Complete mitochondrial genome sequence of <i>Emberiza pallasi</i> (Emberizidae: <i>Emberiza</i>)

Wu, Guiyou; Zhang, Heng; Zhang, Baowei

doi:10.1080/23802359.2019.1616623

Cited by 1 publication

(1 citation statement)

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“…Similarly, a short branch or very shallow divergence, which is suggestive of a misidentification, has been shown in published phylogenies of Charadrius placidus ( Chen et al 2018 ), Aquila heliaca ( Knapp et al 2019 ; Sarker et al 2019a ; Zhou et al 2019 ), Falco naumanni ( Yang et al 2018 ), and Emberiza aureola ( Zhang et al 2016 ; Mackiewicz et al 2019 ; Wu et al 2019 ).…”

Section: Resultsmentioning

confidence: 60%

Sharp Increase of Problematic Mitogenomes of Birds: Causes, Consequences, and Remedies

Sangster

Luksenburg

2021

Genome Biology and Evolution

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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 re-usage in other papers. Of 1876 complete or partial mitogenomes of birds published until 1 January 2020, the authenticity of 1559 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), mislabelling 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 re-used 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until 1 January 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.

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