Sequencing of the complete mitochondrial genome of the common raven Corvus corax (Aves: Corvidae) confirms mitogenome-wide deep lineages and a paraphyletic relationship with the Chihuahuan raven C. cryptoleucus.

Arild Johnsen,Jarl Andreas Anmarkrud,Kevin E Omland,Anna M Kearns

doi:10.1371/journal.pone.0187316

Arild Johnsen, Jarl Andreas Anmarkrud + Show 2 more

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https://doi.org/10.1371/journal.pone.0187316

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Abstract

Previous studies based on single mitochondrial markers have shown that the common raven (Corvus corax) consists of two highly diverged lineages that are hypothesised to have undergone speciation reversal upon secondary contact. Furthermore, common ravens are paraphyletic with respect to the Chihuahuan raven (C. cryptoleucus) based on mitochondrial DNA (mtDNA). Here we explore the causes of mtDNA paraphyly by sequencing whole mitochondrial genomes of 12 common ravens from across the Northern Hemisphere, in addition to three Chihuahuan ravens and one closely related brown-necked raven (C. ruficollis) using a long-range PCR protocol. Our raven mitogenomes ranged between 16925–16928 bp in length. GC content varied from 43.3% to 43.8% and the 13 protein coding genes, two rRNAs and 22 tRNAs followed a standard avian mitochondrial arrangement. The overall divergence between the two common raven clades was 3% (range 0.3–5.8% in 16 regions including the protein coding genes, rRNAs and the control region). Phylogenies constructed from whole mitogenomes recovered the previously found mitochondrial sister relationship between the common raven California clade and the Chihuahuan raven (overall divergence 1.1%), which strengthens the hypothesis that mtDNA paraphyly in the common raven results from speciation reversal of previously distinct Holarctic and California lineages.

Highlights

In the era of genomics and high throughput sequencing, complete mitochondrial genomes are rapidly becoming available for many organisms [1]
45.2% was filtered as polyclonals and 9.3% as low quality reads in the Torrent Suite software
The total length of the raven mitogenomes ranged between 16,925 bp (Californian clade) and 16,928 bp (Holarctic clade), while that of the Chihuahuan raven was 16,928 bp and the brown-necked raven 16,927 bp

Summary

Introduction

In the era of genomics and high throughput sequencing, complete mitochondrial genomes (mitogenomes) are rapidly becoming available for many organisms [1]. In addition to increasing our knowledge of functional aspects of mitochondrial genes and molecular evolution [2, 3], complete mitogenomes offer increased resolution in phylogenetic and phylogeographic. Common raven mitogenomes confirm deep lineages had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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