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

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Nuclear copies of mitochondrial genes (numts) are known in eukaryotes and can complicate phylogenetic analyses.
• Previous avian numt studies, primarily using the chicken genome, suggested they are rare and short in birds.

Purpose of the Study:

• To investigate the prevalence and characteristics of numts in falcons (Falconiformes) using newly sequenced genomes.
• To assess the potential impact of numts on phylogenetic inferences in birds.

Main Methods:

• BLASTN searches were employed to identify numts in Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus) genomes.
• Specific mitochondrial gene sequences (CYTB, ND2, COI) were extracted from identified numts.
• Phylogenetic analyses were conducted using extracted numt sequences alongside authentic mitochondrial DNA sequences from Falconiformes.

Main Results:

• Avian numts appear to be significantly more frequent and longer than previously assumed.
• Multiple independent nuclear insertions of mitochondrial genes were detected throughout Falconiformes' evolutionary history.
• Some publicly available sequences were found to be misidentified numts instead of authentic mitochondrial DNA.

Conclusions:

• The study challenges previous assumptions about the rarity and brevity of avian numts.
• Numts represent a substantial factor to consider in avian systematics and phylogenetic research.
• Advancements in sequencing technologies will facilitate future research on avian numts.