Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus
Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus
Date
2017-07
Authors
Pérez, Trinidad
Rodriguez, Fernando
Fernández, M.
Albornoz, Jesús
Domínguez, Ana
Rodriguez, Fernando
Fernández, M.
Albornoz, Jesús
Domínguez, Ana
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Keywords
Reticulate evolution
Male-dispersal
Chamois
Numts
mtDNA
COI
Cytb
Male-dispersal
Chamois
Numts
mtDNA
COI
Cytb
Abstract
Mitochondrial pseudogenes (numts) inserted in the nuclear genome are frequently
found in population studies. Its presence is commonly connected with problems and
errors when they are confounded with true mitochondrial sequences. In the opposite
side, numts can provide valuable phylogenetic information when they are copies of
ancient mitochondrial lineages. We show that Rupicapra individuals of different
geographic origin from the Cantabrian Mountains to the Apennines and the Caucasus
share a nuclear COI fragment. The numt copies are monophyletic, and their pattern of
differentiation shows two outstanding features: a long evolution as differentiated true
mitochondrial lineage, and a recent integration and spread through the chamois
populations. The COI pseudogene is much older than the present day mitochondrial
clades of Rupicapra and occupies a basal position within the Rupicapra-Ammotragus-
Arabitragus node. Joint analysis of this numt and a cytb pseudogene with a similar
pattern of evolution places the source mitochondrial lineage as a sister branch that
separated from the Ammotragus-Arabitragus lineage 6 million years ago (Mya). The
occurrence of this sequence in the nucleus of chamois suggests hybridization between
highly divergent lineages. The integration event seems to be very recent, more recent
than the split of the present day mtDNA lineages of Rupicapra (1.9 Mya). This
observation invites to think of the spread across the genus by horizontal transfer
through recent male-biased dispersal.
Description
© The Author(s), 2017. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gene 628 (2017): 63-71, doi:10.1016/j.gene.2017.07.035.