The influence of environmental change over geological time on the tempo and mode of biological diversification is a hot topic in biogeography. Of central interest are questions about where, when, and how fast lineages proliferated, suffered extinction, and migrated in response to tectonic events, the waxing and waning of dominant biomes, etc. In this context, the dynamic conditions of the Miocene have received much attention, from studies of many clades and biogeographic regions. Here, Chazot et al.  present an exemplary analysis of butterflies (tribe Ithomiini) in the Neotropics, examining their diversification across the Andes and Amazon. They infer sharp contrasts between these regions in the late Miocene: accelerated diversification during orogeny of the Andes, and greater extinction in the Amazon associated during the Pebas system, with interchange and local diversification increasing following the Pebas during the Pliocene.
Two features of this study stand out. First is the impressive taxon sampling (340 out of 393 extant species). Second is the use of ancestral range reconstructions to compute per-lineage rates of colonization between regions, and rates of speciation within regions, through time. The latter allows for relatively fine-grained comparisons across the 2 fundamental dimensions of historical biogeography, space and time, and is key to the main results. The method resonated with me because I performed a similar analysis in a study showing evidence for uplift-driven diversification in the Hengduan Mountains of China . This analysis is complemented by a variety of other comparative methods for inferring variable diversification across clades, through time, and in response to external factors. Overall, it represents a very nice contribution to our understanding of the effects of Miocene/Pliocene environmental change on the evolution of Neotropical biodiversity.
 Chazot N, Willmott KR, Lamas G, Freitas AVL, Piron-Prunier F, Arias CF, Mallet J, De-Silva DL and Elias M. 2017. Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation. BioRxiv 148189, ver 4 of 19th December 2017. doi: 10.1101/148189
 Xing Y, and Ree RH. 2017. Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot. Proceedings of the National Academy of Sciences of the United States of America, 114: E3444-E3451. doi: 10.1073/pnas.1616063114
DOI or URL of the preprint: 10.1101/148189
Version of the preprint: 1
Dear authors, I now have received reviewers' comments. Based on their evaluation, I would like you to make the modifications they suggest and to reply point by point to their questions. In addition, I also see some caveats -- the most important probably being that extinction is not accounted for in any meaningful sense. More discussion of these would benefit the paper. Also, it is not stated how ancestral ranges at nodes were converted to dispersal events in time, whether at the crowns or stems, or along branches somehow. As noted by the other reviewers, the study makes use of a variety of comparative methods for inferring diversification and geographic range evolution but does not include some that would seem to make sense (e.g., BAMM for inferring shifts in diversification). These omissions are not explained, or rather, the rationale for selecting the methods used is not made clear. In addition to BAMM, the HiSSE model came to mind. Also, details are missing such as: why was both ClaSSE and BiSSE used to study the trait "Andean/non-Andean”?