Visualizing phylogenetic tree landscapes
Visualizing phylogenetic tree landscapes
复制标题
可视化系统发育树景观
作者：
James C. Wilgenbusch;Wen Huang;K. Gallivan
为了更好地理解进化的过程和模式，基因组尺度的序列比对越来越多地用于推断系统发生。这些新排列中的不同分区（如基因、密码子位置和结构特征）往往有利于数百甚至数千个相互竞争的系统发育。使用当前的共识树方法总结和比较从多源数据集获得的系统发育，会丢弃有价值的信息，并可能掩盖潜在的方法问题。发现有效和准确的降维方法，用于在2或3维中立即显示这些相互竞争的系统发生之间的关系，将有助于从业者诊断当前进化模型的局限性，以及在分析大型多源数据集时系统发生重建方法的潜在问题。我们引入了几种降维方法，在2维和3维中可视化从三个大中型线粒体基因组比对中发现的基因分区获得的竞争系统发育之间的关系。我们通过应用几个拟合优度度量来测试这些降维方法的性能。每个数据集的内在维度也被估计，以确定在二维和三维的投影是否可以预期揭示来自不同数据分区的树之间有意义的关系。提出了几种新的方法来帮助比较不同的系统发育景观。结果线性成分分析（CCA）和随机梯度体面（SGD）优化方法对三个线粒体基因组序列的原始树到树距离矩阵给出了最好的表示，大大优于目前用于树木景观可视化的方法。CCA + SGD方法的收敛速度至少与以前用于可视化树木景观的方法一样快。我们证明，对于所有三种mtDNA比对，3D投影显着增加了树到树距离之间的拟合，并有助于解释系统发育树之间的关系。结论降维方法的选择可以显著影响大量竞争系统发育树之间的空间关系。我们强调了选择降维方法来可视化大型多位点系统发育景观的重要性，并证明了线粒体树景观的3D投影更好地捕获了被比较树之间的关系。
BackgroundGenomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented.ResultsCurvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees.ConclusionsWe demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.
影响因子：
6.5
作者：
Nylander, JAA;Ronquist, F;Nieves-Aldrey, JL
通讯作者：
Nieves-Aldrey, JL
影响因子：
6.5
作者：
Alfaro, ME;Huelsenbeck, JP
通讯作者：
Huelsenbeck, JP