Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges
Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges
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DOI：
10.1093/sysbio/sys088
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发表时间：
2013-03-01
影响因子：
6.5
通讯作者：
Roalson, Eric H.
中科院分区：
文献类型：
--
作者：
Hinchliff, Cody E.;Roalson, Eric H.
在本文中，我们使用超矩阵数据挖掘方法，根据GenBank上可获取的核苷酸数据重建了一个庞大且包含度极高的莎草科系统发育树。我们探究了这些树的特性及其在系统发育推断中的效用，并表明即使是超矩阵方法所具有的高度不完整比对，也可能对系统发育产生非常好的估计。我们提出了一种新颖的流程，用于过滤稀疏比对，通过一种我们称为“系统发育支架”的技术，使矩阵本身的部分决定性最大化，从而提高其系统发育效用。我们还提出了一种基于Mesquite软件中实现的I统计量来评估末端不稳定性（即“异常分类群”）的新方法。我们将修改后的统计量称为I - S，它比类似的统计量更易于解释，并且我们对它的应用可以用于大量的大树集合。这里呈现的最大的莎草树包含1500多个末端（约占所有莎草物种的四分之一），并且基于具有20000多个位点且超过90%数据缺失的多基因比对。这些树与先前得到支持的系统发育假说吻合良好，但与经过更严格过滤的树相比，总体支持值较低且分辨率较差。我们分辨率最高的树具有比以往任何已发表的莎草系统发育树更强的支持值，并显示出一些与先前研究不一致的关系。总体而言，我们表明超矩阵方法为进行系统发育研究提供了有力手段，并且这些工具对许多系统生物学家具有很高的潜在价值。
In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I-S, is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to large sets of large trees. The largest sedge trees presented here contain more than 1500 tips (about one quarter of all sedge species) and are based on multigene alignments with more than 20 000 sites and more than 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.