The Permian-Triassic crisis drastically affected invertebrates, especially the benthos but had little effect on conodonts. Most Late Permian species survived the Permian-Triassic reduction of shallow-marine environments and repopulated Early Triassic seaways worldwide from a Tethyan source. For example, important North American Early Triassic species had Tethyan ancestors.

During the Early Triassic, conodont evolution produced diverse and abundant faunas that provide a superior biostratigraphy to that developed from ammonoids. This resurgence was relatively short-lived and during the Middle Triassic, extinction was more pronounced than evolution. Taxonomic reduction continued during Late Triassic and there are few Norian species. Rhaetic species are not known in North America but two species survived in the Tethyan Rhaetic. These Tethyan conodonts were extinct prior to the Jurassic. Post-Triassic conodont reports are of reworked or misidentified material or misidentified stratigraphy.

The reasons for extinction of conodonts are enigmatic. Late Triassic and Early Jurassic sequences in Austria and Nevada were studied to determine if environmental factors interpreted from the carbonate transition rocks could explain conodont extinction. No significant change in carbonate environment throughout the critical intervals was determined. The suggestion that extinction of higher taxa is an expected result of evolution and not the result of deficiencies shared by species of a group, has merit. Unknown factors of nutrients or predation are attractive alternatives to explain extinction but the idea that conodont extinction was plain bad luck or resulted from accumulation of unrelated species level extinctions must be considered.

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