Heteroplasmy and tandem repeats reveal adaptation to elevation in the New World Jays (Aves: Corvidae)

Abstract

Advances in high-throughput sequencing (HTS) and bioinformatic tools have enabled the quick and cost-efficient assembly of complete mitochondrial genomes (mitogenomes) in non-model organisms. Consequently, new evidence of heteroplasmy, recombination and paternal leakage in mitogenomes has increased. In this study, we utilized HTS data from whole-genome sequencing to assemble the first complete mitogenomes of nine species of New World Jays (NWJs), covering all genera. We further investigated the evolution of heteroplasmy, tandem repeats (TRs) and signatures of natural selection. Our results showed a molecular shift in the adaptation to low elevation in the NWJs. Among the species studied, we found 10 heteroplasmic sites either containing TRs in the same site or 1 to 300 nucleotides adjacent; one species-specific TR in a transfer RNA (tRNA-P) potentially associated with low elevation; one phylogenetic branch with evidence of episodic positive selection also associated with low elevation; and 5 codon sites with strong support for positive selection. We referred to the heteroplasmy-TR interaction and its possible role with regulation, recombination and paternal leakage in the mitogenomes. Finally, phylogenetic relationships were in agreement with previous studies and we discussed how selective pressure on genes from the oxidative phosphorylation pathway (OXPHOS) may benefit species from low-elevation habitats. Although these findings in the NWJs require further investigation, this study offers promising insights about the evolution of mitogenomes in birds.