Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons

• Published in: Molecular phylogenetics and evolution Vol. 115; pp. 1 - 6
• Main Authors: Nacer, Deborah F., Raposo do Amaral, Fabio
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2017
• Subjects: Animals; Aves; Cytochromes b - classification; Cytochromes b - genetics; Electron Transport Complex IV - classification; Electron Transport Complex IV - genetics; Falco cherrug; Falco peregrinus; Falconidae; Falconiformes - classification; Mitochondria - genetics; NADH Dehydrogenase - classification; NADH Dehydrogenase - genetics; Phylogeny; Pseudogenes; Synology; Falco cherrug; Pseudogenes; Synology; Falconidae; Aves; Falco peregrinus
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2017.07.002

[Display omitted] •Falcons have considerably more numts than previously thought for birds.•The longest known avian numt was found, with almost 13,000bp.•Multiple independent nuclear insertions of mtDNA sequences occurred in Falconidae.•Some sequences identified as mtDNA in public databases are actually nuclear copies. Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.