No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.
No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.
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DOI：
10.1093/molbev/msw284
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发表时间：
2017-04-01
影响因子：
10.7
通讯作者：
Tautz D
中科院分区：
文献类型：
--
作者：
Domazet-Lošo T;Carvunis AR;Albà MM;Šestak MS;Bakaric R;Neme R;Tautz D
系统地层学是一个计算框架，用于确定DNA和蛋白质序列在一个系统发生中的出现时间。它已被广泛应用于推断基因组进化的模式，包括疾病基因进化，个体发育和从头基因起源的模式。系统地层学通常依赖于BLAST搜索沿着一个物种树，但新的模拟研究提出了关注的能力，BLAST检测远程同源物和它的影响，对地层的推断。在这里，我们重新评估了这些模拟。我们发现，即使可能的整体BLAST假阴性率在11- 15%之间，绝大多数序列分配到最近的进化起源的地层学是不受技术问题的BLAST。在模拟结果确实对先前报道的发现产生怀疑的情况下，我们重复了最初的分析，但现在排除了所有可疑的序列。最初描述的模式基本上保持不变。这些新的分析有力地支持了新地层学的推论，包括：真核生物起源后出现的基因更有可能在果蝇的外胚层中表达，而不是在内胚层或中胚层中表达，并且从非基因序列中重新出现的蛋白质编码基因通过酵母中的原基因中间体发生。我们的结论是，BLAST是一个适当的和足够敏感的工具，在地层学分析，并没有出现引入显着的偏见到进化模式的推断。
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11–15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.