Fisheries Research 93 (2008) 54–63 Contents lists available at ScienceDirect Fisheries Research journal homepage: www.elsevier.com/locate/fishres Resolving species identification problems in the genus Sebastes using nuclear genetic markers Christophe Pampoulie ∗ , Anna Krist´ ın Dan´ ıelsd ´ ottir 1 Marine Research Institute, Population Genetics, Sk´ ulagata 4, 101 Reykjav´ ık, Iceland article info Article history: Received 18 October 2007 Received in revised form 16 February 2008 Accepted 18 February 2008 Keywords: Microsatellite loci Sebastes spp. Species determination Bayesian methods abstract The identification of North Atlantic redfish has been controversial and remains a difficult task due to overlapping of meristic and morphological characters. Here we used nine microsatellite loci to assess the level of genetic differentiation among these species and assess the resolution power of these microsatel- lite loci for individual assignment-based analyses. Conventional analyses as well as individual Bayesian assignment methods clearly separated the four species of North Atlantic redfish as well as the giant form of Sebastes marinus and the so-called “oceanic” and “deep-sea” types of Sebastes mentella. Locus-by-locus analyses revealed that only five microsatellite loci out of nine used could discriminate the concerned species. The advantage of the Bayesian methods relies in the individual information retrieved. It there- fore gave additional information on the interrelationship among species. Indeed, we provide evidence of potential hybridization among species as well as individual misclassification based on morphological identification. We provide a powerful tool to discriminate North Atlantic redfish species, which might be useful for legal issues such as poaching, unintentional harvesting and control label. © 2008 Elsevier B.V. All rights reserved. 1. Introduction Phenotype-based species identification remains a difficult task due to overlapping of meristic and morphological characteristics especially in the case of closely related species. The development of new methods such as polymerase chain reaction (PCR)-based techniques solved several taxonomic as well as management issues. Molecular forensic methods have indeed been increasingly used to tackle issues related to species conservation and stock management such as poaching (An et al., 2007), illegal translocation of individuals (Frantz et al., 2006) and species identification problems (Calo-Mata et al., 2003; Maes et al., 2006; Roques et al., 1999a). Molecular DNA analysis has a tremendous advantage over other genetic techniques such as allozymes and haemoglobin pattern, e.g. the analysis is independent of the sample origin (liver, gonad, flesh) and collec- tion, the information content of DNA is higher compared to that of protein due to degeneracy of genetic code, and finally the DNA molecule is rather stable allowing its extraction from many dif- ferent types of samples such as degraded, processed or archived DNA sources (Nielsen et al., 1999; Poulsen et al., 2006). Although mitochondrial DNA markers (mtDNA) have been intensively used ∗ Corresponding author. Tel.: +354 575 2038; fax: +354 575 2001. E-mail address: chrisp@hafro.is (C. Pampoulie). 1 Current address: The Icelandic Centre for Research-RANNIS, Laugavegi 13, 101 Reykjav´ ık, Iceland. for species identification (Avise, 2004), they are inherited mater- nally and only represent one lineage which might lead to spurious conclusions, especially in the identification of hybrids, admixture events and/or introgression. Microsatellite loci which are short- repeated tandem (STRs) sequence of nucleotide in the genomic DNA have been proved to be particularly useful for species iden- tification (Calo-Mata et al., 2003; Maes et al., 2006; Roques et al., 1999a) due to their high variability, their codominant nature and the high intraspecific discrimination power on small and large geo- graphical scale. However, uncertainty regarding their usefulness for phylogenetic analyses persists because of homoplasy (Estoup et al., 2002). Due to size constraints, microsatellite alleles will mutate back to their former state, resulting in alleles identical by state but not by descent. Although homoplasy might play a smaller role in related species, it nevertheless tends to limit the genetic distance among reproductively isolated species, and may lead to the underestimation of genetic divergence among groups of individuals. This is particularly true in marine fish which exhibit large effective population size, a potentially high mutation rate at the microsatellite loci and a strong size constraint at the alleles (Estoup et al., 2002). One way to assess the presence of homo- plasy would be to analyze an assemblage of microsatellite loci with different level of polymorphism and analyze their contribution to the observed genetic pattern (see Maes et al., 2006; O’Reilly et al., 2004). The genus Sebastes is composed of more than 100 species among which the majority is distributed within the North Pacific. 0165-7836/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.fishres.2008.02.007