Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
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DOI：
10.1093/molbev/msv347
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发表时间：
2016-04-01
影响因子：
10.7
通讯作者：
Kimball, Rebecca T.
中科院分区：
文献类型：
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作者：
Hosner, Peter A.;Faircloth, Brant C.;Kimball, Rebecca T.
大量DNA序列数据集的产生正在改变系统发育推断，但分析此类数据集的最佳实践尚未很好地建立。一个不确定性是对缺失数据的稳健性，特别是在合并框架中。为了了解增加矩阵大小和位点的影响，以增加数据缺失为代价，我们利用目标捕获的超保守元素，建立了90个分类单元、2.2兆碱基、4800个位点的陆禽序列矩阵。然后，我们比较了用串联最大似然估计的系统发育，在串联矩阵上执行的基于四重奏的方法和基因树调和方法，跨越了缺失数据的五个阈值。最大似然分析和四重奏分析的结果是相似的，很好地解决了，并且随着矩阵大小和稀疏度的增加而显示出越来越多的支持。相反，当我们包括所有信息位点时，基因树和解产生了意想不到的关系，与其他方法相比，某些分类群被置于根。对这些分类群的检查发现普遍存在较短的平均contigs，这可能会导致基因树推断的偏差，并导致基因树和解的错误结果。这表明，在基于基因树的分析中，更有问题的缺失数据是部分序列，而不是来自位点比对的整个缺失序列。将基因树和解限制在信息量最大的位点上解决了这个问题，产生了与串联和四重奏方法一致的支持良好的拓扑结构。总的来说，我们的分析为陆禽的系统发育提供了一个很好的解决方案，包括对先前存在问题的关系的有力支持，例如丛林雉（Gallus）之间的关系，并澄清了在以前的分子系统发育研究中未采样的两个神秘的鸡形属（Lerwa, Melanoperdix）的位置。
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.