Mitogenomic analysis of Rüppell’s fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (Vulpes vulpes)

Abstract

The Rüppell’s fox (Vulpes rueppellii) inhabits desert regions across North Africa, the Arabian Peninsula and southwestern Asia. Its phylogenetic relationship with other fox species, especially within the phylogeographic context of its sister species, V. vulpes, remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of V. rueppellii, analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the V. rueppellii mitogenome, obtaining identical sequences except for the incompletely assembled tandem-repeat region within the D-loop. The mitogenome displayed an identical organization, number and length of genes as V. vulpes. We found high support for clustering of both known subclades of V. rueppellii within the Palearctic clade of V. vulpes, rendering the latter species paraphyletic, consistent with previous analyses of shorter mtDNA fragments. More work is needed for a full understanding of the evolutionary drivers and consequences of hybridization in foxes.

Keywords:

• De novo assembly
• mtDNA
• paraphyly
• reference-mapping
• Vulpes rueppellii/Vulpes vulpes

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Correction

Acknowledgements

AEB was supported by the Cardiff University Vice Chancellor’s International Scholarship of Excellence. We thank the Cardiff University School of Biosciences for funding and support, Elizabeth Chadwick for support, Sarah du Plessis for discussions and advice, and the following organizations and individuals for assistance with sample collection: Zoology Department, Faculty of Science, Al-Azhar University, Egypt; Egyptian Environmental Affairs Agency (EEAA), Nature Conservation Sector, Egypt; Dr. Fouad Abdel-Hamid; Dr. Ahmed Badry; Mr. Mohamed Anwar; late Dr. Ali Al-Korey; Dr. Magdy Saleh; Mr. Naser Nabil and Dr. Mahmoud Younes. Sampling was conducted in accordance with national wildlife conservation and veterinary regulations. Sample import was under the Animal and Plant Health Agency (APHA) permit ITIMP21.0069. Bioinformatic analyses were performed on the Cardiff School of Biosciences’ Biocomputing Hub HPC/Cloud infrastructure, and we thank Dr Ian Merrick and Andy Ells for their support. We thank the anonymous reviewers and editor for their helpful suggestions.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

We have deposited the obtained mitogenome sequence from NOVOPlasty in GenBank (accession number: OQ274912) and the raw reads in SRA (BioProject: PRJNA1083499; SRA: SRR28214401).

Correction Statement

This article was originally published with errors, which have now been corrected in the online version. Please see Correction (http://dx.doi.org/10.1080/24701394.2024.2348847)