Direct comparison of mitochondrial markers for the analysis of swordfish population structure

► Compared mitochondrial control region and ND2 in population analysis. ► The control region has a high degree of homoplasy. ► ND2 is better at resolving swordfish population structure within stocks. ► There is structure between eastern and western swordfish spawning areas. ► Genetic markers should be assessed before large-scale studies are performed. When examining the population structure of swordfish ( Xiphias gladius; Linnaeus, 1758) for fisheries management, the traditional marker of choice has been the mitochondrial control region. However, homoplasy within the control region may render it an unsuitable marker. We compared the effectiveness of two mitochondrial markers for examining the population structure between four Indian and one Pacific Ocean sample sites, collected between 2006 and 2009. The control region analysis was unable to detect structure among populations, while ND2 analysis revealed structure between the Seychelles and two other populations, Timor Sea ( Φ ST = 0.012, P = 0.024) and Coral Sea ( Φ ST = 0.011, P = 0.029). The level of homoplasy observed in the control region (HI = 0.736) was considerably higher than that of ND2 (HI = 0.290). These results suggest that use of the control region has likely led in an underestimation of genetic differentiation between populations. Genetic markers should be chosen that are appropriate to the scale of subdivision under investigation.