Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.

中文翻译：

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鸟类有问题的线粒体基因组急剧增加：原因、后果和补救措施


真实的 DNA 序列对于可靠的进化推断至关重要。过去曾多次表达过对 DNA 序列识别的担忧，但定量研究却很少。线粒体基因组在系统发生学、系统发育地理学、群体遗传学和 DNA 鉴定中发挥着重要作用。然而，大量的有丝分裂基因组经常以简短的数据论文形式发表，引发了对其真实性的质疑。在这项研究中，我们量化了鸟类有问题的线粒体基因组及其在其他论文中的重复使用。截至 2020 年 1 月 1 日，已发表 1,876 个鸟类完整或部分线粒体基因组，其中 1,559 个的真实性可以通过同种序列进行评估。其中，78 个 (5.0%) 被发现存在问题，其中包括 45 个精心策划的参考序列。问题是由于错误识别 (33)、两个或三个物种的嵌合体 (23)、测序错误/数字 (18)、不正确的序列组装 (1)、在 GenBank 中标记错误但在最终论文中未标记 (2) 或反之亦然(1).自 2012 年以来，有问题的线粒体基因组数量急剧增加。令人担忧的是，这些有问题的序列已在其他论文中重复使用了 436 次，其中在系统发育中重复使用了 385 次。截至 2020 年 1 月 1 日，发表的所有线粒体基因组系统发育/网络中至少有 53% 包含至少一个有问题的线粒体基因组。有问题的线粒体基因组导致了错误的系统发育假设和无根据的分类学修订的建议，并且可能损害了分歧时间的比较分析和测量。我们的结果表明，有必要对质量控制措施进行重大升级。我们提出了一套全面的措施，可以作为发布线粒体基因组序列的新标准。