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Unlike the gharial, the false gharial's snout broadens considerably towards the base and so is considerably more similar to those of true crocodiles than the gharial, whose osteology indicates a distinct lineage from all other living crocodilians. However, preliminary nuclear genetic sequences may indicate the gharial and false gharial had a shared ancestor at some point in prehistory. Other molecular studies have similarly indicated that it is the nearest relative (the sister taxon) of the gharial. Along with close fossil relatives, such as Maroccosuchus, it is thus increasingly classed in the family Gavialidae.

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