PCR-RFLP technique was employed to amplify about 827bp of mtDNA D-loop hypervariable region of Leuciscus baicalensis, L.merzbacheri and L.idus in Xinjiang. The PCR products of 56 samples with four restriction enzymes were digested: ScaI,HinfI,AluI,DdeI,and RFLP analysis was done then. The study indicates that all of L. species and populations have six haplotypes, L.merzbacheri has two haplotypes: BDAA,BDBA; L.baicalensis has three:AAAA,ABAA,ACAA; L.idus has one:CAAA. It is primarily considered that L.merzbacheri and L.baicalensis have more intra-population mutations. The UPGMA trees with 6 haplotypes and net genetics distance pointed out that L.merzbacheri might be original species, L.baicalensis and L.idus are evolved from L.merzbacheri.

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