Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

By Hojun Song, J. E. Buhay, Michael Whiting, Keith A. Crandall. Proceedings of the National Academy of Sciences of the United States of America, 2008

1,026 citations recorded by the source corpus.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5924c6328c81c1de6fd7054a5624f800085033b5

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Citations in the corpus

Decapod phylogenetics and molecular evolution (2009, background): “Another problem of some mitochondrial genes such as COI is the presence of pseudogenes (nuclear copies of mitochondrial genes) in some species of decapods (Song et al. 2008).”
Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae) (2009, background): “These characteristics are inconsistent with amplification of nuclear pseudogenes (Song et al. 2008).”
Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates (2010, background): “Although there has been considerable criticism of the philosophical and practical underpinnings of DNA barcoding (DeSalle 2006; Fitzhugh 2006; Rubinoff 2006; Rubinoff et al. 2006; Song et al. 2008), its application for species identification has”
Refined Global Analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) Mitochondrial Cytochrome Oxidase 1 to Identify Species Level Genetic Boundaries (2010, neutral): “The inclusion of pseudogenes may overestimate the numbers of species, skew branch structure and lead to spurious results (Buckler et al. 1997, Song et al. 2008).”
Current progress in DNA barcoding and future implications for entomology (2011, background): “This problem has been reported for many insects (Gellissen & Michaelis 1987; Zhang & Hewitt 1996; Bensasson et al. 2000; Brower 2006; Rubinoff et al. 2006; Magnacca & Brown 2010a,b) and can affect the barcoding results (Song et al. 2008).”
Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages (2015, background): “ings, such as overestimation of species richness due to the amplification of nuclear mitochondrial pseudogenes (numts) (Song et al. 2008) or underestimation due to the difficulty of amplification with universal primers covering a broad taxonomic range (Deagle et al.”
DNA Barcodes for Marine Biodiversity: Moving Fast Forward? (2010, background): “pseudogenes [38], contaminants amplified with ‘universal’ primers [39] or cases of mitochondrial introgression [40] (see barcoding reviews [41,42]).”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, background): “…& Knowles, 2006); or because copies become transferred to the nucleus as mitochondrial pseudogenes and show altered patterns of evolution (‘NUMTs’: Song et al., 2008); or because of introgression between species (Ballard & Whitlock, 2004; Monaghan et al., 2005), such as via leakage of paternal…”
Complex patterns of global spread in invasive insects: eco-evolutionary and management consequences (2016, positive): “…this tool is also plagued by problems, such as poor amplification in some groups or the presence of nuclear mitochondrial pseudogenes (numts) that can cause an overestimation of diversity and otherwise confound phylogenetic relationships if not detected (Song et al. 2008; Haran et al. 2015).”
Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes (2010, background): “Recently, DNA barcoding among arthropods was found to overestimate the number of species when numts are coamplified [91], showing that numts introduce serious ambiguity into the DNA barcoding paradigm as arthropods are one the major phyla studied in taxonomy.”
Protecting an ecosystem service: approaches to understanding and mitigating threats to wild insect pollinators (2016, background): “…false 710 negatives (Clarke et al., 2014; Tang et al., 2015), contamination risk and potential co-711 amplification of mitochondrial pseudogenes (Song et al., 2008), and the comparatively short 712 sequence achievable with the current NGS technology, which limits the analysis of the COI…”
“COI-like” Sequences are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies (2009, methodology): “Based on my personal experience with cave Orconectes (Song et al., 2008), I do suspect that the O.”
A practical guide to DNA metabarcoding for entomological ecologists (2020, background): “However, the co-amplification of nuclear mitochondrial pseudogenes (NUMTs) could result in overestimation of the number of true species in DNA metabarcoding studies (Song et al., 2008; Wang et al., 2018).”
How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research (2014, background): “Short PCRs of mt genes are also susceptible to equal or even preferential amplification of numts (Song et al., 2008).”
DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species (2010, neutral): “This suggests that the original sequences came from a nuclear pseudogene, despite containing no stop codons or frame-shift mutations (Song et al. 2008).”