Chimeric mitochondrial genomes: a hazard for phylogenetics and
environmental DNA identification of fishes
Abstract
Chimeric mitogenomes are artifacts resulting from laboratory or sequence
assembly errors. There have been no quantitative studies of chimeric DNA
sequences in animals and their effects on phylogenetics and DNA
identification have not been studied. We describe a new, simple strategy
for detecting chimeras and apply this to a set of 123 mitogenomes of
fishes of the subfamily Schizothoracinae. We detected seven chimeras
(5.7%). The proportion of heterospecific nucleotides ranged from 7.5%
to at least 99.2%. Six chimeras included heterospecific DNA fragments
of at least one marker commonly used for environmental DNA
identification of fishes (12S rRNA, 16S rRNA, COI, cytochrome b). Five
chimeras were placed in an incorrect phylogenetic position in a
mitogenome phylogeny. All seven sequences have been re-used in
subsequent phylogenies and some have also been used in DNA
identification studies. This study shows that chimeras may be common
among published mitogenomes, and affect phylogenetic inference and
environmental DNA identification. Our findings further suggest that
chimeric mitogenomes may remain undetected even if commonly used DNA
identification markers are used to verify their identity. Detecting such
‘cryptic’ chimeras requires additional effort, which currently is not
routinely employed.