Molecular estimation of dispersal for ecology and population genetics

Annual Review of Ecology, Evolution, and Systematics

Volumn 40, Issue , 2009, Pages 193-216

  Broquet, Thomas ^a   Petit, Eric J ^b,c  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b UNIVERSITÉ DE RENNES 1   (France)

^c UNIVERSITÉ DE RENNES 1   (France)

Author keywords

Backward dispersal; Dispersal distance; Gene flow; Genetic inference; Migration rate

Indexed keywords

DISPERSAL; EVOLUTIONARY BIOLOGY; GAMETE; GENE FLOW; GENETIC VARIATION; MOLECULAR ANALYSIS; POPULATION GENETICS; POPULATION MIGRATION; SEED; SPECIES DIVERSITY;

EID: 77951691954     PISSN: 1543592X     EISSN: 15452069     Source Type: Book Series    
DOI: 10.1146/annurev.ecolsys.110308.120324     Document Type: Article

References (139)

1. Abdo Z, Crandall KA, Joyce P. 2004. Evaluating the performance of likelihood methods for detecting population structure and migration. Mol. Ecol. 13:837-851
2. Adams WT, Birkes DS. 1991. Estimating mating patterns in forest tree populations. In Biochemical Markers in the Population Genetics of Forest Trees, ed. S Fineschi, ME Malvolti, F Cannata, HH Hattemer, pp. 157-172 The Hague: SPB Academic Publishing
3. Austerlitz F, Dick CW, Dutech C, Klein EK, Oddou-Muratorio S, et al. 2004. Using genetic markers to estimate the pollen dispersal curve. Mol. Ecol. 13:937-954
4. Austerlitz F, Smouse PE. 2001. Two-generation analysis of pollen flow across a landscape. II. Relation between Φft, pollen dispersal and interfemale distance. Genetics 157:851-857
5. Austerlitz F, Smouse PE. 2002. Two-generation analysis of pollen flow across a landscape. IV Estimating the dispersal parameter. Genetics 161:355-363
6. Bahlo M, Griffiths RC. 2000. Inference from gene trees in a subdivided population. Theor. Popul. Biol. 57:79-95
7. Balloux F, Goudet J. 2002. Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol. Ecol. 11:771-783
8. Barton NH. 1982. The structure of the hybrid zone in Uroderma bilobatum. Evolution 36:863-866
9. Barton NH. 2001. The evolutionary consequences of gene flow and local adaptation: future approaches. In Dispersal, ed. J Clobert, E Danchin, AA Dhondt, JD Nichols, pp. 329-340 New York: Oxford Univ. Press
10. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035
11. Beerli P. 2004. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecol. 13:827-836
12. 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
13. Beerli P, Felsenstein J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98:4563-4568
14. Berry O, Tocher MD, Sarre SD. 2004. Can assignment tests measure dispersal? Mol. Ecol. 13:551-561
15. Blundell GM, Ben-David M, Groves P, Bowyer RT, Geffen E. 2002. Characteristics of sex-biased dispersal and gene flow in coastal river otters: implications for natural recolonization of extirpated populations. Mol. Ecol. 11:289-303
16. Bohonak AJ. 1999. Dispersal, gene flow, and population structure. Q. Rev. Biol. 74:21-45
17. Bossart JL, Prowell DP. 1998. Genetic estimates of population structure and gene flow: limitations, lessons, and new directions. Trends Ecol. Evol. 13:202-206
18. Bowler DE, Benton TG 2005. Causes and consequences of animal dispersal strategies: relating individual behavior to spatial dynamics. Biol. Rev. 80:205-225
19. Broquet T, Johnson CA, Petit E, Thompson ID, Burel F, Fryxell JM. 2006a. Dispersal and genetic structure in the American marten, Martes americana. Mol. Ecol. 15:1689-1697
20. Broquet T, Ray N, Petit E, Fryxell JM, Burel F. 2006b. Genetic isolation by distance and landscape connectivity in the American marten (Martes americana). Landsc. Ecol. 21:877-889
21. Broquet T, Yearsley J, Hirzel AH, Goudet J, Perrin N. 2009. Inferring recent migration rates from individual genotypes. Mol. Ecol. 18:1048-1060
22. Bullock JM, Shea K, Skarpaas O. 2006. Measuring plant dispersal: an introduction to field methods and experimental design. Plant Ecol. 186:217-234
23. Burczyk J, Adams WT, Birkes DS, Chybicki IJ. 2006. Using genetic markers to directly estimate gene flow and reproductive success parameters in plants on the basis of naturally regenerated seedlings. Genetics 173:363-372
24. Burczyk J, Adams WT, Moran GF, Griffin AR. 2002. Complex patterns of mating revealed in a Eucalyptus regnans seed orchard using allozyme markers and the neighbourhood model. Mol. Ecol. 11:2379-2391
25. Burczyk J, DiFazio SP, Adams WT. 2004. Gene flow in forest trees: How far do genes really travel? Forest Genet. 11:1-14
26. Burland TM, Barratt EM, Nichols RA, Racey PA. 2001. Mating patterns, relatedness and the basis of natal philopatry in the brown long-eared bat, Plecotus auritus. Mol. Ecol. 10:1309-1321
27. Carlon DB. 1999. The evolution of mating systems in tropical reef corals. Trends Ecol. Evol. 14:491-495
28. Chapuisat M, Goudet J, Keller L. 1997. Microsatellites reveal high population viscosity and limited dispersal in the ant Formica paralugubris. Evolution 51:475-482
29. Cockerham CC, Weir BS. 1993. Estimation of gene flow from F-statistics. Evolution 47:855-863
30. Crow JF, Aoki K. 1984. Group selection for a polygenic behavioral trait\estimating the degree of population subdivision. Proc. Natl. Acad. Sci. USA Biol. Sci. 81:6073-6077
31. Dale S, Lunde A, Steifetten Ø. 2004. Longer breeding dispersal than natal dispersal in the ortolan bunting. Behav. Ecol. 16:20-24
32. De Iorio M, Griffiths RC. 2004a. Importance sampling on coalescent histories. I. Adv. Appl. Probab. 36:417-433
33. De Iorio M, Griffiths RC. 2004b. Importance sampling on coalescent histories. II: Subdivided population models. Adv. Appl. Probab. 36:434-454
34. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. 2003. Measurably evolving populations. Trends Ecol. Evol. 18:481-488
35. Dyer RJ. 2007. Powers of discerning: challenges to understanding dispersal processes in natural populations. Mol. Ecol. 16:4881-4882
36. Ellstrand NC, Marshall DL. 1985. Interpopulation gene flow by pollen in wild radish, Raphanus sativus. Am. Nat. 126:606-616
37. Ennos RA. 1994. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72:250-259
38. Ennos RA. 2001. Inferences about spatial processesinplant populations from the analysisof molecular markers. In Integrating Ecology and Evolution in a Spatial Context, ed. J Silvertown, J Antonovics, pp. 45-71. Oxford: Blackwell Sci.
39. Epperson BK. 2005. Estimating dispersal from short distance spatial autocorrelation. Heredity 95:7-15
40. Ewing G, Nicholls G, Rodrigo A. 2004. Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 168:2407-2420
41. Ewing G, Rodrigo A. 2006. Coalescent-based estimation of population parameters when the number of demes changes over time. Mol. Biol. Evol. 23:988-996
42. Excoffier L. 2007. Analysis of population subdivision. In Handbook of Statistical Genetics, ed. DJ Balding, M Bishop, C Cannings, pp. 980-1020. New York: John Wiley & Sons. 3rd ed.
43. Faubet P, Gaggiotti OE. 2008. A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 178:1491-1504
44. Fedy BC, Martin K, Ritland C, Young J. 2008. Genetic and ecological data provide incongruent interpretations of population structure and dispersal in naturally subdivided populations of white-tailed ptarmigan (Lagopus leucura). Mol. Ecol. 17:1905-1917
45. Fontanillas P, Petit E, Perrin N. 2004. Estimating sex-specific dispersal rates with autosomal markers in hierarchically structured populations. Evolution 58:886-894
46. Fu Y-X. 2006. Exact coalescent for the Wright-Fisher model. Theor. Popul. Biol. 69:385-394
47. Godoy JA, Jordano P. 2001. Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites. Mol. Ecol. 10:2275-2283
48. Grivet D, Smouse PE, Sork VL. 2005. A novel approach to an old problem: tracking dispersed seeds. Mol. Ecol. 14:3585-3595
49. Hamilton G, Stoneking M, Excoffier L. 2005. Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc. Natl. Acad. Sci. USA 102:7476-7480
50. Hansson B, Bensch S, Hasselquist D. 2003. A new approach to study dispersal: immigration of novel alleles reveals female-biased dispersal in great reed warblers. Mol. Ecol. 12:631-637
51. Hardy O, Vekemans X. 1999. Isolation by distance in a continuous population: reconciliation between spatial autocorrelation and population genetics models. Heredity 83:145-154
52. Hellberg ME. 1995. Stepping-stone gene flow in the solitary coral Balanophyllia elegans: equilibrium and nonequilibrium at different spatial scales. Mar. Biol. 123:573-581
53. Hey J, Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760
54. Hey J, Won Y, Sivasundar A, Nielsen R, Markert JA. 2004. Using nuclear haplotypes with microsatellites to study gene flow between recently separated cichlid species. Mol. Ecol. 13:909-919
55. Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589
56. Ibrahim KM, Nichols RA, Hewitt GM. 1996. Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity 77:282-291
57. Jones B. 2003. Maximum likelihood inference for seed and pollen dispersal distributions. J. Agric. Biol. Environ. Stat. 8:170-183
58. Jones FA, Muller-Landau HC. 2008. Measuring long-distance seed dispersal in complex natural environments: an evaluation and integration of classical and genetic methods. J. Ecol. 96:642-652
59. JordanoP. 2007. Frugivores, seeds and genes: analyzing the key elements of seed shadows. In Frugivory and Seed Dispersal: Theory and Applications in a Changing World, ed. A Dennis, R Green, EW Schupp, D Wescott, pp. 229-251 Wallingford: Commonw. Agric. Bur. Intl.
60. Jordano P, Garcia C, Godoy JA, Garcia-Castaño JL. 2007. Differential contribution of frugivores to complex seed dispersal patterns. Proc. Natl. Acad. Sci. USA 104:3278-3282
61. Kerth G, Petit E. 2005. Colonization and dispersal in a social species, the Bechstein's bat (Myotis bechsteinii). Mol. Ecol. 14:3943-3950
62. Kingman JFC. 1982. The coalescent. Stoch. Process. Appl. 13:235-248
63. Kinlan BP, Gaines SD. 2003. Propagule dispersal in marine and terrestrial environments: a community perspective. Ecology 84:2007-2020
64. Koenig W, Van Vuren D, Hooge P. 1996. Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends Ecol. Evol. 11:514-517
65. Kokko H, López-Sepulcre A. 2006. From individual dispersal to species ranges: perspectives for a changing world. Science 313:789-791
66. Lawson Handley LJ, Perrin N. 2007. Advances in our understanding of mammalian sex-biased dispersal. Mol. Ecol. 16:1559-1578
67. 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 bydistance. Mol. Biol. Evol. 20:491-502
68. Leblois R, Rousset F, Estoup A. 2004. Influence of spatial and temporal heterogeneities on the estimation of demographic parameters in a continuous population using individual microsatellite data. Genetics 166:1081-1092
69. Lebreton J-D, Hines JE, Pradel R, Nichols JD, Spendelow JA. 2003. Estimation by capture-recapture of recruitment and dispersal over several sites. Oikos 101:253-264
70. LenormandT, Bourguet D, Guillemaud T, Raymond M. 1999. Tracking the evolution of insecticide resistance in the mosquito Culex pipiens. Nature 400:861-864 (Pubitemid 29406719)
71. Lenormand T, Guillemaud T, Bourguet D, Raymond M. 1998. Evaluating gene flow using selected markers: a case study. Genetics 149:1383-1392
72. Loiselle BA, Sork VL, Nason J, Graham C. 1995. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82:1420-1425
73. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. 2003. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 4:981-994
74. Manel S, Gaggiotti OE, Waples S. 2005. Assignment methods: matching biological questions with appropriate techniques. Trends Ecol. Evol. 20:136-142
75. Martin CA, Alonso JC, Alonso JA, Palacin C, Magana M, Martin B. 2008. Natal dispersal in great bustards: the effect of sex, local population size and spatial isolation. J. Anim. Ecol. 77:326-334
76. McRae BH. 2006. Isolation by resistance. Evolution 60:1551-1561
77. Nath HB, Griffiths RC. 1996. Estimation in an island model using simulation. Theor. Popul. Biol. 50:227-253
78. Nathan R, Perry G, Cronin JT, Strand AE, Cain ML. 2003. Methods for estimating long-distance dispersal. Oikos 103:261-273
79. Neigel JE. 1997. A comparison of alternative strategies for estimating gene flow from genetic markers. Annu. Rev. Ecol. Syst. 28:105-128
80. Nielsen R, Slatkin M. 2000. Likelihood analysis of ongoing gene flow and historical association. Evolution 54:44-50
81. Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896
82. Oddou-Muratorio S, Klein EK, Austerlitz F. 2005. Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. II. Pollen dispersal and heterogeneity in mating success inferred from parent-offspring analysis. Mol. Ecol. 14:4441-4452
83. Ouborg NJ, Piquot Y, van Groenendael JM. 1999. Population genetics, molecular markers and the study of dispersal in plants. J. Ecol. 87:551-568
84. Paetkau D, Calvert W, Stirling I, Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol. Ecol. 4:347-354
85. Paetkau D, Slade R, Burdens M, Estoup A. 2004. Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol. Ecol. 13:55-65
86. Paradis E, Sutherland WJ, Baillie SR, Gregory RD. 1998. Patterns of natal and breeding dispersal in birds. J. Anim. Ecol. 67:518-536
87. Peacock MM. 1997. Determining natal dispersal patterns in a population of North American pikas (Ochotona princeps) using direct mark-resight and indirect genetic methods. Behav. Ecol. 8:340-350
88. Petit E, Balloux F, Excoffier L. 2002. Mammalian population genetics: Why not Y? Trends Ecol. Evol. 17:28-33
89. Petit E, Balloux F, Goudet J. 2001. Sex-biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters. Evolution 55:635-640
90. Petit E, Valière N. 2006. Estimating population size with noninvasive capture-mark-recapture data. Conserv. Biol. 20:1062-1073
91. Pritchard JK, Stephens M, Donnely P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959
92. Proctor MF, McLellan BN, Strobeck C, Barclay RMR. 2004. Gender-specific dispersal distances of grizzly bears estimated by genetic analysis. Can. J. Zool. 82:1108-1118
93. Ray N, Currat M, Excoffier L. 2003. Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20:76-86
94. Robledo-Arnuncio JJ, Austerlitz F, Smouse PE. 2006. A new method of estimating the pollen dispersal curve independently of effective density. Genetics 173:1033-1045
95. Robledo-Arnuncio JJ, Garcia C. 2007. Estimation of the seed dispersal kernel from exact identification of source plants. Mol. Ecol. 16:5098-5109
96. Rosenberg NA, Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-390
97. Rousset F. 1997. Genetics differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219-1228
98. Rousset F. 1999. Genetic differentiation in populations with different classes of individuals. Theor. Popul. Biol. 55:297-308
99. Rousset F. 2000. Genetic differentiation between individuals. J. Evol. Biol. 13:58-62
100. Rousset F. 2001. Genetic approaches to the estimation of dispersal rates. In Dispersal, ed. J Clobert, E Danchin, AA Dhondt, JD Nichols, pp. 18-28. New York: Oxford Univ. Press
101. Rousset F. 2004. Genetic Structure and Selection in Subdivided Populations. Princeton: Princeton Univ. Press. 288 pp.
102. Rousset F. 2007. Inferences from spatial population genetics. In Handbook of Statistical Genetics, ed. DJ Balding, M Bishop, C Cannings, pp. 945-979 Chichester: John Wiley & Sons Ltd.
103. Rousset F. 2008. Demystifying Moran's I. Heredity 100:231-232
104. Schweizer M, Excoffier L, Heckel G. 2007. Fine-scale genetic structure and dispersal in the common vole (Microtus arvalis). Mol. Ecol. 16:2463-2473
105. Skalski GT. 2007. Joint estimation of migration rate and effective population size using the island model. Genetics 177:1043-1057
106. Slatkin M. 1987. Gene flow and the geographic structure of natural populations. Science 236:787-792
107. Slatkin M. 1993. Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264-279
108. Slatkin M. 1994. Gene flow and population structure. In Ecological Genetics, ed. LA Real, pp. 3-17. Princeton: Princeton Univ. Press
109. Slatkin M. 2005. Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations. Mol. Ecol. 14:67-73
110. Slatkin M, Barton NH. 1989. A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43:1349-1368
111. Slatkin M, Maddison WP. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123:603-613 (Pubitemid 19274683)
112. Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape. I. Male gamete heterogeneity among females. Evolution 55:260-271
113. Smouse PE, Sork VL. 2004. Measuring pollen flow in forest trees: an exposition of alternative approaches. Forest Ecol. Manag. 197:21-38
114. Sork VL, Nason J, Campbell DR, Fernandez JF. 1999. Landscape approaches to historical and contemporary gene flow in plants. Trends Ecol. Evol. 14:219-224
115. Sotka EE, Palumbi SR. 2006. The use of genetic clines to estimate dispersal distances of marine larvae. Ecology 87:1094-1103
116. Sumner J, Rousset F, Estoup A, Moritz C. 2001. Neighbourhood size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods. Mol. Ecol. 10:1917-1927
117. Sutherland GD, Harestad AS, Price K, Lertzman KP. 2000. Scaling of natal dispersal distances in terrestrial birds and mammals. Conserv. Ecol. 4:16
118. Szymura JM, Barton NH. 1986. Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, near Cracow in southern Poland. Evolution 40:1141-1159
119. Turelli M, Barton NH, Coyne JA. 2001. Theory and speciation. Trends Ecol. Evol. 16:330-343
120. Vasemägi A. 2006. The adaptive hypothesis of clinal variation revisited: single-locus clinesas aresult of spatially restricted gene flow. Genetics 173:2411-2414
121. Vekemans X, Hardy O. 2004. New insights from fine-scale genetic structure analyses in plant populations. Mol. Ecol. 13:921-935
122. Vitalis R. 2002. Sex-specific genetic differentiation and coalescence times: estimating sex-biased dispersal rates. Mol. Ecol. 11:125-138
123. Vitalis R, Couvet D. 2001. Estimation of effective population size and migration rate from one-and two-locus identity measures. Genetics 157:911-925
124. Vuillemier S, Possingham HP. 2006. Does colonization asymmetry matter in metapopulations? Proc. R. Soc. London Ser. B 273:1637-1642
125. Vuilleumier S, Perrin N. 2006. Effects of cognitive abilities on metapopulation connectivity. Oikos 113:139-147
126. Wade MJ, McCauley DE. 1988. Extinction and recolonization: their effects on the genetic differentiation of local populations. Evolution 42:995-1005
127. Wakeley J. 1999. Nonequilibrium migration in human history. Genetics 153:1863-1871
128. Wakeley J. 2009. Coalescent Theory: An Introduction. Greenwood Village: Roberts & Company Wang J. 1997. Effective size and F-statistics of subdivided populations. II. Dioecious species. Genetics 146:1465-1474
129. Wang J, Whitlock MC. 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429-446
130. Waples RS, Gaggiotti OE. 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
131. Waser PM, Strobeck C. 1998. Genetic signature of interpopulation dispersal. Trends Ecol. Evol. 13:43-44
132. Watts PC, Rousset F, Saccheri IJ, Leblois R, Kemp SJ, Thompson DJ. 2007. Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of 'neighbourhood size' using a more precise estimator. Mol. Ecol. 16:737-751
133. ST = 1/(4Nm + 1). Heredity 82:117-125
134. Wiegand T, Moloney KA, Naves J, Knauer F. 1999. Finding the missing link between landscape structure and population dynamics: a spatially explicit perspective. Am. Nat. 154:605-627
135. Wilson GA, Rannala B. 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177-1191
136. Wright S. 1931. Evolution in Mendelian populations. Genetics 16:97-159
137. Wright S. 1940. Breeding structure of populations in relation to speciation. Am. Nat. 74:232-248
138. Wright S. 1943. Isolation by distance. Genetics 28:114-138
139. Wright S. 1951. The genetical structure of populations. Ann. Eugen. 15:323-54