Gene Sampling Can Bias Multi-Gene Phylogenetic Inferences: The Relationship between Red Algae and Green Plants as a Case Study
Gene Sampling Can Bias Multi-Gene Phylogenetic Inferences: The Relationship between Red Algae and Green Plants as a Case Study
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DOI：
10.1093/molbev/msp036
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发表时间：
2009-05-01
影响因子：
10.7
通讯作者：
Hashimoto, Tetsuo
中科院分区：
文献类型：
--
作者：
Inagaki, Yuji;Nakajima, Yoshihiro;Hashimoto, Tetsuo
最近对大型多基因数据集(例如，包括30,000个氨基酸[AA]位的数据)进行的系统发育分析中，恢复了包括绿藻、红藻和绿色植物(绿藻和陆地植物)在内的植物单系。另一方面，在不到10,000个氨基酸位置的多基因数据集上，Plantae单体型还没有被稳定地重建。分析了Nozaki等人的5,216个AA头寸。(Nozaki H，Iseki M，Hasegawa M，Misawa K，Nakada T，Sasaki N，Watanabe M.2007.从缓慢进化的核基因推断初级光合作用真核生物的系统发育。摩尔·比奥尔·埃沃。24：1592-1595。)强烈反对Plantae的单调性，而Hackett et al.(Hackett JD，Yoon HS，Li S，Reyes-Prieto A，Rummele SE，Bhattacharya D.2007。系统发育学分析支持隐芽植物和触生植物的单系性，以及根霉属与嗜铬菌属的联系。摩尔·比奥尔·埃沃。24：1702-1713。)在对6,735个AA头寸的分析中，强势恢复了Plantae分支。我们怀疑，两项研究之间观察到的显著不一致是由于多基因系统发育估计中普遍被忽视的偏见，而不是数据大小、分类单元采样或树重建方法。虽然由于缺乏序列数据，蓝藻被排除在我们的分析之外，但我们发现，红藻和绿色植物之间姐妹群关系的恢复主要取决于在系统发育推断中的基因采样。
The monophyly of Plantae including glaucophytes, red algae, and green plants (green algae plus land plants) has been recovered in recent phylogenetic analyses of large multi-gene data sets (e. g., those including >30,000 amino acid [aa] positions). On the other hand, Plantae monophyly has not been stably reconstructed in inferences from multi-gene data sets with fewer than 10,000 aa positions. An analysis of 5,216 aa positions in Nozaki et al. (Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, Watanabe M. 2007. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol Biol Evol. 24: 1592-1595.) strongly rejected the monophyly of Plantae, whereas Hackett et al. (Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol. 24:1702-1713.) robustly recovered the Plantae clade in an analysis of 6,735 aa positions. We suspected that the significant incongruity observed between the two studies was attributable to a bias generally overlooked in multi-gene phylogenetic estimation, rather than data size, taxon sampling, or methods for tree reconstruction. Although glaucophytes were excluded from our analyses due to a shortage of sequence data, we found that the recovery of a sister-group relationship between red algae and green plants primarily depends on gene sampling in phylogenetic inferences from