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Migratory theory mechanisms
There are many theories that attempt to explain monarch migration. Researchers often propose that multiple migratory mechanisms play a role. Not all who study monarch migration agree on the mechanisms that allow the migrating butterflies to find overwintering sites.

Time-Compensated sun compass
The sun plays an integral role in the monarchs’ migratory patterns: they travel during the day and use a circadian clock in conjunction with the sun’s position in the sky to orient themselves. This clock mechanism is time compensated, in that each butterfly entrains to the light-dark cycle of its surroundings and thereby knows how to interpret the changing light patterns throughout the day. The butterflies know to orient South by first adjusting their circadian clocks to environmental cues (such as the time that sunrise and sunset occur) and then using their calibrated clocks to identify South based on the sun's position and the time of day. Various studies have shown this behavior both in natural systems and laboratory settings.

The neural and anatomical mechanisms of the monarch sun compass are among the better understood areas of this theory. Light is first perceived by the monarch’s compound eyes, hitting the retina which registers the azimuthal angle of the light. The light polarization, which is used by various insects for navigation, is then detected by the dorsal rim area, a specialized feature of the compound eye. These cues are then passed on to the central complex of the brain, where they are interpreted. Here, single neurons combine the azimuthal location of the sun and the e-vector angle (angle of polarized skylight). This information is then processed and further combined with other locational and orientational cues in order to produce migratory behavior. Overall, studies agree that the neural processing underlying the monarch’s sun compass occurs in the brain’s central complex; the neural structure found there indicates the butterflies engage in spatial learning, memory and awareness. Further research is needed in order to model the neuronal network and fully understand how spatial cues are modeled and stored in the brain.

While neural processing may occur in the monarch’s brain, research indicates that the actual circadian clock underlying the migratory patterns is located in the butterfly’s antennae. Butterflies with their antennae removed showed no consistent group orientation in their migratory patterns. Painting the antennae black, thereby causing a free running circadian rhythm, led to altered orientation patterns as well. This proved that the antennae are necessary for the circadian clock to function because the paint blocks light information from reaching them. Examination of various genes and proteins involved in circadian rhythms showed that the antennae exhibited their own circadian fluctuations, even when removed from the butterfly and studied in vitro. Overall, the study of antennae-less monarchs as well as the in vitro analysis of the antennae indicate that the antennae are both necessary for the proper functioning of the time-compensated sun compass and contain their own circadian clocks that function even without the butterfly’s brain. Yet there remains much to be researched about the underlying mechanisms for interpreting the orientation and timing cues that lead to the migratory patterns of the monarchs.

Molecular basis of circadian navigation

The importance of the role of the circadian clock in the function of the time-compensated sun compass system has led to much investigation into the molecular basis of the clock mechanism in monarchs. This has resulted in well-characterized models for both a central and a secondary circadian clock.

Similarly to the core mechanisms underlying both the Drosophila and mammalian circadian clocks, the core mechanism of the clock in monarchs relies on a transcriptional-translational negative feedback loop (TTFL). This feedback loop is auto-regulatory and includes both positive and negative elements which function to promote and suppress transcription, driving rhythms in mRNA and protein levels of core circadian clock components.

Despite sharing the conserved core mechanism of the TTFL with many other species, the mechanism of the monarch circadian clock is considered unique because it diverges from other mechanisms in the roles of some of its elements. The most unique aspect of the monarch circadian clock mechanism is that it involves two cryptochrome proteins – CRY1 and CRY2 – which differ in their functions. CRY1 is much like the Drosophila CRY in that it functions as a photoreceptor, while CRY2 is similar to the mammalian CRY in that it functions as one of the major repressors in the feedback loop.[1][2] In the core mechanism of the monarch circadian clock, CRY1 acts as a blue light photoreceptor, providing the clock with a means to entrain to a light-dark cycle. The transcription factors CLOCK (CLK) and CYCLE (CYC) function as positive regulators by binding to promoter sequences (E-boxes) of the genes period (per), timeless (tim), and cry2 and activating transcription. The translated PER, TIM, and CRY2 proteins form complexes in the cytoplasm and after a delay, these complexes translocate back into the nucleus where CRY2 then represses transcription.[1]

In addition to the core feedback loop, a second modulatory feedback loop has also been identified in monarchs. This feedback loop is much like the Drosophila secondary feedback loop and includes genes that encode orthologs of VRILLE and PDP1, which are known to regulate CLK transcription in Drosophila.[3][4]

Bi-directionality of sun compass
Monarchs are known to use their time-compensated sun compass during both the southern migration in the fall and the northern remigration in the spring. The change in directionality necessary to re-orient the monarchs has been shown to depend on the cold temperatures that the monarchs experience while overwintering in the coniferous forests of Mexico. The change in sun compass direction does not depend on the change in photoperiod experienced during the winter months, but this change is likely to affect the timing of the northern remigration in the spring.

An experiment demonstrating the importance of cold exposure for remigration utilized fall monarchs with and without cold temperature exposure in the laboratory. The monarchs that experienced cold temperatures during the winter months successfully changed the direction of their sun compass and oriented north in the spring. In contrast, the monarchs that never experiences the cold temperatures during the winter months oriented south in the spring, and thus did not experience a change in sun compass direction to accompany their migration. Therefore, the cold exposure experienced while overwintering is required for the monarch’s migration cycle.

During the northern remigration of monarchs in the spring, the time-compensated sun compass uses the same substrates as used in the fall. However, the mechanistic differences in these substrates (which can include decreased temperatures, shorter daylight, and older milkweed plants) that allows for a switch in the directionality of the compass is still unknown. RNA-sequencing differences found between the fall and spring butterflies is one avenue of research that could locate the mechanism responsible for the recalibration, which may utilize a temperature sensor to start the switch.

Genetic memory theory
It is proposed that the ability to find overwintering sites in California and Mexico is an inherited trait. It has also been called a genetic memory. The possibility of an inherited map has been posited suggesting that the butterflies may follow streams and recognize landmarks. Other studies provide evidence against the theory of an inherited map.

Landscape theory
Migration theories take into account the terrain monarchs encounter during their migration. Mountains, rivers, lakes and oceans are credited with influencing the migration.Large roosts of migrating monarchs are often formed at a locations that act as obstacles impeding their movement S/SW. Roosting butterflies are thought to form these roosts to wait for ideal weather conditions that will aid them in crossing these landforms, such as lack of rain, temperature, tailwinds, and sunlight. Some years the roosting sites form predictably and consistently year to year. In other instances, roosting sites form in new areas on a transient basis. A roost of migrating monarchs can contain as few as four and as many as thousands. Other geographic features such as the Appalachian Mountains and the Sierra Madres in Mexico 'funnel' the migration, orienting it to the S/SW. One monarch tagged in Ontario was recovered on an oil rig 100 miles south of Galveston, Texas.

Columbus hypothesis
The Columbus Hypothesis is another theory that accounts for the phenomena of the mass migration of the eastern population of the monarch by examining historical records. This theory discusses how many butterflies engage in mass movements to expand their range or relieve pressure on their habitat.According to this theory, the eastern population did not have such an extensive range and did not migrate. Historical observations of animal life during the colonial period in America make no mention of monarch butterflies. Observations of monarchs began and seemed to be related to the deforestation of the Northeast. Monarchs were presumably residents of subtropical and tropical areas but began to move north to breed on the increased numbers of larval host plants that replaced the deforested areas. Populations found in other regions do not migrate over such long distances (in Australia, for example) This may suggest that the migratory behavior of the eastern population of the monarch butterfly developed after other populations of monarchs had become established in other regions.

Other theories
One recent hypothesis suggests that monarchs may be chemically marking certain trees, using an unknown substance and so orienting themselves when they return the following winter.

Another theory denies the existence of the mass migration, but instead explains the movements of monarchs in the fall to weather conditions:"In the fall, monarch adults in Canada and the upper Midwest likely receive an environmental trigger (change in photoperiod or seasonal cold snap) and cease egg laying. When the main jets stream moves south out of Canada, high and low pressure cells become carried across extreme southern Canada and later across the US. At that time, monarchs need merely rise on thermals during clearing conditions and become carried toward the South out of the region in which they were reared. If they have reached sufficient altitude in their ride on thermals, the north winds can carry some of them considerable distance towards Mexico.' Adrian Wenner, professor emeritus of natural history at the University of California, Santa Barbara"