Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size

Molecular Ecology Resources

Volumn 10, Issue 5, 2010, Pages 785-796

  Waples, Robin S ^a  

^a NORTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

Age structure; Contemporary Ne; Long term Ne; Metapopulation; Migration

Indexed keywords

EID: 77955722729     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02876.x     Document Type: Article

References (62)

1. Avise JC, Ball RM, Arnold J. Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Molecular Biology and Evolution 1988, 5:331-344.
2. Balloux F. EASYPOP (version 1.7): a computer program for population genetics simulations. Journal of Heredity 2001, 92:301-302.
3. Balloux F. Heterozygote excess in small populations and the heterozygote-excess effective population size. Evolution 2004, 58:1891-1900.
4. Beerli P, Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences USA 2001, 98:4563-4568.
5. Berendonk TU, Spitze K, Kerfoot WC. Ephemeral metapopulations show high genetic diversity at regional scales. Ecology 2009, 90:2670-2675.
6. Berthier K, Charbonnel N, Glaan M, Chaval Y, J-Cosson F. Migration and recovery of the genetic diversity during the increasing density phase in cyclic vole populations. Molecular Ecology 2006, 15:2665-2676.
7. Biro PA, Dingemanse NJ. Sampling bias resulting from animal personality. Trends in Ecology and Evolution 2009, 24:66-67.
8. Caballero A. Developments in the prediction of effective population size. Heredity 1994, 73:657-679.
9. Charlesworth B. Evolution in Age-Structured Populations 1980, Cambridge University Press, Cambridge, UK
10. Crow JF. Breeding structure of populations. II. Effective breeding number. Statistics and Mathematics in Biology 1954, 543-556. Kempthorne OBancroft TAGowen JWLush JL. eds, Iowa State College Press, Ames, IA
11. Crow JF, Denniston C. Inbreeding and variance effective population numbers. Evolution 1988, 42:482-495.
12. Engen S, Lande R, B-Saether E. Effective size of a fluctuating age-structured population. Genetics 2005, 170:941-954.
13. Felsenstein J. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 1971, 68:581-597.
14. Fraser DJ, Hansen MM, Ostergaard S. Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Molecular Ecology 2007, 16:3866-3889.
15. Gaggiotti OE, Foll M. Quantifying population structure using the F model. Molecular Ecology Resources 2010, 10:821-830.
16. Gaggiotti OE, Vetter RD. Effect of life history strategy, environmental variability, and overexploitation on the genetic diversity of pelagic fish populations. Canadian Journal of Fisheries and Aquatic Sciences 1999, 56:1376-1388.
17. Hedrick PW, Gilpin ME. Genetic effective size of a metapopulation. Metapopulation Biology: Ecology, Genetics, and Evolution 1997, 165-181. Hanski I, Gilpin M. eds, Academic Press, San Diego
18. Henn BM, Gignoux CR, Feldman MW, Mountain JL. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Molecular Biology and Evolution 2009, 26:217-230.
19. Hey J, Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 2004, 167:747-760.
20. Hill WG. Effective size of populations with overlapping generations. Theoretical Population Biology 1972, 3:278-289.
21. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution 2005, 22:1561-1568.
22. Hoffman EA, Schueler FW, Blouin MS. Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog. Evolution 2004, 58:2536-2545.
23. Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C. The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. American Journal of Human Genetics 2003, 72:659-670.
24. Johnson DL. Inbreeding in populations with overlapping generations. Genetics 1977, 87:581-591.
25. Jorde PE, Ryman N. Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 1995, 139:1077-1090.
26. Kuparinen A, Tufto J, Consuegra S, Hindar K, Merila J, de LeanizCG. Effective size of an Atlantic salmon (Salmo salar L.) metapopulation in Northern Spain. Conservation Genetics 2009, http://dx.doi.org/10.1007/s10592-009-9945-6, DOI: 10.1007/s10592-009-9945-6 (published online June 2009
27. Leberg P. Genetic approaches for estimating the effective size of populations. Journal of Wildlife Management 2005, 69:1385-1399.
28. Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 2010, 11:355-373.
29. Morrissey MB, de Kerckhove DT. The maintenance of genetic variation due to asymmetric gene flow in dendritic metapopulations. American Naturalist 2009, 174:875-889.
30. Nei M. Estimation of heterozygosity and genetic distance from a small number of individuals. Genetics 1978, 89:583-590.
31. Nunney L. The effective size of a hierarchically-structured population. Evolution 1999, 53:1-10.
32. Nunney L. The effective size of annual plant populations: the interaction of a seed bank with fluctuating population size in maintaining genetic variation. American Naturalist 2002, 160:195-204.
33. Palstra FP, Ruzzante DE. Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population performance? Molecular Ecology 2008, 17:3428-3447.
34. Ruegg KC, Anderson EC, Baker CS, Vant M, Jackson JA, Palumbi SR. Are Antarctic minke whales unusually abundant because of 20th century whaling? Molecular Ecology 2010, 19:281-291.
35. Storz JF, Beaumont MA. Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 2002, 56:154-166.
36. Tenesa A, Navarro P, Hayes BJ. Recent human effective population size estimated from linkage disequilibrium. Genome Research 2007, 17:520-526.
37. Tufto J, Hindar K. Effective size in management and conservation of subdivided populations. Journal of Theoretical Biology 2003, 222:273-281.
38. Vitalis R, Glémin S, Olivieri I. When genes go to sleep: the population genetic consequences of seed dormancy and monocarpic perenniality. American Naturalist 2004, 163:295-311.
39. Vuilleumier S, Yearsley JM, Perrin N. The fixation of locally beneficial alleles in a metapopulation. Genetics 2008, 178:467-475.
40. Vuilleumier S, Goudet J, Perrin N. Evolution in heterogeneous populations: from migration models to fixation probabilities. in revision
41. Wade MJ. An Experimental Study of Group Selection 1975, PhD Dissertation, Univ. Chicago, Chicago, IL
42. Wakeley J, Sargsyan O. Extensions of the coalescent effective population size. Genetics 2009, 181:341-345.
43. Wang J. Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society, Series B 2005, 360:1395-1409.
44. Wang J, Caballero A. Developments in predicting the effective size of subdivided populations. Heredity 1999, 82:212-226.
45. Wang J, Whitlock MC. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 2003, 163:429-446.
46. Waples RS. Conservation genetics of Pacific salmon. III. Estimating effective population size. Journal of Heredity 1990, 81:277-289.
47. Waples RS. Effective size of fluctuating salmon populations. Genetics 2002a, 161:782-791.
48. Waples RS. Definition and estimation of effective population size in the conservation of endangered species. Population Viability Analysis 2002b, 147-168. Beissinger SRMcCullough DR. eds, University of Chicago Press, Chicago, IL
49. Waples RS. Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology 2005, 14:3335-3352.
50. Waples RS. Seed banks, salmon, and sleeping genes: effective population size in semelparous, age-structured species with fluctuating abundance. American Naturalist 2006, 167:118-135.
51. Waples RS, Do C. Genetic risk associated with supplementation of Pacific salmonids: captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences. 1994, 51(Suppl. 1):310-329.
52. Waples RS, Do C. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 2010, 3:244-262.
53. Waples RS, Yokota M. Temporal estimates of effective population size in species with overlapping generations. Genetics 2007, 175:219-233.
54. Wares JP, Pringle PM. Drift by drift: effective population size is limited by advection. BMC Evolutionary Biology 2008, 8:235. http://dx.doi.org/10.1186/1471-2148-8-235, doi:10.1186/1471-2148-8-235
55. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38:1358-1370.
56. Whitlock MC. Temporal fluctuations in demographic parameters and the genetic variance among populations. Evolution 1992, 46:608-615.
57. Whitlock MC. Fixation probability and time in subdivided populations. Genetics 2003, 164:767-779.
58. Whitlock MC. Selection and drift in metapopulations. Ecology, Genetics and Evolution of Metapopulations 2004, 153-175. Hanski IGaggiotti OE. eds, Elsevier Academic Press, London
59. Whitlock MC, Barton NH. The effective size of a subdivided population. Genetics 1997, 146:427-441.
60. Whitlock MC, Gomulkiewicz R. Probability of fixation in a heterogeneous environment. Genetics 2005, 171:1407-1417.
61. Wright S. Evolution in Mendelian populations. Genetics 1931, 16:97-159.
62. Wright S. Size of population and breeding structure in relation to evolution. Science (USA) 1938, 87:430-431.