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

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 relative...

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Bibliographic Details
Published in:Molecular Phylogenetics and Evolution
Main Authors: Nacer, Deborah F., do Amaral, Fabio Raposo
Format: Article in Journal/Newspaper
Language:English
Published: Academic Press Inc Elsevier Science 2017
Subjects:
Pseudogenes
Synology
Aves
Falconidae
Falco cherrug
Falco peregrinus
Rua
peregrine falcon
Online Access:https://repositorio.unifesp.br/handle/11600/57339
https://doi.org/10.1016/j.ympev.2017.07.002
Description
Summary: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. (C) 2017 Elsevier Inc. All rights reserved. FAPESP Biota Program NSF/Biota FAPESP/NASA Dimensions of Biodiversity Grant CNPq/MCT CAPES Univ Fed Sao Paulo, Dept Ecol & Biol Evolut, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, Brazil Univ Fed Sao Paulo, Dept Ecol & Biol Evolut, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, Brazil BIOTA/FAPESP: 2011/50143-7 BIOTA/FAPESP: 2011/23155-4 BIOTA/FAPESP: 2013/50297-0 DOB/NSF: 1343578 Web of Science

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