Ž . Aquaculture 204 2002 507–516 www.elsevier.comrlocateraqua-online PCR–RFLP analysis of the mitochondrial ND-3 r 4 and ND-5 r 6 gene polymorphisms in the European and East Asian subspecies of common carp ž / Cyprinus carpio L. Riho Gross a, ) , Klaus Kohlmann b , Petra Kersten b a Department of Fish Farming, Institute of Animal Sciences, Estonian Agricultural UniÕersity, 1 Kreutzwaldi St., EE-51015 Tartu, Estonia b Department of Inland Fisheries, Institute of Freshwater Ecology and Inland Fisheries, D-12561 Berlin, Germany Abstract Ž . Polymorphism within the mitochondrial NADH-3,4 dehydrogenase ND-3 r 4 and NADH-5,6 Ž . dehydrogenase ND-5 r 6 gene regions was studied by polymerase chain reaction–restriction Ž . fragment length polymorphism PCR–RFLP analysis among common carp populations belonging Ž . Ž to the European two farmed strains and three wild populations and East Asian Amur wild carp, . Vietnamese wild carp and Japanese Koi carp subspecies, Cyprinus carpio carpio and C. c. haematopterus, respectively. Polymorphism was detected using eight and six restriction enzymes, respectively, and a total of seven composite haplotypes were identified. Both distance-based and maximum likelihood phylogenetic inference methods clustered the haplotypes into four distinct Ž . Ž . Ž . groups—the European two haplotypes , Amur two haplotypes , Vietnamese two haplotypes Ž . and Koi one haplotype , and their distributions strictly follow the geographic origin of popula- Ž tions. The populations are clustered into two highly divergent groups average net nucleotide . divergence, 2.4% , the European and the East Asian populations, suggesting an ancient separation. Ž . Six enzymes HinfI, AluI, HpaII and Taq I at ND-3 r 4; Eco 47I and BsuRI at ND-5 r 6 yielded diagnostic restriction sites for discriminating between the European and East Asian maternal lineages that can be applied to monitoring of genetic purity of the European farmed strains. q 2002 Elsevier Science B.V. All rights reserved. Keywords: Mitochondrial DNA; Polymorphism; Phylogeography; Cyprinus carpio ) Corresponding author. Tel.: q 372-7-313-489; fax: q 372-7-313-429. Ž . E-mail address: rgross@eau.ee R. Gross . 0044-8486r02r$ - see front matter q 2002 Elsevier Science B.V. All rights reserved. Ž . PII: S0044-8486 01 00836-5