Soltis Douglas E, Albert Victor A, Savolainen Vincent, Hilu Khidir, Qiu Yin-Long, Chase Mark W, Farris James S, Stefanović Sasa, Rice Danny W, Palmer Jeffrey D, Soltis Pamela S
Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
Trends Plant Sci. 2004 Oct;9(10):477-83. doi: 10.1016/j.tplants.2004.08.008.
As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although we applaud the use of many genes to resolve phylogenetic patterns, there is a significant caveat. In spite of, or even because of, the abundant data per taxon, whole-genome sequencing for a few exemplars can provide completely resolved and strongly supported, but incorrect, evolutionary reconstructions. We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor.
随着分类学家努力构建生命之树，最近的研究提倡采用基因组规模的方法，即获取少数代表性类群的整个核基因组、质体基因组或线粒体基因组的DNA序列数据。一些人宣称这种比较基因组策略预示着系统发育重建中不一致性问题的终结。尽管我们赞赏使用多个基因来解析系统发育模式，但仍有一个重要的警告。尽管每个类群有丰富的数据，甚至正是因为这些丰富的数据，对少数代表性类群进行全基因组测序可能会提供完全解析且得到有力支持但却是错误的进化重建。我们提供了一个显著的例子，其中包括无油樟，它被认为是所有其他现存被子植物的姊妹类群，突出了在使用全基因组但类群抽样不足时系统发育学的局限性。
