Journal of Plant Research

, Volume 122, Issue 5, pp 509–521 | Cite as

Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae)

  • Kiyomi Tsutsui
  • Atsushi Suwa
  • Kei’ichi Sawada
  • Toshihide Kato
  • Takeshi A. Ohsawa
  • Yasuyuki WatanoEmail author
Regular Paper


Introgression has been considered to be one of main factors leading to phylogenetic incongruence among different datasets at lower taxonomic levels. In the plants of Pinaceae, the mtDNA, cpDNA, and nuclear DNA (nrDNA) may have different evolutionary histories through introgression because they are inherited maternally, paternally and biparentally, respectively. We compared mtDNA, cpDNA, and two low-copy nrDNA phylogenetic trees in the genus Pinus subgenus Strobus, in order to detect unknown past introgression events in this group. nrDNA trees were mostly congruent with the cpDNA tree, and supported the recent sectional and subsectional classification system. In contrast, mtDNA trees split the members of sect. Quinquefoliae into two groups that were not observed in the other gene trees. The factors constituting incongruence may be divided into the following two categories: the different splits within subsect. Strobus, and the non-monophyly of subsect. Gerardianae. The former was hypothesized to have been caused by the past introgression of cpDNA, mtDNA or both between Eurasian and North American species through Beringia. The latter was likely caused by the chimeric structure of the mtDNA sequence of P. bungeana, which might have originated through past hybridization, or through a horizontal transfer event and subsequent recombination.


Introgression Lineage sorting Mitochondrial DNA Phylogeny incongruence Pinus subgenus Strobus 



The authors thank Dr. Yoshihiko Tsumura for providing genomic DNA samples of Pinus sibirica; the Royal Botanic Garden Edinburgh for providing dried leaves of P. albicaulis, P. cembra, P. koraiensis and P. peuce; the Field Science Education and Research Center of Kyoto University for providing leaf samples of many other pine species. This study was partly supported by Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), No. 14340265 and No. 18370033.

Supplementary material

10265_2009_246_MOESM1_ESM.pdf (92 kb)
Table S1. List of species sampled and INSD accessions of the sequences (PDF 92 kb)
10265_2009_246_MOESM2_ESM.pdf (159 kb)
Table S2. Fasta format file of the combined dataset of mtDNA nad1 intron 2 and nad5 intron 1 (PDF 159 kb)


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Copyright information

© The Botanical Society of Japan and Springer 2009

Authors and Affiliations

  • Kiyomi Tsutsui
    • 1
  • Atsushi Suwa
    • 1
  • Kei’ichi Sawada
    • 1
  • Toshihide Kato
    • 1
  • Takeshi A. Ohsawa
    • 2
  • Yasuyuki Watano
    • 2
    Email author
  1. 1.Department of Biology, Faculty of ScienceChiba UniversityChibaJapan
  2. 2.Department of Biology, Graduate School of ScienceChiba UniversityChibaJapan

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