Good references for pre-European contact indigenous populations and environments is The Pristine Landscape by William Denevan, published in The Wilderness Debate, edited by J. Baird Callicott and Michael P. Nelson, and The First Americans: In Pursuit of America’s Greatest Mystery, by J.M. Adovasio with Jake Page.
Carole Mandryk’s article “Invented Traditions and the Ultimate American Origin Myth: In the beginning…there was an ice free-corridor,” in The Settlement of the American Continents, edited by C. Michael Barton, et al., is an excellent presentation of recent archeological investigations into alternative indigenous migration routes and dates to the Americas, as well as Quest for the Lost Land, by Renee Hetherington et.al. that appeared in the February 2004 issue of Geotimes.
Windover: Multidisciplinary Investigation of an Early Archaic Florida Cemetery, by Glen Doran, is an excellent presentation of archaeological and biological evidence about a unique Native American burial site.
The article “How Columbus Sickened the World: Why Were Native Americans so Vulnerable to the Diseases European Settlers Brought With Them,” by D.J. Meltzer (New Scientist, 1992:30-38) is a good summary of the consequences of European diseases in the New World.
For more information about Bartolome’ de las Casas, an accessible article is “Prophet and Apostle: Bartolome’ de las Casas and the Spiritual Conquest of America,” in Christianity and Missions: 1450-1800 edited by J.S. Cummins.
American Indian Population Recovery in the 20th Century by Nancy Shoemaker, is a good historical discussion of indigenous population loss and recovery.
In addition to the archaeology resources cited in the Introduction, An Introduction to Archaeology,by Brain Fagan, is a good presentation of how archaeology is done, with particular reference to North America.
If your library has a copy of the pricey American Indian Linguistics and Literatures by William Bright (English publication by Mouton de Gruyter, 1984) it is an excellent source of information about American Indian languages.
The Oldest Europeans: Who are we? Where do we come from? What made European women different? by J.F. del Giorgio, discusses human migrations to Europe and the history of the Basque people.
There of a number of websites (many of them free) which help people in doing genealogical research about their families.