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The desert is composed of stratified layers of easily erodible siltstone, mudstone, and shale of the Triassic Chinle Formation. These fine grained rock layers contain abundant iron and manganese compounds which provide the pigments for the various colors of the region. Thin resistant lacustrine limestone layers and volcanic flows cap the mesas. Numerous layers of silicic volcanic ash occur in the Chinle and provide the silica for the petrified logs of the area. The erosion of these layers has resulted in the formation of the badlands topography of the region.
In the southern portions of the desert the remains of a Triassic Era coniferous forest have fossilized over millions of years. Wind, water and soil erosion continue to change the face of the landscape by shifting sediment and exposing layers of the Chinle Formation. An assortment of fossilized prehistoric plants and animals are found in the region, as well as dinosaur tracks and the evidence of early human habitation.