Species Phylogeny and Diversification Process of Northeast Asian Pungitius Revealed by AFLP and mtDNA Markers

Mol Phylogenet Evol. 2016 Jun;99:44-52. doi: 10.1016/j.ympev.2016.03.022. Epub 2016 Mar 17.


Pungitius is a highly diversified genus of sticklebacks (Gasterosteidae) occurring widely in northern parts of the Northern Hemisphere. Several ecologically and genetically divergent types that are largely isolated reproductively but occasionally hybridize in sympatry have been discovered in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type localities of the described species. Phylogenetic analyses based on 2683 polymorphic AFLP loci confirmed seven species, each of which (except for one entirely allopatric species P. platygaster) was clearly differentiated from one or two other sympatric species and constituted a highly supported monophyletic clade with conspecific allopatric populations. The phylogeny showed that two lineages arose early; one gave rise to two species (circumpolar species P. pungitius and Paratethys species P. platygaster) and the other to five species endemic to Northeast Asia (P. sinensis, P. tymensis, P. polyakovi, P. kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence of hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region.

Keywords: AFLP; Introgression; Ninespine stickleback; Sea of Japan; Speciation.

MeSH terms

  • Amplified Fragment Length Polymorphism Analysis / methods*
  • Animals
  • Calibration
  • Cytochromes b / genetics
  • DNA, Mitochondrial / genetics*
  • Far East
  • Genetic Markers
  • Genetic Variation*
  • Geography
  • Phylogeny*
  • Smegmamorpha / genetics*
  • Species Specificity
  • Time Factors


  • DNA, Mitochondrial
  • Genetic Markers
  • Cytochromes b