Nature doesn't give anyone rights, no one is born with them. A community of people, who often have a government or recognized authorities, grant and protect the rights of its citizens. Jefferson didn't believe it was "nature" that grants people rights, but God—a transcendental, absolute authority with a kingdom or government. If you don't believe that divine authority granted people their basic rights or an earthly community of human beings, then you have no rights.
Mother nature is a biatch, she doesn't grant rights, but she will provide you with some instinctual patterns of thought and behavior that will keep you from danger, increasing your chances of survival. Those aren't rights they're inherent abilities that contribute to your survival. Your ability to feel pain, and sense a potential predator lurking in the dark, your propensity for social interaction and cooperating with other human beings. All of these attributes that most human beings possess are natural endowments. Rights are given by an earthly community or its authorities/government or a divine, heavenly authority, namely God. Nature doesn't create or protect rights.
Jefferson was a Deist, who believed in God. The source of rights according to him is God, not mother nature.