| Summary: | Capturing the mechanisms leading to the local extirpation of a species in deep-time is a challenge. Combining stable oxygen and carbon isotopic analyses on benthic and planktonic foraminifera and the otoliths of pelagic and benthic fish species, we reveal here the paleoceanographic regime shifts changes that took place in the Eastern Mediterranean from 7.2 to 6.5 Ma, in the precursor phase to the Messinian Salinity Crisis, and discuss the fishes’ response to these events. The step-wise restriction of the Mediterranean–Atlantic gateway impacted the Mediterranean fishes’ metabolisms, particularly those dwelling in the sea bottom. An important shift in the Mediterranean paleoceanographic conditions took place between 6.951 and 6.882 Ma, from predominantly temperature to salinity control, which was probably related to stratification of the water column. A regime shift at 6.814 Ma due to change in the influx amount, source and/or preservation of organic matter led a pelagic–benthic decoupling of the fish fauna. The oxygen isotopic composition of the benthic fish otoliths expresses higher salinity of the lower part of the water column at that time, and is accompanied by a rapid increase and then drop in the carbon isotopic compositions of the otoliths (which is metabolic rate proxy) of the benthic fish, ultimately leading to the local extirpation of the species. Overall, our results confirm that otolith stable oxygen and carbon isotopes are promising proxies for paleoceanographic studies and, when combined with those of foraminifera, can reveal changes in the life history and migration patterns of teleost fishes in deep time.
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