Coral Reefs

, Volume 35, Issue 3, pp 895–899 | Cite as

A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

  • Luke ThomasEmail author
  • Michael Stat
  • Richard D. Evans
  • W. Jason Kennington


Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.


Pocillopora damicornis Cryptic species qPCR Western Australia 



This work was undertaken for the Marine Biodiversity Hub, a collaborative partnership supported through funding from the Australian Government’s National Environmental Research Program. Pilbara and Montebello samples were collected by RE using funds from the Wheatstone Joint Venture Offset Connectivity project. A special thanks to Yvette Hitchen for laboratory consultation.

Supplementary material

338_2016_1430_MOESM1_ESM.docx (17 kb)
Supplementary material 1 (DOCX 17 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Luke Thomas
    • 1
    Email author
  • Michael Stat
    • 2
  • Richard D. Evans
    • 3
  • W. Jason Kennington
    • 4
  1. 1.The UWA Oceans Institute, School of Plant BiologyThe University of Western AustraliaPerthAustralia
  2. 2.Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and AgricultureCurtin UniversityPerthAustralia
  3. 3.Marine Science Program, Science and Conservation DivisionDepartment of Parks and WildlifePerthAustralia
  4. 4.Centre for Evolutionary Biology, School of Animal BiologyThe University of Western AustraliaPerthAustralia

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