Population genetics, molecular markers and the study of dispersal in plants

Journal of Ecology

Volumn 87, Issue 4, 1999, Pages 551-568

  Ouborg, N J ^a,b   Piquot, Y ^b   Van Groenendael, J M ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b CNRS   (France)

Author keywords

Coalescence; Gene flow; Isolation by distance; Paternity analysis; Pollen to seed migration ratio

Indexed keywords

DISPERSAL; MICROSATELLITE DNA; MOLECULAR AND CELLULAR STRUCTURE; POPULATION GENETICS;

GENE FLOW; GENETIC DIFFERENTIATION; GENETIC MARKER; LONG RANGE TRANSPORT; POPULATION GENETICS; SEED DISPERSAL;

EID: 0032788727     PISSN: 00220477     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2745.1999.00389.x     Document Type: Review

References (122)

1. Alvarez-Buylla, E.R. & Garay, A.A. (1994) Population genetic structure of Cecropia obtusifolia, a tropical pioneer tree species. Evolution, 48, 437-453.
2. Amos, W., Sawcer, S.J., Feakes, R.W. & Rubinzstein, D.C. (1996) Microsatellites show mutational bias and heterozygote instability. Nature Genetics, 13, 390-391.
3. Antonovics, J., Thrall, P.H., Jarosz, A.M. & Stratton, D. (1994) Ecological genetics of metapopulations: the Silene-Ustilago plant-pathogen system. Ecological Genetics (ed. L.A. Real), pp. 146-170. Princeton University Press, Princeton, NJ.
4. Arens, P., Coops, H., Jansen, J. & Vosman, B. (1998) Molecular genetic analysis of black poplar (Populus nigra L.) along Dutch rivers. Molecular Ecology, 7, 11-18.
5. Ashley, C.T. & Warren, S.T. (1995) Tri-nucleotide repeat expansion and human disease. Annual Review of Genetics, 29, 703-728.
6. Avise, J.C. (1994) Molecular Markers, Natural History and Evolution. Chapman & Hall, New York, NY.
7. Barrett, S.C.H., Eckert, C.G. & Husband, B.C. (1993) Evolutionary processes in aquatic plant populations. Aquatic Botany, 44, 105-145.
8. Beerli, P. (1998) MIGRATE, http://evolution.genetics.washington.edu/lamarc/migrate.html.
9. Birky, C.W., Fuerst, P. & Maruyama, T. (1989) Organelle gene diversity under migration, mutation and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics, 121, 613-627.
10. Bodmer, W.F. & Cavalli-Sforza, L.L. (1968) A migration matrix model for the study of random genetic drift. Genetics, 59, 565-592.
11. Brown, A.H.D. (1979) Enzyme polymorphism in plant populations. Theoretical Population Biology, 15, 1-42.
12. Brown, J.H. & Kodric-Brown, A. (1977) Turnover rates in insular biogeography: effect of immigration on extinction. Ecology, 58, 445-449.
13. Bruford, M.W., Hanotte, O., Brookfield, J.F.Y. & Burke, T. (1992) Multi-and single-locus fingerprinting. Molecular Analysis of Populations: A Practical Approach (ed. A.R. Hoelzel), pp. 225-269. IRL Press, Oxford, UK.
14. Byrne, M. & Moran, G.F. (1994) Population divergence in the chloroplast genome of Eucalyptus nitens. Heredity, 73, 18-28.
15. Cain, M.L., Damman, H. & Muir, A. (1998) Seed dispersal and the holocene migration of woodland herbs. Ecological Monographs, 68, 325-347.
16. Campbell, D.R. & Dooley, J.L. (1992) The spatial scale of genetic differentiation in a hummingbird-pollinated plant: comparison with models of isolation by distance. American Naturalist, 139, 735-748.
17. Cockerham, C.C. & Weir, B.S. (1993) Estimation of gene flow from F-statistics. Evolution, 47, 855-863.
18. Corriveau, J.L. & Coleman, A.W. (1988) Rapid screening method to detect potential bi-parental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany, 75, 1443-1458.
19. Crow, J.F. & Aoki, K. (1984) Group selection for a polygenie behavioral trait: estimating the degree of population subdivision. Proceedings of the National Academy of Sciences USA, 81, 6073-6077.
20. Dawson, I.K., Waugh, R., Simons, A.J. & Powell, W. (1997) Simple sequence repeats provide a direct estimate of pollen-mediated gene dispersal in the tropical tree Gliricidia sepium. Molecular Ecology, 6, 179-183.
21. Demesure, B., Sodzi, N. & Petit, R.J. (1995) A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology, 4, 129-131.
22. Devlin, B. & Ellstrand, N.C. (1990) The development and application of a refined method for estimating gene flow from angiosperm paternity analysis. Evolution, 44, 248-259.
23. Devlin, B., Roeder, K. & Ellstrand, N.C. (1988) Fractional paternity assignment: theoretical development and comparison to other methods. Theoretical and Applied Genetics, 76, 369-380.
24. Dong, J. & Wagner, D.B. (1994) Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision, and tests of disequilibrium with a maternally inherited mitochondrial polymorphism. Genetics, 136, 1187-1194.
25. Dow, B.D. & Ashley, M.V. (1996) Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Molecular Ecology, 5, 615-627.
26. Ellstrand, N.C. (1992) Gene flow among seed plant populations. New Forests, 6, 241-256.
27. Ellstrand, N.C. & Elam, D.R. (1993) Population genetic consequences of small population size: implications for plant conservation. Annual Review of Ecology and Systematics, 24, 217-242.
28. Ellstrand, N.C. & Hoffman, C.A. (1990) Hybridization as an avenue for escape of engineered genes. Bioscience, 40, 438-442.
29. El Mousadik, A. & Petit, R.J. (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology, 5, 547-556.
30. Ennos, R.A. (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity, 72, 250-259.
31. Epperson, B.K. (1993) Recent advances in correlation studies of spatial patterns of genetic variation. Evolutionary Biology, 27, 95-155.
32. Estoup, A., Garnery, L., Solignac, M. & Cornuet, J.-M. (1995) Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics, 140, 679-695.
33. Excoffier, L., Smouse, P.E. & Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
34. Forcioli, D., Saumitou-Laprade, P., Michaelis, G. & Cuguen, J. (1994) Chloroplast DNA polymorphism revealed by a fast, non-radioactive method in Beta vulgaris ssp. maritima. Molecular Ecology, 3, 173-176.
35. Gielly, L. & Taberlet, P. (1994) The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Molecular Biology and Evolution, 11, 769-777.
36. Giles, B.E. & Goudet, J. (1997) Genetic differentiation in Silene dioica metapopulations: estimation of spatiotemporal effects in a successional plant species. American Naturalist, 149, 507-526.
37. Goudet, J. (1995) FSTAT V-1.2. A computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
38. Govindaraju, D.R. (1988) Relationship between dispersal ability and levels of gene flow in plants. Oikos, 52, 31-35.
39. Grashof-Bokdam, C.J., Jansen, J. & Smulders, M.J.M. (1998) Dispersal patterns of Lonicera periclymenum determined by genetical analysis. Molecular Ecology, 7, 165-174.
40. Gray, A.J. (1996) Genetic diversity and its conservation in natural populations of plants. Biodiversity Letters, 3, 71-80.
41. Greene, D.F. & Johnson, E.A. (1996) Wind dispersal of seeds from a forest into a clearing. Ecology, 77, 595-609.
42. Hamrick, J.L. (1983) The distribution of genetic variation within and among natural plant populations. Genetics and Conservation. A Reference for Managing Wild Animal and Plant Populations (eds CS Schonewald-Cox et al.), pp. 335-346. Benjamin-Cummings, London, UK.
43. Hamrick, J.L. (1987) Gene flow and the distribution of genetic variation in plant populations. Differentiation in Higher Plants (ed. K. Urbanska) pp. 53-67. Academic Press, New York, NY.
44. Hamrick, J.L. & Godt, M.J. (1990) Allozyme diversity in plant species. Population Genetics, Breeding and Genetic Resources (eds A.H.D. Brown, M.T. Clegg, A.L. Kahler & B.S. Weir), pp. 43-63. Sinauer Associates, Sunderland, MA.
45. Hartl, D.L. & Clark, A.G. (1989) Principles of Population Genetics, 2nd edn. Sinauer Associates, Sunderland, MA.
46. Hengeveld, R. (1989) Dynamics of Biological Invasions. Chapman & Hall, London, UK.
47. Hollingsworth, P.M., Preston, C.D. & Gornall, R.J. (1996) Genetic variability in two hydrophilous species of Potamogeton, P. pectinatus and P. filiformis (Potamogetonaceae). Plant Systematics and Evolution, 202, 233-254.
48. Hu, X.-S. & Ennos, R.A. (1997) On estimation of the ratio of pollen to seed flow among plant populations. Heredity, 79, 541-552.
49. Huiskes, A.H.L., Koutstaal, B.P., Herman, P.M.J., Beeftink, W.G., Markusse, M.M. & De Munck, W. (1995) Seed dispersal of halophytes in tidal salt marshes. Journal of Ecology, 83, 559-567.
50. Husband, B.C. & Barrett, S.C.H. (1996) A metapopulation perspective in plant population biology. Journal of Ecology, 84, 461-469.
51. Jarne, P. & Lagoda, P.J.L. (1996) Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution, 11, 424-429.
52. Johansson, M.E. & Nilsson, C. (1993) Hydrochory, population dynamics and distribution of the clonal aquatic plant Ranunculus lingua. Journal of Ecology, 81, 81-91.
53. Kimura, M. (1953) 'Stepping stone' model of population. Annual Report of the National Institute of Genetics, Japan, 3, 62-63.
54. Kreitman, M.E. & Akashi, H. (1995) Molecular evidence for natural selection. Annual Review of Ecology and Systematics, 26, 403-422.
55. Kremer, A., Petit, R.J., Zanetto, A., Fougere, V., Ducousso, A., Wagner, D.B. & Chauvin, C. (1991) Nuclear and organelle gene diversity in Quercus robur and Q. petraea. Genetic Variation in European Populations of Forest Trees (eds G. Müller-Starck & M. Ziehe), pp. 141-166. Sauerländers-Verlag, Frankfurt am Main, Germany.
56. Lönn, M., Prentice, H.C. & Tegelström, H. (1995) Genetic differentiation in Hippocrepis emerus (Leguminosae): allozyme and DNA fingerprint variation in disjunct Scandinavian populations. Molecular Ecology, 4, 39-48.
57. Lynch, M. & Crease, T. (1990) The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution, 7, 377-394.
58. Lynch, M. & Milligan, B.G. (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91-99.
59. McCauley, D.E. (1994) Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants. Proceedings of the National Academy of Sciences USA, 91, 8127-8131.
60. McCauley, D.E. (1995) The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends in Ecology and Evolution, 10, 198-202.
61. McCauley, D.E. (1997) The relative contributions of seed and pollen movement to the local genetic structure of Silene alba. Journal of Heredity, 88, 257-263.
62. McCauley, D.E., Raveill, J. & Antonovics, J. (1995) Local founding events as determinants of genetic structure in a plant metapopulation. Heredity, 75, 630-636.
63. Mader, E., van Vierssen, W. & Schwenk, K. (1998) Clonal diversity in the submerged macrophyte Potamogeton pectinatus L. inferred from nuclear and cytoplasmic variation. Aquatic Botany, 62, 147-160.
64. Mantel, N. (1967) The detection of disease clustering and a generalised regression approach. Cancer Research, 27, 209-220.
65. Masson-Gamer, R.J., Holsinger, K.E. & Jansen, R.K. (1995) Chloroplast DNA haplotype variation within and among populations of Coreopsis grandiflora (Asteraceae). Molecular Biology and Evolution, 12, 371-381.
66. Meagher, T.R. & Thompson, E. (1987) Analysis of parentage for naturally established seedlings of Chamaelirium luteum (Liliaceae). Ecology, 68, 803-812.
67. Michalakis, Y. & Excoffier, L. (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics, 142, 1061-1064.
68. Mogensen, H.L. (1996) The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany, 83, 383-404.
69. Neale, D.B., Saghai-Maroof, M.A., Allard, R.W., Zhang, Q. & Jorgensen, R.A. (1986) Chloroplast DNA diversity in populations of wild and cultivated barley. Genetics, 120, 1105-1110.
70. Nei, M. (1972) Genetic distance between populations. American Naturalist, 106, 283-292.
71. Nei, M. (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences USA, 70, 3321-3323.
72. Neigel, J.E. (1997) A comparison of alternative strategies for estimating gene flow from genetic markers. Annual Review of Ecology and Systematics, 28, 105-128.
73. Nevo, E., Zohary, D., Brown, A.H.D. & Haber, M. (1979) Genetic diversity and environmental associations of wild barley, Hordeum spontaneum in Israel. Evolution, 33, 815-833.
74. Nilsson, C. Gardfjell, M. & Grelsson, G. (1991) Importance of hydrochory in structuring plant communities along rivers. Canadian Journal of Botany, 69, 2631-2633.
75. Olivieri, I., Couvet, D. & Gouyon, P.-H. (1990) The genetics of transient populations: research at the metapopulation level. Trends in Ecology and Evolution, 5, 207-210.
76. Olmstead, R.G. & Palmer, J.D. (1994) Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany, 81, 1205-1224.
77. Ouborg, N.J. (1993) On the relative contribution of genetic erosion to the chance of population extinction. PhD Thesis. University of Utrecht, Utrecht, the Netherlands.
78. Petit, R.J., Kremer, A. & Wagner, D.B. (1993a) Finite island model for organelle and nuclear genes in plants. Heredity, 71, 630-641.
79. Petit, R.J., Kremer, A. & Wagner, D.B. (1993b) Geographic structure of chloroplast DNA polymorphisms in European oaks. Theoretical and Applied Genetics, 87, 122-128.
80. Porter, A.H. & Geiger, H. (1995) Limitations to the inference of gene flow at regional scales - an example from the Pieris napi group (Lepidoptera: Pieridae) in Europe. Biological Journal of the Linnean Society, 54, 329-348.
81. Rannala, B. & Hartigan, J. (1996) Estimating gene flow in island populations. Genetical Research, 67, 147-158.
82. Rannala, B. & Mountain, J. (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA, 94, 9197-9201.
83. Raybould, A.F., Mogg, R.J., Aldam, C., Gliddon, C.J., Thorpe, R.S. & Clarke, R.T. (1998) The genetic structure of sea beet (Beta vulgaris ssp. maritima) populations. III. Detection of isolation by distance at microsatellite loci. Heredity, 80, 127-132.
84. Raybould, A.F., Mogg, R.J. & Clarke, R.T. (1996) The genetic structure of Beta vulgaris ssp. maritima (sea beet) populations: RFLPs and isozymes show different patterns of gene flow. Heredity, 77, 245-250.
85. Raybould, A.F., Mogg, R.J. & Gliddon, C.J. (1997) The genetic structure of Beta vulgaris ssp. maritima (sea beet) populations. II. Differences in gene flow estimated from RFLP and isozyme loci are habitat-specific. Heredity, 78, 532-538.
86. Rousset, F. (1997) Genetic differentiation and estimation of gene flow under isolation by distance. Genetics, 145, 1219-1228.
87. Ruckelshaus, M.H. (1996) Estimation of genetic neighborhood parameters from pollen and seed dispersal in the marine angiosperm Zostera marina L. Evolution, 50, 856-864.
88. Schaal, B.A. (1980) Measurement of gene flow in Lupinus texensis. Nature, 284, 450-451.
89. Silvertown, J. (1991) Dorothy's dilemma and the unification of plant population biology. Trends in Ecology and Evolution, 6, 346-348.
90. Slatkin, M. (1977) Gene flow and genetic drift in a species subject to frequent local extinction. Theoretical Population Biology, 12, 253-262.
91. Slatkin, M. (1985a) Gene flow in natural populations. Annual Review of Ecology and Systematics, 16, 393-430.
92. Slatkin, M. (1985b) Rare alleles as indicators of gene flow. Evolution, 39, 53-65.
93. Slatkin, M. (1987) Gene flow and the geographic structure of natural populations. Science, 236, 787-792.
94. Slatkin, M. (1991) Inbreeding coefficients and coalescent times. Genetical Research Cambridge, 58, 167-192.
95. Slatkin, M. (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264-279.
96. Slatkin, M. (1995) Measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457-462.
97. Slatkin, M. & Barton, N.H. (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution, 43, 1349-1368.
98. Slatkin, M. & Maddison, W. (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics, 123, 603-613.
99. Slatkin, M. & Maddison, W. (1990) Detecting isolation by distance using phylogenies of genes. Genetics, 126, 249-260.
100. Stewart, C.N. & Prakash, C.S. (1998) Chloroplast-transgenic plants are not a gene flow panacea. Nature Biotechnology, 16, 401.
101. Strand, A.E., Leebens-Mack, J. & Milligan, B.G. (1997) Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology, 6, 113-118.
102. Strand, A.E., Milligan, B.G. & Pruitt, C.M. (1996) Are populations islands? Analysis of chloroplast DNA variation in Aquilegia. Evolution, 50, 1822-1829.
103. Tanksley, S.D. (1993) Mapping polygenes. Annual Review of Genetics, 27, 205-233.
104. Thiede, D.A. & Augspurger, C.K. (1996) Intraspecific variation in seed dispersion of Lepidium campestre (Brassicaceae). American Journal of Botany, 83, 856-866.
105. Tufto, J., Engen, S. & Hindar, K. (1996) Inferring patterns of migration from gene frequencies under equilibrium conditions. Genetics, 144, 1911-1921.
106. Van Dorp, D. (1996) Seed dispersal in agricultural habitats and the restoration of species-rich meadows. PhD Thesis. Agricultural University of Wageningen, Wageningen, the Netherlands.
107. Van Dorp, D., van den Hoek, W.P.M. & Daleboudt, C. (1996) Seed dispersal capacity of six perennial grassland species measured in a wind-tunnel at varying wind speed and height. Canadian Journal of Botany, 74, 1956-1963.
108. Voelker, R.A., Schaffer, H.E. & Mukai, T. (1980) Spontaneous allozyme mutations in Drosophila melanogaster: rate of occurrence and nature of mutants. Genetics, 94, 961-968.
109. Wade, M.J. & McCauley, D.E. (1988) Extinction and recolonization: their effects on the genetic differentiation of local populations. Evolution, 42, 995-1005.
110. Wang, X.R. & Szmidt, A.E. (1994) Hybridization and chloroplast DNA variation in a Pinus species complex from Asia. Evolution, 48, 1020-1031.
111. Weber, J.E. & Wong, C. (1993) Mutation of human short tandem repeats. Human Molecular Genetics, 2, 1123-1128.
112. Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates, Sunderland, MA.
113. Weir, B.S. & Cockerham, C.C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
114. Weissing, K., Nybom, H., Wolff, K. & Meyer, W. (1995) DNA Fingerprinting in Plants and Fungi, CRC Press, Boca Ratan, NJ.
115. Whitlock, M.C. (1992) Nonequilibrium population structure in forked fungus beetles: extinction, colonisation, and the genetic variance among populations. American Naturalist, 139, 952-970.
116. Whitlock, M.C. & McCauley, D.E. (1990) Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution, 44, 1717-1724.
117. Williamson, M. (1996) Biological Invasions. Chapman & Hall, London, UK.
118. Wolff, K., El-Akkad, S. & Abbott, R.J. (1997) Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour. Molecular Ecology, 6, 365-372.
119. Wright, S. (1931) Evolution in mendelian populations. Genetics, 16, 97-159.
120. Wright, S. (1940) Breeding structure of populations in relation to speciation. American Naturalist, 74, 232-248.
121. Wright, S. (1943) Isolation by distance. Genetics, 28, 114-138.
122. Wright, S. (1978) Evolution and the Genetics of Populations, Vol. 4. University of Chicago Press, Chicago, III.