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Trying to Remember a Book that explored evolution of Dinosaurs to intelligence and then encountering humans
In this series prehistoric man is constantly fighting a reptilian species that uses genetically altered species to do their bidding. For example, a whale that has a water-tight "hold" they can sit in while the outside is armor plated.
Another thing the book presents is that the female reptiles are the dominant gender. The males mate with two females, the eggs are fertilized in the females, transferred back to males and are finally carried by males until maturation.