Education
Education is one of the predominant themes of the book. Many of the characters' lives are directed by some sort of academic mandate, whether self-imposed or otherwise. For example, Caleb's father tells him that he doesn't have a place within his community and should make use of his peculiar skill set by learning from the white man. This sets his course on college, a goal which he achieves at Harvard. The preacher devotes the latter years of his life to educating these young men, since he is the most qualified in their small village. His devotion to academia inspires the boys to continue their education after his untimely death. Each of them continues on to graduate from college, even though earning the degree is not their ultimate fulfillment. While Caleb and Joel die soon after graduation, they use their collective influence among Native Americans to advocate for more interactions between cultures, especially in academic pursuits. Makepeace learns that school wasn't his real dream, and he does not graduate. He finds his purpose elsewhere. Finally, Bethia is denied many of the rights to education. She's a born academic, though, and finds a husband who believes in more egalitarian methods. Together they make a happy home near Cambridge and study and talk about learned matters.
Death
Death is an inescapable aspect of life in the New World. The Puritans were grossly unprepared for the natural challenges they were to face in building their own towns in New England. Even after they have established themselves, they are still subject to war, famine, and disease. Bethia's father dies by accident when his boat which was returning to England sinks in the Atlantic. He joins his wife who died in childbirth when Bethia was quite young. The Natives don't fare much better. Unprepared to fight off the unique diseases of the Old World, most of them die from disease, including Caleb and Joel. Death is a central part of life for these people living in an unforgiving wilderness.
Social Order
The role of social order is paramount in both of these cultures. For the Puritans, the teachings of the Bible are valued but as their church community interprets. This leads them to subjugate their women to a lesser role in society. They are relegated to the domestic parts of life -- homemaking, childrearing, etc. In their view, women are the inferior sex, and the large majority of citizens agreed. However, Bethia's father does not agree with the more extreme beliefs and practices of the Puritans and moves his family to the island of Great Harbor. He accepts a position there as the village preacher, a role which comes with immense power and prestige. He's one of the town elders to whom the young men are sent for education. Caleb's tribe has its own complex system of social values, to which he does not conform well. His father becomes convinced that Caleb will bring dishonor on them all if he doesn't think creatively, so he sends the boy to the Puritans. He recognizes his son's passionate intellect and tells him to learn all he can from the white man. Both Bethia and Caleb are required to act certain ways in order to satisfy their cultures, but they both find that the obvious answer is not the only one.