DOI: 10.5061/dryad.jdfn2z38x
title: Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America

description: Aim: We investigate the biogeographic history and diversification in a
 treefrog lineage distributed in contrasting (open and forested) ecoregions
 of South America, including three biodiversity hotspots. We evaluate the
 role of dispersal and whether other factors such as diversity-dependence
 or paleotemperatures could explain the diversification pattern for this
 group. Especially focusing on the savanna endemics, we illuminate on
 processes governing the species assembly and evolution of the Cerrado
 savanna. Location: South American ecoregions south of the Amazon (e.g.
 Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern
 Andes). Taxon: Boana pulchella group. Methods: We built the most complete
 time-calibrated phylogeny for the group to date. We then reconstructed
 ancestral ranges using the dispersal-extinction-cladogenesis (DEC) model
 comparing different dispersal scenarios considering distance, adjacency
 and ecological similarity among regions. A center-of-origin hypothesis in
 forest versus open ecoregions was also tested. Using biogeographical
 stochastic mapping, we additionally estimated the contribution of range
 shifts across different biomes. Lastly, we evaluated several
 diversification models, including the effect of time, diversity-dependence
 and temperature-dependence on speciation and extinction rates. Results:
 The Boana pulchella group originated during the Early Miocene (~17.5 MYA)
 and underwent high speciation rates during the Middle Miocene Climatic
 Optimum, with a decreasing trend following the Miocene Climatic
 Transition. We found no support for a single ecoregion acting as a center
 of origin and diversification; instead, we inferred recurrent range shifts
 with dispersal among dissimilar adjacent ecoregions. Speciation linearly
 dependent on paleotemperatures, with either no or very low constant
 extinction rates, best explained the slowdown diversification pattern.
 Main Conclusions: Our results support a species assembly of Cerrado
 savanna in South America during the Miocene with intermittent interchange
 with rainforest habitats. Past climate changes impacted the rate new
 species originated with apparently no impact on extinction. Finally, the
 repeated habitat shifts among open/dry and forested/humid ecoregions,
 rather than long-term in-situ diversification in single areas, highlights
 the very dynamic historical interchange between contrasting habitats in
 South America, possibly contributing to its high species diversity.
description: <strong>BioGeoBEARS_model_selection_&_BSM.R</strong> – BioGeoBEARS script running DEC for models M0, M1, M2, M3, M4 and M5, with a BSM analysis for the selected model (M5: adjacency dispersal). <strong>hyptree_R.tre</strong> – Input tree used for diversification and BioGeoBEARS analyses. <strong>input_BioGeoBEARS.txt</strong> – BioGeoBEARS input file with species biogeographical ranges. <strong>manual_dispersal_multipliers_M1.txt</strong> – Dispersal rate multiplier for M1 model (center of origin E). <strong>manual_dispersal_multipliers_M2.txt</strong> – Dispersal rate multiplier for M2 model (center of origin C). <strong>manual_dispersal_multipliers_M3.txt</strong> – Dispersal rate multiplier for M3 model (center of origin A). <strong>manual_dispersal_multipliers_M4.txt</strong> – Dispersal rate multiplier for M4 model (eco-similarity dispersal). <strong>manual_dispersal_multipliers_M5.txt</strong> – Dispersal rate multiplier for M5 model (adjacency dispersal). <strong>rpanda_pulchella_group.html</strong> – Script used for diversification analyses in R using Rmarkdown exported here as an HTML file (open it in a web browser).