Results
Neotropical Phylogenetic Dataset. We constructed a
dataset of 150 time-calibrated clades of Neotropical tetrapods and
plants derived from densely sampled molecular phylogenies (Fig.
1 and SI Appendix 1 and Fig. S1). The dataset comprises 12,524
species divided into 6,255 species of plants, including gymnosperms and
angiosperms (66 clades, representing 7% of the described Neotropical
seed plants; SI Appendix , Table S1); 900 mammal species (12
clades, 75% of the Neotropical mammals; SI Appendix , Table S2);
2,216 bird species (32 clades, 59% of the Neotropical birds; SI
Appendix , Table S3); 1,148 squamate species (24 clades, 33% of the
Neotropical squamates; SI Appendix , Table S4); and 2,005
amphibian species (16 clades, 69% of the Neotropical amphibian
diversity; SI Appendix , Table S5). Our dataset triplicates
the data presented in previous meta-analyses of the Neotropics in terms
of number of species (214 clades and 4450 species in ref. (Antonelliet al. 2018c), and quadruplicates it in terms of sampling (20.8
species per tree in ref. (Antonelli et al. 2018c) vs . 83.5
in our study). Each clade in our dataset included 7 to 789 species (mean
= 83.5 species), with 53% of the phylogenies including more than 50%
of the described taxonomic diversity (sampling mean = 57%; Fig.
1 and SI Appendix , Fig. S1). Clade ages of current Neotropical
diversity range from 0.9 to 88.5 Myrs (mean = 30.4 Myrs), with the
origin of current squamates (mean = 47.5 Myrs) and amphibians (mean = 66
Myrs) being comparatively older than the age of other groups
(meanbirds = 18.1 Myrs, meanmammals =
25.6, meanplants = 22.5 Myrs; Fig. 1 andSI Appendix , Fig. S1).
Diversification Dynamics in the Neotropics. To
understand the drivers of Neotropical diversification we compared the
fit of birth-death models applied to 150 phylogenies, including models
where diversification rates are constant, vary through time, vary as a
function of past global temperatures, or vary according to past Andean
elevation (see Methods ). Models assuming constant speciation and
extinction rates through time best fit half of the phylogenies in our
study (75 clades; 2,903 species; Fig. 2 and SI Appendix
2 and Table S6 and Fig. S2), often when clades are species-poor
(Kruskal-Wallis chi-squared test: χ2 = 53.675,
df = 3, P = 0.0; SI Appendix , Table S7 and Fig. S2).
Phylogenies best fitting a constant model are also significantly younger
than those fitting Andean uplift and temperature models
(χ2 = 41.96, df = 3, P = 0.0), even
though young clades do not tend to be species-poor (SI Appendix ,
Fig. S3). Taxon sampling does not differ significantly between the four
model categories investigated here, suggesting that there is not a
particular bias due to incomplete sampling in our results
(χ2 = 4.01, df = 3, P = 0.26; SI
Appendix , Table S7 and Fig. S2).
In the other half of the phylogenies analyzed here, representing most of
the Neotropical diversity (75 trees; 9,621 species; Fig. 3 andSI Appendix , Table S8), we find variation in diversification
rates through time, with 42 clades (4,486 species) showing slowdowns of
diversification and 33 increasing diversification (5,135 species). Rate
variation is inferred from models that are able to capture the
dependency of speciation and/or extinction rates over time
(time-dependent models) or over an environmental variable (either
temperature- or uplift-dependent models). Temperature-dependent models
explain diversification in 26% of the phylogenies and 44% of the
species sampled (5,487 species). Time-dependent models best fit 13% of
the clades (1,717 species, 13%). Meanwhile uplift-dependent models
explain 11% of the phylogenies (2,417 species, 19%) (Fig. 2and SI Appendix , Table S9), especially for ancient clades
(χ2 = 53.675, df = 3, P = 0.0; SI
Appendix , Table S7 and Fig. S2). Seven of these clades have an
Amazonean-centered distribution and are better fit by an uplift model.
We did not detect significant differences in diversification trends
(i.e., increasing, constant, decreasing) estimated between
tetrapod lineages living in distinct geographic ranges (Andean-centered,
Amazonian-centered, or other), elevations (lowland [<1000
m], montane [1000 – 3000 m], or highland [>3000
m]) or vegetation types (open tropical vegetation, tropical forest, or
non-tropical vegetation). For plants, we perceived, however, a
marginally non-significant difference in the frequency of
Amazonian-centered clades showing decreasing diversification through
time in comparison with Andean-centered and lineages with other
distribution (χ2 = 5.69, df = 2, P =
0.058).