The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and ~360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with machine learning algorithms to present a phylogenetically-informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. In contrast to other terrestrial vertebrates and their own diversity in the fossil record, extant turtles and crocodilians have not experienced any mass extinctions or shifts in diversification rate, or any significant jumps in rates of body-size evolution over time. We predict threat for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened crocodile and turtle species in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies.

archosauromorpha_Data_SourcesExcel file of all data sources and referencesarchosauromorpha_GenbankGenbank accession numbers for all sequence dataarchosauromorpha_ML_PhylogenyML phylogeny from RAxML in PDF format for viewingarchosauromorpha_ML_PhylogenyML phylogeny from RAxML in Newick format for analysisarchosauromorpha_PASTIS_386_10000Posterior distribution of 10,000 dated, taxonomically-complete phylogenies for non-avian Archosauromorpha, in Newick formatarchosauromorpha_PASTIS_386MrBayes input file for analyis, generated by PASTISarchosauromorpha_Spatial_Distance_MatrixSpatial-distance matrix of range centroids from all turtle and crocodilian speciesarchosauromorphaPartition file for RAxML analysis of phylogenyarchosauromorphaMatrix of DNA-sequence data in PHYLIP format for RAxML analysis