Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

Abstract

Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals.

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References

  1. Al Tawaha M, Benzoni F, Eid E, Abu Awali A (2019) The hard corals of Jordan, a field guide. The Royal Marine Conservation Society of Jordan, Amman

    Google Scholar 

  2. Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Arrigoni R, Stefani F, Pichon M, Galli P, Benzoni F (2012) Molecular phylogeny of the robust clade (Faviidae, Mussidae, Merulinidae, and Pectiniidae): an Indian Ocean perspective. Mol Phylogenet Evol 65:183–193

    PubMed  Google Scholar 

  4. Arrigoni R, Berumen ML, Terraneo TI, Caragnano A, Bouwmeester J, Benzoni F (2015) Forgotten in the taxonomic literature: resurrection of the scleractinian coral genus Sclerophyllia (Scleractinia, Lobophylliidae) from the Arabian Peninsula and its phylogenetic relationships. Syst Biodivers 13:140–163

    Google Scholar 

  5. Arrigoni R, Benzoni F, Terraneo TI, Caragnano A, Berumen ML (2016a) Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea. Sci Rep 6:34612

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Arrigoni R, Berumen ML, Chen CA, Terraneo TI, Baird AH, Payri C, Benzoni F (2016b) Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species. Mol Phylogenet Evol 105:146–159

    PubMed  Google Scholar 

  7. Arrigoni R, Benzoni F, Huang D, Fukami H, Chen CA, Berumen ML, Hoogenboom M, Thomson DP, Hoeksema BW, Budd AF, Zayasu Y, Terraneo TI, Kitano YF, Benzoni F (2016c) When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus. Contrib Zool 85:387–422

    Google Scholar 

  8. Arrigoni R, Maggioni D, Montano S, Hoeksema BW, Seveso D, Shlesinger T, Terraneo TI, Tietbohl MD, Berumen ML (2018) An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea. Coral Reefs 37:967–984

    Google Scholar 

  9. Arrigoni R, Berumen ML, Stolarski J, Terraneo TI, Benzoni F (2019) Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean. Cladistics 35:301–328

    Google Scholar 

  10. Avise JC, Robinson TJ, Kubatko L (2008) Hemiplasy: a new term in the lexicon of phylogenetics. Syst Biol 57:503–507

    PubMed  Google Scholar 

  11. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376

    PubMed  PubMed Central  Google Scholar 

  12. Benzoni F, Stefani F (2012) Porites fontanesii, a new species of hard coral (Scleractinia, Poritidae) from the southern Red Sea, the Gulf of Tadjoura, and the Gulf of Aden. Zootaxa 3447:56–68

    Google Scholar 

  13. Benzoni F, Arrigoni R, Stefani F, Stolarski J (2012) Systematics of the coral genus Craterastrea (Cnidaria, Anthozoa, Scleractinia) and description of a new family through combined morphological and molecular analyses. Syst Biodivers 10:417–433

    Google Scholar 

  14. Berumen ML, Arrigoni R, Bouwmeester J, Terraneo TI, Benzoni F (2019) Corals of the red sea. In: Voolstra CR, Berumen ML (eds) Coral reefs of the red sea. Springer, Berlin, pp 123–155

    Google Scholar 

  15. Boero F (2001) Light after dark: the partnership for enhancing expertise in taxonomy. Trends Ecol Evol 16:266

    CAS  PubMed  Google Scholar 

  16. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Bouckaert RR (2010) DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 26:1372–1373

    CAS  PubMed  Google Scholar 

  18. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchards MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537

    PubMed  PubMed Central  Google Scholar 

  19. Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, Roy-Choudhury A (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917–1932

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Budd AF, Fukami H, Smith ND, Knowlton N (2012) Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia). Zool J Linnean Soc 166:465–529

    Google Scholar 

  21. Cariou M, Duret L, Charlat S (2013) Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol 3:846–852

    PubMed  PubMed Central  Google Scholar 

  22. Carlon DB, Budd AF (2002) Incipient speciation across a depth gradient in a scleractinian coral? Evolution 56:2227–2242

    PubMed  Google Scholar 

  23. Carlon DB, Budd AF, Lippé C, Andrew RL (2011) The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs. Evolution 65:3428–3447

    PubMed  Google Scholar 

  24. Chevalier JP (1975) Les scléractiniaires de la mélanésie francaise (Nouvelle- Calédonie, lies Chesterfield, lies Loyauté, Nouvelles-Hébrides). Expédition Francaise Sur les Récifs Coralliens de la Nouvelle-Calédonie, Deuxieme Partie. Fond Singer-Polignac, Paris

  25. Claereboudt MR (2006) Reef corals and coral reefs of the Gulf of Oman. Historical Association of Oman, Muscat

    Google Scholar 

  26. Crossland C (1952) Madreporaria, Hydrocorallinae, Heliopora and Tubipora. Sci. Rep. Great Barrier Reef Exped. 1928–1929. Bull Br Mus Nat Hist Zool 6:85–257

    Google Scholar 

  27. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genome Project Data Processing Subgroup (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Davey JW, Blaxter ML (2010) RADSeq: next-generation population genetics. Brief Funct Genomics 9:416–423

    CAS  PubMed  Google Scholar 

  29. Dimond JL, Gamblewood SK, Roberts SB (2017) Genetic and epigenetic insight into morphospecies in a reef coral. Mol Ecol 26:5031–5042

    CAS  PubMed  Google Scholar 

  30. Drummond AJ, Bouckaert RR (2015) Bayesian evolutionary analysis with BEAST. Harvard University Press, Cambridge

    Google Scholar 

  31. Eaton DAR, Ree RH (2013) Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae). Syst Biol 62:689–706

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Eaton DA, Spriggs EL, Park B, Donoghue MJ (2017) Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants. Syst Biol 66:399–412

    PubMed  Google Scholar 

  33. Flot JF, 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

    PubMed  PubMed Central  Google Scholar 

  34. Forsman ZH, Barshis DJ, Hunter CL, Toonen RJ (2009) Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites. BMC Evol Biol 9:45

    PubMed  PubMed Central  Google Scholar 

  35. Forsman ZH, Concepcion GT, Haverkort RD, Shaw RW, Maragos JE, Toonen RJ (2010) Ecomorph or endangered coral? DNA and microstructure reveal Hawaiian species complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli. PLoS ONE 5:e15021

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Forsman ZH, Knapp ISS, Tisthammer K, Eaton DAR, Belcaid M, Toonen RJ (2017) Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. compressa. Mol Phylogenet Evol 111:132–148

    CAS  Google Scholar 

  37. Frade PR, Reyes-Nivia MC, Faria J, Kaandorp JA, Luttikhuizen PC, Bak RPM (2010) Semi-permeable species boundaries in the coral genus Madracis: introgression in a brooding coral system. Mol Phylogenet Evol 57:1072–1090

    CAS  PubMed  Google Scholar 

  38. Fukami H, Chen CA, Budd AF, Collins A, Wallace C, Chuang YY, Chen C, Dai CF, Iwao K, Sheppard C, Knowlton N (2008) Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS ONE 3:e3222

    PubMed  PubMed Central  Google Scholar 

  39. García-Roselló E, Guisande C, Manjarrés-Hernández A, González-Dacosta J, Heine J, Pelayo-Villami P, González-Vilas L, Vari RP, Vaamonde A, Granado-Lorencio C, Lobo JM (2015) Can we derive macroecological patterns from primary Global Biodiversity Information Facility data? Global Ecol Biogeog 24:335–347

    Google Scholar 

  40. Garrison E, Marth G (2012) Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907

  41. Gautier M, Gharbi K, Cezard T, Foucaud J, Kerdelhué C, Pudlo P, Cornuet JM, Estoup A (2013) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Mol Ecol 22:3165–3178

    CAS  PubMed  Google Scholar 

  42. Gélin P, Postaire B, Fauvelot C, Magalon H (2017) Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Mol Phylogenet Evol 109:430–446

    PubMed  Google Scholar 

  43. Gélin P, Fauvelot C, Bigot L, Baly J, Magalon H (2018) From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals. Ecol Evol 8:1411–1426

    PubMed  Google Scholar 

  44. Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C (2016) Clustering genes of common evolutionary history. Mol Biol Evol 33:1590–1605

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Hellberg ME (2006) No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol 6:24

    PubMed  PubMed Central  Google Scholar 

  46. Herrera S, Shank TM (2016) RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Mol Phylogenet Evol 100:70–79

    PubMed  Google Scholar 

  47. Hoeksema BW (2007) Delineation of the Indo-Malayan centre of maximum marine biodiversity: the coral triangle. In: Renema W (ed) Biogeography, time and place: distributions, barriers and islands. Springer, Berlin, pp 117–178

    Google Scholar 

  48. Hoeksema BW, Cairns S (2019) World list of scleractinia. Leptastrea Milne Edwards & Haime, 1849. Accessed through: world register of marine species https://www.marinespecies.org/aphia.php?p=taxdetails&id=204278. Accessed 04 Dec 2019

  49. Hou Y, Nowak MD, Mirré V, Bjorå CS, Brochmann C, Popp M (2015) Thousands of RAD-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus Diapensia (Diapensiaceae). PLoS ONE 10:e0140175

    PubMed  PubMed Central  Google Scholar 

  50. Huang D, Benzoni F, Fukami H, Knowlton N, Smith ND, Budd AF (2014a) Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia). Zool J Linnean Soc 171:277–355

    Google Scholar 

  51. Huang D, Benzoni F, Arrigoni R, Baird AH, Berumen ML, Bouwmeester J, Chou LM, Fukami H, Licuanan WY, Lovell ER, Mieri R, Todd PA, Budd AF, Meier R (2014b) Towards a phylogenetic classification of reef corals: the Indo-Pacific genera Merulina, Goniastrea and Scapophyllia (Scleractinia, Merulinidae). Zool Scripta 43:531–548

    Google Scholar 

  52. Huang D, Goldberg EE, Chou LM, Roy K (2018) The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution 72:288–302

    PubMed  Google Scholar 

  53. Hughes TP, Barnes ML, Bellwood DR, Cinner JE, Cumming GS, Jackson JB, Kleypas J, van de Leemput IA, Lough JM, Morrison TH, Palumbi SR, van Nes EH, Scheffer M (2017) Coral reefs in the Anthropocene. Nature 546:82–90

    CAS  PubMed  Google Scholar 

  54. Hughes TP, Anderson KD, Connolly SR, Heron SF, Kerry JT, Lough JM, Baird AH, Baum JK, Berumen ML, Bridge TC, Claar DC, Eakin CM, Gilmour JP, Graham NAJ, Harrison H, Hobbs JPA, Hoey AS, Hoogenboom M, Lowe RJ, McCulloch MT, Pandolfi JM, Pratchett M, Schoepf V, Torda G, Wilson SK (2018) Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359:80–83

    CAS  Google Scholar 

  55. Hughes TP, Kerry JT, Baird AH, Connolly SR, Chase TJ, Dietzel A, Hill T, Hoey AS, Hoogenboom MO, Jacobson M, Kerswell A, Madin JS, Mieog A, Paley AS, Pratchett MS, Torda G, Woods RM (2019) Global warming impairs stock-recruitment dynamics of corals. Nature 568:387–390

    CAS  Google Scholar 

  56. Johnson CN, Balmford A, Brook BW, Buettel JC, Galetti M, Guangchun L, Wilmshurst JM (2017) Biodiversity losses and conservation responses in the Anthropocene. Science 356:270–275

    CAS  PubMed  Google Scholar 

  57. Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón JH, Knapp IS, Toonen RJ (2017) A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci Rep 7:5991

    PubMed  PubMed Central  Google Scholar 

  58. Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773–795

    Google Scholar 

  59. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Keith SA, Baird AH, Hughes TP, Madin JS, Connolly SR (2013) Faunal breaks and species composition of Indo-Pacific corals: the role of plate tectonics, environment and habitat distribution. Proc R Soc Lond 280:20130818

    CAS  Google Scholar 

  61. Klunzinger CB (1879) Die Korallenthiere des Rothen Meeres, 3. Gutmann, Berlin

    Google Scholar 

  62. Kitahara MV, Fukami H, Benzoni F, Huang D (2016) The new systematics of Scleractinia: integrating molecular and morphological evidence. In: Dubinsky Z, Goffredo S (eds) The Cnidaria, past, present and future. Springer, Berlin, pp 41–59

    Google Scholar 

  63. Kitano YF, Benzoni F, Arrigoni R, Shirayama Y, Wallace CC, Fukami H (2014) A phylogeny of the family Poritidae (Cnidaria, Scleractinia) based on molecular and morphological analyses. PLoS ONE 9:e98406

    PubMed  PubMed Central  Google Scholar 

  64. Kitchen SA, Crowder CM, Poole AZ, Weis VM, Meyer E (2015) De novo assembly and characterization of four anthozoan (phylum Cnidaria) transcriptomes. Genes Genom Genet 5:2441–2452

    CAS  Google Scholar 

  65. Knapp IS, Puritz JB, Bird CE, Whitney JL, Sudek M, Forsman ZH, Toonen RJ (2016) ezRAD-an accessible next-generation RAD sequencing protocol suitable for non-model organisms v3. 1. Protocols io life sciences protocol repository. https://dx.doi.org/10.17504/protocols.io.e9pbh5n

  66. Knowlton N (2001) The future of coral reefs. Proc Nat Acad Sci USA 98:5419–5425

    CAS  PubMed  Google Scholar 

  67. Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17–24

    CAS  PubMed  Google Scholar 

  68. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B (2016) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 34:772–773

    Google Scholar 

  69. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Leaché AD, Fujita MK, Minin VN, Bouckaert RR (2014) Species delimitation using genome-wide SNP data. Syst Biol 63:534–542

    PubMed  PubMed Central  Google Scholar 

  71. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    PubMed  PubMed Central  Google Scholar 

  73. Lischer HE, Excoffier L (2011) PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28:298–299

    PubMed  Google Scholar 

  74. Massatti R, Reznicek AA, Knowles LL (2016) Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case study in Carex sect Racemosae. Am J Bot 103:337–347

    CAS  PubMed  Google Scholar 

  75. Matthai G (1914) No. I.—A revision of the recent colonial Astræidæ possessing distinct corallites. Trans Linn Soc Lond 17:1–140

    Google Scholar 

  76. McCauley DJ, Pinsky ML, Palumbi SR, Estes JA, Joyce FH, Warner RR (2015) Marine defaunation: animal loss in the global ocean. Science 347:1255641

    PubMed  PubMed Central  Google Scholar 

  77. McFadden CS, Haverkort-Yeh R, Reynolds AM, Halàsz A, Quattrini AM, Forsman ZH, Benayahu Y, Toonen RJ (2017) Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae). Mol Phylogenet Evol 112:174–184

    Google Scholar 

  78. McFadden CS, Gonzalez A, Imada R, Shi SS, Hong P, Ekins M, Benayahu Y (2019) Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo-Pacific octocoral family Xeniidae. J Biogeogr 46:992–1006

    Google Scholar 

  79. Metzker ML (2010) Sequencing technologies–the next generation. Nat Rev Genet 11:31–46

    CAS  PubMed  Google Scholar 

  80. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the gateway computing environments workshop, New Orleans

  81. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–9248

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Milne Edwards M, Haime J (1849) Recherches sur les polypiers; 4eme mémoire. Monographie des Astréides. Ann Sci Nat 3:95–197

    Google Scholar 

  83. Nishihira M, Veron JEN (1995) Hermatypic corals of Japan. Kaiyusha, Tokyo

    Google Scholar 

  84. Obura DO (2012) The diversity and biogeography of Western Indian Ocean reef-building corals. PLoS ONE 7:e45013

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Obura DO (2016) An Indian Ocean centre of origin revisited: Palaeogene and Neogene influences defining a biogeographic realm. J Biogeogr 43:229–242

    Google Scholar 

  86. Pante E, Abdelkrim J, Viricel A, Gey D, France SC, Boisselier MC, Samadi S (2015) Use of RAD sequencing for delimiting species. Heredity 114:450–459

    CAS  PubMed  Google Scholar 

  87. Paz-García DA, Hellberg ME, García-de-León FJ, Balart EF (2015) Switch between morphospecies of Pocillopora corals. Am Nat 186:434–440

    PubMed  Google Scholar 

  88. Pichon M, Benzoni F, Chaineu C, Dutrieux E (2010) Field Guide to the hard corals of the southern coast of Yemen. Biotope, Paris

    Google Scholar 

  89. Pinzón JH, Sampayo E, Cox E, Chauka LJ, Chen CA, Voolstra CR, LaJeunesse TC (2013) Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia). J Biogeogr 40:1595–1608

    Google Scholar 

  90. Prada C, DeBiasse MB, Neigel JE, Yednock B, Stake JL, Forsman ZH, Baums IB, Hellberg ME (2014) Genetic species delineation among branching Caribbean Porites corals. Coral Reefs 33:1019–1030

    Google Scholar 

  91. Pratchett MS, Caballes CF, Wilmes JC, Matthews S, Mellin C, Sweatman H, Nadler LE, Brodie J, Thmpson CA, Hoey J, Bos AR, Byrne M, Messmer V, Fortunato SA, Chen CCM, Buck ACE, Barbcok RC, Uthicke S (2017) Thirty years of research on crown-of-thorns starfish (1986–2016): scientific advances and emerging opportunities. Diversity 9:41

    Google Scholar 

  92. Puritz JB, Hollenbeck CM, Gold JR (2014) dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ 2:e431

    PubMed  PubMed Central  Google Scholar 

  93. Quattrini AM, Wu T, Soong K, Jeng MS, Benayahu Y, McFadden CS (2019) A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evol Biol 19:116

    PubMed  PubMed Central  Google Scholar 

  94. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67:901–904

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Rancilhac L, Goudarzi F, Gehara M, Hemami MR, Elmer KR, Vences M, Steinfarz S (2019) Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Mol Phylogenet Evol 133:1890–1897

    Google Scholar 

  97. Richards ZT, Berry O, Van Oppen MJ (2016) Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans. Conserv Genet 17:577–591

    Google Scholar 

  98. Roberts CM, McClean CJ, Veron JEN, Hawkins JP, Allen GR, McAllister DE, Mittermeier CG, Schueler FW, Spalding M, Weels F, Vynne C, Werner TB (2002) Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295:1280–1284

    CAS  PubMed  Google Scholar 

  99. Rubin BE, Ree RH, Moreau CS (2012) Inferring phylogenies from RAD sequence data. PLoS ONE 7:e33394

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW (2017) Image J2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 18:529

    PubMed  PubMed Central  Google Scholar 

  101. Sanderson MJ, Driskell AC, Ree RH, Eulenstein O, Langley S (2003) Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol Biol Evol 20:1036–1042

    CAS  PubMed  Google Scholar 

  102. Sargent TD, Jamrich M, Dawid IB (1986) Cell interactions and the control of gene activity during early development of Xenopus laevis. Dev Biol 114:238–246

    CAS  PubMed  Google Scholar 

  103. Scheer G, Pillai CSG (1974) Report on the Scleractinia from the Nicobar Islands. Zoologica 42:1–198

    Google Scholar 

  104. Scheer G, Pillai CSG (1983) Report on the stony corals from the Red Sea. Zoologica 45:1–184

    Google Scholar 

  105. Schettino A, Turco E (2011) Tectonic history of the western Tethys since the Late Triassic. Geol Soc Am Bull 123:89–105

    Google Scholar 

  106. Schmidt-Roach S, Miller KJ, Lundgren P, Andreakis N (2014) With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics. Zool J Linnean Soc 170:1–33

    Google Scholar 

  107. Shearer TL, Van Oppen MJH, Romano SL, Wörheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11:2475–2487

    CAS  PubMed  Google Scholar 

  108. Sheppard CRC, Sheppard ALS (1991) Corals and coral communities of Saudi Arabia. Fauna Arabia 12:1–170

    Google Scholar 

  109. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Stefani F, Benzoni F, Yang SY, Pichon M, Galli P, Chen CA (2011) Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia). Coral Reefs 30:1033–1049

    Google Scholar 

  111. Stobie CS, Cunningham MJ, Oosthuizen CJ, Bloomer P (2019) Finding stories in noise: mitochondrial portraits from RAD data. Mol Ecol Resour 19:191–205

    CAS  PubMed  Google Scholar 

  112. Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N (2017) Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: the fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Mol Phylogenet Evol 114:189–198

    CAS  PubMed  Google Scholar 

  113. Terraneo TI, Berumen ML, Arrigoni R, Waheed Z, Bouwmeester J, Caragnano A, Stefani F, Benzoni F (2014) Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships. ZooKeys 433:1–30

    Google Scholar 

  114. Terraneo TI, Benzoni F, Arrigoni R, Berumen ML (2016) Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea. Mol Phylogenet Evol 102:278–294

    PubMed  Google Scholar 

  115. Terraneo TI, Arrigoni R, Benzoni F, Forsman ZH, Berumen ML (2018a) Using ezRAD to reconstruct the complete mitochondrial genome of Porites fontanesii (Cnidaria: Scleractinia). Mitochondrial DNA B Resour 3:173–174

    Google Scholar 

  116. Terraneo TI, Arrigoni R, Benzoni F, Forsman ZH, Berumen ML (2018b) The complete mitochondrial genome of Porites harrisoni (Cnidaria: Scleractinia) obtained using next-generation sequencing. Mitochondrial DNA B Resour 3:286–287

    Google Scholar 

  117. Todd PA (2008) Morphological plasticity in scleractinian corals. Biol Rev 83:315–337

    PubMed  Google Scholar 

  118. Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1:e203

    PubMed  PubMed Central  Google Scholar 

  119. Van Oppen MV, Willis BL, Vugt HV, Miller DJ (2000) Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyses. Mol Ecol 9:1363–1373

    CAS  PubMed  Google Scholar 

  120. Vaughan TW (1918) Some shoal-water corals from Murray Islands, Cocos Keeling Islands and Fanning Islands. Pap Dep Mar Biol Carnegie Inst Wash 9:51–234

    Google Scholar 

  121. Veron JEN, Pichon M, Wijsman-Best M (1977) Scleractinia of eastern Australia. Part II. Families Faviidae, Trachyphylliidae. Australian Institute of Marine Science, Townsville

    Google Scholar 

  122. Veron JEN (2000) Corals of the World. Australian Institute of Marine Science, Townsville

    Google Scholar 

  123. Veron JEN (2002) New species described in corals of the world. Australian Institute of Marine Science, Townsville

    Google Scholar 

  124. Veron JEN, Stafford-Smith M, DeVantier L, Turak E (2015) Overview of distribution patterns of zooxanthellate Scleractinia. Front Mar Sci 1:81

    Google Scholar 

  125. Verrill A (1867) Synopsis of the polyps and corals of the North Pacific Exploring Expedition, with descriptions of some additional species from the West Coast of North America III Madreporaria. Proc Essex Inst Salem 5:33–50

    Google Scholar 

  126. Vollmer SV, Palumbi SR (2004) Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Mol Ecol 13:2763–2772

    CAS  PubMed  Google Scholar 

  127. Wagner CE, Keller I, Wittwer S, Selz OM, Mwaiko S, Greuter L, Sivasundar A, Seehaunsen O (2013) Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol 22:787–798

    CAS  PubMed  Google Scholar 

  128. Warner PA, Van Oppen MJ, Willis BL (2015) Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity. Mol Ecol 24:2993–3008

    PubMed  Google Scholar 

  129. Wells JW (1956) Scleractinia. In: Moore RC (ed) Treatise on Invertebrate Paleontology, Part F. Geological Society of America, Boulder, pp F328–F444

    Google Scholar 

  130. Wijsman-Best M (1980) Indo-Pacific coral species belonging to the subfamily Montastreinae Vaughan & Wells, 1943 (Scleractinea–Coelenterata) Part II. The genera Cyphastrea, LeptastreaEchinopora and Diploastrea. Zool Meded 55:235–263

    Google Scholar 

  131. Willis SC, Hollenbeck CM, Puritz JB, Gold JR, Portnoy DS (2017) Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage. Mol Ecol Resour 17:955–965

    CAS  PubMed  Google Scholar 

  132. Zhang J, Kobert K, Flouri T, Stamatakis A (2013) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614–620

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This project was supported by funding from KAUST (award # FCC/1/1973-21 and baseline research funds to MLB). This research was undertaken in accordance with the policies and procedures of KAUST. Permissions relevant for KAUST to undertake the research have been obtained from the applicable governmental agencies in the Kingdom of Saudi Arabia. We wish to thank A Gusti (KAUST), the captain and crew of the MV Dream-Master, and the KAUST Coastal and Marine Resources Core Laboratory for fieldwork logistics in the Red Sea. In Yemen, fieldwork organization, logistics, and sampling permits from the relevant authorities were possible thanks to the collaboration of E Dutrieux (Creocean), CH Chaineau (Total SA), R Hirst, and M Abdul Aziz (YLNG). We are grateful to E Karsenti (EMBL) and E Bougois (Tara Expeditions), the OCEANS Consortium for allowing sampling during the Tara Oceans expedition in Djibouti, the Gambier Archipelago, French Polynesia, and Mayotte. We thank the commitment of the following people and additional sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA-003, PROMETHEUS/ANR-09-GENM-031, and TARA-GIRUS/ANR-09-PCS-GENM-218), EU FP7 (MicroB3/No.287589), FWO, BIO5, Biosphere 2, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (https://oceans.taraexpeditions.org). This article is contribution number 103 of the Tara Oceans Expedition 2009–2012. New Caledonia data and specimens were obtained during the IRD CORALCAL1 (https://dx.doi.org/10.17600/7100020), CORALCAL2 (https://dx.doi.org/10.17600/8100050), CORALCAL3 (https://dx.doi.org/10.17600/9100010), CORALCAL4 (https://dx.doi.org/10.17600/12100060), BIBELOT (https://dx.doi.org/10.17600/14003700), and CORALCAL5 (https://dx.doi.org/10.17600/15004300) expeditions on the RV Alis. We are grateful to the chief scientists and cruise organizers C Payri (IRD), C Fauvelot (IRD) for invitation and financial support to join and valuable help with sampling authorizations. Material from Madagascar was collected during the MAD (https://dx.doi.org/10.17600/16004700) expedition on the RV Antea organized by H Magalon (ULR). The MADANG expedition specimens were obtained during the "Our Planet Reviewed" Papua Niugini expedition (https://dx.doi.org/10.17600/12100070) organized by Muséum National d'Histoire Naturelle (MNHN), Pro Natura International (PNI), Institut de Recherche pour le Développement (IRD), and University of Papua New Guinea (UPNG), Principal Investigators P Bouchet, C Payri, and S Samadi. The organizers acknowledge funding from the Total Foundation, Prince Albert II of Monaco Foundation, Fondation EDF, Stavros Niarchos Foundation, and Entrepose Contracting, and in-kind support from the Divine Word University (DWU). Material from Kavieng, PNG, was sampled during the KAVIENG Expedition (https://doi.org/10.17600/14004400). The expedition operated under a permit delivered by the Papua New Guinea Department of Environment and Conservation. Material from the Coral Sea, Australia, was sampled in under Permit No. AU-COM2018-437. The authors wish to thank A.H. Baird (JCU), M. Pratchett (JCU), and Hugo Harrison (JCU), and the relevant staff at Parks Australia, for material collected in the Coral Sea. We are grateful to A. Andouche (MNHN), M. Castellin (MNHN), P. Lozouet (MNHN), C. Lüter (ZMB), T. Bridge (MTQ), P. Muir (MTQ), M. Lowe (NHM), and A. Cabrinovic (NHM) for allowing the study of the museum reference collections. The views expressed are purely those of the writers and may not in any circumstance be regarded as stating an official position of the European Commission, nor of Parks Australia, the Director of National Parks or the Australian Government. We are grateful to Z.H. Forsman (UH Manoa) and one anonymous reviewer for their useful corrections and suggestions.

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Data S1

List of coral samples analyzed in this study with collection information and the sequencing and bioinformatics statistics summary. In particular, the collection information includes voucher numbers, museum/institute where the specimen is deposited, species identification, molecular clade based on SNPs phylogenies, and collection locality. The sequencing and bioinformatics statistics summary includes the total number of raw reads, the total number of reads after trimming and relative percentage, the percentage of trimmed reads mapped to reference sequences (coral transcriptome, coral mitochondrial genome, and coral nuclear ribosomal DNA), average deviation, standard deviation, and the percentage of reference sequence covered. Abbreviations: IRD = Institute de Recherche pour le Développement (Noumea, New Caledonia); KAUST = King Abdullah University of Science and Technology (Thuwal, Saudi Arabia); MNHN = Muséum National d’Histoire Naturelle (Paris, France); UNIMIB = University of Milano-Bicocca (Milan, Italy); refseq_percentage = percentage of reference sequence covered. (XLSX 23 kb)

Data S2

List of the Leptastrea specimens examined for the species treated in this study including museum and collected material in addition to those listed in the Taxonomic Account. Species synonymies and additional taxonomic references cited in the synonymies, but not in the main text, are provided. (DOCX 33 kb)

Data S3

Alignment of nearly complete mitochondrial genomes, including 10,837 bp. (TXT 826 kb)

Data S4

Alignment of nearly complete nuclear ribosomal DNA regions, including 5835 bp. (TXT 445 kb)

Data S5

Average (st. dev.) values of the six Leptastrea skeleton variables measured in this study: v1, maximum calice diameter; v2, minimum calice diameter; v3, maximum columella diameter; v4, minimum columella diameter perpendicular to v3; v5, distance between the centre of the columella and the centre of the columella of the closest adjacent corallite; v6, width of the groove among the corallites. The number of coralla examined per species is given in brackets below the species name. (DOCX 13 kb)

Figure S1

In situ images of colonies of the Leptastrea species analyzed in this study: S1_1 L. purpurea (a) UNIMIB MY143, Mayotte Island; (b) IRD HS3790, Isle of Pines, New Caledonia; (c) KAUST SA0056, Saudi Arabia; (d) KAUST SA0014, Al Lith, Saudi Arabia; (e) UNIMIB PFB776, Kavieng, Papua New Guinea; (f) lagoon pinnacle north of Magareva Island, Gambier Archipelago, French Polynesia (F. Benzoni, 05/07/2011); (g) Aqaba, Jordan (R. Joury, 17/07/2018); S1_2 L. transversa (a) UNIMIB PFB369, Madang, Papua New Guinea; (b) Nakety Bay, Grande Terre, New Caledonia (F. Benzoni, 22/04/2012); (c) KAUST SA0045, Farasan Banks, Saudi Arabia; (d) IRD HS3652, Isle of Pines, New Caledonia; (e) IRD HS3299, Grande Terre, New Caledonia; (f) KAUST SA1027, Magna, Saudi Arabia; (g) Aqaba, Jordan (R. Joury, 17/07/2018); S1_3 L. bottae (a) KAUST SA0736 Ras Al-Ubayd, Saudi Arabia; (b) KAUST SA0011, Al Lith, Saudi Arabia; (c) Aqaba, Jordan (F. Benzoni, 09/07/2018); (d) KAUST SA0044, Farasan Banks, Saudi Arabia; (e) UNIMIB DJ070, Oblal, Djibouti; (f) KAUST SA0011, Al Lith, Saudi Arabia; (g) Aqaba, Jordan (R. Joury, 16/07/2018); S1_4 L. inaequalis (a) UNIMIB BA079, Bir Ali, Yemen; (b) UNIMIB DJ047, Oblal, Djibouti; (c) Aqaba, Jordan (F. Benzoni, 15/07/2018); (d) KAUST SA0043, Farasan Banks, Saudi Arabia; (e) KAUST SA0042, Farasan Banks, Saudi Arabia; (f) Socotra Island, Yemen (F. Benzoni, 18/03/2010); (g) Aqaba, Jordan (R. Joury, 16/07/2018); S1_5 Leptastrea gibbosa sp. n. (a) Lifou Island, Loyalty Islands, New Caledonia (F. Benzoni, 18/02/2014); (b) outer reef south of the Grande Terre, New Caledonia (F. Benzoni, 08/11/2017); (c) IRD HS3167, Moneo, Grande Terre, New Caledonia; (d) UNIMIB PFB805, Kavieng, Papua New Guinea; (e) IRD HS3740, Isle of Pines, New Caledonia; (f) IRD HS3653, Isle of Pines, New Caledonia; (g) Mellish Reef, Australia (F. Benzoni, 02/12/2018); S1_6 Leptastrea magaloni sp. n. (a) IRD MD266, Nosy Sakatia, Madagascar; (b) IRD MD260, Nosy Be, Madagascar; (c) IRD MD222, Nosy Lava, Madagascar; (d) MNHN-IK-2012-9823, Bouzi, Mayotte Island; (e) IRD MD225, Nosy Lava, Madagascar; (f) IRD MD183, Nosy Mitsio, Madagascar; (g) IRD MD274, Nosy Sakatia, Madagascar; (h) same colony as in g with retracted tentacles. All in situ specimen images by F. Benzoni. For specimens, site and date metadata can be found in Data S1. (PDF 6043 kb)

Figure S2

Maximum Likelihood (ML) phylogenetic tree of Leptastrea estimated with RAxML v8.2.10 using (a) the concatenated “holobiont-min” supermatrix (2075 loci including a total of 2141 SNPs); (b) the concatenated “coral-min” supermatrix (2366 loci including a total of 2479 SNPs). Branch support is based on ML bootstrap analyses. (PDF 992 kb)

Figure S3

Maximum Likelihood (ML) phylogenetic tree of Leptastrea estimated with RAxML v8.2.10 using (a) the barcoding portion of the cytochrome oxidase subunit I gene of the mitochondrial genome (COI); (b) the complete ITS1, 5.8S, and ITS2 regions of the nuclear ribosomal DNA (ITS). Branch support is based on ML bootstrap analyses. (PDF 906 kb)

Figure S4

Variability of skeleton morphology across specimens of the Leptastrea species examined in this study included in the genomic and morphometric analyses: L. purpurea (a–h), L. transversa (i–l), L. gibbosa sp. n. (m–p), L. inaequalis (q–t), L. bottae (u–x), L. magaloni sp. n. (y-ab). (a) UNIMIB BA081; (b) UNIMIB MY247; (c) UNIMIB MY245; (d) IRD HS3045; (e) UNIMIB PFB776; (f) UNIMIB GA097; (g) UNIMIB GA170; (h) UNIMIB GA076; (i) UNIMIB DJ297; (j) UNIMIB MY202; (k) UNIMIB PFB252; (l) IRD HS3247; (m) UNIMIB PFB805; (n) IRD HS3740; (o) and (p) IRD HS2344; (q) UNIMIB DJ292; (r) UNIMIB BA044; (s) UNIMIB BA079; (t) UNIMIB DJ047; (u) UNIMIB AD040; (v) UNIMIB DJ070; (w) UNIMIB BAL144; (x) UNIMIB DJ335; (y) UNIMIB MY333; (z) IRD MD260; (aa) IRD MD183; (ab) IRD MD222. All images were taken at the same magnification (scale bar shown in a). Colour code same as in Figures 4, 5, 6 and 7. Collection metadata for L. magaloni sp. n. and L. gibbosa sp. n. specimens are in the Taxonomic Account, for all the other species in Data S1. (JPEG 411 kb)

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Arrigoni, R., Berumen, M.L., Mariappan, K.G. et al. Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific. Coral Reefs 39, 1001–1025 (2020). https://doi.org/10.1007/s00338-020-01924-8

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Keywords

  • ezRAD
  • dDocent
  • Holobiont
  • SNAPP
  • Bayes factor delimitation
  • Morphometrics
  • New species