Abstract
The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid species complex containing three geographical lineages: ND, NE and SE. Here, complete mitochondrial genomes of these three lineages were analyzed to estimate the genetic differentiation among them and to identify their phylogenetic placement in genus Pungitius. Although the overall genome structure was identical among those three lineages, the genome sizes were slightly different from each other, ranging from 16,489 to 16,500 bp. Upon robust phylogenetic tree inferred by Bayesian algorithm, ND and SE showed relatively higher affinity, and those three lineages formed a monophyletic group with Russian P. tymensis, clearly supporting previous studies
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