The authors do not understand phylogeny, and have a very limited understanding of the biological vocabular and issues. They propose that if common descent is correct, then:
A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).Explore Evolution, p. 57
This is simply wrong.
Genes and organisms are very different things; gene family trees and organism family trees can, and do, differ. Contrary to the book's statements, evolutionary biology does not expect these trees to match up exactly. Rather, the relationship between genes and organisms is an issue in biology that is under active research in a wide range of fields.