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Missing the mark(er): pseudogenes identified through whole mitochondrial genome sequencing provide new insight into invasive lionfish genetics

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Abstract

As documented marine invasions rise, determining the underlying molecular mechanisms of successful invasions is an immediate concern to management, but the relevance of such genetic studies hinges upon choosing the right markers. Most invasive lionfish phylogeography studies have used only the mitochondrial D-loop marker. For this study, three markers were targeted in invasive lionfish (n = 148): D-loop (mitochondrial), cytochrome oxidase I (mitochondrial), and S7 ribosomal intron-1 (nuclear). Using both mitochondrial and nuclear markers showed evidence of hybridization. At the D-loop marker, all sequences grouped with the Pacific Ocean lineage represented by Pterois volitans. At the S7 intron-1, all sequences grouped with the Indian Ocean S7 intron-1 haplotype associated with the Indian Ocean lineage represented by Pterois miles, showing discordance between the mitochondrial and nuclear markers. Further, at the COI marker, three out of 163 individuals sequenced matched P. miles. High throughput sequencing of the entire mitochondrial genome (n = 7) revealed that incongruence between mtDNA markers may be due to the insertion of mitochondrial DNA from P. volitans into the nuclear genome of fish genetically identified as P. miles. These data suggest hybridization and demonstrate that careful marker choice is important in future studies of lionfish genetics and invasive species in general.

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Acknowledgements

We acknowledge and thank Amy Brower, Margaret Hunter, Kirsty McFarland, Captain Andrew Ross, Tyler Steube, Divers Supply (Jacksonville), Suncoast Spearfishing Challenge, Pensacola Lionfish Awareness & Removal Day, Florida Fish and Wildlife Conservation Commission, Upper Keys Lionfish Derby (Key Largo), and Forfar Field Station (Andros Island) for help in collection of tissue samples.

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  1. Nicholls State University, 906 East 1st Street, Thibodaux, LA, 70301, USA

    Justine M. Whitaker

  2. University of West Florida, 11000 University Parkway, Bldg. 58, Office 60, Pensacola, FL, 32514, USA

    Alexis M. Janosik

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AMJ conceived the research and coordinated sampling. Laboratory work, including DNA extractions and PCR, and subsequent analyses were performed by JW and reviewed by AMJ JW wrote the manuscript with significant review performed by AMJ.

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Correspondence to Justine M. Whitaker.

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10592_2020_1263_MOESM1_ESM.xlsx

Supplementary file1 (XLSX 21 kb). Appendix 1. Sample identification number, location and match when Saner sequence results were queried against BLASTn database. D-loop and COI sequences are identified in Genbank as P. volitans or P. miles, and S7 intron-1 sequences are identified as Indian Ocean lineage (representing P. miles), and Pacific Ocean lineage (representing P. volitans/russelli/lunulata)

10592_2020_1263_MOESM2_ESM.xlsx

Supplementary file2 (XLSX 98 kb). Appendix 2. Single nucleotide polymorphisms identified when aligned to the P. volitans reference, accession #KM488633.1

10592_2020_1263_MOESM3_ESM.xlsx

Supplementary file3 (XLSX 143 kb). Appendix 3. Single nucleotide polymorphisms identified when aligned to the P. miles reference, accession #K022697.1

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Whitaker, J.M., Janosik, A.M. Missing the mark(er): pseudogenes identified through whole mitochondrial genome sequencing provide new insight into invasive lionfish genetics. Conserv Genet 21, 467–480 (2020). https://doi.org/10.1007/s10592-020-01263-9

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