Mitochondrial genomes of the bird genus Piranga: rates of sequence evolution, and discordance between mitochondrial and nuclear markers

Luke C Campillo,Kevin J Burns,Robert G Moyle,Joseph D Manthey

doi:10.1080/23802359.2019.1637286

Abstract

We report the characteristics of the mitochondrial genomes of 22 individuals in the bird genus Piranga, including all currently recognized species in the genus (n = 11). Elements follow the standard avian mitogenome series, including two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein coding genes, and the mitochondrial control region. Excluding tRNA sequences, sequence divergence rate was lowest in rRNA genes and highest in genes encoding NADH (specifically ND1, ND2, ND3) and the control region. Gene trees assembled from 16 elements (non-tRNAs) varied greatly in topological concordance compared to the recognized species tree (based on thousands of nuclear loci), with no one gene tree precisely recovering all relationships in the genus. We also investigated patterns of concordance between the mitogenome tree and the nuclear species tree and found some discrepancies. Across non-tRNA gene trees (n = 16), the species tree topology was recovered by as few as three elements at a particular node and complete concordance (i.e. 16/16 gene trees matched the species tree topology) was recovered at only one node. We found mitochondrial gene regions that are often used in vertebrate systematics (e.g. CytB, ND2) recovered nearly the exact same topology as the nuclear species tree topology.

Highlights

Mitochondrial DNA has long been used to elucidate phylogenetic relationships across the tree of life
For ribosomal RNA (rRNA) (12S and 16S), we recovered greater than 90% identical nucleotides for each respective gene region
We investigated patterns of topological concordance with the nuclear species tree identified using thousands of loci (Manthey et al 2016) but failed to recover a single mitochondrial element that was completely concordant with the species tree

Summary

Introduction

Mitochondrial DNA (mtDNA) has long been used to elucidate phylogenetic relationships across the tree of life. In the bird genus Piranga, several studies have used mtDNA to investigate phylogenetic relationships (Burns 1998; Barker et al 2015), but reconstructions varied in topology and nodal support depending on the mtDNA genes used (CytB or CytB þ ND2, respectively). We used restriction-site associated DNA sequencing (RAD-seq; Miller et al 2007) and target capture of ultraconserved elements (UCEs; Faircloth et al 2012) to resolve the phylogeny of the genus, producing topologically identical species tree reconstructions with high support across nodes for both sequencing methods (Manthey et al 2016), but different from previous, mtDNA-based phylogenies We used restriction-site associated DNA sequencing (RAD-seq; Miller et al 2007) and target capture of ultraconserved elements (UCEs; Faircloth et al 2012) to resolve the phylogeny of the genus, producing topologically identical species tree reconstructions with high support across nodes for both sequencing methods (Manthey et al 2016), but different from previous, mtDNA-based phylogenies (i.e. Burns 1998; Barker et al 2015)

Methods

Results

Conclusion