High similarity of genetic population structure in the false clown anemonefish (Amphiprion ocellaris) found in microsatellite and mitochondrial control region analysis

Conservation Genetics

Volumn 13, Issue 3, 2012, Pages 693-706

  Timm, J ^a   Planes, S ^b   Kochzius, M ^a,c  

^a UNIVERSITY OF BREMEN   (Germany)

^b CNRS   (France)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

Anemone fish; Clownfish; Coral triangle; Genetic markers; Indo Malay archipelago; Southeast Asia

Indexed keywords

CORAL REEF; DISCRIMINANT ANALYSIS; DISPERSAL; DIVERGENCE; GENETIC MARKER; GENETIC STRUCTURE; MITOCHONDRIAL DNA; PERCIFORM; POPULATION SIZE; RESOLUTION; SEA LEVEL;

SOUTHEAST ASIA;

AMPHIPRION OCELLARIS; ANEMONE; ANTHOZOA;

EID: 84860449163     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-012-0318-1     Document Type: Article

References (78)

1. Allen GR, Werner TB (2002) Coral reef fish assessment in the "coral triangle" of southeastern Asia. Environ Biol Fish 65: 209-214.
2. Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2002) Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences. Mol Ecol 11: 659-674.
3. Barrière A, Félix M (2007) Temporal dynamics and linkage disequilibrium in natural Caenorhabditis elegans populations. Genetics 176: 999-1011.
4. Barrowclough GF, Zink RM (2009) Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Mol Ecol 18: 2934-2936.
5. Bazin E, Glémin S, Galtier N (2006) Population size does not influence mitochondrial genetic diversity in animals. Science 312: 570-572.
6. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300.
7. Bentzen P, Taggart CT, Ruzzante DE, Cook D (1996) Microsatellite polymorphism and the population structure of Atlantic cod (Gadus morhua) in the northwest Atlantic. Can J Fish Aquat Sci 53: 2706-2721.
8. Berry OF (2006) Mitochondrial DNA and population size. Science 314: 1388.
9. Borsa P (2003) Genetic structure of the round scad mackerel Decapterus macrosoma (Carangidae) in the Indo-Malay archipelago. Mar Biol 142: 575-581.
10. Bradbury IR, Snelgrove PVR (2001) Contrasting larval transport in demersal fish and benthic invertebrates: the role of behaviour and advective processes in determining spatial pattern. Can J Fish Aquat Sci 58: 811-823.
11. Briggs JC (2000) Centrifugal speciation and centres of origin. J Biogeogr 27: 1183-1188.
12. Buston PM, Bogdanowicz AW, Harrison RG (2007) Are clownfish groups composed of close relatives? An analysis of microsatellite DNA variation in Amphiprion percula. Mol Ecol 16: 3671-3678.
13. De Innocentiis S, Sola L, Catandella S, Bentzen P (2001) Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea. Mol Ecol 10: 2163-2175.
14. Edwards S, Bensch S (2009) Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Mol Ecol 18: 2930-2933.
15. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: an integrated software package for population genetics data analysis. Evol Bioinf Online 1: 47-50.
16. Eyre-Walker A (2006) Size does not matter for mitochondrial DNA. Science 312: 537-538.
17. Fautin DG, Allen GR (1994) Anemonenfische und ihre Wirte. Tetra-Verlag, Melle, pp 1-168.
18. Fauvelot C, Bernardi G, Planes S (2003) Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change. Evolution 57: 1571-1583.
19. Froukh T, Kochzius M (2007) Genetic population structure of the endemic fourline wrasse (Larabicus quadrilineatus) suggests limited larval dispersal distances in the Red Sea. Mol Ecol 16: 1359-1367.
20. Froukh T, Kochzius M (2008) Species boundaries and evolutionary lineages in the blue green damselfishes Chromis viridis and Chromis atripectoralis (Pomacentridae). J Fish Biol 72: 451-457.
21. García De Leon FJ, Chikhi L, Bonhomme F (1997) Microsatellite polymorphism and population subdivision in natural populations of European sea bass Dicentrarchus labrax (Linnaeus 1758). Mol Ecol 6: 51-62.
22. Garza JC, Slatkin M, Freimer NB (1995) Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol Biol Evol 12: 594-603.
23. Glaubitz JC (2004) CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4: 309-310.
24. Goudet J (1995) Fstat version 1. 2: a computer program to calculate F-statistics. J Hered 86: 485-486.
25. Györffy B, Kocsis I, Vásárhelyi B (2004) Biallelic genotype distributions in papers published in gut between 1998 and 2003: altered conclusions after recalculating the Hardy-Weinberg equilibrium. Int J Gastroenterol Hepatol 53: 614-616.
26. Hall R (1996) Reconstructing cenozoic SE Asia. In: Hall R, Blundell D (eds) Tectonic evolution of southeast Asia. Geological Society of London Special Publication No. 106, pp. 153-184.
27. Hartl DL (2000) A primer of population genetics, vol 3rd. Sinauer Associates, Inc. Publishers, Sunderland, pp 70-74.
28. Hauser L, Adcock GJ, Smith PJ, Bernal Ramírez JH, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagus auratus). Proc Natl Acad Sci USA 99: 11742-11747.
29. Hoarau G, Piquet AM-T, van der Veer HW, Rijnsdorp AD, Stam WT, Olsen JL (2004) Population structure of plaice (Pleuronectes platessa L.) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data. J Sea Res 51: 183-190.
30. 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, vol 29. Springer, Dordrecht, pp 117-178.
31. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6: 1-6.
32. Jones GP, Planes S, Thorrold SR (2005) Coral reef fish larvae settle close to home. Curr Biol 15: 1314-1318.
33. Knittweis L, Krämer WE, Timm J, Kochzius M (2009) Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts. Conserv Genet 10: 241-249.
34. Kochzius M (2009) Trend in fishery genetics. In: Beamish R, Rothschild B (eds) The future of fisheries science in north America, fish & fisheries series. Springer, Dordrecht, pp 453-493.
35. Kochzius M, Nuryanto A (2008) Strong genetic population structure in the boring giant clam Tridacna crocea across the Indo-Malay Archipelago: implications related to evolutionary processes and connectivity. Mol Ecol 17: 3775-3787.
36. Kochzius M, Söller R, Khalaf MA, Blohm D (2003) Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Mol Phylogenet Evol 28: 396-403.
37. Kochzius M, Seidel C, Hauschild J, Kirchhoff S, Mester P, Meyer-Wachsmuth I, Nuryanto A, Timm J (2009) Genetic population structures of the blue starfish Linckia laevigata and its gastropod ectoparasite Thyca crystallina. Mar Ecol Prog Ser 396: 211-219.
38. Kuhnt W, Holbourn A, Hall R, Zuvela M, Käse R (2004) Neogene history of the Indonesian throughflow. In: Clift P, Hayes D, Kuhnt W, Wang P (eds) Continent-ocean interactions in the East Asian marginal seas, vol 149. AGU Monograph, Washington, pp 299-320.
39. Laan M, Pääbo S (1997) Demographic history and linkage disequilibrium in human populations. Nat Genet 17: 435-438.
40. Lee JY, Edwards SV (2008) Divergence across Australia's carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 62: 3117-3134.
41. Lourie SA, Green DM, Vincent ACJ (2005) Dispersal, habitat differences, and comparative phylogeography of Southeast Asien seahorses (Syngnathidae: Hippocampus). Mol Ecol 14: 1073-1094.
42. Mann HB, Whitney DR (1947) On a test of whether one of two random variables is stochastically larger than the other. Ann Math Stat 18: 50-60.
43. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
44. Moll H (1983) Zonation and diversity of Scleractinia on reef off S. W. Sulawesi, Indonesia. PhD Thesis, University of Leiden, The Netherlands.
45. Mulligan CJ, Kitchen A, Miyamoto MM (2006) Comment on "populatin size does not influence mitochondrial genetic diversity in animals". Science 314: 1390a.
46. Nauta MJ, Weissing FJ (1996) Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143: 1021-1032.
47. Nelson JS, Hoddell RJ, Chou LM, Chan WK, Phang VPE (2000) Phylogeographic structure of false clownfish, Amphiprion ocellaris, explained by sea level changes on the Sunda shelf. Mar Biol 137: 727-736.
48. Nugroho E, Takagi M, Sugama K, Taniguchi N (1998) Detection of GT repeats microsatellite loci and their polymorphism for grouper of the genus Epinephelus. Fish Sci 64: 836-837.
49. Nuryanto A, Kochzius M (2009) Highly restricted gene flow and deep evolutionary lineages in the giant clam Tridacna maxima. Coral Reefs 28: 607-619.
50. Perrin C, Borsa P (2001) Mitochondrial DNA analysis of the geographic structure of Indian scad mackerel in the Indo-Malay archipelago. J Fish Biol 59: 1421-1426.
51. Planes S, Jones GP, Thorroldd SR (2009) Larval dispersal connects fish populations in a network of marine protected areas. Proc Natl Acad Sci USA 106: 5693-5697.
52. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
53. Quenouille B, Bouchenak-Khelladi Y, Hervet C, Planes S (2004) Eleven microsatellite loci for the saddleback clownfish Amphiprion polymnus. Mol Ecol Notes 4: 291-293.
54. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
55. Reilly A, Elliott NG, Grewe PM, Clabby C, Powell R, Ward RD (1999) Genetic differentiation between Tasmanian cultured Atlantic salmon (Salmon salar L.) and their ancestral Canadian population: comparison of microsatellite DNA and allozyme and mitochondrial DNA variation. Aquaculture 173: 459-469.
56. Renema W, Troelstra SR (2001) Larger foraminifera distribution on a mesotrophic carbonate shelf in SW Sulawesi (Indonesia). Palaeogeogr Palaeoclimatol Palaeoecol 175: 125-146.
57. Rohfritsch A, Borsa P (2005) Genetic structure of Indian scad mackerel Decapterus russelli: Pleistocene vicariance and secondary contact in the central Indo-West Pacific seas. Heredity 95: 315-326.
58. Rousset F, Raymond M (1995) Testing heterozygote excess and deficiency. Genetics 140: 1413-1419.
59. Ruzzante DE (1998) A comparison of several measures of genetic distance and population structure with microsatellite data: bias and sampling variance. Can J Fish Aquat Sci 55: 1-14.
60. Saenz-Agudelo P, Jones GP, Thorrold SR, Planes S (2009) Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Mol Ecol 18: 1765-1776.
61. Santini S, Polacco G (2006) Finding Nemo: molecular phylogeny and evolution of the unususal life style of anemonefish. Gene 385: 19-27.
62. Shaw PW, Pierce GJ, Boyle PR (1999) Subtle population structuring within a highly vagile marine invertebrate, the veined squid, Loligo forbesi, demonstrated with microsatellite DNA markers. Mol Ecol 8: 407-417.
63. Sokal RR, Rohlf FJ (1981) Biometry: the principles and practice of statistics in biological research. W. H. Freeman and Company, New York.
64. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17: 6463-6471.
65. Timm J, Kochzius M (2008) Geological history and oceanography of the Indo-Malay Archipelago shape the population structure in the false clown anemonefish (Amphiprion ocellaris). Mol Ecol 17: 3999-4014.
66. Timm J, Figiel M, Kochzius M (2008) Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity. Mol Phylogenet Evol 49: 268-276.
67. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-538.
68. Vázquez JF, Pérez T, Albornoz J, Dominguez A (2000) Estimation of microsatellite mutation rates in Drosophila melanogaster. Genet Res 76: 323-326.
69. Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and durations. J Biogeogr 27: 1153-1167.
70. Wabnitz C, Taylor M, Green E, Razak T (2003) From ocean to aquarium. UNEP-WCMC, Cambridge.
71. Wahlund S (1928) Zusammensetzung von Populationen und Korrelationserscheinungen vom Standpunkt der Vererbungslehre aus betrachtet. Hereditas 11: 65-106.
72. Wares JP, Barber PH, Ross-Ibarra J, Sotka EE, Toonen RJ (2006) Mitochondrial DNA and population size. Science 314: 1388-1389.
73. Weber JL, Wong C (1993) Mutation of short tandem repeats. Hum Mol Genet 2: 1123-1128.
74. Whitten T, Mustafa M, Henderson GS (2002) The EcOLOGY Of Sulawesi. ecology of Indonesia series, vol IV. Periplus Editions Ltd, Hong Kong.
75. Williams ST (2000) Species boundaries in the starfish genus Linckia. Mar Biol 136: 137-148.
76. Wyrtki K (1961) Physical oceanography of the Southeast Asien waters. In: NAGA Report, vol. 2, University of California, Scripps Institution of Oceanography, LaJolla, California.
77. Zavattari P, Deidda E, Whalen M, Lampis R, Mulargia A, Loddo M, Eaves L, Mastio G, Todd JA, Cucca F (2000) Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection. Hum Mol Genet 9: 2947-2957.
78. Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Mol Ecol 17: 2107-2121.