Most modern phylogenetic inference methods assume that data should be fitted to a set of possible trees, from which the optimal tree is to be identified. A bifurcat ing tree-like diagram is thought to best represent evo lutionary history. This expectation follows largely from the view that (i) simultaneous divergence of multiple organismal lineages from the same common ancestor is likely to be rare (Hennig, 1966), hence the bifurcat ing attribute; and (ii) reticulate patterns of relationship caused by hybridization, horizontal gene transfer, and gene conversion and recombination are relatively mi nor deviations from an underlying single bifurcating pattern of evolution (Brown et al., 2001; Daubin et al., 2003). Whether most of the pattern of evolutionary history is truly bifurcating is still uncertain, but it has become in creasingly evident that complications such as hybridiza tion, horizontal gene transfer, and lineage sorting of ancestral polymorphisms are not as rare as once sup posed (Takahashi et al., 2001; P??bo, 2003; Zhaxybayeva et al., 2004; Gogarten and Townsend, 2005). Under these conditions, individual gene histories may not be con gruent with the general pattern of species or higher taxon relationships, and a phylogenetic tree estimated from the combined (concatenated) gene sequence rep resents an oversimplified version of the genetic history (Huber and Moulton, 2005; Morrison, 2005; Huson and Bryant, 2006). An usual alternative to simultaneous anal ysis of combined sequences from multiple gene parti tions is to present a consensus tree as a representation of relationships common to each individual gene tree, but this also suffers from oversimplification (Swofford, 1991) and can be performed only when each gene tree has the same taxon representation. A solution to the oversimplification and taxon constraints to topological congruence would allow visualization of both the princi pal conflicting patterns among individual gene trees and the phylogenetic patterns common among trees that may not overlap completely in taxon representation (partial trees). Huson et al. (2004) presented the Z-closure method for constructing a supernetwork from a set of partial trees. In cases where gene trees contain numerous dif ferent incongruent relationships, the resulting supernet work can, however, be too complex to visualize and interpret. Huson et al. (2006), therefore, extended the supernetwork approach to enable filters to remove re lationships (splits) from the supernetwork that are rep resented only once or sporadically among the source trees. The result is a network that summarizes the rela

中文翻译：

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用于从不一致的基因树中提取和可视化循环信号的过滤 Z 闭合超网络

大多数现代系统发育推断方法都假设数据应该适合一组可能的树，从中可以确定最佳树。分叉树状图被认为最能代表进化历史。这种预期主要源于以下观点：(i) 来自同一共同祖先的多个生物谱系同时发生分歧可能很少见 (Hennig, 1966)，因此存在分叉属性；(ii) 由杂交、水平基因转移以及基因转换和重组引起的网状关系模式与潜在的单一分叉进化模式的偏差相对较小（Brown 等人，2001 年；Daubin 等人，2003 年）。进化史的大部分模式是否真的分叉还不确定，但越来越明显的是，诸如杂交、水平基因转移和祖先多态性谱系分选等并发症并不像人们想象的那么罕见（Takahashi 等，2001；P??bo，2003；Zhaxybayeva 等., 2004; Gogarten 和 Townsend, 2005)。在这些条件下，个体基因历史可能与物种的一般模式或更高的分类群关系不一致，并且从组合（串联）基因序列估计的系统发育树代表了遗传历史的过度简化版本（Huber 和 Moulton， 2005 年；莫里森，2005 年；休森和布莱恩特，2006 年）。同时分析来自多个基因分区的组合序列的一种常用替代方法是呈现一个共识树作为每个单独基因树共有关系的表示，但这也存在过于简化的问题（Swofford，1991），并且只有当每个基因树具有相同的分类单元表示时才能执行。拓扑一致性的过度简化和分类约束的解决方案将允许可视化单个基因树之间的主要冲突模式和树之间常见的系统发育模式，这些模式在分类单元表示（部分树）中可能不完全重叠。胡森等人。(2004) 提出了从一组部分树构建超网络的 Z 闭包方法。然而，在基因树包含许多不同的不一致关系的情况下，产生的超网络工作可能过于复杂而无法可视化和解释。胡森等人。(2006) 因此，扩展了超网络方法，使过滤器能够从超网络中移除仅在源树中表示一次或偶尔出现的关系（分裂）。结果是一个总结了关系的网络