Timing of seasonal reproduction by flying-foxes is apparently dependent on an endogenous circannual rhythm, coded in their genome. Ultimately, evolution of an endogenous rhythm aligns an important reproductive stage, such as lactation, with resource availability such as the occurrence of maximum plant productivity; animals then do not have to rely on proximate factors to predict conditions nine months in advance. External influences that re-align reproduction to match a phase-shift in environmental conditions have to either adjust the period of the biological clock, or else induce a phase-shift, to bring breeding back into line with prevailing conditions. These are non-genomic factors: they influence the expression of genes, and therefore phenotype, without altering the DNA.

Stages of reproduction relate temporally with the endogenous rhythm, but individual flying-foxes may need to make fine adjustments in their own timing. To do this they probably monitor a suite of environmental conditions. It has been proposed that if a signal changed in isolation from other factors it would be ignored. For example, it is important that a nomadic species be not directly responsive to photoperiod since this differs when they move between latitudes. A reproductive stage would, however, be inhibited if several cues warned against proceeding, e.g. inadequate forage combined with long commuting distances at a time of unfavourable temperatures.

What non-genomic factors regulate flying-fox reproduction? It is likely that rainfall is part of the regulation for the overall rhythm, while current energy balance is probably important for individual animals during many stages of their reproduction.