Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
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TLDR
It is demonstrated that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding, which strives for rapid and inexpensive generation of molecular species tags.Abstract:
Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. They can be easily coamplified with orthologous mtDNA by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms by using a short fragment of the mitochondrial cytochrome c oxidase I (COI) gene. Here, we study the effect of numts on DNA barcoding based on phylogenetic and barcoding analyses of numt and mtDNA sequences in two divergent lineages of arthropods: grasshoppers and crayfish. Single individuals from both organisms have numts of the COI gene, many of which are highly divergent from orthologous mtDNA sequences, and DNA barcoding analysis incorrectly overestimates the number of unique species based on the standard metric of 3% sequence divergence. Removal of numts based on a careful examination of sequence characteristics, including indels, in-frame stop codons, and nucleotide composition, drastically reduces the incorrect inferences of the number of unique species, but even such rigorous quality control measures fail to identify certain numts. We also show that the distribution of numts is lineage-specific and the presence of numts cannot be known a priori. Whereas DNA barcoding strives for rapid and inexpensive generation of molecular species tags, we demonstrate that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding.read more
Citations
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Refined global analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) mitochondrial cytochrome oxidase 1 to identify species level genetic boundaries.
TL;DR: This new analysis, which constructs consensus sequences and uses these as a standard against which unknown sequences can be compared, provides for the first time a consistent means of identifying the genetic bounds of each species with a high degree of certainty.
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Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes
TL;DR: The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency.
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Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces
TL;DR: The effectiveness of DNA barcoding in determining the diets of bat species that specialize in eating different taxa of arthropod prey is investigated and a comparison of data with parallel morphological analyses revealed a close correlation between the two methods.
Journal ArticleDOI
The Effect of Geographical Scale of Sampling on DNA Barcoding
Johannes Bergsten,David T. Bilton,Tomochika Fujisawa,Miranda Elliott,Michael T. Monaghan,Michael Balke,Lars Hendrich,Joja Geijer,Jan Herrmann,Garth N. Foster,Ignacio Ribera,Anders N. Nilsson,Timothy G. Barraclough,Alfried P. Vogler +13 more
TL;DR: A CO1 data set of aquatic predaceous diving beetles of the tribe Agabini is presented and it is shown that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation, showing that the geographical scale of sampling has a critical impact on the global application of DNA barcoding.
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DNA Barcoding of Marine Metazoa
TL;DR: This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene.
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