Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches.
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches.
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DOI：
10.1186/1471-2148-9-37
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发表时间：
2009-02-11
影响因子：
3.4
通讯作者：
Donoghue, Michael J.
中科院分区：
文献类型：
--
作者：
Smith, Stephen A.;Beaulieu, Jeremy M.;Donoghue, Michael J.
生物学越来越认识到有必要建立和利用更大的遗传学来解决广泛的进化问题。大规模的植物遗传学促进了树木和草本植物之间分子进化速率差异的发现。它们帮助我们理解了哺乳动物的多样化模式以及种子进化的模式。除了这些广泛的进化问题，人们越来越认识到大型生物多样性对于解决生物多样性热点和应对全球变化等保护问题的重要性。两大类方法已被用来完成大型树的建设任务：超树和超矩阵。虽然这些方法正在不断发展，但它们还没有被比较生物学家完全使用，使得非常大的树木非常罕见。在这里，我们描述和演示了一个修改后的超矩阵方法，称为大规模遗传学，使用数据库序列以及分类层次结构，使非常大的树与密度矩阵比超矩阵。大规模超矩阵遗传学面临的两个主要挑战是从数据库中组装大型数据矩阵和从这些数据集重建树。巨型发电厂的方法解决了前者，因为后者是通过采用最近开发的方法，大大减少了大型发电厂建设的运行时间。我们提出了一个算法，需要相对较少的人为干预。实现的算法被证明与一个数据集和系统发生的紫菀目（内桔梗科）包含4954种和12,033个网站和一个rbcL矩阵的绿色植物（Viridiplantae）13,533种和1,401个网站。通过研究更大的遗传学，我们发现了一些在其他方面看不见的模式。Viridiplantae的基因组发生成功地重建了维管植物的主要关系，而这些关系以前需要更多的基因。这些演示强调了使用大的遗传算法来揭示重要的进化模式的重要性，我们提出了一个快速，简单的方法来构建这些遗传算法。
Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies.
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