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Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch ( Perca flavescens ), Eurasian perch ( Perca fluviatilis ), pike perch ( Sander lucioperca ), and ruffe ( Gymnocephalus cernua ), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the  D .  rerio  branch to the sub-branch clustered by  P .  flavescens  and  P .  fluviatilis . The specific 93 fast-evolving genes and 57 positively selected genes in  P .  flavescens , compared with 22 shared fast-evolving genes among  P .  fluviatilis ,  G .  cernua , and  S .  lucioperca , showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in  S .  lucioperca  drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.

Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species