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

杂交和基因渗入被认为是导致不同数据集之间系统发育不一致的主要因素之一。在松科植物中，由于cpDNA和mtDNA分别是父本遗传和母本遗传，叶绿体dna和线粒体dna通过渗入可能具有不同的进化历史。事实上，松属物种的繁殖屏障不足，已经报道了许多渐渗杂交的例子。因此，松木物种可能容易因杂交和渐渗而产生系统发育偏差。本研究重建了松亚属的cpDNA树、mtDNA树和4个核DNA树，并对它们进行了比较，以发现导致基因树不一致的隐性和古性基因渗入事件。利用油松GapCp、PgiC和ESTs的部分序列（PtIFG_9008、PtIFG_0464）构建了4棵nrDNA树。根据nad1内含子2和nad5内含子的部分序列生成MtDNA树。CpDNA树基于Wang等人（1999）的数据集和我们的附加数据。在nrDNA树中，Strobus组属单系，Parrya组属副系。在Parrya节，Gerardianae分节的两个种形成了一个分支，这是Strobus分节的姐妹。CpDNA树与nrDNA树在区段和亚区段之间的关系上基本一致。另一方面，mtDNA树显示了三个分支，其中两个分支由来自s . Strobus和s . Parrya亚段的成员组合而成。Gerardianae。由于nrDNA和cpDNA树显示的系统发育关系是一致的，在形态方面也是合理的，不一致的原因可能是mtDNA树的偏差。可能，不同区段的种间早就发生了mtDNA渗入。

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.