The best book on the subject is Conquest and Pestilence in the Early Spanish Philippines by Linda Newson. The conventional thinking was that since the Philippines participated in Old World trade networks, the people had already developed immunity to common diseases. Newson argues that because of the widely dispersed population previous imported epidemics would not have had the chance to spread through the population and therefore most people would have lacked any immunity. Using records from Church archives she tries to calculate populations region by region pre and post conquest and estimates that population fell by over 50% at one point.