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Faunal Remains Liang Bua cave includes many faunal remains. This assemblage has well-preserved mollusc, reptile, mammal, and bird remains, many of which show examples of island gigantism or dwarfism. Stegodon and komodo dragon remains in the cave are attributed to Homo floresienses, who probably preyed upon juvenile specimens, while smaller remains are attributed to local predatory birds. There are at least 47 Stegodon (Stegodon florensis insularis) individuals experiences insular, or island, dwarfism in the excavated areas of Liang Bua, represented by mostly dental remains. These dental remains show a 30% linear size reduction from its Early/Middle Pleistocene ancestor (Stegodon florensis florensis). The stegodon reached central Flores ~880ka, replacing the extinct, more dwarfed species, Stegodon sondaari. By approximately 900,000 years ago, komodo dragon remains are present on Flores. Giant rats are found in the cave, and could grow to a length of 115cm (tail included). The four species of giant rat recorded at Liang Bua are now extinct. Middle and smaller-sized rats also existed in the cave, as well as many introduced mammal species, including the Sulawesi warty pig (~7ka), Eurasian pig, Javanese porcupine, Masked palm civet, and Long-tailed macaque (~4ka). Nearly all of the avian remains in the cave are still present on Flores today, and occur only sporadically throughout the cave's archaeological sequence. The birds that no longer exist include a giant species of Leptoptilos, a large endemic Tyto species, and all Vini species. Mollusc remains only appear relatively recently in the Liang Bua deposits, and were certainly leftovers of human consumption.

Extinction By ~17ka, researchers no longer see Stegodon florensis insularis and H. floresiensis in the Liang Bua fossil record, along with some endemic bird species. This may be attributed to a volcanic eruption ~17ka, which deposited a thick silt layer in the cave. The eruption may have had a snowball effect, disrupting ecological processes and systems, and influencing flora-related productivity. Compounding this incidence is evidence of a changing climate toward the end of the Pleistocene (17-11ka). The climate seems to have gotten wetter, which thickened the soil and resulted in the loss of many bird taxa. The extinction on Flores at this time is mirrored on many other Pacific and Southeast Asian islands. Modern humans arrived to Liang Bua ~11ka. Aside from modern skeletons, researchers also find stone artifacts, deliberate disposal of the dead, and evidence for the transport of goods ~40km away, all indicated a modern human presence.