Marine Biodiversity

, Volume 49, Issue 1, pp 395–404 | Cite as

Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the Great Barrier Reef

  • Song HeEmail author
  • Jacob L. Johansen
  • Andrew S. Hoey
  • Melissa K. Pappas
  • Michael L. Berumen
Original Paper


To date, more than 81 species of tropical coral reef fish have been reported to hybridize in nature, spanning multiple families, including the Chaetodontidae, Pomacanthidae, and Labridae. Hybridization, however, is seemingly rare among benthic nesting species that engage in pair spawning, such as the Pomacentridae. Here, we present evidence for the first molecularly confirmed record of hybridization within the genus Dascyllus; D. aruanus and D. reticulatus. Interestingly, although many hybridization events are attributed to peripheral range effects or areas of limited overlap among otherwise allopatric species, this hybrid individual was collected from the northern Great Barrier Reef, centrally located within the distribution ranges of both species. The hybrid exhibited coloration and meristic counts intermediate between D. aruanus and D. reticulatus. Diagnostic genetic markers and subsequent microsatellites analysis confirmed that this individual was a hybrid offspring of D. aruanus and D. reticulatus, with the latter providing the maternal contribution. The occurrence of the D. aruanus × D. reticulatus hybrid on the Great Barrier Reef represents an exception to the otherwise species-specific haplotypes. The nuclear diagnostic marker which was identified during this study could serve as a hybrid indicator and benefit future hybrid investigations for hybridization between these two species.


Damselfish Natural hybridization Molecular identification 



This study was conducted under Great Barrier Reef Marine Park Authority permit G11/34319.1 and QLD Fisheries permit 103256. Ethical approval was obtained from James Cook University (permit A1267). We thank the Lizard Island Research Station staff for fieldwork support and the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory for laboratory support. We thank Gerry Allen, Tane Sinclair-Taylor, and Jean-François Flot for the useful discussions and/or assistance with figures. We thank Prof. Zeng Xiaoqi from the Ocean University of China for sharing the samples collected from Paracel Islands, South China Sea. Financial support was provided by the Australian Research Council (DE130100688 to ASH) and KAUST baseline research funds (to MLB).

Supplementary material

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ESM 1 (DOCX 1032 kb)
12526_2017_819_MOESM2_ESM.xlsx (58 kb)
ESM 2 (XLSX 58 kb)


  1. Allen GR (1973) Amphiprion leucokranos, a new species of pomacentrid fish, with notes on other anemonefishes of new Guinea. Pac Sci 27:319–326Google Scholar
  2. Allen GR (1975) Damselfishes of the south seas. TFH Publications, Neptune City, New JerseyGoogle Scholar
  3. Asoh K (2003) Gonadal development and infrequent sex change in a population of the humbug damselfish, Dascyllus aruanus, in continuous coral-cover habitat. Mar Biol 142:1207–1218CrossRefGoogle Scholar
  4. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48CrossRefGoogle Scholar
  5. Bernardi G, Crane NL (1999) Molecular phylogeny of the humbug damselfishes inferred from mtDNA sequences. J Fish Biol 54:1210–1217CrossRefGoogle Scholar
  6. Bernardi G, Holbrook SJ, Schmitt RJ, Crane NL, DeMartini E (2002) Species boundaries, populations and colour morphs in the coral reef three-spot damselfish (Dascyllus trimaculatus) species complex. Proc R Soc Lond B Biol Sci 269:599–605CrossRefGoogle Scholar
  7. Bernardi G, Noguchi R, Anderson AB, Floeter SR, Ferreira CEL (2013) Sargo Amarelo, a traditionally recognized hybrid between two species of Brazilian reef fishes. Mar Biodivers 43:255–256CrossRefGoogle Scholar
  8. Borsa P, Sembiring A, Fauvelot C, Chen W-J (2014) Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.) Comptes Rendus Biologies 337:709–716CrossRefGoogle Scholar
  9. Carvalho MC, Streiff R, Guillemaud T, Afonso P, Santos RS, Cancela ML (2000) Isolation and characterization of polymorphic microsatellite markers in Abudefduf luridus (Pisces: Pomacentridae). Mol Ecol 9:993–994CrossRefGoogle Scholar
  10. Coker DJ, Pratchett MS, Munday PL (2012) Influence of coral bleaching, coral mortality and conspecific aggression on movement and distribution of coral-dwelling fish. J Exp Mar Biol Ecol 414:62–68CrossRefGoogle Scholar
  11. Coleman RR, Gaither MR, Kimokeo B, Stanton FG, Bowen BW, Toonen RJ (2014) Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawai’i promotes genetic swamping of the endemic congener A. abdominalis. Mol Ecol 23:5552–5565CrossRefGoogle Scholar
  12. Cooper WJ, Smith LL, Westneat MW (2009) Exploring the radiation of a diverse reef fish family: phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera. Mol Phylogenet Evol 52:1–16CrossRefGoogle Scholar
  13. Cuif M, Kaplan DM, Fauvelot C, Lett C, Vigliola L (2015) Monthly variability of self-recruitment for a coral reef damselfish. Coral Reefs 34:759–770CrossRefGoogle Scholar
  14. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772CrossRefGoogle Scholar
  15. De’ath G, Fabricius KE, Sweatman H, Puotinen M (2012) The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc Nat Acad Sci U S A 109:17995–17999CrossRefGoogle Scholar
  16. DiBattista JD, Rocha LA, Hobbs J-PA, He S, Priest MA, Sinclair-Taylor TH, Bowen BW, Berumen ML (2015) When biogeographical provinces collide: hybridization of reef fishes at the crossroads of marine biogeographical provinces in the Arabian Sea. J Biogeogr 42:1601–1614CrossRefGoogle Scholar
  17. Fauvelot C, Smith-Keune C, Jerry DR, Buston PM, Planes S (2009) Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae). Mol Ecol Resour 9:651–653CrossRefGoogle Scholar
  18. Flot J-F (2007) Champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Mol Ecol Resour 7:974–977CrossRefGoogle Scholar
  19. Flot J-F (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Mol Ecol Resour 10:162–166CrossRefGoogle Scholar
  20. Flot J-F, Tillier S (2006) Molecular phylogeny and systematics of the scleractinian coral genus Pocillopora in Hawaii. In: Proceedings of the 10th International Coral Reef Symposium, pp 24–29Google Scholar
  21. Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle’s “field for recombination” approach and its application to the coral genus Pocillopora in Clipperton. BMC Evol Biol 10:372CrossRefGoogle Scholar
  22. Flot J-F, Blanchot J, Charpy L, Cruaud C, Licuanan WY, Nakano Y, Payri C, Tillier S (2011) Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecol 11:22CrossRefGoogle Scholar
  23. Gainsford A, Herwerden L, Jones GP (2015) Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish. J Evol Biol 28:205–222CrossRefGoogle Scholar
  24. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available online at:
  25. Harrison HB, Feldheim KA, Jones GP, Ma K, Mansour H, Perumal S, Williamson DH, Berumen ML (2014) Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecol Evol 4:2046–2057Google Scholar
  26. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755CrossRefGoogle Scholar
  27. Johansen JL, He S, Frank G, Pappas MK, Berumen ML, Hoey AS (2017) Hybridization between damselfishes Dascyllus aruanus and D. reticulatus on the Great Barrier Reef. Coral Reefs 36:717. CrossRefGoogle Scholar
  28. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405CrossRefGoogle Scholar
  29. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94CrossRefGoogle Scholar
  30. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G (2009) Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread indo-Pacific three-spot damselfish, Dascyllus trimaculatus, and closely related D. auripinnis. Mol Ecol Resour 9:213–215CrossRefGoogle Scholar
  31. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G (2010) Allopatric divergence and speciation in coral reef fish: the three-spot dascyllus, Dascylus trimaculatus, species complex. Evolution 64:1218–1230Google Scholar
  32. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefGoogle Scholar
  33. Liu SYV, Chang FT, Borsa P, Chen WJ, Dai CF (2014) Phylogeography of the humbug damselfish, Dascyllus aruanus (Linnaeus, 1758): evidence of indo-Pacific vicariance and genetic differentiation of peripheral populations. Biol J Linn Soc 113:931–942CrossRefGoogle Scholar
  34. Mackiewicz A, Ratajczak W (1993) Principal components analysis (PCA). Comput Geosci 19:303–342CrossRefGoogle Scholar
  35. Maruska KP, Peyton KA (2007) Interspecific spawning between a recent immigrant and an endemic damselfish (Pisces: Pomacentridae) in the Hawaiian islands. Pac Sci 61:211–221CrossRefGoogle Scholar
  36. McCafferty S, Bermingham E, Quenouille B, Planes S, Hoelzer G, Asoh K (2002) Historical biogeography and molecular systematics of the indo-Pacific genus Dascyllus (Teleostei: Pomacentridae). Mol Ecol 11:1377–1392CrossRefGoogle Scholar
  37. McCormick MI, Hoey AS (2004) Larval growth history determines juvenile growth and survival in a tropical marine fish. Oikos 106:225–242CrossRefGoogle Scholar
  38. McMillan WO, Weigt LA, Palumbi SR (1999) Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterflyfishes (Chaetodontidae). Evolution 53:247–260CrossRefGoogle Scholar
  39. Montanari SR, van Herwerden L, Pratchett MS, Hobbs J-PA, Fugedi A (2012) Reef fish hybridization: lessons learnt from butterflyfishes (genus Chaetodon). Ecol Evol 2:310–328CrossRefGoogle Scholar
  40. Montanari SR, Hobbs J-PA, Pratchett MS, van Herwerden L (2016) The importance of ecological and behavioural data in studies of hybridisation among marine fishes. Rev Fish Biol Fish 26:181–198CrossRefGoogle Scholar
  41. Mullen SP, Little K, Draud M, Brozek J, Itzkowitz M (2012) Hybridization among Caribbean damselfish species correlates with habitat degradation. J Exp Mar Biol Ecol 416:221–229CrossRefGoogle Scholar
  42. Pratchett MS, Coker DJ, Jones GP, Munday PL (2012) Specialization in habitat use by coral reef damselfishes and their susceptibility to habitat loss. Ecol Evol 2:2168–2180CrossRefGoogle Scholar
  43. Quenouille B, Bermingham E, Planes S (2004) Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 31:66–88CrossRefGoogle Scholar
  44. R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available online at:
  45. Randall HA, Allen GR (1977) A revision of the damselfish genus Dascyllus (Pomacentridae) with the description of a new species. Rec Aust Mus 31:349–385CrossRefGoogle Scholar
  46. Randall JE, Randall HA (2001) Dascyllus auripinnis, a new pomacentrid fish from atolls of the Central Pacific Ocean. Zool Stud Taipei 40:61–67Google Scholar
  47. Randall JE, Allen GR, Steene RC (1977) Five probable hybrid butterfly fishes of the genus Chaetodon from the central and western Pacific. Rec West Aust Mus 6:3–26Google Scholar
  48. Randall JE, Allen GR, Steene RC (1997) Fishes of the Great Barrier Reef and Coral Sea. University of Hawaii Press, Honolulu, HawaiiGoogle Scholar
  49. Rocha LA, Craig MT, Bowen BW (2007) Phylogeography and the conservation of coral reef fishes. Coral Reefs 26:501–512CrossRefGoogle Scholar
  50. Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106CrossRefGoogle Scholar
  51. Schwarz AL, Smith LC (1990) Sex change in the damselfish Dascyllus reticulatus (Richardson) (Perciformes: Pomacentridae). Bull Mar Sci 46:790–798Google Scholar
  52. Schweitzer JA, Martinsen GD, Whitham TG (2002) Cottonwood hybrids gain fitness traits of both parents: a mechanism for their long-term persistence? Am J Bot 89:981–990CrossRefGoogle Scholar
  53. Song CB, Near TJ, Page LM (1998) Phylogenetic relations among percid fishes as inferred from mitochondrial cytochrome b DNA sequence data. Mol Phylogenet Evol 10:343–353CrossRefGoogle Scholar
  54. Steinke D, Zemlak TS, Hebert PD (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4:e6300CrossRefGoogle Scholar
  55. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162–1169CrossRefGoogle Scholar
  56. Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA (2002) Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution 56:961–971CrossRefGoogle Scholar
  57. Sweatman HPA (1983) Influence of conspecifics on choice of settlement sites by larvae of two pomacentrid fishes (Dascyllus aruanus and D. reticulatus) on coral reefs. Mar Biol 75:225–229CrossRefGoogle Scholar
  58. Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, Warman ML (2000) Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques 29:52–54CrossRefGoogle Scholar
  59. van der Meer MH, Jones GP, Hobbs J-PA, van Herwerden L (2012) Historic hybridization and introgression between two iconic Australian anemonefish and contemporary patterns of population connectivity. Ecol Evol 2:1592–1604CrossRefGoogle Scholar
  60. van Herwerden L, Choat JH, Dudgeon CL, Carlos G, Newman SJ, Frisch A, van Oppen M (2006) Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: introgressive hybridisation or ancestral polymorphisms. Mol Phylogenet Evol 41:420–435CrossRefGoogle Scholar
  61. Walter RP, Kessel ST, Alhasan N, Fisk AT, Heath DD, Chekchak T, Klaus R, Younis M, Hill G, Jones B et al (2014) First record of living Manta alfredi × Manta birostris hybrid. Mar Biodivers 44:1–2CrossRefGoogle Scholar
  62. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci 360:1847–1857CrossRefGoogle Scholar
  63. Yaakub SM, Bellwood DR, van Herwerden L, Walsh FM (2006) Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae). Mol Phylogenet Evol 40:84–100CrossRefGoogle Scholar

Copyright information

© Senckenberg Gesellschaft für Naturforschung and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
  2. 2.Marine Science InstituteUniversity of Texas at AustinAustinUSA
  3. 3.ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleAustralia

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