Lemurs, primates belonging to the suborder Strepsirrhini which branched off from other primates less than 63 million years ago, evolved on the island of Madagascar, for at least 40 million years. They share some traits with the most basal primates, and thus are often confused as being ancestral to modern monkeys, apes, and humans. Instead, they merely resemble ancestral primates.

Lemurs are thought to have evolved during the Eocene or earlier, sharing a closest common ancestor with lorises, pottos, and galagos (lorisoids). Fossils from Africa and some tests of nuclear DNA suggest that lemurs made their way to Madagascar between 40 and 52 mya. Other mitochondrial and nuclear DNA sequence comparisons offer an alternative date range of 62 to 65 mya. An ancestral lemur population is thought to have inadvertently rafted to the island on a floating mat of vegetation, although hypotheses for land bridges and island hopping have also been proposed. 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.

Having undergone their own independent evolution on Madagascar, lemurs have diversified to fill many niches normally filled by other types of mammals. They include the smallest primates in the world, and once included some of the largest. Since the arrival of humans approximately 2,000 years ago, lemurs are now restricted to 10% of the island, or approximately , with many facing extinction.

Evolutionary history Lemurs are primates belonging to the suborder Strepsirrhini. Like other strepsirrhine primates, such as lorises, pottos, and galagos, they share ancestral traits with early primates. In this regard, lemurs are popularly confused with ancestral primates; however, lemurs did not give rise to monkeys and apes, but evolved independently on Madagascar.

Primates first evolved sometime between the Middle Cretaceous and the early Paleocene periods on either the supercontinent of Laurasia or in Africa. According to molecular clock studies, the last common ancestor of all primates dates to around 79.6 mya, although the earliest known fossil primates are only 54–55 million years old. The closest relatives of primates are the extinct plesiadapiforms, the modern colugos (commonly and inaccurately named "flying lemurs"), and treeshrews. Some of the earliest known true primates are represented by the fossil groups Omomyidae, Eosimiidae, and Adapiformes.

The relationship between known fossil primate families remains unclear. A conservative estimate for the divergence of haplorhines (tarsiers, monkeys, apes, and humans) and strepsirrhines is 58 to 63 mya. A consensus is emerging that places omomyids as a sister group to tarsiers, eosimiids as a stem group to simians (non-tarsier haplorhines), and Djebelemur, an African genus likely to be related to an early Asian branch of cercamoniine adapiforms, as a stem group to modern strepsirrhines, including lemurs. In 2009, a highly publicized and scientifically criticized publication proclaimed that a 47-million-year-old adapiform fossil, Darwinius masillae, demonstrated both adapiform and simian traits, making it a transitional form between the prosimian and simian lineages. Media sources inaccurately dubbed the fossil as a "missing link" between lemurs and humans.

Lemurs were traditionally thought to have evolved during the Eocene (55 to 37 mya) based on the fossil record, although molecular tests suggest the Paleocene (66 to 56 mya) or later. Until recently, they were thought to have descended directly from the diverse group of adapiforms due to several shared postcranial traits, as well as long snouts and small brains. Although adapiforms also had lemur-like auditory bullae, a prosimian characteristic, they had smaller brains and longer snouts than lemurs. There are also several other morphological differences. 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. Unlike lemurs, adapiforms exhibited a fused mandibular symphysis (a characteristic of simians) and also possessed four premolars, instead of three or two.

Comparative studies of the cytochrome b gene, which are frequently used to determine phylogenetic relationships among mammals—particularly within families and genera—have been used to show that lemurs share common ancestry with lorisoids. This conclusion is also corroborated by the shared strepsirrhine toothcomb, an unusual trait that is unlikely to have evolved twice. If adapiforms were the ancestors of the living strepsirrhines, then the last common ancestor of modern strepsirrhines would have to predate the early Eocene, a view supported by molecular phylogenetic studies by Anne D. Yoder and Ziheng Yang in 2004, which showed that lemurs split from lorises approximately 62 to 65 mya. These dates were confirmed by more extensive tests by Julie Horvath et al. in 2008. These molecular studies also showed that lemuroids diversified before the modern lorisoids. Using a more limited data set and only nuclear genes, another study in 2005 by Céline Poux et al. dated the split between lemurs and lorises at 60 mya, lemur diversification at 50 mya, and the lemur colonization of Madagascar somewhere between these two approximate dates. However, the 2003 discovery of fossil lorisoids at the Fayum Depression in Egypt pushed the date of lorisoid divergence back to the Eocene, matching the divergence dates predicted by Yoder and Horvath.

The fossil record tells a different story. Although it cannot show the earliest possible date for the appearance of a taxonomic group, other concerns have arisen about these vastly earlier divergence dates predicted independently of the fossil record. First, palaeontologists have expressed concerns that if primates have been around for significantly more than 66 million years, then the first one-third of the primate fossil record is missing. Another problem is that some of these molecular dates have overestimated the divergence of other mammalian orders, such as Rodentia, suggesting primate divergence might also be overestimated. One of the oldest known strepsirrhines, Djebelemur, dates from the early Eocene of northern Africa and lacks a fully differentiated toothcomb. Based on fossils and other genetic tests, a more conservative estimate dates the divergence between lemurs and lorises to around 50 to 55 mya.

To complicate the ancestry puzzle, no terrestrial Eocene or Paleocene fossils have been found on Madagascar, and the fossil record from both Africa and Asia around this time is not much better. Fossil sites in Madagascar are restricted to only five windows in time, which omit most of the Cenozoic, from 66 mya to ~26,000 years ago. What little fossil-bearing rock exists from this vast span of time is dominated by marine strata along the west coast. The oldest lemur fossils on Madagascar are actually subfossils dating to the Late Pleistocene.

Colonization of Madagascar Once part of the supercontinent Gondwana, Madagascar broke away from eastern Africa, the most likely source of the ancestral lemur population, about 160 mya and then from Antarctica between 80 and 130 mya. 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. Around that time, it split with India, leaving it isolated in the Indian Ocean and separated from nearby Africa by the Mozambique Channel, a deep channel with a minimum width of approximately . 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, an evolutionary process known as vicariance. In support of this, mammalian fossils on Madagascar from the Cretaceous (see Mesozoic mammals of Madagascar) include gondwanatheres and other mammalian groups that would not have been ancestral to lemurs or the other endemic mammals present on the island today.

With Madagascar already geographically isolated by the Paleocene and lemur diversification dating to the same time, an explanation was needed for how lemurs had made it to the island. 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. By the early 20th century, oceanic dispersal emerged as the most popular explanation for how lemurs reached the island. The idea first took shape under the anti-plate tectonics movement of the early 1900s, when renowned paleontologist William Diller Matthew proposed the idea in his influential article "Climate and Evolution" in 1915. In the article, Matthew could only account for the presence of lemurs in Madagascar by "rafting". In the 1940s, American paleontologist George Gaylord Simpson coined the term "sweepstakes dispersal" for such unlikely events.

As plate tectonics theory took hold, oceanic dispersal fell out of favor and was even considered by many researchers to be "miraculous" if it occurred. 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. 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.

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. Such a trait in a small, nocturnal lemur ancestor would have facilitated the ocean voyage and could have been passed on to its descendants. 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.

Because only five terrestrial orders of mammals have made it to the island, each likely to have derived from a single colonization, and since these colonizations date to either the early Cenozoic or the early Miocene, the conditions for oceanic dispersal to Madagascar seem to have been better during two separate periods in the past. A report published in January 2010 supported this assumption by demonstrating that both Madagascar and Africa were south of their present-day positions around 60 mya, placing them in a different ocean gyre and reversing the strong current that presently flows away from Madagascar. 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.