Study of diversity at the nucleotide sequence level across the whole genome has provided a useful understanding of numerous processes. However, until recently these studies have been largely focussed within a species but using different populations. This is set to change with the explosion of datasets that are being generated in many species across the globe. We have made our tiny bit of contribution to the use of such an approach with a recent pre-print on bioRxiv "Genome-wide signatures of genetic variation within and between populations - a comparative perspective".
Many other studies (Singhal et al., Van Doren et al., Ludo et al.) have shown this pattern of correlated landscapes of diversity and divergence. Some have even addressed other questions related to speciation rates, habitat preference as well as their impact on the diversity and divergence landscape. We are also seeing studies in other species groups such as primates and trees. Theoretically oriented groups have also started getting into the nitty gritty of things by trying to understand the patterns better and get into the processes driving them.
The figure-1 (b) from the bioRxiv paper is very interesting as I managed to sneak in the flags of both Germany and Sweden :). We had to cut it in our paper now published with a different title "Genome-wide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa". Our paper even got featured on the Molecular Ecologist blog with a write-up by Arun Sethuraman.