Identifying localized biases in large datasets: A case study using the avian tree of life
Identifying localized biases in large datasets: A case study using the avian tree of life
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DOI：
10.1016/j.ympev.2013.05.029
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发表时间：
2013-12-01
影响因子：
4.1
通讯作者：
Braun, Edward L.
中科院分区：
文献类型：
--
作者：
Kimball, Rebecca T.;Wang, Ning;Braun, Edward L.
大规模的多位点研究在分子遗传学中已经变得很常见，新的研究不断添加到以前的数据集，以充分解决生命树。总的证据分析，结合联合收割机现有的数据与新收集的数据，预计将增加系统发育分析的力量，以解决困难的关系。然而，它们可能会受到局部偏差的影响，一个或几个位点对结果具有强烈的和潜在的误导性影响。为了检验这种可能性，我们将新收集的包括所有主要鸟类谱系的代表的31个基因座数据集与具有可比数量的位点的19个基因座的公开数据集（Hackett等人，2008. Science 320，1763 - 1768）。这使我们能够探索进行全证据分析的优势，并确定分析独立于已发表数据集的新数据集是否也很重要。总证据分析得出的结果与已发表的结果非常相似，只有少数节点的支持率略有增加。然而，分别分析31个和19个位点的数据集突出了几个差异。两个进化枝在已发表的数据集和总证据分析中得到了强有力的支持，但支持似乎反映了单个位点（β-纤维蛋白原[FGB]）的偏倚。支持这些关系的FGB中的信号足以导致它们在自举支持下的恢复，即使当与缺乏该信号的49个位点组合时。FGB似乎对物种树方法的结果没有实质性影响，但另一个位点（脑源性神经营养因子[BDNF]）确实对这些分析产生了影响。这些结果表明，本地化的偏见可以影响大规模的系统发育分析，但他们也表明，考虑独立的证据和探索多种分析方法可以揭示他们。(C)2013 Elsevier Inc. All rights reserved.
Large-scale multi-locus studies have become common in molecular phylogenetics, with new studies continually adding to previous datasets in an effort to fully resolve the tree of life. Total evidence analyses that combine existing data with newly collected data are expected to increase the power of phylogenetic analyses to resolve difficult relationships. However, they might be subject to localized biases, with one or a few loci having a strong and potentially misleading influence upon the results. To examine this possibility we combined a newly collected 31-locus dataset that includes representatives of all major avian lineages with a published dataset of 19 loci that has a comparable number of sites (Hackett et al., 2008. Science 320, 1763-1768). This allowed us to explore the advantages of conducting total evidence analyses, and to determine whether it was also important to analyze new datasets independent of published ones. The total evidence analysis yielded results very similar to the published results, with only slightly increased support at a few nodes. However, analyzing the 31- and 19-locus datasets separately highlighted several differences. Two clades received strong support in the published dataset and total evidence analysis, but the support appeared to reflect bias at a single locus (beta-fibrinogen [FGB]). The signal in FGB that supported these relationships was sufficient to result in their recovery with bootstrap support, even when combined with 49 loci lacking that signal. FGB did not appear to have a substantial impact upon the results of species tree methods, but another locus (brain-derived neurotrophic factor [BDNF)) did have an impact upon those analyses. These results demonstrated that localized biases can influence large-scale phylogenetic analyses but they also indicated that considering independent evidence and exploring multiple analytical approaches could reveal them. (C) 2013 Elsevier Inc. All rights reserved.