Madagascar is thought to have been colonized comparatively late compared to other landmasses, with the first evidence of human occupation coming from less than 2000 years ago. As a consequence, the extinction of Malagasy megafauna occurred much later. Originally home to all number of large vertebrates, including elephant birds and several species of giant sloth-lemur, all native species weighing over 20 kilograms, as well as several weighing less than that, were eventually wiped out. Due to the unique nature of Madagascar’s megafauna, restoring the ecological functions left empty by these species is difficult, however, there are several taxa that might be introduced in order to restore some lost trophic effects.

The first of these is the tortoises (Testudinidae). There are four native species of tortoise in Madagascar, including two members of the genus Pixys and two members of Astrochelys. Before occupation by humans, however, there were also two members of the genus Aldabrachelys, which is still represented by the giant tortoises of Aldabra and the Seychelles. The two extinct species, †Aldabrachelys abrupta and †Aldabrachelys grandidieri differed in that the former was a dome-shelled grazer, and the latter was a saddle-backed browser. There are three subspecies of the living Aldabrachelys gigantea, two of which (gigantea and hololissa) are domed and one of which (arnoldi) is saddled. Specimens of the saddled morph are rare, but easily bred, and a colony on Madagascar would likely represent a valuable conservation opportunity. The Malagasy domed tortoise could likely be replaced by either the Aldabra (gigantea) or Seychelles (hololissa) domed tortoise, but the latter would likely benefit more from additional breeding populations. It is quite possible that if they were alive today, the Malagasy giant tortoises would also be considered as subspecies of this quite variable taxon since the current tortoises of Aldabra are known to have migrated there from Madagascar only in the past 100,000 years. Tortoises are incredibly important as herbivores, seed distributors, and nutrient cyclers, especially in systems with few other large herbivores. Because native plants tend to have adaptations against overgrazing by giant tortoises, the animals often prefer to eat alien species instead, opening up more space for native plants to grow. Tortoises are unlikely to conflict much with humans, as they are docile and easily restricted from agricultural areas.

Besides tortoises, another group of large, ecologically important herbivores in Madagascar was the hippopotamuses. There were three distinct species of hippopotamus that lived in Madagascar before human arrival. Two of these, †Hippopotamus? lemerlei and †Hippopotamus? madagascariensis were similar in size to the modern pygmy hippopotamus, Choeropsis liberiensis. While the latter was a forest-dwelling, more terrestrial species, probably quite similar ecologically to the pygmy hippo, the former was apparently more similar to the common hippopotamus (Hippopotamus amphibius) in that it was mostly tied to freshwater rivers and lakes. The third species, †Hippopotamus? laloumena, was apparently almost as large as the common hippopotamus, but very little is known about it. While the introduction of the larger common hippopotamus would likely be problematic due to its aggressiveness, need for large territories, and questionable similarity to the extinct species, the introduction of pygmy hippopotamuses might be a more reasonable proposal. This smaller species from the rainforests of West Africa is far less dangerous than its larger cousins and fills an ecological role more similar to that of tapirs, eating mostly browse and fruit. Like tortoises, Malagasy hippopotamuses would have played an important role in seed dispersal and nutrient cycling.

Another important member of the Malagasy herbivore was the goose. There were two native species of large, grazing waterfowl present in Madagascar before human arrival. The first, †Centrornis majori, was the only member of its genus and its relationship to other species is unclear. The second, †Alopochen sirabensis, however, seems to have been very closely related to the living Egyptian goose, Alopochen aegyptiaca. This species is still very common in Africa and in several areas outside of its natural distribution, and could quite easily be acquired and introduced in order to fill the role of its extinct congeneric. Like tortoises and hippos, large waterfowl are keystone grazers, feeding on many kinds of plants and acting as seed distributors.

Eagles are another group of birds that have suffered a loss of diversity in Madagascar. Two species, the Malagasy fish-eagle (Haliaeetus vociferoides) and the Malagasy serpent-eagle (Eutriorchis astur), are still present, though both are endangered. Fossils show that one or two species of the genus Aquila were formerly present but it is unknown how they were related to any of the extant species. A clearer relationship is drawn between the extinct Malagasy crowned eagle (†Stephanoaetus mahery) and the living African crowned eagle (Stephanoaetus coronatus). Crowned eagles are specialist predators of arboreal mammals, especially monkeys, and as such the Malagasy crowned eagle was probably a lemur specialist. It may have disappeared as a result of some of the larger (but not giant) lemur species, such as †Archaeolemur, †Babakotia, †Hadropithecus, and †Mesopropithecus. It is worth noting, however, that many living lemur species display avoidance behaviours towards birds of prey, despite the fact that no living raptor from Madagascar is large enough to hunt adult lemurs. This would suggest that the crowned eagle preyed on these species as well. Introduction of a top predator like the crowned eagle is likely not a good idea while lemur numbers are low but at a later stage of restoration they could be an important factor in controlling numbers and in mediating interspecies competition between lemur taxa.

Another important large carnivore, the crocodiles are an interesting example of what could be called accidental trophic rewilding. In prehistory the only native crocodilian in Madagascar was †Voay robustus,which was related to, but much larger than, the African dwarf crocodiles (Osteolaemus tetraspis). Since the extinction of this species, Madagascar has subsequently been colonized by the Nile crocodile (Crocodylus niloticus). It is likely that the ecological roles of these two species were similar enough to prevent the latter to colonize while the former was still present. †Voay robustus was probably the top predator of pre-human Madagascar, just as the Nile crocodile is today. Crocodiles have been known to prey on pygmy hippos and giant tortoises elsewhere, and it is likely that these two species were part of †Voay’s diet, alongside smaller vertebrates. The Madagascan subspecies of Nile crocodile is today restricted to the western and southern parts of the island, but it was formerly widespread. Cessation of poaching and an increase in potential prey may aid in its recolonization.

Overall there is a fair amount of work that could be done to help reinvigorate ecosystem dynamics in Madagascar. However, it is worth noting that there were five whole families of native tetrapods that have gone completely extinct. The smallest elephant birds,†Mullerornis, were similar in size to an emu (Dromaius) or a cassowary (Casuarius), but differed in being at least partially nocturnal, while the largest elephant birds, †Aepyornis, were over four times heavier than an ostrich (Struthio). A large insectivore dubbed †Plesiorycteropus was initially thought to have been a close relative of the aardvark (Orycteropus) but is now known to have been a large tenrec, which evolved a similar niche through convergent evolution. Three families of medium-large lemur have gone extinct, with two genera, †Megaladapis and †Palaeopropithecus reaching 50 kilograms in weight and one, †Archaeoindris, weighing over 150 kilograms, comparable in size to a gorilla. There are no obvious stand-ins for these taxa, as there are for the aforementioned groups, and so their role in the ecosystem may need to go unfilled for the time being. Sometimes it will not be possible to restore all or even most of the lost functionality in the ecosystem, and in these situations, the goal will just be to restore as much as possible and to make sure that the region in question has the resources it needs to start repairing itself. The giant lemurs and tenrecs are gone, but there are still smaller representatives of these groups which might eventually fill new niches if given the space and time. The elephant birds are also gone, but perhaps the introduction of cassowaries or other ratites could be considered in order to restore some of the same dynamics, and possibly encourage convergent evolution. The future ecosystems of Madagascar will never be the same as in the past, but if the right decisions are made, they may be much more diverse and impressive than they are in the present.