Dodo

The dodo (Latin: Raphus cucullatus, Dutch: doedaars), sometimes called a didus, was a type of large, flightless pigeon that was found only on Mauritius. (NSA: The Last Dodo) According to the First Doctor, it was well known for its extinction. (TVC: The Didus Expedition) Nevertheless, several "last Dodos" were known to have existed — all of whom the Doctor encountered at one point or another; one of them was kept in his TARDIS. (ST: Echo)

According to the Tenth Doctor, the English word dodo came from the Dutch doedaars, which literally meant "fat ass" — or as he more modestly put it, "fat, um, rear". (NSA: The Last Dodo)

Biology
The dodo had a large curved beak, a featherless face, a curly grey tail and yellow tips to its wings. (NSA: The Last Dodo)

History
The dodo became extinct in 1681, wiped out by humans who had introduced species like pigs.

The last dodo was saved and kept in the Museum of the Last Ones. This specimen was cloned by Eve and used to plant bombs on Earth which would destroy the planet. The original dodo was returned by the Tenth Doctor to Mauritius. Though Martha did not understand why, the Doctor had named the bird "Dorothea", a reference to his former companion, Dorothea "Dodo" Chaplet. (NSA: The Last Dodo)

In later centuries, the expression "dead as a dodo," referring to their extinction, was common. (BFA: The Wrath of the Iceni)

Another dodo was held in the TARDIS zoo. Ace found it while exploring the ship. She let it out, but it bit her and fled down the corridors. She caught it and returned it to the zoo. (ST: Echo)

Yet another "last dodo" was found at a zoo on an unnamed planet. This dodo escaped — because a monkey had opened its cage — shortly before the First Doctor, John and Gillian visited the zoo. The travellers offered to find the bird. They set off into the jungle surrounding the zoo and were quickly beset by a hostile tribe who believed the bird lucky and captured it. The Doctor tricked the tribesmen with a false bird of paradise that John quickly carved and returned the didus to the zoo. The bird's eggs hatched after that, creating yet more "last dodos" (TVC: The Didus Expedition)

Other references

 * The I-Spyder Book of Earth Creatures gave 800 points for seeing a dodo. (NSA: The Last Dodo)
 * Griffin had a dodo in his collection. (EDA: Unnatural History)
 * The feasibility generator looked like a dodo. (IW: The Land of Wonder)
 * The Eleventh Doctor planned to save the dodos if he survived his death at Lake Silencio. (DW: The Wedding of River Song)
 * Charles Darwin was said to have eaten dodo. (TWN: Risk Assessment)

Behind the scenes
Another Latin name for the bird is Didus ineptus. When the First Doctor calls the bird a didus in The Didus Expedition, he's therefore speaking Latin, not naming an entirely different species that happens to have the same features and backstory of the dodo. In the zoological community, Didus ineptus was an attempt at a new, and more obvious, Latin name. However, many zoologists favour the older Raphus cucullatus. In any case, the two terms are synonymous.