Emergent patterns of population genetic structure for a coral reef community

Molecular Ecology

Volumn 23, Issue 12, 2014, Pages 3064-3079

  Selkoe, Kimberly A ^a,b   Gaggiotti, Oscar E ^c   Bowen, Brian W ^a   Toonen, Robert J ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^c UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

chaotic genetic heterogeneity; community genetics; Hawa i; marine connectivity; pelagic larval duration; stepping stone dispersal

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOTA; CHAOTIC GENETIC HETEROGENEITY; COMMUNITY GENETICS; CORAL REEF; ECOSYSTEM; FISH; GENETICS; HAWAÌI; INVERTEBRATE; ISLAND (GEOLOGICAL); MARINE CONNECTIVITY; PELAGIC LARVAL DURATION; POPULATION GENETICS; STATISTICAL MODEL; STEPPING STONE DISPERSAL; UNITED STATES;

CHAOTIC GENETIC HETEROGENEITY; COMMUNITY GENETICS; HAWAÌI; MARINE CONNECTIVITY; PELAGIC LARVAL DURATION; STEPPING STONE DISPERSAL;

ANIMALS; BIOTA; CORAL REEFS; DNA, MITOCHONDRIAL; ECOSYSTEM; FISHES; GENETICS, POPULATION; HAWAII; INVERTEBRATES; ISLANDS; LINEAR MODELS; MICROSATELLITE REPEATS; MODELS, GENETIC;

EID: 84902440112     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12804     Document Type: Article

References (70)

1. Andrews KR, Moriwake V, Wilcox C, Grau EG, Pyle RL, Bowen BW, (2014) Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (Family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago. PLoS ONE, 9, e91665. doi: 10.1371/journal.pone. 0091665.
2. Arnaud-Haond S, Vonau V, Rouxel C, et al,. (2008) Genetic structure at different spatial scales in the pearl oyster (Pinctada margaritifera cumingii) in French Polynesian lagoons: beware of sampling strategy and genetic patchiness. Marine Biology, 155, 147-157.
3. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
4. Baums ILB, Miller M, Hellberg ME, (2006) Geographic variation in clonal structure in a reef-building Caribbean coral, Acropora palmata. Ecological Monographs, 76, 503-519.
5. Beaumont MA, (2010) Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics, 41, 379-406.
6. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F, (2002) GENETIX 4.04, logiciel sous WindowsTM pour la genetique des populations. Laboratoire Genome, Populations, Interactions. CNRS UMR 500, Universite de Montpellier II, Montpellier, France.
7. Bird CE, Smouse PE, Karl SA, Toonen RJ, (2011a) Detecting and measuring genetic differentiation. In: Crustacean Issues: Phylogeography and Population Genetics in Crustacea (eds, Koenemann S, Held C, Schubart C,), pp. 31-55. CRC Press, Boca Raton, Florida.
8. Bird CE, Holland BS, Bowen BW, Toonen RJ, (2011b) Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago. Molecular Ecology, 20, 2128-2141.
9. Bradbury IR, Laurel B, Snelgrove PVR, Bentzen P, Campana SE, (2008) Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history. Proceedings of the Royal Society Series B, Biological Sciences, 275, 1803-1809.
10. Broquet T, Viard F, Yearsley JM, (2012) Genetic drift and collective dispersal can result in chaotic genetic patchiness. Evolution, 67, 1660-1675.
11. Burnham KP, Anderson DR, (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer-Verlag, New York, New York.
12. Carpenter KE, Barber PH, Crandall ED, et al,. (2011) Comparative phylogeography of the coral triangle and implications for marine management. Journal of Marine Biology, 2011, 1-14.
13. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW, (2009) The merging of community ecology and phylogenetic biology. Ecology Letters, 12, 693-715.
14. Crawford N, (2010) SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources, 10, 556-557.
15. Darriba D, Taboada GL, Doallo R, Posada D, (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.
16. Dawson M, (2014) Natural experiments and meta-analyses in comparative phylogeography. Journal of Biogeography, 41, 52-65.
17. Díaz-Ferguson E, Haney RA, Haney R, et al,. (2010) Population genetics of a trochid gastropod broadens picture of Caribbean Sea connectivity. PLoS ONE, 5, e12675. doi: 10.1371/journal.pone.0012675.
18. Eble J, Toonen R, Sorenson L, Basch L, Papastamatiou Y, Bowen B, (2011) Escaping paradise: larval export from Hawaii in an Indo-Pacific reef fish, the yellow tang Zebrasoma flavescens. Marine Ecology Progress Series, 428, 245-258.
19. Etter RJ, Rex MA, Chase MR, Quattro JM, (2005) Population differentiation decreases with depth in deep-sea bivalves. Evolution; International Journal of Organic Evolution, 59, 1479-1491.
20. Excoffier L, Lischer HE, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
21. Faurby S, Barber PH, (2012) Theoretical limits to the correlation between pelagic larval duration and population genetic structure. Molecular Ecology, 21, 3419-3432.
22. Foster NL, Paris CB, Kool JT, et al,. (2012) Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow. Molecular Ecology, 21, 1143-1157.
23. Gaither MR, Toonen RJ, Bowen BW, (2012) Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai'i. Proceedings of the Royal Society Series B, Biological Sciences, 279, 3948-3957.
24. Galindo HM, Pfeiffer-Herbert AS, McManus MA, Chao Y, Chai F, Palumbi SR, (2010) Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal. Molecular Ecology, 19, 3692-3707.
25. Hedgecock D, (1994) Temporal and spaial genetic structure of marine animal populations in the California Current. CalCOFI Reports, 35, 73-81.
26. Hedgecock D, Pudovkin AI, (2011) Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bulletin of Marine Science, 87, 971-1002.
27. Hickerson MJ, Meyer CP, (2008) Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evolutionary Biology, 8, 322.
28. Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellend M, (2008) Ecological consequences of genetic diversity. Ecology Letters, 11, 609-623.
29. Iacchei M, Ben-Horin T, Selkoe KA, Bird CE, García- Rodríguez FJ, Toonen RJ, (2013) Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations. Molecular Ecology, 22, 3476-3494.
30. Johnson MS, Black R, (1982) Chaotic genetic patchiness in an intertidal limpet, Siphonaria sp. Marine Biology, 70, 157-164.
31. Jost L, (2008) GST and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.
32. Kalinowski ST, (2002) How many alleles per locus should be used to estimate genetic distances? Heredity, 88, 62-65.
33. Kelly RP, Eernisse DJ, (2007) Southern hospitality: a latitudinal gradient in gene flow in the marine environment. Evolution, 61, 700-707.
34. Kelly RP, Palumbi SR, (2010) Genetic structure among 50 species of the northeastern Pacific rocky intertidal community. PLoS ONE, 5, e8594.
35. Kobayashi D, (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.
36. Kokko H, Lõpez-Sepulcre A, (2007) The ecogenetic link between demography and evolution: can we bridge the gap between theory and data? Ecology Letters, 10, 773-782.
37. Lang WH, Young AM, (1977) The larval development of Clibanarius vittatus (Bosc) (Crustacea: decapoda: diogenidae) reared in the laboratory. Biological Bulletin, 152, 84-104.
38. Legendre P, Legendre L, (2012) Numerical Ecology. Elsevier B.V, Amsterdam.
39. Lischer HEL, Excoffier L, (2012) PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28, 298-299.
40. Lowe WH, Allendorf FW, (2010) What can genetics tell us about population connectivity? Molecular Ecology, 19, 3038-3051.
41. Manel S, Schwartz MK, Luikart G, Taberlet P, (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189-197.
42. Marko P, (2004) 'What's larvae got to do with it?' Disparate patterns of post-glacial population structure in two benthic marine gastropods with identical dispersal potential. Molecular Ecology, 13, 597-611.
43. Marko PB, Hart MW, (2011a) Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea. Evolutionary Ecology, 26, 291-315.
44. Marko PB, Hart MW, (2011b) The complex analytical landscape of gene flow inference. Trends in Ecology & Evolution, 26, 448-456.
45. Meirmans PG, (2012) The trouble with isolation by distance. Molecular Ecology, 21, 2839-2846.
46. Meirmans PG, Hedrick PW, (2011) Assessing population structure: F(ST) and related measures. Molecular Ecology Resources, 11, 5-18.
47. Meirmans P, van Tienderen PH, (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Heredity, 93, 43-50.
48. Meirmans PG, Goudet J, Gaggiotti OE, (2011) Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Molecular Ecology, 20, 3144-3155.
49. Poortvliet M, Longo GC, Selkoe KA, et al,. (2013) Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality. Ecology and Evolution, 3, 4558-4571.
50. Puritz JB, Toonen RJ, (2011) Coastal pollution limits pelagic larval dispersal. Nature Communications, 2, 226.
51. Qiu B, Koh D, Lumpkin C, Flament P, (1997) Existence and formation mechanism of the North Hawaiian Ridge Current. Journal of Physical Oceanography, 27, 431-444.
52. Riginos C, Douglas KE, Jin Y, Shanahan DF, Treml EA, (2011) Effects of geography and life history traits on genetic differentiation in benthic marine fishes. Ecography, 34, 566-575.
53. Rivera MAJ, Andrews KR, Kobayashi DR, 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, 2011, 1-11.
54. Robertson DR, (2001) Population maintenance among tropical reef fishes: inference from small island endemics. Proceedings of the National Academy of Sciences USA, 98, 5667-5670.
55. Rousset F, (2004) Genetic Structure and Selection in Subdivided Populations. Princeton University Press, Princeton, New Jersey.
56. Schultz ET, Cowen RK, (1994) Recruitment of coral-reef fishes to Bermuda: local retention or long-distance transport? Marine Ecology Progress Series, 109, 15-28.
57. 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.
58. Selkoe KA, Henzler CM, Gaines SD, (2008) Seascape genetics and the spatial ecology of marine populations. Fish and Fisheries, 9, 363-377.
59. Selkoe KA, Watson JR, White C, 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.
60. Storfer A, Murphy MA, Evans JS, et al,. (2007) Putting the "landscape" in landscape genetics. Heredity, 98, 128-142.
61. Taberlet P, Zimmermann NE, Englisch T, et al,. (2012) Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecology Letters, 15, 1439-1448.
62. Theisen TC, Bowen BW, Lanier W, Baldwin JD, (2008) High connectivity on a global scale in the pelagic wahoo, Acanthocybium solandri (tuna family Scombridae). Molecular Ecology, 17, 4233-4247.
63. Toonen RJ, Grosberg RK, (2011) Causes of chaos: spatial and temporal genetic heterogeneity in the intertidal anomuran crab Petrolisthes cinctipes. In: Phylogeography and Population Genetics in Crustacea (eds, Koenemann S, Held C, Schubart C,) Ch. 4, pp. 75-107. CRC Press Crustacean Issues Series, ISBN 1439840733.
64. Toonen RJ, Andrews KR, Baums IB, et al,. (2011) Defining boundaries for ecosystem-based management: a multispecies case study of marine connectivity across the Hawaiian Archipelago. Journal of Marine Biology, 2011, 1-13.
65. Wares JP, (2002) Community genetics in the Northwestern Atlantic intertidal. Molecular Ecology, 11, 1131-1144.
66. Weersing K, Toonen R, (2009) Population genetics, larval dispersal, and connectivity in marine systems. Marine Ecology Progress Series, 393, 1-12.
67. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
68. White C, Selkoe KA, Watson J, Siegel DA, Zacherl DC, Toonen RJ, (2010) Ocean currents help explain population genetic structure. Proceedings of the Royal Society Series B, Biological Sciences, 277, 1685-1694.
69. Wright S, (1943) Isolation by distance. Genetics, 28, 114-138.
70. Yearsley JM, Viard F, Broquet T, (2013) The effect of collective dispersal on the genetic structure of a subdivided population. Evolution, 67, 1649-1659.