The removal from family
Tobias does whatever he can to sacrifice for his family, but when the Civil War erupts, the Confederacy drafts him into their forces, which leaves his family ironically without support. The Confederacy is a force against the good of his family, because it makes him give his entire resources to the government while the people the government was supposedly designed to protect, his family of citizens, suffers and struggles.
The plagues
As if to add insult to injury, fate brings even more plagues and pestilence to the family, as if the war and the Confederate agenda were not disruptive enough. The family is burgled, beset by mosquitoes, and their livestock dies. The untimely nature of the plagues is an ironic portrait of how the war really damaged the family, because the family was made to endure harsh trials without the support of Tobias.
The ironic enmity of nature
Although nature is often celebrated for its restorative, cathartic qualities, this family is practically devastated by nature again and again. This culminates in a crisis when the family mother is attacked by a bear. Zecheriah must fight a bear to save his mother, and even in the aftermath the Florida wilderness is foreboding. They must worry about predators of all different kinds, as if nature intends to kill them. Ironically, one could make the argument that nature is literally designed for the survival of the fittest.
Zecheriah's replacement
When Zecheriah replaces Tobias as the head of the family, that is their way of accepting that Tobias is lost. That is ironic, because they have struggled this whole time, hoping along the way that perhaps Tobias will return one day, but instead, they experience a different outcome from the passage of time. Through the struggle, and through time, Zecheriah becomes qualified to replace his father, which would have inevitably happened anyway, so that Tobias is unnecessary.
The bitter feud
As in Biblical folklore, two sons fight bitterly as their father dies, late in this novel. Solomon and Toby make peace as Zecheriah's son Solomon is dying. In the passage of time, the family has made millions of dollars through land development, but the success of the family stands between them. Their ironic feud is the inverse opposite of Zecheriah and his mother's closeness. Struggle brought them together, and success ironically drives them apart.