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Subfossil specimens

Until 1860, the only known dodo remains were the four incomplete 17th-century specimens. Philip Burnard Ayres found the first subfossil bones in 1860, which were sent to Richard Owen at the British Museum, who did not publish the findings. In 1863, Owen requested the Mauritian Bishop Vincent Ryan to spread word that he should be informed if any dodo bones were found. In 1865, George Clark, the government schoolmaster at Mahébourg, finally found an abundance of subfossil dodo bones in the swamp of Mare aux Songes in Southern Mauritius, after a 30-year search inspired by Strickland and Melville's monograph. In 1866, Clark explained his procedure to The Ibis, an ornithology journal: he had sent his coolies to wade through the centre of the swamp, feeling for bones with their feet. At first they found few bones, until they cut away herbage that covered the deepest part of the swamp, where they found many fossils. Harry Pasley Higginson, a railway engineer from Yorkshire, reports discovering the Mare aux Songes bones at the same time as Clark and there is some dispute over who found them first. Higginson sent boxes of these bones to Liverpool, Leeds and York museums. The swamp yielded the remains of over 300 dodos, but very few skull and wing bones, possibly because the upper bodies were washed away or scavenged while the lower body was trapped. The situation is similar to many finds of moa remains in New Zealand marshes. Most dodo remains from the Mare aux Songes have a medium to dark brown colouration.

Clark's reports about the finds rekindled interest in the bird. Sir Richard Owen and Alfred Newton both wanted to be first to describe the post-cranial anatomy of the dodo, and Owen bought a shipment of dodo bones originally meant for Newton, which led to rivalry between the two. Owen described the bones in Memoir on the Dodo in October 1866, but erroneously based his reconstruction on the Edwards's Dodo painting by Savery, making it too squat and obese. In 1869 he received more bones and corrected its stance, making it more upright. Newton moved his focus to the Réunion solitaire instead. The remaining bones not sold to Owen or Newton were auctioned off or donated to museums. In 1889, Théodor Sauzier was commissioned to explore the "historical souvenirs" of Mauritius and find more dodo remains in the Mare aux Songes. He was successful, and also found remains of other extinct species.

In 2005, after a hundred years of neglect, a part of the Mare aux Songes swamp was excavated by an international team of researchers (International Dodo Research Project). To prevent malaria, the British had covered the swamp with hard core during their rule over Mauritius, which had to be removed. Many remains were found, including bones of at least 17 dodos in various stages of maturity (though no juveniles), and several bones obviously from the skeleton of one individual bird, which have been preserved in their natural position. These findings were made public in December 2005 in the Naturalis museum in Leiden. 63% of the fossils found in the swamp belonged to turtles of the extinct genus Cylindraspis, and 7.1% belonged to dodos, which had been deposited within several centuries, 4,000 years ago. Subsequent excavations suggested that dodos and other animals became mired in the Mare aux Songes while trying to reach water during a long period of severe drought about 4,200 years ago. Furthermore, cyanobacteria thrived in the conditions created by the excrements of animals gathered around the swamp, which died of intoxication, dehydration, trampling, and miring. Though many small skeletal elements were found during the recent excavations of the swamp, few were found during the 19th century, probably owing to the employment of less refined methods when collecting.

Louis Étienne Thirioux, an amateur naturalist at Port Louis, also found many dodo remains around 1900 from several locations. They included the first articulated specimen, which is the first subfossil dodo skeleton found outside the Mare aux Songes, and the only remains of a juvenile specimen, a now lost tarsometatarsus. The former specimen was found in 1904 in a cave near Le Pouce mountain, and is the only known complete skeleton of an individual dodo. Thirioux donated the specimen to the Museum Desjardins (now Natural History Museum at Mauritius Institute). Thrioux's heirs sold a second mounted composite skeleton (composed of at least two skeletons, with a mainly reconstructed skull) to the Durban Museum of Natural Science in South Africa in 1918. Together, these two skeletons represent the most completely known dodo remains, including bone elements previously unrecorded (such as knee-caps and wing bones). Though some contemporary writers noted the importance of Thrioux's specimens, they were not scientifically studied, and were largely forgotten until 2011, when sought out by a group of researchers. The mounted skeletons were laser scanned, from which 3-D models were reconstructed, which became the basis of a 2016 monograph about the osteology of the dodo. In 2006, explorers discovered a complete skeleton of a dodo in a lava cave in Mauritius. This was only the second associated skeleton of an individual specimen ever found, and the only one in recent times.

Worldwide, 26 museums have significant holdings of dodo material, almost all found in the Mare aux Songes. The Natural History Museum, American Museum of Natural History, Cambridge University Museum of Zoology, the Senckenberg Museum, and others have almost complete skeletons, assembled from the dissociated subfossil remains of several individuals. In 2011, a wooden box containing dodo bones from the Edwardian era was rediscovered at the Grant Museum at University College London during preparations for a move. They had been stored with crocodile bones until then.