At the time of the fall of Nojpetén, there are estimated to have been 60,000 Maya living around Lake Petén Itzá, including a large number of refugees from other areas. It is estimated that 88% of them died during the first ten years of colonial rule owing to a combination of disease and war. Although disease was responsible for the majority of deaths, Spanish expeditions and internecine warfare between indigenous groups also played their part. Catholic priests from Yucatán founded several mission towns around Lake Petén Itzá in 1702-1703. The first towns to be concentrated into colonial reducciones were Ixtutz, which became the new town of San José, and neighbouring San Andrés, both on the north shore of Lake Petén Itzá. They were first subjugated by one of Ursúa's officers, Cristobal de Sologaistoa, before being passed into the care of the Dominican friars for the Christian conversion of the inhabitants. Surviving Itza and Kowoj were resettled in the new colonial towns by a mixture of persuasion and force. Kowoj and Itza leaders in these mission towns rebelled against their Spanish overlords in 1704 and almost retook Nojpetén, but although well-planned, the rebellion was quickly crushed. Its leaders were executed, and most of the mission towns were abandoned; by 1708 only about 6,000 Maya remained in central Petén. The reductions failed in large part because the missionaries charged with converting the inhabitants could not speak the Itza language.

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