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Origin and evolution

Scientists have been proposing since the 1910s that flatfishes evolved from percoid ancestors. There has been some disagreement whether they are a monophyletic group. Some palaeontologists think that some percomorph groups other than flatfishes were "experimenting" with head asymmetry during the Eocene, and certain molecular studies conclude that the primitive family of Psettodidae evolved their flat bodies and asymmetrical head independently of other flatfish groups. Many scientists, however, argue that pleuronectiformes are monophyletic.

The fossil record indicates that flatfishes might have been present before the Eocene, based on fossil otoliths resembling those of modern pleuronectiforms dating back to the Thanetian and Ypresian stages (57-53 million years ago).

Flatfishes have been cited as dramatic examples of evolutionary adaptation. Richard Dawkins, in The Blind Watchmaker, explains the flatfishes' evolutionary history thus:

...bony fish as a rule have a marked tendency to be flattened in a vertical direction.... It was natural, therefore, that when the ancestors of took to the sea bottom, they should have lain on one side.... But this raised the problem that one eye was always looking down into the sand and was effectively useless. In evolution this problem was solved by the lower eye 'moving' round to the upper side.

The origin of the unusual morphology of flatfishes was enigmatic up to the 2000s, and early researchers suggested that it came about as a result of saltation rather than gradual evolution through natural selection, because a partially migrated eye were considered to have been maladaptive. This started to change in 2008 with a study on the two fossil genera Amphistium and Heteronectes, dated to about 50 million years ago. These genera retain primitive features not seen in modern types of flatfishes. In addition, their heads are less asymmetric than modern flatfishes, retaining one eye on each side of their heads, although the eye on one side is closer to the top of the head than on the other. The more recently described fossil genera Quasinectes and Anorevus have been proposed to show similar morphologies and have also been classified as "stem pleuronectiforms". Suchs findings lead Friedman to conclude that the evolution of flatfish morphology "happened gradually, in a way consistent with evolution via natural selection —not suddenly, as researchers once had little choice but to believe."

To explain the survival advantage of a partially migrated eye, it has been proposed that primitive flatfishes like Amphistium rested with the head propped up above the seafloor (a behaviour sometimes observed in modern flatfishes), enabling them to use their partially migrated eye to see things closer to the seafloor.

While known basal genera like Amphistium and Heteronectes support a gradual acquisition of the flatfish morphology, they were probably not direct ancestors to living pleuronectiforms, as fossil evidence indicate that most flatfish lineages living today were present in the Eocene and contemporaneous with them. It has been suggested that the more primitive forms were eventually outcompeted.