Cronon, William. Changes in the Land: Indians, Colonists, and the Ecology of New England. Hill and Wang. New York. 1983. By far the most well read work on this subject. An invaluable source for anyone interested in the topic of Native American and Colonial land uses, or the time period in general.
Crosby, Alfred. Ecological Imperialism: The Biological Expansion of Europe 900-1900. Cambridge University Press. Cambridge. 1986. Easy to read book with a lot of pertinent information on disease ecology, and the destructive qualities of disease.
Diamond, Jared. Guns, Germs, and Steel. Norton and Company. New York. 1997. Popular book on the NY Times best seller list. Large, but very interesting book that does a good job at making the reader think about why history happened the way it did. Its wide appeal to many different readers explains it long stint on the best seller list, but there is a great deal of important information to be learned from this book.
Foster, David "The Importance of Land-Use Legacies to Ecology and Conservation" Bioscience. January 2003. Vol. 53. A scholarly article with insights on Native American land uses in Central America.
Hill, Kim. Hillard Kaplan, Kristen Hawkes, and Magdelena Hurtado. "Foraging Decisions Among Ache Hunter-Gatherers: New Date and Implications for Optimal Foraging Models" Ecology and Sociobiology. Vol. 8: 1-36 (1987) A scholarly article assigned as reading in our seminar. This work explains Optimal Foraging Theory in detail, discussing how organisms, (Ache Hunter-Gatherers of South America in this case) make economic decisions regarding when and how to forage for food.