Comparison of chloroplast, mitochondrial and multiple nuclear DNA trees in genus Pinus subgenus Stnobus

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Hybridization and introgression have been considered to be one of the main factors that lead to phylogenetic incongruence among different data sets. In the plants of Pinaceae, chloroplast and mitochondrial DNAs may have different evolutionary histories through introgression because cpDNA and mtDNA are inherited paternally and maternally, respectively. In fact, Pinus species have insufficient reproductive barriers, and many examples of introgressive hybridization have been reported. Pinus species, therefore, could be susceptible to phylogenetic bias by hybridization and introgression. In the present study, we reconstructed cpDNA tree, mtDNA tree, and four nuclear DNA trees in the genus Pinus subgenus Strobus, and compared them in order to detect cryptic and ancient introgression episodes which caused incongruence among gene trees. Four nrDNA trees were constructed based on partial sequences of GapCp, PgiC and ESTs of Pinus taeda (PtIFG_9008, PtIFG_0464). MtDNA tree was generated based on partial sequences of intron2 of nad1 and intronl of nad5 genes. CpDNA tree was based on the dataset of Wang et al. (1999) and our additional data. In nrDNA trees, species of the section Strobus were monophyletic, and the species of the other section (Parrya) were paraphyletic. In the sec. Parrya, two species of the subsection Gerardianae formed a clade, which was a sister to the sec. Strobus. CpDNA tree was consistent with the nrDNA trees in the relationship among sections and subsections. On the other hand, mtDNA tree showed three clades, and in the two of them, each clade consisted of the combined members both from sec. Strobus and from sec Parrya subsec. Gerardianae. Because phylogenetic relationships suggested by the nrDNA and cpDNA trees are congruent and also reasonable in morphological respects, the cause of incongruence could be attributed to the bias in the mtDNA tree. Possibly, mtDNA introgression had occurred anciently between species of different sections.