Phylogenetic identification of lateral genetic transfer events.
Phylogenetic identification of lateral genetic transfer events.
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横向遗传转移事件的系统发育鉴定。
DOI：
10.1186/1471-2148-6-15
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发表时间：
2006-02-11
影响因子：
3.4
通讯作者：
Hamilton N
中科院分区：
文献类型：
--
作者：
Beiko RG;Hamilton N
横向遗传转移可导致包含来自同一组分类群的序列的系统发育树之间的分歧。当拓扑不一致被认为是通过遗传转移事件产生的，树比较可以用来识别可能共享遗传信息的谱系。一个或多个传输事件的“编辑路径”可以用一系列子树修剪和重新移植（SPR）操作来表示，但找到最佳的此类操作集对于有根树之间的比较来说是NP难的，对于无根树也可能如此。EEEP（Efficient Evaluation of Edit Paths）是一种新的树比较算法，它使用进化上合理的约束来识别和消除许多无效的搜索途径，从而减少解决许多编辑路径问题所需的时间。EEEP的性能比较有利的其他算法时，适用于严格的分叉树与指定数量的SPR操作。我们还使用EEEP从超过19000个无根的、不完全解析的蛋白质树中恢复编辑路径，这些蛋白质树包含多达144个分类群，作为大型基因组研究的一部分。虽然推断的蛋白质树与参考超树的相似性远远超过随机树之间的相似性，但随机与推断的转移事件所跨越的系统发育距离是相似的，这表明真实的转移事件最常发生在密切相关的生物体之间，但也可以跨越大的系统发育距离。虽然这里检查的大多数蛋白质树与参考超树非常相似，需要零个或一个编辑操作进行调和，但一些树暗示在单个蛋白质的正向组内多达40个转移事件。由于序列树通常没有隐含的根，并可能包含未解决的或多分叉的节点，在EEEP中实现的策略是最合适的基因组分析。推断的蛋白质树之间的高度一致性表明，垂直遗传是进化的主导模式，至少对于这里考虑的生物体。然而，使用EEEP推断的编辑路径表明遗传转移在微生物基因组进化中也起着重要作用。
Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer events, tree comparisons can be used to identify the lineages that may have shared genetic information. An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between rooted trees, and may be so for unrooted trees as well. Efficient Evaluation of Edit Paths (EEEP) is a new tree comparison algorithm that uses evolutionarily reasonable constraints to identify and eliminate many unproductive search avenues, reducing the time required to solve many edit path problems. The performance of EEEP compares favourably to that of other algorithms when applied to strictly bifurcating trees with specified numbers of SPR operations. We also used EEEP to recover edit paths from over 19 000 unrooted, incompletely resolved protein trees containing up to 144 taxa as part of a large phylogenomic study. While inferred protein trees were far more similar to a reference supertree than random trees were to each other, the phylogenetic distance spanned by random versus inferred transfer events was similar, suggesting that real transfer events occur most frequently between closely related organisms, but can span large phylogenetic distances as well. While most of the protein trees examined here were very similar to the reference supertree, requiring zero or one edit operations for reconciliation, some trees implied up to 40 transfer events within a single orthologous set of proteins. Since sequence trees typically have no implied root and may contain unresolved or multifurcating nodes, the strategy implemented in EEEP is the most appropriate for phylogenomic analyses. The high degree of consistency among inferred protein trees shows that vertical inheritance is the dominant pattern of evolution, at least for the set of organisms considered here. However, the edit paths inferred using EEEP suggest an important role for genetic transfer in the evolution of microbial genomes as well.
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横向遗传转移事件的系统发育鉴定。
影响因子：
3.4
作者：
Beiko RG;Hamilton N
通讯作者：
Hamilton N
影响因子：
1.1
作者：
Hein, J;Jiang, T;Zhang, KZ
通讯作者：
Zhang, KZ
DOI：
10.2307/2413326
发表时间：
1985-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
ESTABROOK, GF;MCMORRIS, FR;MEACHAM, CA
通讯作者：
MEACHAM, CA
影响因子：
1.1
作者：
DasGupta, B;He, X;Tromp, J
通讯作者：
Tromp, J
影响因子：
10.7
作者：
Fitzpatrick, DA;Creevey, CJ;McInerney, JO
通讯作者：
McInerney, JO