Single nucleotide polymorphism markers for genotyping hawksbill turtles (Eretmochelys imbricata)

Abstract

Assessing population connectivity and identifying conservation units are critical to formulating effective management plans for marine turtles. We combined a multiplexed targeted enrichment capture technique and high-throughput sequencing to discover single nucleotide polymorphisms (SNPs) and to genotype hawksbill turtles (Eretmochelys imbricata) to examine population structure. Our approach discovered 455 potential informative SNPs for hawksbill turtles. We optimized 25 of the 455 SNPs discovered and used them to identify preliminary evidence of hawksbill population structure, suggesting that these markers will be informative in discerning conservation units when applied to larger sample sizes in future studies.

This is a preview of subscription content, access via your institution.

Fig. 1

Data availability

Array Designs & Sequences: GEO Repository ID: GPL21262. Analysis pipeline R scripts: Dryad data repository https://doi.org/10.5061/dryad.cv35b.

References

  1. Archer F, Adams P, Schneiders B (2017) strataG: an R package for manipulating, summarizing, and analyzing population genetic data. Mol Ecol Resour 17:5–11

    CAS  Article  Google Scholar 

  2. Dutton PH, Roden SE, Stewart KR, LaCasella EL, Tiwari M, Formia A et al (2013) Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers. Conserv Genet 14:625–636

    Article  Google Scholar 

  3. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  Article  Google Scholar 

  4. Gaos A, Lewison R, Liles M et al (2016) Hawksbill turtle terra incognita: conservation genetics of Eastern Pacific rookeries. Ecol Evol 6:1251–1264

    Article  Google Scholar 

  5. Hancock-Hanser BL, Frey A, Leslie MS et al (2013) Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics. Mol Ecol Resour 13:254–268

    CAS  Article  Google Scholar 

  6. Hendricks S, Anderson EC, Antao T, Bernatchez L et al (2018) Recent advances in conservation and population genomics data analysis. Evol Appl 11:1197–1211

    Article  Google Scholar 

  7. Mortimer JA, Donnelly M, IUCN SSC Marine Turtle Specialist Group (2008) Eretmochelys imbricata. The IUCN red list of threatened species. Accessed 17 Apr 2019

  8. Jakobsson M, Rosenberg N (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806

    CAS  Article  Google Scholar 

  9. Jones M, Good J (2016) Targeted capture in evolutionary and ecological genomics. Mol Ecol 25:185–202

    Article  Google Scholar 

  10. Komoroske L, Miller M, O’Rourke S et al (2018) A versatile rapture (RAD-capture) platform for genotyping marine turtles. Mol Ecol Resour 19:497–511

    Article  Google Scholar 

  11. LeRoux R, Dutton P, Abreu-Grobois F et al (2012) Re-examination of population structure and phylogeography of hawksbill turtles in the Wider Caribbean using longer mitochondrial DNA sequences. J Hered 103:806–820

    CAS  Article  Google Scholar 

  12. Morin PA, McCarthy M (2007) Highly accurate SNP genotyping from historical and low-quality samples. Mol Ecol Notes 7:937–946

    CAS  Article  Google Scholar 

  13. Morin PA, Luikart G, Wayne RK, SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  14. Mullins RB, McKeown NJ, Sauer WHH et al (2018) Genomic analysis reveals multiple mismatches between biological and management units in yellowfin tuna (Thunnus albacares). ICES J Mar Sci 75:2145–2152

    Article  Google Scholar 

  15. Nishizawa H, Joseph J, Chong YK (2016) Spatio-temporal patterns of mitochondrial DNA variation in hawksbill turtles (Eretmochelys imbricata) in Southeast Asia. J Exp Mar Biol Ecol 474:164–170

    CAS  Article  Google Scholar 

  16. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Article  Google Scholar 

  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  19. Vargas S, Jensen M, Ho S et al (2015) Phylogeography, genetic diversity, and management units of hawksbill turtles in the Indo-Pacific. J Hered 107:199–213

    Article  Google Scholar 

  20. Zolgharnein H, Salari-Aliabadi MA, Forougmand AM et al (2001) Genetic population structure of Hawksbill turtle (Eretmochelys imbricta) using microsatellite analysis. Iran J Biotechnol 9:56–62

    Google Scholar 

Download references

Acknowledgements

We would like to thank Tammy Summers, David Graff, Alden Tagarino, Nancy Fitzsimmons, Neca Marcovaldi, Joca Thome, Brian Bowen, Jeanne Mortimer, Emma Harrison and George Balazs, Velkiss Gadea, Eduardo Altamirano, Didiher Chacon, Felipe Vallejo, Christina Miranda, Equilibrio Azul, Lauren Kurpita, Mark MacDonald, Sofía Chavarría, Neftaly Sánchez, Carlos Pacheco, Centro Tamar/ICMbio and Projeto Tamar/Fundação Pro Tamar, The Sea Turtle Conservancy, American Samoa Department of Marine and Wildlife Resources, CNMI Division of Fish and Wildlife & Department of Lands & Natural Resources and NOAA-Fisheries Pacific Islands Science Center, Fauna & Flora International, Latin American Sea Turtles, Hawaiian Island Hawksbill Project for sample contributions. We also are grateful to Steve Head and the TSRI DNA Array Core Facility for library sequencing and advice about the library preparation procedure. At the Southwest Fisheries Science Center, we thank Gabriela Serra-Valente and Amy Lanci for processing samples and Robin LeRoux, Amanda Bowman, and Vicki Pease for technical and logistical assistance, and Michael Jensen and Karen Martien for constructive feedback that improved the manuscript.

Funding

This study was funded by NOAA Fisheries (NMFS West Coast Regional Office and Southwest Fisheries Science Center).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Lisa M. Komoroske.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Banerjee, S.M., Komoroske, L.M., Frey, A. et al. Single nucleotide polymorphism markers for genotyping hawksbill turtles (Eretmochelys imbricata). Conservation Genet Resour 12, 353–356 (2020). https://doi.org/10.1007/s12686-019-01112-z

Download citation

Keywords

  • DNA capture array
  • Sea turtle
  • Conservation
  • SNP
  • Genotyping by sequencing