The crevalle jack Caranx hippos (Carangidae: Caranginae) is a commercially important carangid, especially along the Brazilian Northeastern coast. However, little is known about its population structure and genetic diversity, which is crucial information for species conservation. Using mitochondrial [barcode region COI and control region] and nuclear (first intron S7) data, we investigated the genetic structure and demographic history of C. hippos along the Brazilian Northeastern coast, and included the COI public database to provide a latitudinal approach. Both mitochondrial markers revealed two coexistent lineages along the Brazilian Northeastern coast, while the nuclear DNA did not recover any signals of structure. This mitonuclear discordance can be explained by both male dispersal and demographic history, which seem to be closely related to the Pleistocene period. Over the glacial cycles, the lineages may have used different refuges, regaining contact during the interglacial cycles. This hypothesis of previous allopatry is reinforced by the profound genetic distance found. The latitudinal approach reveals a deep differentiation between the Carolina and both Brazilian and Caribbean Provinces, with high and significant FST pairwise values, such that the tropical-temperate climate transition may be acting as a gene flow barrier between them. Thus, we suggest two preliminary stocks for C. hippos in the Atlantic: (1) Carolina and (2) Brazilian and Caribbean Provinces.
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