title: Meta-population structure in a coral reef fish demonstrated by genetic data on patterns of migration, extinction and re-colonisation.
abstract: BACKGROUND
  Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined.
  
  
  RESULTS
  Acanthochromis polyacanthus displayed strong genetic structure among regions (PhiST = 0.81, P < 0.0001) that supported an equilibrium isolation-by-distance model (r = 0.77, P = 0.001). Significant structuring across the continental shelf was only evident in the northern region (PhiST = 0.31, P < 0.001) and no evidence of isolation-by-distance was found within any region. Pairwise PhiST values indicated overall strong but variable genetic structure (mean PhiST among reefs within regions = 0.28, 0.38, 0.41), and asymmetric migration rates among reefs with low genetic structure. Genetic differentiation among younger reefs was greater than among older reefs supporting a meta-population propagule-pool colonisation model. Variation in genetic diversities, demographic expansion and population growth estimates indicated more frequent genetic bottlenecks/founder effects and subsequent population expansion in the central and southern regions compared to the northern one.
  
  
  CONCLUSIONS
  Our findings provide genetic evidence for meta-population dynamics in a direct developing coral reef fish and we reject the equilibrium island and isolation-by distance models at local spatial scales. Instead, strong non-equilibrium genetic structure appears to be generated by genetic bottlenecks/founder effects associated with population reductions/extinctions and asymmetric migration/(re)-colonisation of such populations. These meta-population dynamics varied across the geographical range examined with edge populations exhibiting lower genetic diversities and higher rates of population expansion than more central populations. Therefore, coral reef species may experience local population reductions/extinctions that promote overall meta-population genetic differentiation.
authors.affiliation: School of Marine and Tropical Biology, James Cook University, Townsville, Qld 4811, Australia. line.bay@jcu.edu.au
authors.forename: Line K
authors.initials: LK
authors.lastname: Bay
authors.forename: M Julian M
authors.initials: MJ
authors.lastname: Caley
authors.forename: Ross H
authors.initials: RH
authors.lastname: Crozier
mesh_terms: D025041:Animal Migration; D000818:Animals; D001315:Australia; D001482:Base Composition; D004272:DNA, Mitochondrial / Q000235:genetics; D017753:Ecosystem; D019143:Evolution, Molecular; D053476:Extinction, Biological; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D008957:Models, Genetic; D010473:Perciformes / Q000235:genetics*; D011157:Population Dynamics; D016415:Sequence Alignment
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers
references.citation: Mol Ecol. 2002 Mar;11(3):289-303
references.pmid: 11928704
references.citation: Genetics. 1997 Oct;147(2):915-25
references.pmid: 9335623
references.citation: Mar Genomics. 2008 Sep-Dec;1(3-4):129-34
references.pmid: 21798164
references.citation: Mol Ecol. 2007 Feb;16(4):771-84
references.pmid: 17284210
references.citation: J Mol Evol. 1997 Nov;45(5):473-84
references.pmid: 9342395
references.citation: Evolution. 2001 Nov 11;55(11):2263-73
references.pmid: 11794786
references.citation: Philos Trans R Soc Lond B Biol Sci. 2000 Dec 29;355(1404):1851-64
references.pmid: 11205346
references.citation: Bioinformatics. 1998;14(9):817-8
references.pmid: 9918953
references.citation: Science. 2007 May 4;316(5825):742-4
references.pmid: 17478720
references.citation: Evolution. 1996 Jun;50(3):1167-1175
references.pmid: 28565289
references.citation: Science. 1987 May 15;236(4803):787-92
references.pmid: 3576198
references.citation: Bioinformatics. 2012 Oct 1;28(19):2537-9
references.pmid: 22820204
references.citation: Proc Biol Sci. 2002 Oct 22;269(1505):2079-86
references.pmid: 12396481
references.citation: Theor Popul Biol. 1977 Dec;12(3):253-62
references.pmid: 601717
references.citation: Science. 1995 Feb 10;267(5199):880-3
references.pmid: 7846530
references.citation: Trends Ecol Evol. 1991 Jan;6(1):5-8
references.pmid: 21232411
references.citation: Genetics. 1943 Mar;28(2):114-38
references.pmid: 17247074
references.citation: Mol Biol Evol. 2003 Jan;20(1):76-86
references.pmid: 12519909
references.citation: Genetics. 1931 Mar;16(2):97-159
references.pmid: 17246615
references.citation: Comput Appl Biosci. 1989 Jul;5(3):233-4
references.pmid: 2766009
references.citation: Evolution. 1997 Aug;51(4):1232-1243
references.pmid: 28565481
references.citation: Evolution. 2003 Jul;57(7):1571-83
references.pmid: 12940362
references.citation: Evolution. 2000 Feb;54(1):226-37
references.pmid: 10937199
references.citation: Mol Ecol. 2005 Apr;14(5):1367-75
references.pmid: 15813777
references.citation: Evolution. 1997 Oct;51(5):1506-1517
references.pmid: 28568622
references.citation: Genetics. 1998 May;149(1):429-34
references.pmid: 9584114
references.citation: Bioinformatics. 2003 Dec 12;19(18):2496-7
references.pmid: 14668244
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Genetics. 1999 Jun;152(2):763-73
references.pmid: 10353916
references.citation: Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4563-8
references.pmid: 11287657
references.citation: Curr Biol. 2005 Jul 26;15(14):1314-8
references.pmid: 16051176
references.citation: Evol Bioinform Online. 2007 Feb 23;1:47-50
references.pmid: 19325852
references.citation: Genetics. 1983 Oct;105(2):437-60
references.pmid: 6628982
references.citation: Ecol Appl. 1992 Feb;2(1):18-29
references.pmid: 27759195
references.citation: J Evol Biol. 2006 Jan;19(1):239-52
references.pmid: 16405595
references.citation: Evolution. 2000 Oct;54(5):1590-605
references.pmid: 11108587
references.citation: Mol Biol Evol. 2002 Dec;19(12):2092-100
references.pmid: 12446801
references.citation: Mol Ecol. 2004 Apr;13(4):853-64
references.pmid: 15012760
references.citation: Trends Ecol Evol. 1996 Apr;11(4):180-3
references.pmid: 21237801
references.citation: Evolution. 2003 May;57(5):949-61
references.pmid: 12836814
references.citation: Genetics. 1992 Jun;131(2):479-91
references.pmid: 1644282
references.citation: Science. 2003 Aug 15;301(5635):929-33
references.pmid: 12920289
references.citation: Trends Ecol Evol. 1990 Jul;5(7):207-10
references.pmid: 21232356
references.citation: Am Nat. 2000 Feb;155(2):252-265
references.pmid: 10686164
references.citation: Mol Biol Evol. 1993 May;10(3):512-26
references.pmid: 8336541
references.citation: Proc Natl Acad Sci U S A. 1955 Mar 15;41(3):144-50
references.pmid: 16589632
references.citation: Evolution. 1984 Nov;38(6):1358-1370
references.pmid: 28563791
references.citation: Genetics. 1964 Apr;49(4):561-76
references.pmid: 17248204
references.citation: Evolution. 1990 Nov;44(7):1717-1724
references.pmid: 28567815
references.citation: J Hered. 2006 Jan-Feb;97(1):1-12
references.pmid: 16394255
references.citation: Int Rev Cytol. 1992;141:173-216
references.pmid: 1452431
references.citation: Evolution. 1999 Jun;53(3):664-676
references.pmid: 28565620
references.citation: Mol Ecol. 2008 May;17(9):2234-44
references.pmid: 18363661
references.citation: Nature. 2000 Aug 17;406(6797):692-3
references.pmid: 10963585
references.citation: Evolution. 2002 Feb;56(2):378-99
references.pmid: 11926506
references.citation: Evolution. 1988 Sep;42(5):995-1005
references.pmid: 28581169
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):858-63
references.pmid: 17213323
references.citation: Mol Ecol. 2004 Apr;13(4):837-51
references.pmid: 15012759
references.citation: Mol Ecol. 2004 Jan;13(1):67-80
references.pmid: 14653789