Supplementary material from "The Paleozoic assembly of the holocephalan body plan far preceded post-Cretaceous radiations into the ocean depths"

Among cartilaginous fishes, Holocephali represents the species-depauperate, morphologically conservative sister to sharks, rays, and skates and the last survivor of a once far greater Paleozoic and Mesozoic diversity. Currently, holocephalan diversity is concentrated in deep-sea species, suggesting that this lineage might contain relictual diversity that persisted in the ocean depths. Yet, the relationships of living holocephalans to their extinct relatives and the timescale of diversification of living species remains unclear. Here, we reconstruct the evolutionary history of holocephalans using comprehensive morphological and DNA sequence datasets. Our results suggest that crown holocephalans entered and diversified in deep (>1000 m) ocean waters after the Cretaceous-Paleogene mass extinction, contrasting with the hypothesis that this ecosystem has acted as a refugium of ancient cartilaginous fishes. These invasions were decoupled from the evolution of key features of the holocephalan body plan, including crushing dentition, a single frontal clasper, and holostylic jaw suspension, during the Paleozoic Era. Yet, they considerably postdated the appearance of extant holocephalan families by 150 million years ago during a major period of biotic turnover in oceans termed the Mesozoic Marine Revolution. These results clarify the origins of living holocephalans as the recent diversification of a single surviving clade among numerous Paleozoic lineages.