The book provides a reconstruction of the categories of thinking that are at work in the structural, historical, and the structuro-historical methods as they are applied in modern genetics, paleogenetics, and paleogenomics and that enable the growth and extension of knowledge. These categories are as follows: appearances, underlying structures, mechanisms of underlying structures, manifestations of underlying structures, transformations of underlying structures, historical interaction events between underlying structures. The scope of the book ranges from classics in sciences like those by Mendel, Newton, and Jean Perrin to authors like Svante Pääbo et al. with their recent contributions to paleogenomics. In philosophy and philosophy of science the authors addressed range from Kant and Hegel to philosophers of science who belong to the tradition of the modern mechanistic philosophy of science. The target audience are philosophers of natural science, philosophers of biological sciences, philosophers of physics, graduate students interested in philosophy of science, paleogeneticists, and paleoanthropologists.