Sequencing errors in Native American mitogenomes: Impact on clade definitions, haplogroup assignation, and beyond

• Published in: Mitochondrion Vol. 70; pp. 54 - 58
• Main Authors: Aquilano, Eliana, de la Fuente, Constanza, Rodríguez Golpe, Daniela, Motti, Josefina M.B., Bravi, Claudio M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-05-2023
• Subjects: American Indian or Alaska Native; Artificial recombination; DNA, Mitochondrial; Genome, Mitochondrial; Haplogroup; Haplotypes; Humans; Mitochondrial DNA; Mitogenome; Native American; Phylogeny; Haplogroup; Mitochondrial DNA; Mitogenome; Artificial recombination; Native American
• ISSN: 1567-7249; 1872-8278
• DOI: 10.1016/j.mito.2023.03.005

•This paper presents evidence of artificial recombination in published mitogenomes of Native American origin.•Some errors stem from preferential scoring of the original Cambridge Reference sequence.•Other errors include mismatched control and coding regions, as well as intra- and inter-haplogroup chimaeras.•Given that some errors led to an incorrect definition of haplogroup B2h, a revised definition is proposed here.•Preventive quality control measures are suggested for the field.
Available evidence allows the interpretation that some cases of absence of otherwise expected variation, based on phylogenetic expectations in mitogenomes of Native American origin, are due to artificial recombination rather than to homoplasy, while other more complex scenarios involving combination of original Cambridge Reference Sequence mistakes plus incomplete or incorrect scoring of variation are also showed. Several instances of mismatched control and coding regions as well as partially duplicated HV2 are observed in Peruvians, while intra-haplogroup chimaeras of different D1 subhaplogroups are referred to in Mexican Native Americans. A revised definition for haplogroup B2h is proposed, and preventive quality control measures are suggested.