Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibian diversity is composed of both older, depauperate lineages and extensive, more recent tropical radiations found in select clades. Frog and salamander diversification increased strongly after the Cretaceous–Palaeogene boundary, preceded by a potential mass-extinction event in salamanders. Diversification rates of subterranean caecilians varied little over time. Biogeographically, the Afro- and Neotropics harbour a particularly high proportion of Gondwanan relicts, comprising species with high evolutionary distinctiveness (ED). These high-ED species represent a large portion of the branches in the present tree: around 28% of all phylogenetic diversity comes from species in the top 10% of ED. The association between ED and imperilment is weak, but many species with high ED are now imperilled or lack formal threat status, suggesting opportunities for integrating evolutionary position and phylogenetic heritage in addressing the current extinction crisis. By providing a phylogenetic estimate for extant amphibians and identifying their threats and ED, we offer a preliminary basis for a quantitatively informed global approach to conserving the amphibian tree of life.
amph_shl_new_Backbone
Species chosen from the 4,061-species matrix for representation in the 175-species backbone tree.
amph_shl_new_Classification
Classification of 7,238 amphibian species, indication of data presence/absence, and dimensions of available sequence data.
amph_shl_new_Consensus_7238
Consensus of 10,000 fully-sampled trees from the posterior, containing both data species (4,061) and imputed taxa (3,177).
amph_shl_new_GenBank
GenBank accession numbers for the 4,061 species in the 15-gene matrix.
amph_shl_new.ED.1000
ED values for 7,238 species calculated from 1,000 randomly sampled trees from the posterior.
amph_shl_new
Best-fit evolutionary models for the 15-gene, 4,061-species alignment.
amph_shl_new.phy
The 15-gene, 4,061-species alignment, zipped.
amph_shl_new
The NNI-optimized ML phylogeny containing 4,061 species, from 15-gene alignment, with SHL support values.
Supplemental_Figures_S1-12
Supplementary Figures S1-12
Global_Ecoregion_Assignments
Assignment of 7238 amphibian species to 12 global ecoregions. Some species are listed two or three times, as they occur in multiple ecoregions, for a total of 7474 entries.
Amphibian_ED_Threat_EDGE_Isaac
Primary results from the phylogenetic analyses, including the ED score of all 7,238 species, the upper and lower 2.5% range of ED scores per species, the threat status of each species, its EDGE score, and the ED and EDGE scores reported for 4,307 species by Isaac et al.
amph_shl_new_Posterior_7238.1000.trees
First 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.2000.trees
Second 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.3000.trees
Third 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.4000.trees
Fourth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.5000.trees
Fifth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.6000.trees
Sixth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.7000.trees
Seventh 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.8000.trees
Eighth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.9000.trees
Ninth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.
amph_shl_new_Posterior_7238.10000.trees
Tenth 1000 taxonomically complete, dated trees, containing 7,238 amphibian species.