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全面进行棕榈科(Arecaceae)的类群水平系统发育分析,并比较了超级树和超级矩阵方法。

Complete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches.

机构信息

Royal Botanic Gardens, Kew, Richmond, Surrey, UK.

出版信息

Syst Biol. 2009 Apr;58(2):240-56. doi: 10.1093/sysbio/syp021. Epub 2009 May 30.

Abstract

Supertree and supermatrix methods have great potential in the quest to build the tree of life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap-weighted matrix elements performed most effectively in this case, generating trees with the greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Nonindependence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations, with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semistrict consensus, enumerating shared clades and compatible clades. The semistrict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate 2 composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods.

摘要

系统发育树和超级矩阵方法在构建生命之树方面具有巨大的潜力,但它们仍然存在争议,大多数研究人员选择一种方法,而很少同时使用两种方法。在这里,我们同时使用这两种方法构建了所有掌状科(棕榈科)属的系统发育树,这是一个具有重要经济价值的标志性被子植物科。我们组装了一个超级矩阵,其中包含 16 个分区,包括所有属的 DNA 序列数据、质体限制片段长度多态性数据和形态学数据,尽管存在大量缺失数据,但仍构建了一个高度分辨率和高度支持的系统发育树。为了构建超级树,我们使用了基于直接从超级矩阵子样本生成的输入树的基于矩阵表示的简约分析(MRP)的变体。所有超级树都得到了很好的解决。在这种情况下,标准的 MRP 与基于 bootstrap-weighted 矩阵元素的方法表现最佳,生成的树与超级矩阵树的一致性最高,没有任何输入树支持的分支最少。由于基于数据分区组合的输入树导致的非独立性是提高超级树性能的可接受的权衡。不可逆的 MRP 和仅使用严格独立的输入树并没有提供明显的好处。与之前的说法相反,我们发现,在某些 MRP 实现下,没有支持的分支并不罕见,在一些不可逆的 MRP 超级树中,多达 13%的分支没有任何输入树的支持。为了构建正式的综合分析,我们使用半严格共识来评估超级矩阵树和变体超级树之间的交叉证实,枚举共享分支和兼容分支。超级矩阵树和最一致的超级树的半严格共识包含 160 个分支(最多 204 个),其中 137 个分支存在于两棵树中。这些树恢复的关系强烈支持掌状科的当前系统发育分类。我们评估了 2 种综合超级树支持度量(rQS 和 V),并得出结论,报告支持或与给定超级树分支冲突的输入树的数量更具信息量。这项研究表明,超级树和超级矩阵方法可以为综合不连续的系统发育证据提供有效、明确和互补的机制,同时强调需要进一步改进超级树方法。

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