Nature is running a little online feature 15 Evolutionary Gems that have been published on its pages over the past 10 years.
One of the interesting things you'll note is the amount of molecular biology appearing in the section on the fossil record. Nevertheless, fossils have given us next to zero molecular data (even what is known is a infinitesimally small proportion of fossils in the fossil record). The reason this is possible is because of the way in which fossils fit into the tree of life: they intercalate into the branches between living branches. Thus, they act as a sort of "control" on how we propose hypotheses of morphological change -- in fact they often tell us all we can know about morphological change.
But there's more to this than just fossils: stories from population-level studies show us how the mechanisms of evolution act. Fossils and gene expression data tell us about patterns, but population studies tell us about evolution at the level of process. How natural selection and other forces act to shape the morphology, physiology, and behaviour of organisms can only be studied in real time, using population-based analyses. The work highlighted by Nature tackles important topics such as the role of natural selection in speciation, co-evolution, and the contingent nature of evolution -- the necessary consideration of phylogenetic history in studying adaptation.
Finally, we marry these two through the study of molecular processes. Mutation, gene regulation, epigenetics, these are all forces that influence the possibilities of evolution. These are the driving forces of diversification, but also the conservative nature of descent with modification. It is a slow and stumbling processes. Nature illuminates these issues by covering gene regulation studies in Galapagos finches, insects, among other worthwhile reads.
My main problem with this piece, however, is the way in which item #13 suggests that there is a fundamentally different macroevolution and microevolution. It attributes perceived large steps in evolution as real and refers to them as "macroevolutionary". This reads to me like saltationism, which seems to be bore strictly out of the argument from ignorance or the assumption that gaps in the fossil record are real. Nevertheless, it's a nice summary and worth checking out.
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