Unlike the original peopling of the Caribbean islands, which came late in the human settlement of the Americas, it was in these islands that the secondary – Columbian – colonization of the continents had its beginning. This was not the only significant difference between the two colonizations. The secondary phase, which reached the islands in 1492 with Columbus did not have roots in the tropical rimland, as did the first colonization, but rather had its origins far away across the Atlantic, in Europe. It brought in its wake peoples, plants, animals, and technologies not only from Europe but from across the globe – particularly Africa, but also from the world beyond the Atlantic, from Asia and the Pacific. Further, whereas the first colonization peopled the islands, the initial impact of the secondary wave was characterized not by an augmentation of island populations but their destruction.

When Europeans first voyaged to the Caribbean, the Taíno population they encountered was relatively homogeneous and derived from a limited continental source. In the islands, the founder effect was so powerful that genetic diversity was being reduced rather than expanded. The first colonizers of the Caribbean brought with them few animals, but over time reduced the species diversity of the islands through extinctions. They carried with them a wider variety of plants and some of these, notably cassava, were fundamental to the food supply of a growing population, but at the same time the spread of agriculture was accompanied by the burning of forest.