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 globa...

在系统发育研究（phylogenetic studies）中，分子序列的演化通常被认为是沿着现存物种（extant species）的祖先所溯源的系统发育路径展开的。然而，若存在水平基因转移（Lateral Gene Transfer, LGT），这一假设则未必成立——因为携带被转移基因的物种谱系可能已然灭绝，或是尚未被纳入采样范围。由于无法完整指定或重建所有物种的系统发育树，我们需要通过对催生完整系统发育树的物种形成动力学（speciation dynamics）进行建模，来描述未被当前系统发育树涵盖的基因演化过程。本研究证实，当采样物种（sampled species）的数量远少于现存物种的总数量时，绝大多数基因转移事件均涉及指向灭绝或未采样谱系的物种形成过程，以及沿这些谱系进行的基因演化。我们进一步证明，灭绝或未采样谱系上的基因演化，在极佳近似条件下可被视作由若干全局参数所描述的独立演化谱系的演化过程。