The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines

Abstract

Coral reefs within the Coral Triangle (CT) are home to the greatest marine diversity on the globe and are an important supplier of marine resources to densely populated coastal regions. Many coral reefs within the CT and around the world are under threat from over-exploitation. Marine protected areas (MPAs) have been proven to be effective tools in restoring fish stocks. However, the role that MPAs play in promoting connectivity at greater distances through larval dispersal is still unknown. RADseq was used to discover 4253 SNPs from 81 individuals of the dusky parrotfish (Scarus niger) collected from three sites within the Philippines. A lack of population structure suggested a high rate of gene flow (F ST = 0.007). Estimates of Ne from linkage disequilibrium are relatively large, ranging from 1200 to 2000. A sibling analysis revealed one pair of well-supported full siblings (r = 0.773) and one pair of putative half siblings (r = 0.191) between sites separated by more than 500 km. The low F ST values indicate a high degree of gene flow between the reefs within the sampling area while the sibling analysis suggests demographic connectivity between the Sibuyan Sea and the Sulu Sea. The Mindoro–Panay throughflow is a likely vector by which larvae are transported between these sites, suggesting that reefs in Romblon are sources for reefs near Basay, 400 km to the south. Given the reliance of a vast majority of coral reef fishes on larval dispersal, this study reveals that MPAs established within the central Philippines can supply varying levels of larvae to overfished reefs.

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Acknowledgments

We are thankful for the Philippine National Fisheries Research and Development Institute (NFRDI) and Bureau of Fisheries and Aquatic Research (BFAR) assistance in granting collection permits (0208/FRP/SM/IX/2009). We thank Silliman University and particularly Hilconida Calumpong for providing laboratory space. This work was supported by NSF-PIRE (OISE-0,730,256) grant to KE Carpenter and PH Barber and by GIZ ACCCoast (No. 83099096). Additional funding was provided by a grant from the Gordon and Betty Moore Foundation to LWS. WAL was supported by an NSF Graduate Research Fellowship (Grant # DGE-0718124). The views expressed herein do not necessarily reflect the views of those organizations. We would like to thank individuals that aided in fieldwork and collection of samples, including K Hachenberg, CR Jadloc, O Paderanga and A Scalabrin. We would like to thank Seeb Lab members Carita Pascal and Marissa Jones for lab instruction and Jim Seeb for comments on the manuscript.

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Correspondence to Brian L. Stockwell.

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Stockwell, B.L., Larson, W.A., Waples, R.K. et al. The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines. Conserv Genet 17, 239–249 (2016). https://doi.org/10.1007/s10592-015-0776-3

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Keywords

  • Parrotfish
  • Population genetics
  • Restriction site associated DNA sequencing
  • Single nucleotide polymorphism
  • Larval connectivity
  • Marine protected areas