Department of Evolutionary Biology, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, 3498838, Israel.
BMC Genomics. 2018 Aug 13;19(Suppl 6):570. doi: 10.1186/s12864-018-4921-5.
Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.
In this work we tackle this question, using real and simulated data. We first tighten a recent related theoretical result in this field. In a simulation study, we infer individual quartet topologies, and then use the inferred quartets to reconstruct simulated species trees. We demonstrate that accurate tree reconstruction is feasible despite surprisingly high rates of HGT. In a real data study, we construct phylogenies of two sets of prokaryotes, and show that our tree reconstruction scheme is comparable with (and complementary better than) other commonly used methods.
Using a blend of theoretical and empirical investigations, our study proves the feasibility of accurate quartet-based phylogenetic reconstruction, the vast impact of HGT events notwithstanding.
解析地球上生命的历史长期以来一直被视为生物学中最核心的任务之一。在过去的几年中，已经揭示了原核生物同源基因的进化历史在不同群体之间存在广泛的不一致，主要是由于水平基因转移（HGT）。尽管存在 HGT 事件，但仍发现了支持进化树状信号的证据。因此，一项具有挑战性的任务是从所有非树状事件源引起的噪声中提取出这种树状信号。
在这项工作中，我们使用真实和模拟数据来解决这个问题。我们首先收紧了该领域最近的一个相关理论结果。在模拟研究中，我们推断了个体四重体拓扑结构，然后使用推断的四重体来重建模拟的种系发生树。我们证明，尽管存在令人惊讶的高 HGT 率，但准确的树状重建是可行的。在真实数据研究中，我们构建了两组原核生物的系统发育，结果表明我们的树状重建方案可与（且优于）其他常用方法相媲美。
通过理论和经验研究的结合，我们的研究证明了准确的基于四重体的系统发育重建的可行性，尽管 HGT 事件的影响巨大。
