Soltis Douglas E, Kuzoff Robert K
Department of Botany, Washington State University, Pullman, Washington, 99164-4238.
Evolution. 1995 Aug;49(4):727-742. doi: 10.1111/j.1558-5646.1995.tb02309.x.
Various factors, including taxon density, sampling error, convergence, and heterogeneity of evolutionary rates, can potentially lead to incongruence between phylogenetic trees based on different genomes. Particularly at the generic level and below, chloroplast capture resulting from hybridization may distort organismal relationships in phylogenetic analyses based on the chloroplast genome, or genes included therein. However, the extent of such discord between chloroplast DNA (cpDNA) trees and those trees based on nuclear genes has rarely been assessed. We therefore used sequences of the internal transcribed spacer regions (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) to reconstruct phylogenetic relationships among members of the Heuchera group of genera (Saxifragaceae). The Heuchera group presents an important model for the analysis of chloroplast capture and its impact on phylogenetic reconstruction because hybridization is well documented within genera (e.g., Heuchera), and intergeneric hybrids involving six of the nine genera have been reported. An earlier study provided a well-resolved phylogenetic hypothesis for the Heuchera group based on cpDNA restriction-site variation. However, trees based on ITS sequences are discordant with the cpDNA-based tree. Evidence from both morphology and nuclear-encoded allozymes is consistent with the ITS trees, rather than the cpDNA tree, and several points of phylogenetic discord can clearly be attributed to chloroplast capture. Comparison of the organellar and ITS trees also raises the strong likelihood that ancient events of chloroplast capture occurred between lineages during the early diversification of the Heuchera group. Thus, despite the many advantages and widespread use of cpDNA data in phylogeny reconstruction, comparison of relationships based on cpDNA and ITS sequences for the Heuchera group underscores the need for caution in the use of organellar variation for retrieving phylogeny at lower taxonomic levels, particularly in groups noted for hybridization.
包括分类单元密度、抽样误差、趋同以及进化速率的异质性等多种因素，都可能导致基于不同基因组构建的系统发育树之间出现不一致。特别是在属及以下分类水平，杂交导致的叶绿体捕获可能会在基于叶绿体基因组或其中所含基因的系统发育分析中扭曲生物间的关系。然而，叶绿体DNA（cpDNA）树与基于核基因构建的树之间这种不一致的程度很少被评估。因此，我们使用核糖体DNA（rDNA）的内部转录间隔区（ITS - 1和ITS - 2）序列来重建矾根属组（虎耳草科）各成员间的系统发育关系。矾根属组是分析叶绿体捕获及其对系统发育重建影响的重要模型，因为属内（如矾根属）杂交现象有充分记录，并且已报道涉及九个属中六个属的属间杂种。一项早期研究基于cpDNA限制性位点变异为矾根属组提供了一个解析度良好的系统发育假说。然而，基于ITS序列构建的树与基于cpDNA构建的树不一致。形态学和核编码同工酶的证据都与基于ITS构建的树一致，而非基于cpDNA构建的树，并且系统发育不一致的几个点可以明确归因于叶绿体捕获。细胞器树与ITS树的比较也极大地表明，在矾根属组早期多样化过程中，叶绿体捕获的古老事件发生在不同谱系之间。因此，尽管cpDNA数据在系统发育重建中有诸多优势且被广泛使用，但对矾根属组基于cpDNA和ITS序列的关系进行比较强调了在较低分类水平使用细胞器变异来检索系统发育时需谨慎，特别是在以杂交著称的类群中。
