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Peer-reviewedCC BY 4.0Ecology and Evolution

A Genetic Method for Distinguishing Cryptic Pocillopora Species in French Polynesia Without Sequencing

  • Francesca M. Cohn1,2
  • Erika C. Johnston3
  • Scott C. Burgess4,5
  • Jordan A. Sims1
  • Krithika Layagala1
  • Pierrick Harnay6
  • Hollie M. Putnam7
  • Adrienne M. S. Correa1
7 affiliations
  1. 1Department of Environmental Science, Policy, and Management University of California Berkeley California USA
  2. 2Department of Developmental Biology Stanford University Stanford California USA
  3. 3Hawaii Institute of Marine Biology University of Hawaii at Manoa Kaneohe Hawaii USA
  4. 4Department of Biological Science Florida State University Tallahassee Florida USA
  5. 5Department of Biology Norwegian University of Science and Technology Trondheim Norway
  6. 6Leon H. Charney School of Marine Sciences University of Haifa Haifa Israel
  7. 7Department of Biological Sciences College of the Environment and Life Sciences, University of Rhode Island Kingston Rhode Island USA
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Abstract

Pocillopora is a widespread, dominant reef‐building coral genus in the Indo‐Pacific; many species within this group exhibit high morphological similarity and plasticity. Given this, genetic tools are needed to robustly identify Pocillopora individuals to the species level. Quick and accurate identification approaches for Pocillopora species are critical to estimating biodiversity patterns under current and future environmental challenges. In recent years, the mitochondrial open reading frame (mtORF) and a histone region (PocHistone) have been validated using genome‐wide data to become the most widely used species‐level markers for Pocillopora . However, Sanger sequencing of a large number of samples can be prohibitively expensive and sequencing facilities are not always readily available. Therefore, we present restriction fragment length polymorphism (RFLP) digests here that identify the six species of Pocillopora ( P. acuta , P. cf. effusa , P. grandis , P. meandrina , P. tuahiniensis , and P. verrucosa ) found in French Polynesia, without sequencing. In uninformed validation tests (in silico and in vitro), our protocol identified each Pocillopora species with 100% accuracy. Given their cost‐effective, rapid nature, the tailoring of additional RFLP digest protocols to identify cryptic coral species in reef regions around the world will support foundational reef science, conservation and restoration initiatives.

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Cite

BibTeXRIS
BibTeX
@article{cohn2026genetic,
  title = {{A Genetic Method for Distinguishing Cryptic Pocillopora Species in French Polynesia Without Sequencing}},
  author = {Francesca M. Cohn and Erika C. Johnston and Scott C. Burgess and Jordan A. Sims and Krithika Layagala and Pierrick Harnay and Hollie M. Putnam and Adrienne M. S. Correa},
  journal = {Ecology and Evolution},
  year = {2026},
  month = oct,
  doi = {10.1002/ece3.74409},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.74409},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - A Genetic Method for Distinguishing Cryptic Pocillopora Species in French Polynesia Without Sequencing
AU  - Francesca M. Cohn
AU  - Erika C. Johnston
AU  - Scott C. Burgess
AU  - Jordan A. Sims
AU  - Krithika Layagala
AU  - Pierrick Harnay
AU  - Hollie M. Putnam
AU  - Adrienne M. S. Correa
PY  - 2026
DA  - 2026/10/02
JO  - Ecology and Evolution
DO  - 10.1002/ece3.74409
UR  - https://onlinelibrary.wiley.com/doi/10.1002/ece3.74409
AB  - Pocillopora is a widespread, dominant reef‐building coral genus in the Indo‐Pacific; many species within this group exhibit high morphological similarity and plasticity. Given this, genetic tools are needed to robustly identify Pocillopora individuals to the species level. Quick and accurate identification approaches for Pocillopora species are critical to estimating biodiversity patterns under current and future environmental challenges. In recent years, the mitochondrial open reading frame (mtORF) and a histone region (PocHistone) have been validated using genome‐wide data to become the most widely used species‐level markers for Pocillopora . However, Sanger sequencing of a large number of samples can be prohibitively expensive and sequencing facilities are not always readily available. Therefore, we present restriction fragment length polymorphism (RFLP) digests here that identify the six species of Pocillopora ( P. acuta , P. cf. effusa , P. grandis , P. meandrina , P. tuahiniensis , and P. verrucosa ) found in French Polynesia, without sequencing. In uninformed validation tests (in silico and in vitro), our protocol identified each Pocillopora species with 100% accuracy. Given their cost‐effective, rapid nature, the tailoring of additional RFLP digest protocols to identify cryptic coral species in reef regions around the world will support foundational reef science, conservation and restoration initiatives.
SN  - 2045-7758
SN  - 2045-7758
ER  -