Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Andrews, Kimberly R ^a,b   Moriwake, Virginia N ^a,c   Wilcox, Christie ^a,d   Grau, E Gordon ^a   Kelley, Christopher ^a,e   Pyle, Richard L ^f   Bowen, Brian W ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b DURHAM UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF HAWAII   (United States)

^d UNIVERSITY OF HAWAII   (United States)

^e UNIVERSITY OF HAWAII   (United States)

^f BISHOP MUSEUM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; MICROSATELLITE DNA; MITOCHONDRIAL DNA; NUCLEOTIDE;

ADULT; ARTICLE; COMPARATIVE STUDY; ETELIS CORUSCANS; ETELIS MARSHI; FEMALE; FISH; FISHERY MANAGEMENT; GENE LOCUS; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC VARIABILITY; HYPORTHODUS QUERNUS; LARVA; NONHUMAN; PHYLOGEOGRAPHY; POPULATION DIFFERENTIATION; POPULATION STRUCTURE; PRISTIPOMOIDES FILAMENTOSUS; QUALITY CONTROL; SPECIES CONSERVATION; SPECIES HABITAT; UNITED STATES; ALLELE; ANIMAL; BAYES THEOREM; CLUSTER ANALYSIS; FISHERY; GENETICS; GENOTYPE; GEOGRAPHY; POPULATION GENETICS; SAMPLE SIZE;

ALLELES; ANIMALS; BAYES THEOREM; CLUSTER ANALYSIS; CYTOCHROMES B; DNA, MITOCHONDRIAL; FISHERIES; FISHES; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; GEOGRAPHY; HAWAII; MICROSATELLITE REPEATS; NUCLEOTIDES; PHYLOGEOGRAPHY; SAMPLE SIZE;

EID: 84899514925     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0091665     Document Type: Article

References (80)

1. Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion GT, et al. (2011) Defining boundaries for ecosystem-based management: A multispecies case study of marine connectivity across the Hawaiian Archipelago. Journal of Marine Biology Article ID 460173.
2. Rivera MAJ, Kelley CD, Roderick GK (2004) Subtle population genetic structure in the Hawaiian grouper, Epinephelus quernus (Serranidae) as revealed by mitochondrial DNA analyses. Biological Journal of the Linnean Society 81: 449- 468.
3. Rivera MAJ, Andrews KR, Kobayashi D, Wren J, Kelley C, et al. (2011) Genetic analyses and simulations of larval dispersal reveal distinct populations and directional connectivity across the range of the Hawaiian Grouper (Epinephelus quernus). Journal of Marine Biology Article ID 765353.
4. Gaither MR, Jones SA, Kelley C, Newman SJ, Sorenson L, et al. (2011) High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with Isolation of the Hawaiian Archipelago. Plos One 6: e28913. doi:28910.21371/journal.pone.0028913
5. Kobayashi DR (2006) Colonization of the Hawaiian Archipelago via Johnston Atoll: a characterization of oceanographic transport corridors for pelagic larvae using computer simulation. Coral Reefs 25: 407-417.
6. Craig MT, Eble JA, Bowen BW, Robertson DR (2007) High genetic connectivity across the Indian and Pacific Oceans in the reef fish Myripristis berndti (Holocentridae). Marine Ecology Progress Series 334: 245-254. (Pubitemid 46657924)
7. Ramon ML, Nelson PA, De Martini E, Walsh WJ, Bernardi G (2008) Phylogeography, historical demography, and the role of post-settlement ecology in two Hawaiian damselfish species. Marine Biology 153: 1207-1217.
8. Eble JA, Toonen RJ, Bowen BW (2009) Endemism and dispersal: comparative phylogeography of three surgeonfishes across the Hawaiian Archipelago. Marine Biology 156: 689-698.
9. Craig MT, Eble JA, Bowen BW (2010) Origins, ages and population histories: comparative phylogeography of endemic Hawaiian butterflyfishes (genus Chaetodon) . Journal of Biogeography 37: 2125-2136.
10. Gaither MR, Bowen BW, Toonen RJ, Planes S, Messmer V, et al. (2010) Genetic consequences of introducing allopatric lineages of Bluestriped Snapper (Lutjanus kasmira) to Hawaii. Molecular Ecology 19: 1107-1121.
11. DiBattista JD, Wilcox C, Craig MT, Rocha LA, Bowen BW (2011) Phylogeography of the Pacific Blueline Surgeonfish Acanthurus nigroris reveals a cryptic species in the Hawaiian Archipelago. Journal of Marine Biology Article ID 839134.
12. Eble JA, Rocha LA, Craig MT, Bowen B (2011) Not all larvae stay close to home: Insights into marine population connectivity with a focus on the Brown Surgeonfish (Acanthurus nigrofuscus). Journal of Marine Biology, Article ID 518516.
13. Reece JS, Bowen BW, Smith DG, Larson A (2011) Comparative phylogeography of four Indo-Pacific moray eel species (Muraenidae) reveals comparable ocean-wide genetic connectivity despite five-fold differences in available adult habitat. Marine Ecology Progress Series 437: 269-277.
14. Timmers MA, Toonen RJ, Andrews K, deMaintenton MJ, Brainard R (2011) Widespread dispersal of the crown-of-thorns sea star, Acanthaster planci, across the Hawaiian Archipelago and Johnston Atoll. Journal of Marine Biology Article ID 934269.
15. Skillings D, Bird CE, Toonen RJ (2011) Gateways to Hawai'i: Genetic population structure of the tropical sea cucumber Holothuria atra. Journal of Marine Biology Article ID 783030.
16. WPRFMC (2012) Final fishery management plan for coral reef ecosystems of the western Pacific region, volume III, Essential Fish Habitat for Management Unit Species, Appendix 3, Essential Fish Habitat descriptions, Part 1: Hawaiian bottomfish.
17. WPRFMC (1988) Amendment 2 to the fishery management plan for the bottomfish and seamount groundfish fisheries of the Western Pacific Region. Western Pacific Regional Fishery Management Council, Honolulu.
18. DeMartini EE, Friedlander AM (2004) Spatial patterns of endemism in shallow-water reef fish populations of the Northwestern Hawaiian Islands. Marine Ecology-Progress Series 271: 281-296. (Pubitemid 38681904)
19. Moffitt RB, Parrish FA (1996) Habitat and life history of juvenile Hawaiian Pink Snapper, Pristipomoides filamentosus. Pacific Science 50: 371-381.
20. DeMartini EE, Lau BB (1999) Morphometric criteria for estimating sexual maturity in two snappers, Etelis carbunculus and Pristipomoides sieboldii. Fishery Bulletin 97: 449-458. (Pubitemid 29341960)
21. Ralston S (1979) A description of the bottomfish fisheries of Hawaii, American Samoa, Guam and the Northern Marianas. Honolulu: Western Pacific Regional Fisheries Management Council.
22. Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology 69: 82-90.
23. Cummings SA, Thorgaard GH (1994) Extraction of DNA from fish blood and sperm. Biotechniques 17: 426-430. (Pubitemid 2139767)
24. Meeker ND, Hutchinson SA, Ho L, Trecle NS (2007) Method for isolation of PCR-ready genomic DNA from zebrafish tissues. Biotechniques 43: 610-614. (Pubitemid 350174911)
25. Meyer A (1993) Molecular phylogenetic studies of fishes. In: Beaumont AR, editor. Evolution and Genetics of Aquatic Organisms. London: Chapman and Hall.
26. Taberlet P, Meyer A, Bouvet J (1992) Unusual mitochondrial DNA polymorphism in two local populations of blue tit Parus caeruleus. Molecular Ecology 1: 27-36.
27. Gaither MR, Toonen RJ, Sorenson L, Bowen BW (2010) Isolation and characterization of microsatellite markers for the Crimson Jobfish, Pristipomoides filamentosus (Lutjanidae). Conservation Genetics Resources 2: 169-172.
28. Park SDE (2001) Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection [PhD thesis]. Dublin: University of Dublin.
29. Excoffier L, Laval LG, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
30. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICROCHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535-538. (Pubitemid 39147523)
31. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24: 621-631.
32. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512-526. (Pubitemid 23157236)
33. Posada D (2008) jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
34. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices, http://www2.unil.ch/popgen/softwares/fstat.htm. Accessed: 2014 Feb 17.
35. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48. (Pubitemid 29024937)
36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
37. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332.
38. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249.
39. Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8: 103-106.
40. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
41. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
42. Aris-Brosou S, Excoffier L (1996) The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Molecular Biology and Evolution 13: 494-504. (Pubitemid 26066101)
43. Tajima F (1989) The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
44. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
45. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19: 2092-2100. (Pubitemid 35440445)
46. Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR (2001) Phylogeography of the trumpetfishes (Aulostomus) : Ring species complex on a global scale. Evolution 55: 1029-1039. (Pubitemid 32550570)
47. Reece JS, Bowen BW, Smith DG, Larson A (2010) Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean. Molecular Phylogenetics and Evolution 57: 829-835.
48. Brodziak J, Courtney D, Wagatsuma L (2011) Stock assessment of the main Hawaiian Islands Deep7 bottomfish complex through 2010. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-29.
49. Andrews AH, Kalish JM, Newman SJ, Johnston JM (2011) Bomb radiocarbon dating of three important reef-fish species using Indo-Pacific D14C chronologies. Marine and Freshwater Research 62: 1259-1269.
50. Selkoe KA, Toonen RJ (2011) Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal. Marine Ecology-Progress Series 436: 291-305.
51. Leis J (1987) Review of the early life history of tropical groupers (Serranidae) and snappers (Lutjanidae). In: Polovina J, Ralston S, editors. Tropical snappers and groupers: biology and fisheries management. Boulder, CO: Westview Pr. pp. 189-237.
52. Leis JM, Lee K (1994) Larval development in the lutjanid subfamily Etelinae (Pisces): The genera Aphareus, Aprion, Etelis and Pristipomoides. Bulletin of Marine Science 55: 46-125. (Pubitemid 2135774)
53. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, et al. (2010) Allopatric divergence and speciation in coral reef fish: the three-spot Dascyllus, Dascyllus trimaculatus, species complex. Evolution 64: 1218-1230.
54. Briggs JC, Bowen BW (2012) A realignment of marine biogeographic provinces with particular reference to fish distributions. Journal of Biogeography 39: 12-30.
55. Grigg RW (1981) Acropora in Hawaii USA 2. Zoogeography. Pacific Science 35: 15-24.
56. Grigg RW, Wells JW, Wallace C (1981) Acropora in Hawaii USA 1. History of the scientific record, systematics and ecology. Pacific Science 35: 1-13.
57. Maragos JE, Jokiel PL (1986) Reef corals of Johnston Atoll: one of the world's most isolated reefs. Coral Reefs 4: 141-150.
58. Mundy BC (2005) Checklist of the fishes of the Hawaiian archipelago. Bishop Museum Press, Honolulu, Hawaii.
59. Randall JE (2007) Reef and shore fishes of the Hawaiian Islands: Sea Grant College Program, University of Hawaii, Honolulu, Hawaii. 546 p.
60. Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15: 1419-1439.
61. Ryman N, Palm S, Andre C, Carvalho GR, Dahlgren TG, et al. (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Molecular Ecology 15: 2031-2045. (Pubitemid 43876449)
62. Avise JC (2004) Molecular Markers, Natural History, and Evolution. Sunderland, MA: Sinauer Associates, Inc.
63. DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW (2012) Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. Journal of Heredity 103: 617-629.
64. Karl SA, Toonen RJ, Grant WS, Bowen BW (2012) Common misconceptions in molecular ecology: Echos of the modern synthesis. Molecular Ecology 21: 4171-4189.
65. Waples RS (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Conservation Biology 89: 438-450.
66. Waples RS, Punt AE, Cope JM (2008) Integrating genetic data into management of marine resources: how can we do it better? Fish and Fisheries 9: 423-449.
67. Rivera MAJ (2002) Population Genetic Structure of the Commercially Important Hawaiian Grouper Epinephelus quernus (Serranidae) using Mitochondrial and Nuclear Microsatellite DNA: PhD thesis, University of California, Berkeley, 145 pp.
68. Lesser MP, Slattery M, Leichter JJ (2009) Ecology of mesophotic coral reefs. Journal of Experimental Marine Biology and Ecology 375: 1-8.
69. Ovenden JR, Salini J, O'Connor S, Street R (2004) Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle. Molecular Ecology 13: 1991-1999. (Pubitemid 38847601)
70. Gaither MR, Bowen BW, Bordenave TR, Rocha LA, Newman SJ, et al. (2011) Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific barrier with contemporary overlap in the coral triangle. BMC Evolutionary Biology 11: 189 doi:10.1186/1471-2148- 11-189
71. 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. (Pubitemid 36953646)
72. Ludt WB, Bernal MA, Bowen BW, Rocha LA (2012) Living in the past: Phylogeography and population histories of Indo-Pacific wrasses (Genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One 7: e38042 doi:10.1371/journal.pone.0038042
73. Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography 27: 1153-1167.
74. Pooley SG (1987) Demand considerations in fisheries management - Hawaii's market for bottom fish. In: Polovian JJ, Ralston S, editors. Tropical Snappers and Groupers: Biology and Fisheries Management. Boulder, CO: Westview Press. pp. 605-638.
75. Hospital J, Pan M (2009) Demand for Hawaii bottomfish revisited: incorporating economics into total allowable catch management. U.S. Department of Commerce, NOAA Technical Memo, NOAA-TM-NMFS-PIFSC-20. 19 pgs+ Appendix p.
76. Martel SJD, Korman J, Darcy M, Christensen LB, Zeller D (2011) Status and trends of the Hawaiian bottomfish stocks: 1948-2006. A report submitted under Contract No. JJ133F-06-SE-2510 September 2006. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Ser., NOAA, Honolulu, HI 96822-2396. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-11-02C.
77. Bowen BW, Karl SA (2007) Population genetics and phylogeography of sea turtles. Molecular Ecology 16: 4886-4907. (Pubitemid 350157765)
78. Waples RS, Hendry AP (2008) Evolutionary perspectives on salmonid conservation and management. Evolutionary Applications 1: 183-188.
79. Selkoe KA, Watson JR, White C, Ben Horin T, Iacchei M, et al. (2010) Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Molecular Ecology 19: 3708-3726.
80. White C, Selkoe KA, Watson J, Siegel DA, Zacherl DC, et al. (2010) Ocean currents help explain population genetic structure. Proceedings of the Royal Society B 277: 1685-1694.