Interplay between isolation by distance and genetic clusters in the red coral Corallium rubrum: Insights from simulated and empirical data

Conservation Genetics

Volumn 14, Issue 3, 2013, Pages 705-716

  Aurelle, Didier ^a   Ledoux, Jean Baptiste ^a,b,c  

^a AVIGNON UNIVERSITÉ   (France)

^b INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^c UNIVERSITY OF PORTO   (Portugal)

Author keywords

Clustering; Genetic structure; Isolation by distance; Red coral; Simulations

Indexed keywords

CLUSTER ANALYSIS; CORAL; DATA INTERPRETATION; ECOLOGICAL MODELING; EMPIRICAL ANALYSIS; ENDANGERED SPECIES; GENETIC STRUCTURE; HARVESTING; ISOLATION EFFECT; POPULATION GENETICS; SAMPLING; SPECIES CONSERVATION;

ANTHOZOA; CORALLIUM RUBRUM;

EID: 84877789238     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-013-0464-0     Document Type: Article

References (60)

1. Aurelle D, Ledoux J-B, Rocher C, Borsa P, Chenuil A, Féral J-P (2011) Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian. Genetica 139: 855-869.
2. Barnosky AD, Hadly EA, Bascompte J et al (2012) Approaching a state shift in earth's biosphere. Nature 486: 52-58.
3. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13: 969-980.
4. Blair C, Weigel DE, Balazik M, Keeley ATH, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N (2012) A simulation-based evaluation of methods for inferring linear barriers to gene flow. Mol Ecol Res 12: 822-833.
5. Bruckner AW (2009) Rate and extent of decline in Corallium (pink and red coral) populations: existing data meet the requirements for a CITES Appendix II listing. Mar Ecol Prog Ser 397: 319-332.
6. Castric V, Bernatchez L (2003) The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis Mitchill). Genetics 163(3): 983-996.
7. Chen C, Durand E, Forbes F (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7: 747-756.
8. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15: 2833-2843.
9. Corander J, Waldmann P, Sillanpää MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163(1): 367-374.
10. Corander J, Marttinen P, Siren J, Tang J (2008a) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinform 9(1): 539.
11. Corander J, Sirén J, Arjas E (2008b) Bayesian spatial modelling of genetic population structure. Comput Stat 23: 111-129.
12. Costantini F, Fauvelot C, Abbiati M (2007a) Fine-scale genetic structuring in Corallium rubrum: evidence of inbreeding and limited effective larval dispersal. Mar Ecol Prog Ser 340: 109-119.
13. Costantini F, Fauvelot C, Abbiati M (2007b) Genetic structuring of the temperate gorgonian coral (Corallium rubrum) across the western Mediterranean sea revealed by microsatellites and nuclear sequences. Mol Ecol 16: 5168-5182.
14. Costantini F, Taviani M, Remia A, Pintus E, Schembri PJ, Abbiati M (2010) Deep-water Corallium rubrum (L., 1758) from the Mediterranean Sea: preliminary genetic characterisation. Mar Ecol 31: 261-269.
15. Dawson KJ, Belkhir K (2001) A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res Camb 78: 59-77.
16. Dawson KJ, Belkhir K (2009) An agglomerative hierarchical approach to visualization in Bayesian clustering problems. Heredity 103: 32-45.
17. Dellicour S, Frantz A, Colyn M, Bertouille S, Chaumont F, Flamand M-C (2011) Population structure and genetic diversity of red deer (Cervus elaphus) in forest fragments in north-western France. Cons Gen 12: 1287-1297.
18. Durand E, Jay F, Gaggiotti OE, François O (2009) Spatial inference of admixture proportions and secondary contact zones. Mol Biol Evol 26(9): 1963-1973.
19. Earl D, vonHoldt B (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Cons Gen Res 4(2): 359-361.
20. Epperson BK, McRae BH, Scribner K, Cushman SA, Rosenberg MS, Fortin M-J, James PMA et al (2010) Utility of computer simulations in landscape genetics. Mol Ecol 19(17): 3549-3564.
21. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8): 2611-2620.
22. Excoffier, Laval LG, Schneider S (2005) Arlequin ver. 3. 0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
23. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
24. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4): 1567-1587.
25. François O, Durand E (2010) Spatially explicit Bayesian clustering models in population genetics. Mol Ecol Res 10: 773-784.
26. Frankham R, Ballou JD, Briscoe DA (2010) Introduction to conservation genetics, 2nd edn. Cambridge University Press, New York.
27. Frantz AC, Cellina S, Krier A, Schley L, Burke T (2009) Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? J Appl Ecol 46: 493-505.
28. Garrabou J, Coma R, Bensoussan N et al (2009) Mass mortality in northwestern Mediterranean rocky benthic communities: effects of the 2003 heat wave. Glob Change Biol 15(5): 1090-1103.
29. Gauffre B, Estoup A, Bretagnolle V, Cosson JF (2008) Spatial genetic structure of a small rodent in a heterogeneous landscape. Mol Ecol 17: 4619-4629.
30. Giraudel JL, Aurelle D, Lek S, Berrebi P (2000) Application of the self-organizing mapping and fuzzy clustering to microsatellite data: how to detect genetic structure in brown trout (Salmo trutta) populations. In: Lek S, Guégan JF (eds) Artificial neuronal networks. Springer, Berlin, pp 187-202.
31. Guillot G, Estoup A, Mortier F, Cosson JF (2005) A spatial statistical model for landscape genetics. Genetics 170(3): 1261-1280.
32. Guillot G, Leblois R, Coulon A, Frantz AC (2009) Statistical methods in spatial genetics. Mol Ecol 18: 4734-4756.
33. Heller R, Siegismund HR (2009) Relationship between three measures of genetic differentiation G ST, D EST and G' ST: how wrong have we been? Mol Ecol 18: 2080-2083.
34. Hoban S, Bertorelle G, Gaggiotti OE (2012) Computer simulations: tools for population and evolutionary genetics. Nat Rev Gen 13: 110-122.
35. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405.
36. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11(1): 94.
37. Kalinowski ST (2011) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106(4): 625-632.
38. Kimura M, Weiss GH (1964) Stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49: 561-576.
39. Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OEJ (2006) Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Cons Gen 7: 295-302.
40. Laval G, Excoffier L (2004) SIMCOAL 2. 0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20(15): 2485-2487.
41. Leblois R, Estoup A, Rousset F (2003) Influence of mutational and sampling factors on the estimation of demographic parameters in a "Continuous" population under isolation by distance. Mol Biol Evol 20(4): 491-502.
42. Leblois R, Estoup A, Rousset F (2009) IBD Sim: a computer program to simulate genotypic data under Isolation by Distance. Mol Ecol Res 9: 107-109.
43. Ledoux J-B, Garrabou J, Bianchimani O, Drap P, Féral J-P, Aurelle D (2010a) Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum. Mol Ecol 19(19): 4204-4216.
44. Ledoux J-B, Mokhtar-Jamaï K, Roby C, Féral J-P, Garrabou J, Aurelle D (2010b) Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation. Mol Ecol 19(4): 675-690.
45. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18(4): 189-197.
46. Orozco-Ter Wengel P, Corander J, Schlötterer C (2011) Genealogical lineage sorting leads to significant but incorrect Bayesian multilocus inference of population structure. Mol Ecol 20: 1108-1121.
47. Palsbøll PJ, Bérubé M, Allendorf FW (2006) Identification of management units using population genetic data. Trends Ecol Evol 22(1): 11-16.
48. Palumbi SR (2003) Population genetics, demographic connectivity, and the design of marine reserves. Ecol Appl 13(sp1): 146-158.
49. Perrier C, Guyomard R, Baglinière J-L, Evanno G (2011) Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences. Mol Ecol 20(20): 4231-4245.
50. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959.
51. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 49: 1283-1286.
52. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145(4): 1219-1228.
53. Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Res 8: 103-106.
54. Rousset F, Leblois R (2012) Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals. Mol Biol Evol 29(3): 957-973.
55. Safner T, Miller MP, McRae BH, Fortin M-J, Manel S (2011) Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics. Int J Mol Sci 12: 865-889.
56. Schwartz MK, McKelvey KS (2009) Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Cons Genet 10(2): 441-452.
57. Viard F, Franck P, Dubois M-P, Estoup A, Jarne P (1998) Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species. J Mol Evol 47: 42-51.
58. 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. Mol Ecol 15: 1419-1439.
59. Weir B, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
60. Zellmer AJ, Hanes MM, Hird SM, Carstens BC (2012) Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Syst Biol 61(5): 763-777.