In Colonial códices, the tlacuilos, master artist-scribes and experts in the application of color, continued the tradition of representing visually many aspects of the history and cultures of Mesoamerica. They employed traditional materials such as paper made of bark, cloth, and animal skins, as well as dyes made from plants and mineral pigments. European paper began to be used in the 16th century, yielding códices in book form, a change from the earlier accordion format. Roman Catholic evangelizing of the Indians led to the destruction of many códices, because they preserved indigenous religions and were thus considered dangerous. Some colonial códices nevertheless document religious practices, since the Spanish friars needed this knowledge for their missionary work. The need to establish effective communication between conqueror and colonized explains the appearance of what is referred to as "mixed" códices, characterized by a combination of glyphs and figures from the indigenous tradition with dates and numbers in Arabic and roman characters, as well as written text. Some texts were written in Spanish, others in native languages, and still others in bilingual form.

Approximately 500 Colonial códices are currently known. This number is likely to increase, however, as more manuscripts no doubt await discovery in remote towns and provinces. Some communities have preserved such treasured documents for centuries; some are in private hands and are therefore inaccessible to scholars.

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