Goremykin V V, Nikiforova S V, Cavalieri D, Pindo M, Lockhart Peter
FEM Research and Innovation Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy;
Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand; and Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
Syst Biol. 2015 Sep;64(5):879-91. doi: 10.1093/sysbio/syv028. Epub 2015 May 20.
Support for Amborella as the sole survivor of an evolutionary lineage that is sister to all other angiosperms comes from positions in DNA multiple-sequence alignments that have a poor fit to time-reversible substitution models. These sites exhibit significant levels of homoplasy, compositional heterogeneity, and strong heterotachy. We report phylogenetic analyses with observed, randomized, and simulated data which show there is little or no expectation that these sites provide useful information for understanding relationships among basal angiosperms. Their inclusion in phylogenetic analyses leads to a long-branch attraction artifact that favors Amborella as sister to other angiosperms in reconstructed phylogenies. Using parametric simulations, we show that sites in chloroplast sequences that exhibit less homoplasy between angiosperms and gymnosperms provide more reliable information for inferring basal angiosperm relationships. We confirm our earlier findings that the basal angiosperm Amborella is most closely related to aquatic herbs. Our current and previously reported (Goremykin et al. 2013) analyses highlight an essential aspect of the total evidence approach to phylogenetic inference. They suggest that data partitioning aimed at identifying components of the data that better fit evolutionary models is a more reliable approach to phylogeny reconstruction at deep taxonomic levels.
支持无油樟作为所有其他被子植物姐妹进化支系的唯一幸存者的证据，来自于DNA多序列比对中与时间可逆替换模型拟合不佳的位置。这些位点表现出显著水平的平行进化、组成异质性和强烈的异速进化。我们报告了对观察到的数据、随机数据和模拟数据的系统发育分析，结果表明，几乎没有期望这些位点能为理解基部被子植物之间的关系提供有用信息。将它们纳入系统发育分析会导致一种长枝吸引假象，在重建的系统发育树中，这种假象会使无油樟成为其他被子植物的姐妹。通过参数模拟，我们表明，在被子植物和裸子植物之间表现出较少平行进化的叶绿体序列位点，为推断基部被子植物的关系提供了更可靠的信息。我们证实了我们早期的发现，即基部被子植物无油樟与水生草本植物关系最为密切。我们目前的分析以及之前报道的（戈雷米金等人，2013年）分析突出了系统发育推断的总证据方法的一个重要方面。这些分析表明，旨在识别更符合进化模型的数据成分的数据划分，是在深层次分类水平上进行系统发育重建的一种更可靠的方法。
