Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.
复制标题
通过递归合并和重排来比较系统发育树，从而扣除了横向基因转移的可能事件。
DOI：
10.1186/1471-2148-5-27
复制
发表时间：
2005-04-08
影响因子：
3.4
通讯作者：
Bapteste E
中科院分区：
文献类型：
--
作者：
MacLeod D;Charlebois RL;Doolittle F;Bapteste E
当基于单标记基因序列的生物系统发育没有得到很好的解决时，一个合乎逻辑的方法是增加更多的标记，假设微弱但一致的系统发育信号将在这样的多基因树中得到加强。只有当几个标记确实具有相同的系统发育时，这种方法才有效，这是许多多基因方法(如使用串联基因序列或组装超级树)没有直接解决的问题。事实上，即使真实的历史是一些基因的垂直遗传和其他基因的横向基因转移(LGT)的混合，这种方法也会产生独特的拓扑结构。我们已经开发了一种软件，目的是从一组基因树中提取垂直和横向遗传的证据，并与任意的参考树进行比较。这一证据随后被显示为对树的垂直遗传的支持的合成，覆盖着推断在树的历史上发生的显式侧向基因转移(LGT)事件。与拆分树方法一样，可以识别发生冲突的节点。此外，人们还可以对垂直和横向信号做出合理的推断，指定假定的供体和受体。像我们这样的工具可以通过高分辨率地剖析垂直和横向遗传来探索分子进化的网状维度。我们的意思是，不仅可以检查单个节点的一致性，而且还可以检查LGT的一致性。我们断言，我们的工具将促进系统发育树的比较，并解释相互冲突的数据。
When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies. We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients. A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data.
登录
查看更多内容
影响因子：
3.4
作者：
Andersson JO;Roger AJ
通讯作者：
Roger AJ
影响因子：
6.5
作者：
Levasseur, C;Lapointe, FJ
通讯作者：
Lapointe, FJ
影响因子：
12.3
作者：
Daubin V;Lerat E;Perrière G
通讯作者：
Perrière G
影响因子：
5.8
作者：
Creevey, CJ;McInerney, JO
通讯作者：
McInerney, JO
影响因子：
64.8
作者：
Nelson, KE;Clayton, RA;Fraser, CM
通讯作者：
Fraser, CM