Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
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DOI：
10.1093/sysbio/syr079
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发表时间：
2011-12-01
影响因子：
6.5
通讯作者：
Parr, Cynthia
中科院分区：
文献类型：
--
作者：
Cho, Soowon;Zwick, Andreas;Parr, Cynthia
本文讨论的问题是，是否可以经济地提高鲁棒性的分子遗传学估计增加基因采样的类群的一个子集，而不会有失效的分析所产生的文物大块缺失的数据。我们的案例研究源于一个正在进行的努力，以解决知之甚少的更深层次的关系，在大型分支Ditrysia（> 150,000种）的昆虫命令鳞翅目（蝴蝶和蛾）。为了弥补在123个样本中基于5个核基因（6.6 kb）的初步研究中对更深层次分歧的总体弱支持，我们将总基因样本增加了近两倍（至26个基因，18.4 kb），但仅在三分之一（41）的分类群中。由此产生的部分增强的数据矩阵（45%故意缺失的数据）一致地增加了对先前在五基因（几乎）完整矩阵中确定的分组的自举支持，同时没有引入预测缺失数据会产生的那种矛盾分组。我们的研究结果增加了越来越多的证据表明，在基因和分类单元采样的数据集差异很大，往往可以安全和有利可图的组合。最强的整体支持节点以上的家庭水平来自包括所有核苷酸的变化，而分区网站成组经历大多数非同义与大多数同义的变化。相比之下，支持最深的节点，任何有说服力的分子证据（78-85%自举）还没有出现，是弱或不存在的，除非同义的变化被完全排除，一个结果可能归因于组成的异质性。这个节点（Gelechioidea + Apoditrysia），暂时提出了由以前的作者的基础上的四个形态学synapomorphies，是第一个主要的亚群ditrysian超家族，以获得强有力的统计支持，在任何系统发育研究。一个“更多的基因，只有”数据集（41 taxax 26基因）也给出了强烈的信号，第二个深分组（Macrolepidoptera），这是模糊的，但不强烈矛盾，在更多的分类单元丰富的分析。
This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxax26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.