.

An individual’s energy environment fluctuates in cycles throughout its life. These cycles can occur over the individual’s life span responding to intra- and intergenerational influences, recur annually in response to seasons, occur monthly relative to the reproductive cycle, or recur daily based on activity and feeding. All of these cyclic changes require reversible alterations in bioenergetic physiology, which cannot be achieved through static genetic changes.

Cyclic changes that occur over tens of years require moderate stability. These are achieved through epigenomic changes: modification of DNA by methylation or of histones through phosphorylation, acetylation, and methylation. Shorter-term reversible changes are accomplished through modulation of transcription factors and alterations in signal transduction pathways. All of these changes must be cued to changes in the energetic environment. Therefore, cyclic changes in the epigenome and signafling pathways are all mediated by changes in the intracellular concentrations of energetic intermediates including ATP for phosphorylation, acetyl-CoA for acetylation, NAD⁺ for Sirtuin-mediated deacetylation, S-adenosyl-methionine (SAM) for methylation, oxidation-reduction (redox) state for thiol-disulfide regulation, and reactive oxygen species (ROS) for driving oxidative reactions (Wallace and Fan, 2010).

Since the publication of the Darwin–Wallace hypothesis of natural selection, numerous examples have been reported of anatomical changes associated with speciation. The earliest report of anatomical changes associated with exploitation of alternative energy resources was that of Darwin’s Galapagos finches, discussed by Darwin and Gould before the Geological Society of London in January 1839. More recently, the change in beak size of these finches has been attributed in part to changes in calmodulin expression (Abzhanov et al., 2006). Comparable studies have continued for more than a hundred years, culiminating in the recent report that pelvic loss in stickleback fish is due to deletion of a tissue-specific enhancer of the Pituitary homeobox transcription factor 1 (Pitx1) gene (Chan et al., 2010). Although these studies confirm the importance of anatomical change in speciation, they belie the complexity of the physiological adaptations that are required for a species to occupy a new bioenergetic niche.