HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion.
HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion.
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DOI：
10.4161/mge.19030
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发表时间：
2011-11-01
期刊：
影响因子：
--
通讯作者：
Palmer JD
中科院分区：
文献类型：
--
作者：
Hao W;Palmer JD
水平基因转移（HGT）常常导致系统发育不一致。当“重复 HGT”引入预先存在的基因的第二个副本时，这两个副本可能会进行基因转换，从而产生系统发育镶嵌基因。当重复的 HGT 伴随着后代谱系之间的差异基因转换时，如在 DH-DC 模型下，系统发育分析变得更加复杂。为了探索 DH-DC 对系统发育重建的影响，我们分析了两组序列：（1）一组增强的植物线粒体 atp1 序列，我们最近发表了 DH-DC 的证据； (2)一组模拟序列，我们改变了嵌合程度、嵌合基因的数量和核苷酸取代率。我们表明，进化嵌合基因的系统发育行为是高度不稳定的，并且取决于嵌合程度和分析中存在的差异嵌合基因的数量。此外，我们发现基因树中嵌合基因的存在可以虚假地影响纯天然序列的系统发育位置，特别是通过将这些序列吸引到树中的基础位置。我们提出术语“HGT 湍流”来描述进化嵌合基因对系统发育结果的这些复杂影响。
Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When “duplicative HGT” introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term “HGT turbulence” to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.