Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer
Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer
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DOI：
10.1186/1471-2148-11-259
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发表时间：
2011-09-16
影响因子：
3.4
通讯作者：
Stiller, John W.
中科院分区：
文献类型：
--
作者：
Stiller, John W.
越来越多的来自不同真核生物的基因组研究正在研究基因树之间的冲突，作为水平基因转移的证据。如果在给定的基因组中发现来自同一真核谱系的多个外源基因，则越来越多地将其解释为生物体进化历史中的隐蔽内共生期间的协同基因转移，也称为“内共生基因转移”或EGT。一些挑衅性的假设丢失或连续取代内共生体已经先进，但到目前为止，这些推论主要是事后的解释基因树之间的全基因组冲突。由于数据集像真核生物基因组序列一样庞大而复杂，因此研究基因组内系统发育冲突的替代解释至关重要，特别是从方向偏差和统计噪声中预期有多少冲突信号。基因组水平数据的可用性允许并需要使用严格的统计方法和明确定义的实验对照来测试明确的水平基因转移的先验预测的基因组学。
A growing number of phylogenomic investigations from diverse eukaryotes are examining conflicts among gene trees as evidence of horizontal gene transfer. If multiple foreign genes from the same eukaryotic lineage are found in a given genome, it is increasingly interpreted as concerted gene transfers during a cryptic endosymbiosis in the organism's evolutionary past, also known as "endosymbiotic gene transfer" or EGT. A number of provocative hypotheses of lost or serially replaced endosymbionts have been advanced; to date, however, these inferences largely have been post-hoc interpretations of genomic-wide conflicts among gene trees. With data sets as large and complex as eukaryotic genome sequences, it is critical to examine alternative explanations for intra-genome phylogenetic conflicts, particularly how much conflicting signal is expected from directional biases and statistical noise. The availability of genome-level data both permits and necessitates phylogenomics that test explicit, a priori predictions of horizontal gene transfer, using rigorous statistical methods and clearly defined experimental controls.