Data from: Lateral gene transfer from the dead

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modelling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared to the total number of existing species, the overwhelming majority of gene transfers involve speciation to, and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events − 28% – appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.

在系统发育研究中，分子序列的演化被认为是沿着现存物种祖先所溯源的系统发育树（phylogeny）展开的。然而，当存在横向基因转移（Lateral Gene Transfer, LGT）时，这一假设未必成立——因为承载转移基因的物种谱系可能已然灭绝，或未被纳入采样范围。由于完整构建并明确界定所有物种的系统发育树并不可行，我们需要通过建模催生完整系统发育树的物种形成动力学（speciation dynamics），来描述未被纳入采样系统发育树的基因演化过程。
我们的研究表明，若采样物种数量远低于现存物种总规模，绝大多数基因转移事件均涉及发生于灭绝或未采样谱系的物种形成，以及沿此类谱系的演化过程。我们进一步证明，在良好近似的前提下，灭绝或未采样谱系上的基因演化可被视为由若干全局参数描述的独立演化谱系。基于这一结论，我们推导得出一种算法，可在已知采样物种系统发育树的前提下，计算基因树（gene tree）的概率，并复原最大似然基因树-物种树调和（maximum likelihood reconciliation）结果。
通过分析来自36种蓝细菌（Cyanobacteria）的473个近通用基因家族数据集，我们发现近三分之一的转移事件（占比28%）呈现出沿灭绝物种演化的拓扑特征；但仅有约6%的转移事件可将其祖先追溯至采样蓝细菌共同祖先之前。