Indigenous issues extend into environmental and food insecurity concerns throughout the Navajo Nation. Other issues are generational or learned behavior due to colonization, forced sterilization, religious conversion, boarding schools, domestic violence, and alcoholism.

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A major factor of indigenous issues both past and present deal with the colonization and mass extermination of indigenous peoples in America. This was conducted actively through mass genocide, bounties on local animals, such as the buffalo, forced education through boarding schools, and religious conversion. In secrecy, the government sanctioned the involuntary sterilization of indigenous women. Through genetics and learned behavior this has lead to domestic violence, alcoholism, and other serious mental, emotional, and physical health problems.