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Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America

Cite this dataset

Vasconcellos, Mariana (2020). Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America [Dataset]. Dryad.


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.

Usage notes

BioGeoBEARS_model_selection_&_BSM.R – BioGeoBEARS script running DEC for models M0, M1, M2, M3, M4 and M5, with a BSM analysis for the selected model (M5: adjacency dispersal).

hyptree_R.tre – Input tree used for diversification and BioGeoBEARS analyses.

input_BioGeoBEARS.txt – BioGeoBEARS input file with species biogeographical ranges.

manual_dispersal_multipliers_M1.txt – Dispersal rate multiplier for M1 model (center of origin E).

manual_dispersal_multipliers_M2.txt – Dispersal rate multiplier for M2 model (center of origin C).

manual_dispersal_multipliers_M3.txt – Dispersal rate multiplier for M3 model (center of origin A).

manual_dispersal_multipliers_M4.txt – Dispersal rate multiplier for M4 model (eco-similarity dispersal).

manual_dispersal_multipliers_M5.txt – Dispersal rate multiplier for M5 model (adjacency dispersal).

rpanda_pulchella_group.html – Script used for diversification analyses in R using Rmarkdown exported here as an HTML file (open it in a web browser).


National Science Foundation, Award: DEB 0334952 and DEB 1311517