DOI: 10.5061/dryad.kwh70rz4w
title: Diversification dynamics in the Neotropics through time, clades and biogeographic regions

description: The origins and evolution of the outstanding Neotropical biodiversity are
 a matter of intense debate. A comprehensive understanding is hindered by
 the lack of deep-time comparative data across wide phylogenetic and
 ecological contexts. Here, we quantify the prevailing diversification
 trajectories and drivers of Neotropical diversification in a sample of 150
 phylogenies (12,512 species) of seed plants and tetrapods and assess their
 variation across Neotropical regions and taxa. Analyses indicate that
 Neotropical diversity has mostly expanded through time (70% of the
 clades), while scenarios of saturated and declining diversity account for
 21% and 9% of Neotropical diversity, respectively. Five biogeographic
 areas are identified as distinctive units of long-term Neotropical
 evolution, including Pan-Amazonia, the Dry Diagonal, and
 Bahama-Antilles. Diversification dynamics do not differ across these
 areas, suggesting no geographic structure in long-term Neotropical
 diversification. In contrast, diversification dynamics differ across taxa:
 plant diversity mostly expanded through time (88%), while a substantial
 fraction (43%) of tetrapod diversity accumulated at a slower pace or
 declined toward the present. These opposite evolutionary patterns may
 reflect different capacities for plants and tetrapods to cope with past
 climate changes
description: Dataset 1. Chronogram dataset. To compile this dataset,
 Neotropical clades were extracted from large-scale time-calibrated
 phylogenies of frogs and toads (Hutter <em>et al.</em> 2017),
 salamanders (Pyron <em>et al.</em> 2013; Pyron, 2014), lizards
 and snakes (Pyron & Burbrink 2014), birds (Jetz <em>et
 al.</em> 2012) (including only species for which genetic data was
 available), mammals (Bininda-Emonds <em>et al.</em> 2007; Kuhn
 <em>et al.</em> 2011), and plants (Zanne <em>et
 al.</em> 2014). To identify independent Neotropical radiations,
 species in these large-scale phylogenies were coded as distributed in the
 Neotropics – delimited by the World Wide Fund for Nature WWF – or
 elsewhere using the R package <em>speciesgeocodeR</em> 1.0-4
 (Töpel et al., 2017), and their geographical ranges extracted from the
 Global Biodiversity Information Facility “GBIF” (https://www.gbif.org/), the PanTHERIA database (https://omictools.com/pantheria-tool), BirdLife (http://www.birdlife.org) and eBird (http://ebird.org/content/ebird), all accessed in 2018, in a procedure similar to (Meseguer et al., 2020). Next, we pruned the trees to extract the most inclusive clades that contained at least 80% Neotropical species, as previously defined. This procedure ensures that the diversification signal pertains to the Neotropics. In addition, phylogenies of particular lineages not represented in the global trees (or with improved taxon sampling) were obtained from published studies or reconstructed <em>de novo</em> in this study (for caviomorph rodents, including 199 species; see SI). In the case of plants and mammals, most phylogenies were obtained from individual studies, given the low taxon sampling of the plant and mammal large-scale trees. However, whenever possible, we extracted phylogenies from a single dated tree rather than performing a meta-analysis of individual trees from different sources (Hoorn <em>et al.</em> 2010; Jansson <em>et al.</em> 2013), such that divergence times would be comparable. The resulting independent Neotropical radiations could represent clades of different taxonomic ranks. We did not perform any specific selection on tree size, crown age, or sampling fraction, but tested the effect of these factors on our results. Note that some of the phylogenies used in this study (10 trees) cannot be provided here, because they were obtained from third parties. These input phylogenies have to be obtained individually from the original sources Dataset 2. Diversification results for each clade show the strength of support for constant, time-, temperature- and Andean uplift-dependent models by computing Akaike information criterion (AICc), ∆AICc, and Akaike weights (AICω). For each model category, we fitted three models in which speciation (B) and/or extinction (D) remain constant (cst), or vary continuously with time, with temperature changes, or with the elevation of the Andes. Abbreviations: NP = number of parameters; logL = log likelihood.
description: Both Datasets 1 and 2 could be opened with a simple text
 editor. The 150 phylogenetic trees (Datasets 1), and
 the corresponding diversification results for each of these trees (Dataset
 2), are presented concatenated to minimise the number of files
 uploaded.