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)

References

• Anijalg P, Ho SYW, Davison J, Keis M, Tammeleht E, Bobowik K, Tumanov IL, Saveljev AP, Lyapunova EA, Vorobiev AA, et al. 2018. Large-scale migrations of brown bears in Eurasia and to North America during the Late Pleistocene. J Biogeogr. 45(2):394–405. doi:10.1111/jbi.13126.
   Web of Science ®Google Scholar
• Arnason U, Gullberg A, Janke A, Kullberg M, Lehman N, Petrov EA, Väinölä R. 2006. Pinniped phylogeny and a new hypothesis for their origin and dispersal. Mol Phylogenet Evol. 41(2):345–354. doi:10.1016/j.ympev.2006.05.022.
   PubMed Web of Science ®Google Scholar
• Basuony AE, Saleh M, Sarhan M, Younes M, Abdel-Hamid F, Rodriguez Fernandes C, Vercammen P, Aboshaala F, Bounaceur F, Chadwick EA, et al. 2023. Paraphyly of the widespread generalist red fox (Vulpes vulpes): introgression rather than recent divergence of the arid-adapted Rüppell’s fox (Vulpes rueppellii)? Biol J Linn Soc. 138(4):453–469. doi:10.1093/biolinnean/blad001.
   Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi:10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Briscoe AG, Hopkins KP, Waeschenbach A. 2016. High-throughput sequencing of complete mitochondrial genomes. In: Bourlat SJ, editor. Marine genomics. vol. 1452. New York: Springer. p. 45–64.
   Google Scholar
• Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) ‘99, GCB, 45–56; Hannover, Germany.
   Google Scholar
• Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. doi:10.1093/nar/gkw955.
   PubMed Web of Science ®Google Scholar
• Du Plessis SJ, Hong S, Lee B, Koepfli KP, Chadwick EA, Hailer F. 2023a. Mitochondrial genome-based synthesis and timeline of Eurasian otter (Lutra lutra) phylogeography. Animal Cells and Syst. 27(1):366–377. doi:10.1080/19768354.2023.2283763.
   Web of Science ®Google Scholar
• Du Plessis SJ, Blaxter M, Koepfli K-P, Chadwick EA, Hailer F. 2023b. Genomics reveals complex population history and unexpected diversity of Eurasian otters (Lutra lutra) in Britain relative to genetic methods. Mol Biol Evol. 40(11):msad207. doi:10.1093/molbev/msad207.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797. doi:10.1093/nar/gkh340.
   PubMed Web of Science ®Google Scholar
• Finstermeier K, Zinner D, Brameier M, Meyer M, Kreuz E, Hofreiter M, Roos C. 2013. A Mitogenomic Phylogeny of Living Primates. PLoS One. 8(7):e69504. doi:10.1371/journal.pone.0069504.
   PubMed Web of Science ®Google Scholar
• Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, et al. 2021. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol. 22(1):120. doi:10.1186/s13059-021-02336-9.
   PubMed Web of Science ®Google Scholar
• Geffen E, Mercure A, Girman DJ, Macdonald DW, Wayne RK. 1992. Phylogenetic relationships of the fox-like canids: mitochondria1 DNA restriction fragment, site and cytochrome b sequence analyses. J Zool. 228(1):27–39. doi:10.1111/j.1469-7998.1992.tb04430.x.
   Google Scholar
• Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads - A baiting and iterative mapping approach. Nucleic Acids Res. 41(13):e129. doi:10.1093/nar/gkt371.
   PubMed Web of Science ®Google Scholar
• Ip EK, Troup M, Xu C, Winlaw DS, Dunwoodie SL, Giannoulatou, E, 13. 2022. Benchmarking the effectiveness and accuracy of multiple mitochondrial DNA variant callers: practical implications for clinical application. Front Genet. 13:692257. doi:10.3389/fgene.2022.692257.
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589. doi:10.1038/nmeth.4285.
   PubMed Web of Science ®Google Scholar
• Keis M, Remm J, Ho W, Davison SY, Tammeleht J, Tumanov E, Saveljev IL, Männil AP, Kojola P, Abramov I, et al. 2013. Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia. J Biogeogr. 5:916–927. doi:10.1111/jbi.12043.
   Google Scholar
• Koepfli KP, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, et al. 2015. Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Curr Biol. 25(16):2158–2165. doi:10.1016/j.cub.2015.06.060.
   PubMed Web of Science ®Google Scholar
• Kukekova A. v, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova A, Herbeck V, Serdyukova Y, Xiong NA, et al. 2018. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol. 2(9):1479–1491. doi:10.1038/s41559-018-0611-6.
   PubMed Web of Science ®Google Scholar
• Leite JV, Álvares F, Velo-Antón G, Brito JC, Godinho R. 2015. Differentiation of North African foxes and population genetic dynamics in the desert—insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes. Org Divers Evol. 15(4):731–745. doi:10.1007/s13127-015-0232-8.
   Web of Science ®Google Scholar
• Lenain DM. 2000. Fox populations of a protected area in Saudi Arabia [master’s thesis]. University of Hertfordshire.
   Google Scholar
• Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14):1754–1760. doi:10.1093/bioinformatics/btp324.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078–2079. doi:10.1093/bioinformatics/btp352.
   PubMed Web of Science ®Google Scholar
• Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 438(7069):803–819. doi:10.1038/nature04338.
   PubMed Web of Science ®Google Scholar
• Machado DJ, Lyra ML, Grant T. 2016. Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs. Mol Ecol Resour. 16(3):686–693. doi:10.1111/1755-0998.12492.
   PubMed Web of Science ®Google Scholar
• Mallon D, Murdoch JD, Wacher T. 2015. “Vulpes rueppellii”. IUCN Red List of Threatened Species. 2015: e.T23053A46197483. doi:10.2305/IUCN.UK.2015-4.RLTS.T23053A46197483.en.
   Google Scholar
• Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195. doi:10.1093/molbev/mst024.
   PubMed Web of Science ®Google Scholar
• Murdoch JD, Drew C, Llanes IB, Tourenq C. 2007. Rüppell’s foxes in Al Dhafra, United Arab Emirates. Canid News. 10:1–6.
   Google Scholar
• Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, et al. 2017. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. Curr Biol. 27(22):3487–3498.e10. 7 doi:10.1016/j.cub.2017.09.047.
   PubMed Web of Science ®Google Scholar
• Rivero ERC, Neves AC, Silva-Valenzuela MG, Sousa SOM, Nunes FD. 2006. Simple salting-out method for DNA extraction from formalin-fixed, paraffin-embedded tissues. Pathol Res Pract. 202(7):523–529. doi:10.1016/j.prp.2006.02.007.
   PubMed Web of Science ®Google Scholar
• Rocha LJ, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, et al. 2023. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol. 7(8):1267–1286., doi:10.1038/s41559-023-02094-w.
   PubMed Web of Science ®Google Scholar
• Rosevear DR. 1974. The carnivores of West Africa. Trustees of the British museum (Natural History). Publication no. 723, London, United Kingdom.
   Google Scholar
• Scornavacca C, Galtier N. 2017. Incomplete lineage sorting in mammalian phylogenomics. Syst Biol. 66(1):112–120. doi:10.1093/sysbio/syw082.
   PubMed Web of Science ®Google Scholar
• Sillero-Zubiri C, Hoffmann M, Macdonald DW. 2004. Canids: foxes, Wolves, Jackals and Dogs: status survey and conservation action plan. Gland, Switzerland: IUCN/SSC Canid Specialist Group.
   Google Scholar
• Statham MJ, Murdoch J, Janecka J, Aubry KB, Edwards CJ, Soulsbury CD, Berry O, Wang Z, Harrison D, Pearch M, et al. 2014. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories. Mol Ecol. 23(19):4813–4830. doi:10.1111/mec.12898.
   PubMed Web of Science ®Google Scholar
• Sun LW, Yang Y, Li GY. 2019. The complete mitochondrial genome of the raccoon dogs (Canidae: nyctereutes ussurienusis) and intraspecific comparison of three Asian raccoon dogs. Mitochondrial DNA B Resour. 4(1):670–671. doi:10.1080/23802359.2017.1419081.
   Web of Science ®Google Scholar
• Sun W-L, Zhong W, Bao K, Liu H-L, Ya-Han Y, Wang Z, Li G-Y. 2016. The complete mitochondrial genome of silver fox (Caniformia: Canidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(5):3348–3350. doi:10.3109/19401736.2015.1018216.
   PubMedGoogle Scholar
• Tamashiro RA, White ND, Braun MJ, Faircloth BC, Braun EL, Kimball RT. 2019. What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Mol Phylogenet Evol. 130:132–142. doi:10.1016/j.ympev.2018.10.008.
   PubMed Web of Science ®Google Scholar
• Termignoni-Garcia F, Bougiouri K, Edwards SV. 2023. Heteroplasmy and tandem repeats reveal adaptation to elevation in the New World Jays (Aves: corvidae). bioRxiv (2023):2023-12. doi:10.1101/2023.12.05.570157.
   Google Scholar
• Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq - Versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. doi:10.1093/nar/gkx391.
   PubMed Web of Science ®Google Scholar
• Toews DPL, Brelsford A. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol. 21(16):3907–3930. doi:10.1111/j.1365-294X.2012.05664.x.
   PubMed Web of Science ®Google Scholar
• Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44(W1):W232–W235. doi:10.1093/nar/gkw256.
   PubMed Web of Science ®Google Scholar
• Williams JB, Lenain D, Ostrowski S, Tieleman BI, Seddon PJ. 2002. Energy expenditure and water flux of Rüppell’s foxes in Saudi Arabia. Physiol Biochem Zool. 75(5):479–488. doi:10.1086/344490.
   PubMed Web of Science ®Google Scholar
• Yan SQ, Guo PC, Yue Y, Li WH, Bai CY, Li YM, Sun JH, Zhao ZH. 2016. The complete sequence of the mitochondrial genome of Arctic fox (Alopex lagopus). Mitochondrial DNA A DNA Mapp Seq Anal. 27(6):4095–4096. doi:10.3109/19401736.2014.1003860.
   PubMedGoogle Scholar
• Yang X, Zhao C, Zhang H, Zhang J, Chen L, Sha W, Liu G. 2016. Complete mitochondrial genome of the fennec fox (Vulpes zerda). Mitochondrial DNA A DNA Mapp Seq Anal. 27(1):637–638. doi:10.3109/19401736.2014.908467.
   PubMedGoogle Scholar
• Yu JN, Kim S, Oh K, Kwak M. 2012. Complete mitochondrial genome of the Korean red fox Vulpes vulpes (Carnivora, Canidae). Mitochondrial DNA. 23(2):118–119. doi:10.3109/19401736.2011.653800.
   PubMed Web of Science ®Google Scholar
• Zhang J, Zhang H, Zhao C, Chen L, Sha W, Liu G. 2015. The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana). Mitochondrial DNA. 26(5):739–741. doi:10.3109/19401736.2013.845766.
   PubMed Web of Science ®Google Scholar
• Zhao C, Zhang H, Liu G, Yang X, Zhang J. 2016. The complete mitochondrial genome of the Tibetan fox (Vulpes ferrilata) and implications for the phylogeny of Canidae. C R Biol. 339(2):68–77. doi:10.1016/j.crvi.2015.11.005.
   PubMed Web of Science ®Google Scholar
• Zhong HM, Zhang HH, Sha WL, Zhang CD, Chen YC. 2010. Complete mitochondrial genome of the red fox (Vulpes vulpes) and phylogenetic analysis with other canid species. Dongwuxue Yanjiu. 31(2):122–130. doi:10.3724/SP.J.1141.2010.02122.
   PubMedGoogle Scholar