Accurate population genetic measurements require cryptic species identification in corals
- 649 Downloads
Correct identification of closely related species is important for reliable measures of gene flow. Incorrectly lumping individuals of different species together has been shown to over- or underestimate population differentiation, but examples highlighting when these different results are observed in empirical datasets are rare. Using 199 single nucleotide polymorphisms, we assigned 768 individuals in the Acropora hyacinthus and A. cytherea morphospecies complexes to each of eight previously identified cryptic genetic species and measured intraspecific genetic differentiation across three geographic scales (within reefs, among reefs within an archipelago, and among Pacific archipelagos). We then compared these calculations to estimated genetic differentiation at each scale with all cryptic genetic species mixed as if we could not tell them apart. At the reef scale, correct genetic species identification yielded lower FST estimates and fewer significant comparisons than when species were mixed, raising estimates of short-scale gene flow. In contrast, correct genetic species identification at large spatial scales yielded higher FST measurements than mixed-species comparisons, lowering estimates of long-term gene flow among archipelagos. A meta-analysis of published population genetic studies in corals found similar results: FST estimates at small spatial scales were lower and significance was found less often in studies that controlled for cryptic species. Our results and these prior datasets controlling for cryptic species suggest that genetic differentiation among local reefs may be lower than what has generally been reported in the literature. Not properly controlling for cryptic species structure can bias population genetic analyses in different directions across spatial scales, and this has important implications for conservation strategies that rely on these estimates.
KeywordsAcropora Connectivity Genetic differentiation Scleractinian corals
This study was conducted over many years—from sample collection to initial discovery of cryptic species to a focus on expanded sample sizes—and as a result was improved by many people while they were in the SRP lab, including Jason Ladner, Kelly Barr, Hannah Jaris, and Deborah Johnson. Dan Griffin helped in much of the sample collection. This Project was funded through Grants to S.R.P. from the Gordon and Betty Moore Foundation and the National Science Foundation (RAPID-1547921), as well as support from the Stanford University Office of International Affairs, Stanford University Bio-X, the US National Park Service, Conservation International, and the Palau International Coral Reef Center.
Reference DNA sequences for seven exons and one mt control region locus. SNP genotypes for each individual along with sample location and cryptic genetic species identification: Stanford Digital Repository https://purl.stanford.edu/dr174rj9968.
- Hare MP, Palumbi SR (2002) Genetic distinctiveness of inshore and offshore Spisula clams. Journal of Shellfish Research 21:381Google Scholar
- Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias-Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME (2007) Coral reefs under rapid climate change and ocean acidification. Science 318:1737–1742CrossRefPubMedGoogle Scholar
- Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, Folke C, Grosberg R, Hoegh-Guldberg O, Jackson JBC, Kleypas J, Lough JM, Marshall P, Nyström M, Palumbi SR, Pandolfi JM, Rosen B, Roughgarden J (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301:929–933CrossRefPubMedGoogle Scholar
- Veron J (2000) Corals of the World. Australian Institute of Marine Science, Townsville, QueenslandGoogle Scholar
- Wallace CC (1999) Staghorn Corals of the World: A revision of the Coral Genus Acropora (Scleractinia; Astrocoeniina; Acroporidae) Worldwide, with Emphasis on Morphology. Phylogeny and Biogeography, CSIRO, Collingwood, VictoriaGoogle Scholar
- Williamson DH, Harrison HB, Almany GR, Berumen ML, Bode M, Bonin MC, Bonin M, Choukroun S, Doherty PJ, Frisch AJ, Saenz-Agudelo P, Jones GP (2016) Large-scale, multidirectional connectivity among coral reef populations in the Great Barrier Reef Marine Park. Molecular Ecology 25:6039–6054CrossRefPubMedGoogle Scholar
- Wilson K, Li YT, Whan V, Lehnert S, Byrne K, Moore S, Pongsomboon S, Tassanakajon A, Rosenberg G, Ballment E, Fayazi Z, Swan J, Kenway M, Benzie J (2002) Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture 204:297–309CrossRefGoogle Scholar