从死者身上进行横向基因转移
Lateral Gene Transfer from the Dead
摘要：
在系统发育研究中，分子序列的进化被认为是沿着现存物种的祖先所追踪的系统发育发生的。然而，在横向基因转移（LGT）的情况下，情况可能并非如此，因为基因转移的物种谱系可能已经灭绝或没有被采样。因为它是不可行的，以指定或重建所有物种的完整的进化，我们必须通过建模的物种形成动力学，产生了完整的进化，描述所代表的进化之外的基因的进化。我们证明，如果采样物种的数量是小的现有物种的总数相比，绝大多数的基因转移涉及物种形成，并沿着灭绝或未采样的谱系进化。我们表明，沿灭绝或未采样的谱系的基因的进化可以很好的近似被视为由几个全局参数描述的独立进化的谱系。使用这个结果，我们推导出一个算法来计算基因树的概率，并恢复最大似然和解给定的采样物种的遗传。检查473个近普遍的基因家族从36蓝藻，我们发现，近三分之一的转移事件- 28% -似乎有拓扑特征的进化沿灭绝的物种，但只有约6%的转让追溯其祖先之前的采样蓝藻的共同祖先。
英文摘要：
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.
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