Sang T, Donoghue M J, Zhang D
Department of Botany and Plant Pathology, Michigan State University, East Lansing, Michigan 48824, USA.
Mol Biol Evol. 1997 Oct;14(10):994-1007. doi: 10.1093/oxfordjournals.molbev.a025716.
Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an additional gene, Adh1B, is also present in section Moutan. Phylogenetic analyses of exon sequences of the Adh genes of Paeonia and a variety of other angiosperms imply that duplication of Adh1 and Adh2 occurred prior to the divergence of Paeonia species and was followed by a duplication resulting in Adh1A and Adh1B. Concerted evolution appears to be absent between these paralogous loci. Phylogenetic analysis of only the Paeonia Adh exon sequences, positioning the root of the tree between the paralogous genes Adh1 and Adh2, suggests that the first evolutionary split within the genus occurred between the shrubby section Moutan and the other two herbaceous sections Oneapia and Paeonia. Restriction of Adh1B genes to section Moutan may have resulted from deletion of Adh1B from the common ancestor of sections Oneapia and Paeonia. A relative-rate test was designed to compare rates of molecular change among lineages based on the divergence of paralogous genes, and the results indicate a slower rate of evolution within the shrubby section Moutan than in section Oneapia. This may be responsible for the relatively long branch length of section Oneapia and the short branch length between section Moutan and the other two sections found on the Adh, ITS (nrDNA), and matK (cpDNA) phylogenies of the genus. Adh1 and Adh2 intron sequences cannot be aligned, and we therefore carried out separate analyses of Adh1A and Adh2 genes using exon and intron sequences together. The Templeton test suggested that there is not significant incongruence among Adh1A, ITS, and matK data sets, but that these three data sets conflict significantly with Adh2 sequence data. A combined analysis of Adh1A, ITS, and matK sequences produced a tree that is better resolved than that of any individual gene, and congruent with morphology and the results of artificial hybridization. It is therefore considered to be the current best estimate of the species phylogeny. Paraphyly of section Paeonia in the Adh2 gene tree may be caused by longer coalescence times and random sorting of ancestral alleles.
通过聚合酶链反应（PCR）扩增、克隆并测序了来自芍药属被子植物11个假定非杂交物种的乙醇脱氢酶基因。利用乙醇脱氢酶（Adh）基因的5个外显子和6个内含子区域的序列来重建这些物种的系统发育。发现了两个旁系同源基因，Adh1A和Adh2；另外一个基因Adh1B也存在于牡丹组中。对芍药属和其他多种被子植物的Adh基因外显子序列进行系统发育分析表明，Adh1和Adh2的复制发生在芍药属物种分化之前，随后发生了一次复制，产生了Adh1A和Adh1B。这些旁系同源位点之间似乎不存在协同进化。仅对芍药属Adh外显子序列进行系统发育分析，将树的根部定位在旁系同源基因Adh1和Adh2之间，结果表明该属内的第一次进化分支发生在灌木状的牡丹组与另外两个草本组独叶草组和芍药组之间。Adh1B基因仅限于牡丹组，可能是由于独叶草组和芍药组的共同祖先中Adh1B的缺失所致。设计了一个相对速率检验，以根据旁系同源基因的差异比较各谱系间的分子变化速率，结果表明灌木状的牡丹组内的进化速率比独叶草组慢。这可能是导致独叶草组在Adh、ITS（nrDNA）和matK（cpDNA）系统发育树上分支长度相对较长，而牡丹组与其他两组之间分支长度较短的原因。Adh1和Adh2的内含子序列无法比对，因此我们使用外显子和内含子序列一起对Adh1A和Adh2基因进行了单独分析。Templeton检验表明，Adh1A、ITS和matK数据集之间没有显著的不一致，但这三个数据集与Adh2序列数据存在显著冲突。对Adh1A、ITS和matK序列进行联合分析得到的一棵树比任何单个基因的树分辨率更高，并且与形态学以及人工杂交结果一致。因此，它被认为是目前对物种系统发育的最佳估计。Adh2基因树中芍药组的并系现象可能是由于较长的合并时间和祖先等位基因的随机分选造成的。
