Unravelling the history of Neotropical plant diversification
Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent
Recommendation: posted 28 September 2017, validated 29 September 2017
South American rainforests, particularly the Tropical Andes, have been recognized as the hottest spot of plant biodiversity on Earth, while facing unprecedented threats from human impact [1,2]. Considerable research efforts have recently focused on unravelling the complex geological, bioclimatic, and biogeographic history of the region [3,4]. While many studies have addressed the question of Neotropical plant diversification using parametric methods to reconstruct ancestral areas and patterns of dispersal, Pirie et al.  take a distinct, complementary approach. Based on a new, near-complete molecular phylogeny of two Neotropical genera of the flowering plant family Annonaceae, the authors modelled the ecological niche of each species and reconstructed the history of niche differentiation across the region. The main conclusion is that, despite similar current distributions and close phylogenetic distance, the two genera experienced rather distinct processes of diversification, responding differently to the major geological events marking the history of the region in the last 20 million years (Andean uplift, drainage of Lake Pebas, and closure of the Panama Isthmus).
As a researcher who has not personally worked on Neotropical biogeography, I found this paper captivating and especially enjoyed very much reading the Introduction, which sets out the questions very clearly. The strength of this paper is the near-complete diversity of species the authors were able to sample in each clade and the high-quality data compiled for the niche models. I would recommend this paper as a nice example of a phylogenetic study aimed at unravelling the detailed history of Neotropical plant diversification. While large, synthetic meta-analyses of many clades should continue to seek general patterns [4,6], careful studies restricted on smaller, but well controlled and sampled datasets such as this one are essential to really understand tropical plant diversification in all its complexity.
 Antonelli A, and Sanmartín I. 2011. Why are there so many plant species in the Neotropics? Taxon 60, 403–414.
 Mittermeier RA, Robles-Gil P, Hoffmann M, Pilgrim JD, Brooks TB, Mittermeier CG, Lamoreux JL and Fonseca GAB. 2004. Hotspots revisited: Earths biologically richest and most endangered ecoregions. CEMEX, Mexico City, Mexico 390pp
 Antonelli A, Nylander JAA, Persson C and Sanmartín I. 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution. Proceedings of the National Academy of Science of the USA 106, 9749–9754. doi: 10.1073/pnas.0811421106
 Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, Sanmartín I, Sanchez-Meseguer A, Anderson CL, Figueiredo JP, Jaramillo C, Riff D, Negri FR, Hooghiemstra H, Lundberg J, Stadler T, Särkinen T and Antonelli A. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931. doi: 10.1126/science.1194585
 Pirie MD, Maas PJM, Wilschut R, Melchers-Sharrott H and Chatrou L. 2017. Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent. bioRxiv, 141127, ver. 3 of 28th Sept 2017. doi: 10.1101/141127
 Bacon CD, Silvestro D, Jaramillo C, Tilston Smith B, Chakrabartye P and Antonelli A. 2015. Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Science of the USA 112, 6110–6115. doi: 10.1073/pnas.1423853112
Hervé Sauquet (2017) Unravelling the history of Neotropical plant diversification. Peer Community in Evolutionary Biology, 100033. 10.24072/pci.evolbiol.100033
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
Evaluation round #1
DOI or URL of the preprint: 10.1101/141127
Version of the preprint: 1
Author's Reply, 28 Aug 2017
Decision by Hervé Sauquet, posted 07 Jul 2017
Your preprint has now been reviewed by Thomas Couvreur and myself. You will find our comments attached. Although I was less critical than Thomas, who has more expertise in this field, I agree with most of his comments and believe that addressing them would make a stronger manuscript. Upon second thought, I also realize that this study did not use any of the recent parametric methods to reconstruct ancestral areas and biogeographic scenarios (such as Lagrange and BioGeoBears), yet most of the paper focuses on the biogeographic history of these two clades. It would be worthwhile explaining why in your text as some readers might also wonder about this.
I hope you will find these comments useful and would be very happy to recommend your preprint if you could address them. Although PCI Evol Biol is not a formal publication yet and we are all learning and testing the system here, I would suggest to treat this invitation to revise as you would for a traditional publication: please provide a point-by-point response to our comments and highlight your modifications in the revised manuscript.
I look forward to receiving your revised preprint.