The first chapter describes the physical geography and geology of the islands with particular attention to the role of volcanoes and earthquakes. It also discusses the overall pattern of the flora and fauna including the fact that the islands can be divided, by what would eventually become known as the Wallace line, into two parts, those whose animals are more closely related to those of Asia and those whose fauna is closer to that of Australia.

The following chapters describe in detail the places Wallace visited. Wallace includes numerous observations on the people, their languages, ways of living, and social organization, as well as on the plants and animals found in each location. He talks about the biogeographic patterns he observes and their implications for natural history, in terms both of the movement of species and of the geologic history of the region. He also narrates some of his personal experiences during his travels. The final chapter is an overview of the ethnic, linguistic, and cultural divisions among the people who live in the region and speculation about what such divisions might indicate about their history.

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