Due to their vulnerability to fishing pressure, many species of skate (Rajidae) in the Northeast Atlantic are undergoing declines in abundance. The assessment of stock status and subsequent proposal of management measures are often complicated by high levels of species diversity and endemism, coupled with morphological and ecological conservatism, which makes distinguishing between species difficult. To improve the identification of skates and investigate the phylogenetic position of endemic species the cytochrome c oxidase subunit I (COI) was sequenced in 12 species (Dipturus oxyrinchus, Leucoraja naevus, Leucoraja circularis, Neoraja iberica, Raja brachyura, Raja clavata, Raja maderensis, Raja microocellata, Raja miraletus, Raja montagui, Raja undulata, Rostroraja alba) inhabiting the Portuguese waters. Based on sequence divergence R. maderensis and R. clavata only differ by 1% of the 652 bp COI sequence, questioning the recognition of R. maderensis (considered to be endemic to Madeira and the Azores), as a reproductively isolated species. Otherwise, there was clear phylogenetic support for the different genera and all the remaining species, although the genetic divergence was low compared to other chordates. In particular, COI analysis allowed clear identification of the morphologically similar species R. brachyura and R. montagui.
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