The Paleolithic Period, which ranges from the Middle Pleistocene (1.2 million years BP) to the Middle to Late Holocene (4000 years BP), is characterized by a hunting and gathering way of life and utilization of stone tools.

Research on this period intensified when Dr. Robert Fox explored and eventually excavated the Tabon Cave in Lipuun Point, Quezon, Palawan in the early 1960s, where flake tools assemblages, and human fossils from this collection were recovered. From Palawan, his attention was shifted to the north, in Cagayan Valley, where explorations and excavations of caves and open air sites in search for the early human were pursued. Sites in this region contain stone tools, and fragments and pieces of fossil bones of Middle Pleistocene fauna as surface finds. Direct association between the stone tools and the fossils could not be established for many years, until the discovery of a site in Rizal, Kalinga in 2014 by a composite team of French and Filipino archaeologists led by Dr. Thomas Ingicco. The fossil bones of an almost complete disarticulated rhinoceros exhibiting signs of butchery were retrieved within the same layer as stone tools, and other faunal remains, resulting in the earliest evidence of early human activity in the Philippines at about 709 thousand years ago.

Fossils and subfossils, or the preserved and partially preserved remains of humans, animals and plants whose parts were replaced by minerals until hardening into rocks, are around 10,000 years old or more. These fossilized materials aid in the reconstruction of paleoenvironments and chronobiostratigraphy of a time leading to or during early human occupation. Through analysis of faunal assemblages and archaeobotanical research from different sites, coupled with evidence of activities such as the presence of stone tools and other human activity-related remains, early hominin dispersal during the Quaternary can be inferred. Fossilized and subfossilized remains of humans, animals and plants from open air sites, cave sites, shell midden sites and other Late Pleistocene to Holocene sites comprise this collection.

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