The caste system derives from a Portuguese labeling system.
There was a history of religious conflict in Portugal that led to the development of a kind of classification system. When Portuguese colonists came to India, they applied similar practices to the native people.
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In the 1300s, the Christian Portuguese were persecuting the Jewish people. Under pressure from the empire, many Jews converted to Christianity. However, when those converts rose to prominent positions in the Church, they drew the resentment of "original" Christian clergy. Furthermore, those converts' subsequent affiliation with tax collectors made them unpopular with poor Christians. Thus, persecution continued against Jewish-descended Christians. Christian leaders began to declare that only "original" Christians were worthy of acknowledgement. The idea of a "casta," a classification based on descent, was formed. And members of the Jewish "casta" were barred from opportunity. When Portuguese colonists came to India, they applied the same classification system to the native people. They believed that different groups stayed separate to preserve a purity of bloodline, just as they did in Portugal. This idea propagated in India and became integral to its history. Not only the title, but also the very nature of the caste system, was given by the influence of the Portuguese.
The Portuguese influence on the caste system was nothing more than putting a name to a pre-existing practice of separation they observed on arrival, as Guha's article implies. They didn't invent the practice; they simply gave it the name we know it by today. But the practice itself has deep historical roots - far earlier than when the Portuguese arrived.