This paper describes Harvard archaeologist John Shea who has proposed that human cognition has not changed much since the species homo sapien arose and that the more 'complex' culture that we see today is really just a product of different environmental challenges.
This paper called Fossils Versus Clocks details some of the challenges and benefits of using either method to determine dates of speciation and emergence of species.
This paper used molecular phylogenetic analysis to determine the placental mammal ancestor and the geographic spread and speciation of major clades of placental mammals after the Cretaceous-Paleogene boundaries.
This Science News article shows that the appendix evolved over 30 times in mammals. They did this by mapping species with the appendix onto a phylogenetic tree and seeing that these species were spread out all over the tree.