Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.
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DOI：
10.1093/sysbio/syv053
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发表时间：
2015-11
影响因子：
6.5
通讯作者：
Stamatakis A
中科院分区：
文献类型：
--
作者：
Leaché AD;Banbury BL;Felsenstein J;de Oca AN;Stamatakis A
单核苷酸多态性（SNPs）是系统发育研究的有用标记，部分原因是它们在整个基因组中普遍存在且易于收集。限制性位点相关DNA测序（RADseq）方法在SNP数据收集中越来越受欢迎，但缺乏对在遗传学中使用这些数据的最佳方法的评估。我们使用计算机模拟，和新的双消化RADseq（ddRADseq）数据的蜥蜴科Phrynosomatidae，研究RAD基因座的系统发育推断的准确性。我们比较了在系统发育分析期间使用RAD基因座的两种主要方式，包括全序列分析（即，SNP连同不变位点），或者在排除不变位点之后对SNP本身进行分析。我们发现，从分支长度和拓扑准确性的角度来看，使用全序列而不仅仅是SNP是优选的，但不是计算时间。我们介绍了两个新的收购偏差校正处理对齐组成的SNP，条件似然法和重组DNA的方法。条件似然方法仅以可变特征的存在为条件（未采样但已知存在的不变位点的数量不被考虑），而重构DNA方法要求用户在分析之前指定未采样不变位点的确切数量。在模拟下，对于两种采集偏差校正方法，分支长度偏差随着缺失数据量的增加而增加，但是与条件似然方法相比，重构DNA方法中的分支长度准确度得到了很大提高。系统发育分析的经验数据，使用串联或聚结为基础的物种树的方法提供了强有力的支持许多被接受的关系之间的phrynosomatid蜥蜴，这表明RAD基因座包含有用的系统发育信号在一个范围内的分歧时间，尽管存在缺失的数据。RAD基因座的系统发育分析需要仔细注意模型假设，特别是如果下游分析依赖于分支长度。
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.