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Diagnostic nuclear markers for hybrid Nemos in Kimbe Bay, PNG-Amphiprion chrysopterus x Amphiprion sandaracinos hybrids

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Abstract

Hybridization among clownfish (genus Amphiprion) is common in the aquarium trade and has also been reported in natural environments. Putative hybrids between Amphiprion chrysopterus and Amphiprion sandaracinos have been identified in a previous genetic study. However, convenient diagnostic tools for hybrid detection for this case are still missing. During the present study, several potential nuclear markers were tested on both parental species and their hybrids collected from Kimbe Bay, Papua New Guinea. Two diagnostic nuclear markers were found that can confidently discriminate the parent species and their hybrids. A haploweb analysis based on those two diagnostic nuclear markers indicated that one backcrossed hybrid was misclassified as one of the purebred parent species. Identification results from these two diagnostic markers were supported by results from microsatellites, mitochondrial gene markers, and morphological traits analysis.

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References

  • Allen GR (1973) Amphiprion leucokranos, a new species of pomacentrid fish, with notes on other anemonefishes of new Guinea. Pac Sci 27:319–326

    Google Scholar 

  • Almany GR, Planes S, Thorrold SR, Berumen ML, Bode M, Saenz-Agudelo P, Bonin MC, Frisch AJ, Harrison HB, Messmer V (2017) Larval fish dispersal in a coral-reef seascape. Nature Ecology and Evolution. https://doi.org/10.1038/s41559-017-0148

  • Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    Article  CAS  PubMed  Google Scholar 

  • Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G (2009) Isolation and characterization of eight polymorphic microsatellite markers from the orange-fin anemonefish, Amphiprion chrysopterus. Conserv Genet Resour 1:333–335

    Article  Google Scholar 

  • 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 43:255–256

    Article  Google Scholar 

  • Buston PM (2004) Territory inheritance in clownfish. Proc R Soc Lond B Biol Sci 271:252–254

    Article  Google Scholar 

  • Buston PM, Cant MA (2006) A new perspective on size hierarchies in nature: patterns, causes, and consequences. Oecologia 149:362–372

    Article  PubMed  Google Scholar 

  • Camp EF, Hobbs J-PA, De Brauwer M, Dumbrell AJ, Smith DJ (2016) Cohabitation promotes high diversity of clownfishes in the coral triangle. Proc R Soc B Biol Sci 283:20160277. https://doi.org/10.1098/rspb.2016.0277

    Article  CAS  Google Scholar 

  • Chow S, Hazama K (1998) Universal PCR primers for S7 ribosomal protein gene introns in fish. Mol Ecol 7:1255–1256

    CAS  PubMed  Google Scholar 

  • Coleman RR, Gaither MR, Kimokeo B, Stanton FG, Bowen BW, Toonen RJ (2014) Large-scale introduction of the indo-Pacific damselfish Abudefduf vaigiensis into Hawaii promotes genetic swamping of the endemic congener A. abdominalis. Mol Ecol 23:5552–5565

    Article  PubMed  Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772–772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DiBattista JD, Rocha LA, Hobbs JPA, 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 42:1601–1614

    Article  Google Scholar 

  • Fautin D, Allen G (1997) Anemonefishes and their host sea anemones. Western Australian Museum Perth

  • Fautin DG (1986) Why do anemonefishes inhabit only some host actinians? Environ Biol Fish 15:171–180

    Article  Google Scholar 

  • Flot J-F, Tillier S (2006) Molecular phylogeny and systematics of the scleractinian coral genus Pocillopora in Hawaii. Proc 10th Int Coral Reef Symp 1:24–29

    Google Scholar 

  • 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 10:372–386

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 11:22–36

    Article  PubMed  PubMed Central  Google Scholar 

  • Flot JF (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Mol Ecol Resour 10:162–166

    Article  CAS  PubMed  Google Scholar 

  • Fricke HW (1979) Mating system, resource defence and sex change in the anemonefish Amphiprion akallopisos. Ethology 50:313–326

    Google Scholar 

  • Gainsford A, Herwerden L, Jones G (2015) Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish. J Evol Biol 28:205–222

    Article  CAS  PubMed  Google Scholar 

  • Gordon AK, Bok AW (2001) Frequency and periodicity of spawning in the clownfish Amphiprion akallopisos under aquarium conditions. Aquar Sci Conserv 3:293–299

    Article  Google Scholar 

  • 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 4:2046–2057

    PubMed  PubMed Central  Google Scholar 

  • Hattori A (1991) Socially controlled growth and size-dependent sex change in the anemonefish Amphiprion frenatus in Okinawa, Japan. Jpn J Ichthyol 38:165–177

    Article  Google Scholar 

  • He S, Johansen JL, Hoey AS, Pappas MK, Berumen ML (2017) Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the great barrier reef. Mar Biodivers. https://doi.org/10.1007/s12526-12017-10819-12528

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  CAS  PubMed  Google Scholar 

  • Ignatius B, Rathore G, Jagadis I, Kandasamy D, Victor A (2001) Spawning and larval rearing technique for tropical clown fish Amphiprion sebae under captive condition. J Agric Trop 16:241–249

    Google Scholar 

  • Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405

    Article  CAS  PubMed  Google Scholar 

  • Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94–109

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar TA, Balasubramanian T (2009) Broodstock development, spawning and larval rearing of the false clown fish, Amphiprion ocellaris in captivity using estuarine water. Curr Sci 97:1483–1486

    Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  PubMed  Google Scholar 

  • Mackiewicz A, Ratajczak W (1993) Principal components analysis (PCA). Comput Geosci 19:303–342

    Article  Google Scholar 

  • McMillan WO, Weigt LA, Palumbi SR (1999) Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterflyfishes (Chaetodontidae). Evolution 53:247–260

    Article  PubMed  Google Scholar 

  • Mitchell JS (2003) Social correlates of reproductive success in false clown anemonefish: subordinate group members do not pay-to-stay. Evol Ecol Res 5:89–104

    Google Scholar 

  • 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 26:181–198

    Article  Google Scholar 

  • Montanari SR, Van Herwerden L, Pratchett MS, Hobbs JPA, Fugedi A (2012) Reef fish hybridization: lessons learnt from butterflyfishes (genus Chaetodon). Ecol Evol 2:310–328

    Article  PubMed  PubMed Central  Google Scholar 

  • Moyer JT, Nakazono A (1978) Protandrous hermaphroditism in six species of the anemonefish genus Amphiprion in Japan. Jpn J Ichthyol 25:101–106

    Google Scholar 

  • Oudet G (2001) FSTAT, A program to estimate and test gene diversities and fixation indices (version 2.9. 3)

  • R Core Team (2015) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna URL http://www.r-project.org/

    Google Scholar 

  • Richards ZT, van Oppen MJ, Wallace CC, Willis BL, Miller DJ (2008) Some rare Indo-Pacific coral species are probable hybrids. PLoS One 3:e3240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rocha L, Craig M, Bowen B (2007) Phylogeography and the conservation of coral reef fishes. Coral Reefs 26:501–512

    Article  Google Scholar 

  • Ross RM (1990) The evolution of sex-change mechanisms in fishes. Environ Biol Fish 29:81–93

    Article  Google Scholar 

  • Rousset F (2008) Genepop 007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Schweitzer JA, Martinsen GD, Whitham TG (2002) Cottonwood hybrids gain fitness traits of both parents: a mechanism for theirlong-term persistence? Am J Bot 89:981–990

    Article  PubMed  Google Scholar 

  • Seehausen O (2006) Conservation: losing biodiversity by reverse speciation. Curr Biol 16:334–337

    Article  CAS  Google Scholar 

  • Song CB, Near TJ, Page LM (1998) Phylogenetic relations among percid fishes as inferred from mitochondrial CytochromebDNA sequence data. Mol Phylogenet Evol 10:343–353

    Article  CAS  PubMed  Google Scholar 

  • Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162–1169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Streelman J, Alfaro M, Westneat M, Bellwood D, Karl S (2002) Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution 56:961–971

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Truett G, Heeger P, Mynatt R, Truett A, Walker J, Warman M (2000) Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques 29:52–54

    Article  CAS  PubMed  Google Scholar 

  • Van der Meer M, Jones G, Hobbs J-PA, Van Herwerden L (2012) Historic hybridization and introgression between two iconic Australian anemonefish and contemporary patterns of population connectivity. Ecol Evol 2:1592–1604

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Herwerden L, Choat J, Dudgeon C, Carlos G, Newman S, 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 41:420–435

    Article  CAS  PubMed  Google Scholar 

  • Walter R, Kessel S, Alhasan N, Fisk A, Heath D, Chekchak T, Klaus R, Younis M, Hill G, Jones B (2014) First record of living Manta alfredi × Manta birostris hybrid. Mar Biodivers 44:1–2

    Article  Google Scholar 

  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc B: Biol Sci 360:1847–1857

    Article  CAS  Google Scholar 

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Acknowledgments

We thank Nathalie Tolou from EPHE, PSL Research University and King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory for laboratory support. We thank Jean-François Flot for useful discussions and valuable suggestions. We also thank anonymous reviewers for their constructive comments.

Funding

Financial support was provided by KAUST baseline research funds (BAS/1/1010-01-01) to M. L. B. and ANR grants to S. P.

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Authors and Affiliations

  1. Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia

    Song He, Tane H. Sinclair-Taylor & Michael L. Berumen

  2. State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian Province, China

    Song He

  3. Laboratoire d’Excellence “CORAIL”, EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, 66360, Perpignan, France

    Serge Planes

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  1. Song He
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Correspondence to Song He.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed by the authors.

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All necessary permits for sampling and observational field studies have been obtained by the authors from the competent authorities.

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Communicated by R. Thiel

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He, S., Planes, S., Sinclair-Taylor, T.H. et al. Diagnostic nuclear markers for hybrid Nemos in Kimbe Bay, PNG-Amphiprion chrysopterus x Amphiprion sandaracinos hybrids. Mar Biodiv 49, 1261–1269 (2019). https://doi.org/10.1007/s12526-018-0907-4

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  • DOI: https://doi.org/10.1007/s12526-018-0907-4

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