Testing the consistency of connectivity patterns for a widely dispersing marine species

Heredity

Volumn 111, Issue 4, 2013, Pages 345-354

  Thomas, L ^a,b   Bell, J J ^a  

^a VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

connectivity; dispersal; rock lobster

Indexed keywords

CONSERVATION MANAGEMENT; DISPERSAL; GENE FLOW; GENETIC STRUCTURE; LOBSTER; MITOCHONDRIAL DNA; POPULATION DYNAMICS; POPULATION STRUCTURE; ROCK; SELECTION; SOURCE-SINK DYNAMICS;

NEW ZEALAND;

JASUS EDWARDSII;

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; AQUATIC SPECIES; ARTICLE; ECOSYSTEM; GENE FLOW; GENETICS; NEW ZEALAND; PALINURIDAE; POPULATION GENETICS; THEORETICAL MODEL;

ANIMALS; AQUATIC ORGANISMS; DNA, MITOCHONDRIAL; ECOSYSTEM; GENE FLOW; GENETICS, POPULATION; MICROSATELLITE REPEATS; MODELS, THEORETICAL; NEW ZEALAND; PALINURIDAE;

EID: 84888005602     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2013.58     Document Type: Article

References (83)

1. Allendorf FW (1986). Genetic drift and the loss of alleles versus heterozygosity. Zool Biol 5: 181-190.
2. Allison GW, Gaines SD, Lubchenco J, Possingham HP (2003). Ensuring persistence of marine reserves: Catastrophes require adopting an insurance factor. Ecol Appl 13: 8-24.
3. Antao T, Lopes A, Lopes RJ, Beia-Pereira A, Luikart G (2008). LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323.
4. Beaumont MA, Nichols RA (1996). Evaluating loci for use in the genetic analysis of population structure. Proc Royal Soc B 263: 1619-1626. (Pubitemid 27055553)
5. Becker BJ, Levin LA, Fodrie FJ, McMillan PA (2007). Complex larval connectivity patterns among marine invertebrate populations. Proc Natl Acad Sci USA 104: 3267-3272. (Pubitemid 46364148)
6. Beerli P (2010). MIGRATE Documentation Version 3.2. Florida State University: Tallahassee, FL, USA.
7. Beerli P, Felsenstein J (1999). Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-773. (Pubitemid 29272726)
8. Bell JJ (2008). Connectivity between island marine protected areas and the mainland. Biol Conservation 141: 2870-2820.
9. Bell JJ, Okamura B (2005). Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design. Proc R Soc 272: 1067-1074. (Pubitemid 40943957)
10. Berry O, Tocher MD, Sarre SD (2004). Can assignment tests measure dispersal? Mol Ecol 13: 551-561. (Pubitemid 38260939)
11. Berumen ML, Almany GR, Planes S, Jones GP, Saenz-Agudelo P, Thorrold SR (2012). Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network. Ecol Evol 2: 444-452.
12. Booth JD, Breen PA (1992). Stock structure in the New Zealand red rock lobster, Jasus edwardsii. Report No. 92/20 Ministry of Agriculture and Fisheries: Wellington, New Zealand.
13. Booth JD, Ovenden JR (2000). Distribution of Jasus spp (Decapoda: Palinuridae) phyllosomas in southern waters: implications for larval recruitment. Mar Ecol Prog Ser 200: 241-255.
14. Booth JD, Phillips BF (1994). Early life history of spiny lobster. Proceedings from the fourth international workshop on lobster biology and management. Crustaceana 66: 271-294.
15. Booth JD, Street RJ, Smith PJ (1990). Systematic status of the rock lobsters Jasus edwardsii from New Zealand and J. novaehollandiae from Australia. NZ J Mar Freshw Res 24: 239-249.
16. Bradbury IR, Laurel B, Snelgrove PV, Bentzen P, Campana SE (2008). Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history. Proc Royal Soc B 275: 1803-1809. (Pubitemid 351839872)
17. Chiswell S, Booth JD (1999). Rock lobster Jasus edwardsii larval retention by the Wairarapa Eddy off New Zealand. Mar Ecol Prog Ser 183: 227-2440.
18. Chiswell S, Roemmich D (1998). The East Cape Current and two eddies: a mechanism for larval retention? NZ J Mar Freshw Res 32: 385-397. (Pubitemid 29000597)
19. Chiswell SM (1994). Variability in sea surface temperature around New Zealand from AVHRR images. NZ J Mar Freshw Res 28: 179-192.
20. Chiswell SM, Booth JD (2008). Sources and sinks of larval settlement in Jasus edwardsii around New Zealand: where do larvae come from and where do they go? Mar Ecol Prog Ser 354: 201-217. (Pubitemid 351327401)
21. Chiswell SM, Wilkin J, Booth JD, Stanton B (2003). Trans-Tasman Sea larval transport: Is Australia a source for New Zealand rock lobsters? Mar Ecol Prog Ser 247: 173-182. (Pubitemid 36229867)
22. Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999). New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153: 1989-2000.
23. Cowen RK, Gawarkiewicz G, Pineda J, Thorrold SR, Werner F (2007). Population connectivity in marine systems: an overview. Oceanography 20: 14-21.
24. Cowen RK, Paris CB, Srinivasan A (2006). Scaling of connectivity in marine populations. Science 311: 522-527. (Pubitemid 43157730)
25. Cowen RK, Sponaugle S (2009). Larval Dispersal and marine population connectivity. Ann Rev Mar Sci 1: 443-466.
26. Coyer J, Hoarau G, Pearson G, Mota C, Jü terbock A, Alpermann T et al. (2011). Genomic scans detect signatures of selection along a salinity gradient in populations of the intertidal seaweed Fucus serratus on a 12 km scale. Mar Genomics 4: 41-49.
27. Earl DA, VonHoldt BM (2011). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4: 359-361.
28. Evano G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 14: 2611-2620. (Pubitemid 40886055)
29. Excoffier L, Laval G, Schneider S (2005). Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Biol Online 1: 47-50.
30. Gardner JPA, Bell JJ, Constable HB, Ritchie PA, Zuccarello GC (2010). Multi-species coastal marine connectivity: a literature review with recommendations for further research. NZ Aquatic Environment Biodiversity Report 58: 1-47.
31. Gonzalez EG, Zardoya R (2007). Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus). BMC Evolutionary Biology 7: 197-209.
32. Goudet J (1995). FSTAT (version 1.2): a computer program to calculate F-statistics. Heredity 86: 485-486.
33. Hauser L, Adcock GJ, Smith PJ, Ramiréz JHB, Carvalho GR (2002). Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc Nat Acad Sci USA 99: 11742-11747. (Pubitemid 34994469)
34. Heath R (1985). A review of the physical oceanography of the seas around New Zealand-1982. New Zeal J Mar Freshwater Res 19: 79-124.
35. Heath RA (1980). Eastward oceanic flow past northern New Zealand. NZ J Mar Freshwa Res 14: 169-182.
36. Hedgecock D, Barber PH, Edmands S (2007). Genetic approaches to measuring connectivity. Oceanography 20: 70-79.
37. Hubisz M, Falush D, Stephens M, Pritchard J (2009). Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9: 1322-1332.
38. Hughes TP, Graham NAJ, Jackson JBC, Mumby PJ, Steneck RS (2010). Rising to the challenge of sustaining coral reef resilience. Trends Ecol Evol 25: 633-642.
39. Hutchinson WF, Carvalho GR, Rogers S (2001). Marked genetic structuring in localized spawning populations of cod Gadus morhua in the North Sea and adjoining waters as revealed by microsatellites. Mar Ecol Prog Series 223: 251-260. (Pubitemid 34067281)
40. Jakobsson M, Rosenberg NA (2007). CLUMPP: a cluster match-ing and permutation program for dealing with label switch-ing and multimodality in analysis of population structure. Bioinformatics 23: 1801.
41. Jones GP, Planes S, Thorrold SR (2005). Coral reef fish larvae settle close to home. Curr Biol 15: 1314-1318. (Pubitemid 41026599)
42. Kelly RP, Palumbi S (2010). Genetic structure among 50 species of the northeastern Pacific rocky intertidal community. PLoS One 5: 1-13.
43. Kinlan BP, Gaines SD (2003). Propagule dispersal in marine and terrestrial environments: a community perspective. Ecology 84: 2007-2020. (Pubitemid 37435675)
44. Korbie DJ, Mattick JS (2008). Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc 3: 1452-1456.
45. Lesser JHR (1978). Phyllosoma larvae of Jasus edwardsii (Hutton) (Crustacea: Decapoda: Palinuridae) and their distribution off the east coast of the North Island, New Zealand. NZ J Mar Freshwa Res 12: 357-370.
46. Leis JM, van Herwerden L, Patterson HM (2011). Estimating connectivity in marine fish populations: what works best? Oceanogr Mar Biol 49: 193-234.
47. Lewis KB, Carter L, Davey FJ (1994). The opening of the Cook Straight: interglacial tidal scour and aligning basins at a subduction to transform plate edge. Mar Geol 116: 293-312. (Pubitemid 24425807)
48. Lowe WH, Allendorf FW (2010). What can genetics tell us about population connectivity? Mol Ecol 19: 3038-3051.
49. Manel S, Gaggiotti OE, Waples RS (2005). Assignment methods:matching biological questions with appropriate techniques. Trends Ecol Evol 20: 136-142. (Pubitemid 40257094)
50. Meirmans P (2006). Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60: 2399-2402. (Pubitemid 44925478)
51. Meirmans PG, Hedrick PW (2011). Assessing population structure: F(ST) and related measures. Mol EcolResources 11: 5-18.
52. National Rock Lobster Management Group. (2010) NRLMG 2010. Annual Report. http://www.fish.govt.nz/
53. Nei M. (1987). Molecular Evolutionary Genetics. Columbia Univ. Press: New York, NY, USA.
54. Nielsen EE, Hansen MM, Meldrup D (2006). Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Mol Ecol 15: 3219-3229. (Pubitemid 44379728)
55. Ovenden JR, Brasher DJ, White RWG (1992). mDNA analysis of the red rock lobster Jasus edwardsii shows an apparent absence of population subdivisions throughout Australasia. Mar Biol 326: 319-326. (Pubitemid 23395228)
56. Paetkau D, Calvert W, Stirling I, Strobeck C (1995). Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4: 347-354.
57. Paetkau D, Slade R, Burden M, Estoup A (2004). Direct, real-time estimation of migration rate using assignment methods: a simulation-based exploration of accuracy and power. Mol Ecol 13: 55-65. (Pubitemid 38106473)
58. Paetkau D, Waits LP, Clarkson PL, Craigheadg L (1997). An empirical evaluation of genetic distance statistics using microsatellite data from Bear (Ursidae) populations. Genet Soc Am 147: 1943-1957. (Pubitemid 27525481)
59. Palumbi SR (2003). Population genetics, demographic connectivity, and the design of marine reserves. Ecological Applications 13: 146-158.
60. Peakall R, Smouse PE (2006). GenAlEx 6: genetic analy-sis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295. (Pubitemid 43373825)
61. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004). GeneClass2: a software for genetic assignment and first-generation migrant detection. Heredity 95: 536-539. (Pubitemid 39383165)
62. Planes S, Lenfant. P (2002). Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success. Mol Ecol 11: 1515-1524.
63. Polato NR, Concepcion GT, Toonen RJ, Baums IB (2010). Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata. Mol Ecol 19: 4661-4677.
64. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
65. Pritchard J (2010). Structure (Online). Website last modified in 2010 (accessed January 20 2012). Available at http://pritch.bsd.uchicago.edu/ software/install-v.2.3.1.html.
66. Rannala B, Mountain JL (1997). Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci 94: 9197-9201. (Pubitemid 27357806)
67. Rice WR (1989). Analyzing tables of statistical tests. Evolution 43: 223-235.
68. Rosenberg NA (2004). DISTRUCT: a program for the graphical dis-play of population structure. Mol Ecol Notes 4: 137-138. (Pubitemid 38261335)
69. 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.
70. Selkoe KA, Toonen RJ (2006). Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9: 615-629.
71. Selkoe KA, Toonen RJ (2011). Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal. Mar Ecol Prog Ser 436: 291-305.
72. Shanks AL, Grantham BA, Carr MH (2003). Propagule dispersal distance and the size and spacing of marine reserves. Ecological Applications 13: 159-169.
73. Shears N, Babcock R (2003). Continuing trophic cascade effects after 25 years of no-take marine reserve protection. Mar Ecol Prog Ser 246: 1-16. (Pubitemid 36198867)
74. Swearer SE, Caselle JE, Lea DW, Warner RR (1999). Larval retention and recruitment in an island population of a coral-reef fish. Nature 402: 799-802.
75. Thomas L, Bell JJ (2011). Characterization of polymorphic microsatellite markers for the red rock lobster, Jasus edwardsii (Hutton 1875). Conservation Genet Resour 4: 319-321.
76. Thorrold SR, Jones GP, Hellberg ME, Burton RS, Swearer SE, Neigel JE et al. (2002). Quantifying larval retention and connectivity in marine populations with artificial and natural markers. Bulletin of Marine Science 70: 291-308. (Pubitemid 34696167)
77. Underwood J N, Smith L D, Van Oppen M J H, Gilmour J P (2007). Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol Ecol 16: 771-784. (Pubitemid 46233099)
78. van Oosterhout C, Hutchinson W, Wills D, Shipley P (2004). MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-538. (Pubitemid 39147523)
79. Weersing KA, Toonen RJ (2009). Population genetics, larval dispersal, and demographic connectivity in marine systems. Mar Ecol Prog Ser 393: 1-12.
80. Whitlock M C, McCauley D E (1999). Indirect measures of gene flow and migration: FST not equal to 1/(4Nm\+1). Heredity 82: 117-125. (Pubitemid 29120325)
81. Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370. (Pubitemid 16277759)
82. Wooster WS, Bailey KM (1989). Recruitment of marine fishes revisited. In Effects of ocean variability on recruitment and an evaluation of parameters used in stock assessment modelsBeamish RJ, McFarlane. GA (eds). Canadian Special Publication of Fisheries and Aquatic Science 108: 153-159.
83. Wright S. (1951). The genetical structure of populations. Ann. Eugethcs 15: 323-354.