Lemurs are thought to have evolved during the Eocene or earlier, sharing a closest common ancestor with lorises, pottos, and galagos (lorisoids).
The timing and number of hypothesized colonizations has traditionally hinged on the phylogenetic affinities of the aye-aye, the most basal member of the lemur clade.
[4] The closest relatives of primates are the extinct plesiadapiforms, the modern colugos (commonly and inaccurately named "flying lemurs"), and treeshrews.
[13] Until recently, they were thought to have descended directly from the diverse group of adapiforms due to several shared postcranial traits,[14] as well as long snouts and small brains.
Most noticeably, adapiforms lack a key derived trait, the toothcomb, and possibly the toilet-claw, found not only in extant (living) strepsirrhines but also in tarsiers.
[17] Comparative studies of the cytochrome b gene, which are frequently used to determine phylogenetic relationships among mammals—particularly within families and genera[18]—have been used to show that lemurs share common ancestry with lorisoids.
One of the oldest known strepsirrhines, Djebelemur, dates from the early Eocene of northern Africa and lacks a fully differentiated toothcomb.
Initially, the island drifted south from where it split from Africa (around modern Somalia) until it reached its current position between 80 and 90 mya.
[17] These separation dates and the estimated age of the primate lineage preclude any possibility that lemurs could have been on the island before Madagascar pulled away from Africa,[31] an evolutionary process known as vicariance.
In the 19th century, prior to the theory of continental drift, scientists including Philip Sclater, Étienne Geoffroy Saint-Hilaire, and Ernst Haeckel suggested that Madagascar and India were once part of a southern continent—named Lemuria by Sclater—that has since disappeared under the Indian Ocean.
[30] Despite the low likelihood of its occurrence, oceanic dispersal remains the most accepted explanation for numerous vertebrate colonizations of Madagascar, including that of the lemurs.
[30][35] Although unlikely, over long periods of time terrestrial animals can occasionally raft to remote islands on floating mats of tangled vegetation, which get flushed out to sea from major rivers by floodwaters.
[17][34][36] Any extended ocean voyage without fresh water or food would prove difficult for a large, warm-blooded (homeothermic) mammal, but today many small, nocturnal species of lemur exhibit heterothermy, which allows them to lower their metabolism and become dormant while living off fat reserves.
[36] However, this trait has not been observed in the closely related lorisoids studied to date, and could have evolved on Madagascar in response to the island's harsh environmental conditions.
The currents were even shown to be stronger than they are today, shortening the rafting time to approximately 30 days or less, making the crossing much easier for a small mammal.
Over time, as the continental plates drifted northward, the currents gradually changed, and by 20 mya the window for oceanic dispersal had closed.
The most parsimonious explanation, given the genetic evidence and the absence of toothcombed primates in European fossil sites,[17] is that stem strepsirrhines evolved on the Afro-Arabian landmass, dispersing to Madagascar and more recently from Africa to Asia.
[12] An alternative form of oceanic dispersal that had been considered was island hopping, where the lemur ancestors might have made it to Madagascar in small steps by colonizing exposed seamounts during times of low sea level.
[12] Geological studies have shown that following the collision of India and Asia, the Davie fracture zone had been pushed up by tectonic forces, possibly high enough to create a land bridge.
By the early Miocene, the East African Rift created tension along the fault, causing it to subside beneath the ocean.
Using both mitochondrial and nuclear DNA sequences, a single colonization has been estimated at 62 to 65 mya based on the split between the aye-aye and the rest of the lemurs.
[25] Monkeys had evolved by the Oligocene, and their intelligence, aggression, and deceptiveness may have given them the advantage in exploiting the environment over the diurnal adapiform primates in Africa and Asia, ultimately driving them to extinction and leaving only the nocturnal lorisoids.
[45] As Madagascar edged above the subtropical ridge and India moved closer to Asia, the climate became less dry and the arid spiny bush retreated to the south and southwest.
[21][22] The dates for this divergence window span the Eocene–Oligocene extinction event, during which time climate cooling took place and changes in ocean currents altered weather patterns.
[21][12] Outside of Madagascar, these dates also coincide with the divergence of the lorisoid primates and five major clades of squirrels, all occupying niches similar to those of lemurs.
[47] Most surprising were the mouse lemurs, a group which is now thought to contain cryptic species, meaning they are indistinguishable from each other based solely on appearance.
[47] Although the divergence estimates for these two genera are imprecise, they overlap with a change to a wetter climate in Madagascar, as new weather patterns generated monsoons and likely influenced the plant life.
The center of the island, the Hauts-Plateaux, was converted by early settlers to rice paddies and grassland through slash-and-burn agriculture, known locally as tavy.
[14] Having evolved in Madagascar's challenging environment, replete with poor soils, extreme shifts in poor, seasonal plant productivity, and devastating climatic events such as extended droughts and annual cyclones,[13] lemurs have adopted unique combinations of unusual traits to survive, distinguishing them significantly from other primates.
Now represented only by recent or subfossil remains, they were modern forms and are counted as part of the rich lemur diversity that evolved in isolation.