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Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

机译：系统发育重建方法对单基因座数据对物种划界鲁棒性的影响

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list list-type="1" id="mee312246-list-0001"> Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. doi origin="wiley" registered="yes">10.1111/(ISSN)2041-210X/doi
机译：基于联盟的物种定界方法结合了种群遗传学和系统发生学理论，为描述进化上重要的多样性单位提供了一种客观手段。广义混合Yule合并（GMYC）和泊松树过程（PTP）是使用超度（GMYC或PTP）或非超度（PTP）基因树作为输入的方法，主要用于单基因座数据（例如DNA）条码。在这里，我们评估了GMYC和PTP对不同的系统发育重建和分支平滑方法的鲁棒性。我们使用系统发育和平滑方法的多达30种不同组合重建了400棵超大型树，并在16个经验数据集中执行了2000多个单独的物种定界分析。然后，我们根据物种的界定，系统发育和平滑方法，就丰富度和同一性而言，评估可变多样性的估计数。 PTP方法通常会产生对不同系统发育方法更可靠的多样性估计。 GMYC更为敏感，但是可以为BEAST树提供一致的估计。 GMYC估计的较低一致性可能是由于平滑步骤引入的基因树之间存在差异。未解决的节点（实际异常或方法假象）会影响GMYC和PTP估计，但对GMYC估计的影响更大。分支平滑是一个困难的步骤，并且可能是偏见的未得到充分理解的原因，这种偏见可能在多样性和多元化研究中普遍存在。但是，仔细选择系统发育方法确实会产生等效的PTP和GMYC多样性估计。我们建议将PTP模型与任何基于模型的基因树（例如RAxML）和GMYC方法与BEAST树同时使用，以获取物种假设。 10.1111 /（ISSN）2041-210X

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