Biodiversity and Conservation

, Volume 21, Issue 2, pp 343–361 | Cite as

Island endemism, morphological stasis, and possible cryptic speciation in two coral reef, commensal Leucothoid amphipod species throughout Florida and the Caribbean

  • Vincent P. Richards
  • Michael J. Stanhope
  • Mahmood S. Shivji
Original Paper


Coral reefs are believed to be one of the most diverse ecosystems, but the true magnitude of their biodiversity and patterns of endemism is uncertain. This uncertainty stems partly from the relative paucity of investigations on the small, difficult to collect taxa (cryptofauna) that may make up the majority of reef biodiversity and require specialized expertise for morphological identification. To assess the extent of diversity in some of the reef micro-cryptofauna, we analyzed 414 bp of the mitochondrial cytochrome oxidase subunit I gene from 556 individuals representing two brooding amphipod species (Leucothoe ashleyae and Leucothoe kensleyi). These amphipods are commensal inside the branching vase sponge Callyspongia vaginalis, and were sampled throughout Florida and the Caribbean. Phylogenetic analyses revealed 11 deeply divergent, strongly supported lineages (seven L. ashleyae and four L. kensleyi) each with very narrow geographic ranges. The level of intraspecific lineage divergence for both morphospecies was among the highest reported for any marine crustacean (12.4–26.0% uncorrected), and exceeded that of congeners from nine diverse amphipod families, as well as the patristic genetic distance suggested as a threshold for crustacean species delineation. These findings suggest a history of cryptic speciation within each morphospecies, concomitant with a pronounced period of morphological stasis involving each of the morphotypes. The observation of multiple, highly divergent, evolutionary significant units, each endemic to Florida and Caribbean island locations, supports the emerging view that coral reef biodiversity, especially in the cryptofaunal component, is likely vastly underestimated.


Cryptic species Morphological stasis Coral reef species diversity Leucothoid amphipods 



We thank B. Riegl, S. Purkis, J. Thomas, D. Chapman, R. Hernandez, Caribbean Research and Management of Biodiversity (CARMABI) in Curaçao, Anthony’s Key Resort in Roatan, the Smithsonian research facility at Carrie Bow Cay, the WCS research facility at Glovers Reef for help with sample collections, and M. Debiasse, K. Klebba for lab assistance. This study was supported by a National Oceanic and Atmospheric Administration Coastal Ocean Program (#NA16OA2413) grant to the National Coral Reef Institute and by the Guy Harvey Research Institute. This contribution is NCRI publication number 137.


  1. Adachi J, Hasegawa M (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 42:459–468PubMedCrossRefGoogle Scholar
  2. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, CambridgeGoogle Scholar
  3. Baums IB, Miller MW, Hellberg ME (2005) Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata. Mol Ecol 14:1377–1390PubMedCrossRefGoogle Scholar
  4. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155PubMedCrossRefGoogle Scholar
  5. Bradford T, Adams M, Humphreys WF, Austin AD, Cooper SJB (2010) DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia’s arid zone. Mol Ecol Res 10:41–50CrossRefGoogle Scholar
  6. Buhay JE (2009) ‘COI-like’ sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crust Biol 29:96–110CrossRefGoogle Scholar
  7. Costa FO, deWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295CrossRefGoogle Scholar
  8. Costa FO, Henzler CM, Lunt DH, Whiteley NM, Rock J (2009) Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Sys Biodivers 7:365–379CrossRefGoogle Scholar
  9. De Queiroz K (1998) The general lineage concepts of species, species criteria, and the process of speciation. In: Howard D, Berlocher S (eds) Endless forms: species and speciation. Oxford University Press, New York, pp 57–75Google Scholar
  10. Eldridge MDB, King JM, Loupis AK, Spencer PBS, Taylor AC, Pope LC, Hall GP (1999) Unprecedented low levels of genetic variation and inbreeding depression in an island population of the black-footed rock-wallaby. Conserv Biol 13:531–541CrossRefGoogle Scholar
  11. Emerson BC (2002) Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process. Mol Ecol 11:951–966 Google Scholar
  12. Finston TL, Johnson MS, Humphreys WF, Eberhard SM, Halse SA (2007) Cryptic speciation in two widespread subterranean amphipod genera reflects historical drainage patterns in an ancient landscape. Mol Ecol 16:355–365PubMedCrossRefGoogle Scholar
  13. Flot J-F, Wöerheide G, Dattagupta S (2010) Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy. BMC Evol Biol 10:1–13CrossRefGoogle Scholar
  14. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299PubMedGoogle Scholar
  15. Fourment M, Gibbs MJ (2006) PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6:1PubMedCrossRefGoogle Scholar
  16. Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10:1500–1508CrossRefGoogle Scholar
  17. Garcia-Rodriguez AI, Bowen BW, Domning D, Mignucci-Giannoni AA, Marmontel M, Montoya-Ospina RA, Morales-Vela B, Rudin M, Bonde RK, McGuire PM (1998) Phylogeography of the West Indian manatee (Trichechus manatus): how many populations and how many taxa? Mol Ecol 7:1137–1149PubMedCrossRefGoogle Scholar
  18. Geller JB, Walton ED, Grosholz ED, Ruiz GM (1997) Cryptic invasions of the crab Carcinus detected by molecular phylogeography. Mol Ecol 6:901–906PubMedCrossRefGoogle Scholar
  19. Goodbody-Gringley G, Vollmer SV, Woollacott RM, Giribet G (2010) Limited gene flow in the brooding coral Favia fragum (Esper, 1797). Mar Biol 157:2591–2602CrossRefGoogle Scholar
  20. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704PubMedCrossRefGoogle Scholar
  21. Hellberg ME (2009) Gene flow and isolation among populations of marine animals. Ann Rev Ecol Evol Syst 40:291–310CrossRefGoogle Scholar
  22. Hickerson MJ, Meyer CP, Moritz C (2006) DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55:729–739PubMedCrossRefGoogle Scholar
  23. Huelsenbeck J, Ronquist F (2001) MRBAYES: a program for bayesian inference of phylogeny. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  24. 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, Nystrom M, Palumbi SR, Pandolfi JM, Rosen B, Roughgarden J (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301:929–933PubMedCrossRefGoogle Scholar
  25. King JL, Hanner R (1998) Cryptic species in a “living fossil” lineage: taxonomic and phylogenetic relationships within the genus Lepidurus (Crustacea: Notostraca) in North America. Mol Phylogenet Evol 10:23–36PubMedCrossRefGoogle Scholar
  26. Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420:73–90CrossRefGoogle Scholar
  27. Knowlton N, Jackson JBC (2008) Shifting baselines, local impacts, and global change on coral reefs. PLoS Biol 6:215–220CrossRefGoogle Scholar
  28. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  29. Lee CE (2000) Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate “populations”. Evolution 54:2014–2027PubMedCrossRefGoogle Scholar
  30. Lee T, Ó Foighil D (2004) Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Mol Ecol 13:3527–3542PubMedCrossRefGoogle Scholar
  31. Lee T, Ó Foighil D (2005) Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex. Evolution 59:2139–2158PubMedGoogle Scholar
  32. Lefébure T, Douady CJ, Gouy M, Gibert J (2006) Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol 40:435–447PubMedCrossRefGoogle Scholar
  33. Lefébure T, Douady CJ, Malard F, Gibert J (2007) Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis). Mol Phylogenet Evol 42:676–686PubMedCrossRefGoogle Scholar
  34. Lessios HA (2008) The great American schism: divergence of marine organisms after the rise of the Central American Isthmus. Annu Rev Ecol Evol Syst 39:63–91CrossRefGoogle Scholar
  35. Lessios HA, Kessing BD, Pearse JS (2001) Population structure and speciation in tropical seas: global phylogeography of the sea urchin Diadema. Evolution 55:955–975PubMedCrossRefGoogle Scholar
  36. Lyle M, Dadey KA, Farrell JW (1995) Proceedings of the ocean drilling program. In: Pisias NG, Mayer LA, Janecek TR, Palmer-Julson A, van Andel TH (eds) Scientific results, vol 138. College Station, TX (Ocean Drilling Program), pp 69–82Google Scholar
  37. Macdonald KS III, Yampolsky L, Duffy JE (2005) Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Mol Phylogenet Evol 35:323–343PubMedCrossRefGoogle Scholar
  38. Markow TA, Pfeiler E (2010) Mitochondrial DNA evidence for deep genetic divergences in allopatric populations of the rocky intertidal isopod Ligia occidentalis from the eastern Pacific. Mol Phylogenet Evol 56:468–473PubMedCrossRefGoogle Scholar
  39. Meyer CP, Geller JB, Paulay G (2005) Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods. Evolution 59:113–125PubMedGoogle Scholar
  40. Mitton JB, Berg CJ Jr, Orr KS (1989) Population structure, larval dispersal, and gene flow in the queen conch, Strombus gigas, of the Caribbean. Biol Bull 177:356–362CrossRefGoogle Scholar
  41. Moritz C (1994) Defining ‘evolutionary significant units’ for conservation. Trends Ecol Evol 9:373–375PubMedCrossRefGoogle Scholar
  42. Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2:e354PubMedCrossRefGoogle Scholar
  43. Murphy NP, Adams M, Austin AD (2009) Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia’s Great Artesian Basin. Mol Ecol 18:109–122PubMedGoogle Scholar
  44. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford & New YorkGoogle Scholar
  45. Nicholas K, Nicholas HJ, Deerfield DI (1997) GENEDOC: analysis and visualization of genetic variation. Embnew News 4:14Google Scholar
  46. Nichols S, Wörheide G (2005) Sponges: new views of old animals. Integr Comp Biol 45:333–334PubMedCrossRefGoogle Scholar
  47. Okano T, Suzuki H, Hiwatashi Y, Nagoshi F, Miura T (2000) Genetic divergence among local populations of the Japanese freshwater crab Geothelphusa dehaani (Decapoda, Brachyura, Potamidae) from southern Kyushu, Japan. J Crust Biol 20:759–768CrossRefGoogle Scholar
  48. Paetkau D, Shields GF, Strobeck C (1998) Gene flow between insular, coastal and interior populations of brown bears in Alaska. Mol Ecol 7:1283–1292PubMedCrossRefGoogle Scholar
  49. Palumbi SR, Benzie J (1991) Large mitochondrial DNA differences between morphologically similar penaeid shrimp. Mol Mar Biol Biotechnol 1:27–34PubMedGoogle Scholar
  50. Plaisance L, Knowlton N, Paulay G, Meyer C (2009) Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding. Coral Reefs 28:977–986CrossRefGoogle Scholar
  51. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818PubMedCrossRefGoogle Scholar
  52. Radulovici AE, Sainte-Marie B, Dufresne F (2009) DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach. Mol Ecol Res 9:181–187CrossRefGoogle Scholar
  53. Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7:355–364. Google Scholar
  54. Richards VP, Thomas JD, Stanhope MJ, Shivji MS (2007) Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies. Mol Ecol 16:139–157PubMedCrossRefGoogle Scholar
  55. Roberts CM, Hawkins JP (1999) Extinction risk in the sea. Trends Ecol Evol 14:241–246PubMedCrossRefGoogle Scholar
  56. Roberts CM, McClean CJ, Veron JEN, Hawkins JP, Allen GR, McAllister DE, Mittermeier CG, Schueler FW, Spalding M, Wells F, Vynne C, Werner TB (2002) Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295:1280–1284PubMedCrossRefGoogle Scholar
  57. Rocha LA, Robertson DR, Roman J, Bowen BW (2005) Ecological speciation in tropical reef fishes. Proc R Soc Biol Sci Ser B 272:573–579Google Scholar
  58. Roth J, Droxler A, Kameo K (2000) Proceedings of the ocean drilling program. In: Leckie R, Sigurdsson H, Acton G, Draper G (eds) Scientific results, vol 165, College Station, TX (Ocean Drilling Program), pp 249–273Google Scholar
  59. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497PubMedCrossRefGoogle Scholar
  60. Samadi S, Bottan L, Macpherson E, De Forges BR, Boisselier M-C (2006) Seamount endemism questioned by the geographic distribution and population genetic structure of marine invertebrates. Mar Biol 149:1463–1475CrossRefGoogle Scholar
  61. Santos SR (2006) Patterns of genetic connectivity among anchialine habitats: a case study of the endemic Hawaiian shrimp Halocaridina rubra on the island of Hawaii. Mol Ecol 15:2699–2718PubMedCrossRefGoogle Scholar
  62. Schmittner A, Sarnthein M, Kinkel H, Bartoli G, Bickert T, Crucifix M, Crudeli D, Groeneveld J, Kosters F, Mikolajewicz U, Millo C, Reijmer J, Schafer P, Schmidt D, Schneider B, Schulz M, Steph S, Tiedemann R, Weinelt M, Zuvela M (2004) Global impact of the Panamanian seaway closure. EOS 85:526CrossRefGoogle Scholar
  63. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116Google Scholar
  64. Silberman JD, Sarver SK, Walsh PJ (1994) Mitochondrial DNA variation and population structure in the spiny lobster Panulirus argus. Mar Biol 120:601–608CrossRefGoogle Scholar
  65. Stanhope MJ, Hartwick B, Baillie D (1993) Molecular phylogeographic evidence for multiple shifts in habitat preference in the diversification of an amphipod species. Mol Ecol 2:99–112CrossRefGoogle Scholar
  66. Stevens MI, Hogg ID (2003) Long-term isolation and recent range expansion from glacial refugia revealed for the endemic springtail Gomphiocephalus hodgsoni from Victoria Land, Antarctica. Mol Ecol 12:2357–2369PubMedCrossRefGoogle Scholar
  67. Swofford D (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, SunderlandGoogle Scholar
  68. Taylor MS, Hellberg ME (2003) Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science 299:107–109PubMedCrossRefGoogle Scholar
  69. Taylor MS, Hellberg ME (2006) Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean. Mol Ecol 15:695–707PubMedCrossRefGoogle Scholar
  70. Thomas JD, Klebba KN (2007) New species and host associations of commensal leucothoid amphipods from coral reefs in Florida and Belize (Crustacea: Amphipoda). Zootaxa 1494:1–44Google Scholar
  71. Vollmer SV, Palumbi SR (2007) Restricted gene flow in the Caribbean staghorn coral Acropora cervicornis: implications for the recovery of endangered reefs. J Hered 98:40–50PubMedCrossRefGoogle Scholar
  72. Wellborn GA, Broughton RE (2008) Diversification on an ecologically constrained adaptive landscape. Mol Ecol 17:2927–2936PubMedCrossRefGoogle Scholar
  73. Wheeler QD, Platnick NI (2000) The phylogenetic species concept (sensu Wheeler and Platnick). In: Wheeler QD, Meier R (eds) Species concepts and phylogenetic theory a debate. Columbia University Press, New York, pp 55–69Google Scholar
  74. Witt JDS, Hebert PDN (2000) Cryptic species diversity and evolution in the amphipod genus Hyalella within central glaciated North America: a molecular phylogenetic approach. Can J Fish Aquat Sci 57:687–698CrossRefGoogle Scholar
  75. Witt JDS, Blinn DW, Hebert PDN (2003) The recent evolutionary origin of the phenotypically novel amphipod Hyalella montezuma offers an ecological explanation for morphological stasis in a closely allied species complex. Mol Ecol 12:405–413PubMedCrossRefGoogle Scholar
  76. Witt JDS, Threloff DL, Hebert PDN (2006) DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Mol Ecol 15:3073–3082PubMedCrossRefGoogle Scholar
  77. Xia X, Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. J Hered 92:371–373PubMedCrossRefGoogle Scholar
  78. Xia X, Xie Z, Salemi M, Chen L, Wang Y (2003) An index of substitution saturation and its application. Mol Phylogenet Evol 26:1–7PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Vincent P. Richards
    • 1
    • 2
  • Michael J. Stanhope
    • 3
  • Mahmood S. Shivji
    • 1
  1. 1.Oceanographic CenterNational Coral Reef Institute, Nova Southeastern UniversityDania BeachUSA
  2. 2.Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthacaUSA
  3. 3.Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthacaUSA

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