Calculating N e and N e/N in age-structured populations: A hybrid Felsenstein-Hill approach

Ecology

Volumn 92, Issue 7, 2011, Pages 1513-1522

  Waples, Robin S ^a   Do, Chi ^a   Chopelet, Julien ^b  

^a NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Age structured population; Effective number of breeders; Leslie matrix; Overdispersed variance; Overlapping generations; Reproductive success; Sex reversal; Software

Indexed keywords

AGE STRUCTURE; ECOLOGICAL MODELING; EFFECTIVE POPULATION SIZE; FERTILITY; GENERATION TIME; HYBRID; MATHEMATICAL ANALYSIS; MATRIX; NEON; NITROGEN; POPULATION STRUCTURE; REPRODUCTIVE SUCCESS; SOFTWARE; SURVIVAL;

AGE DISTRIBUTION; ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; ECOSYSTEM; FEMALE; MALE; POPULATION DENSITY; REPRODUCIBILITY; REPRODUCTION; SEX RATIO;

AGE DISTRIBUTION; ANIMALS; COMPUTER SIMULATION; ECOSYSTEM; FEMALE; MALE; MODELS, BIOLOGICAL; POPULATION DENSITY; REPRODUCIBILITY OF RESULTS; REPRODUCTION; SEX RATIO; SOFTWARE;

EID: 79960442320     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/10-1796.1     Document Type: Article

References (47)

1. Allsop, D. J., and S. A. West. 2003. Changing sex at the same relative body size. Nature 425:783-784. (Pubitemid 37351455)
2. Anderson, E. C., and K. K. Dunham. 2005. SPIP 1.0: a program for simulating pedigrees and genetic data in agestructured populations. Molecular Ecology Notes 5:459-461. (Pubitemid 40772406)
3. Berkeley, S. A., C. Chapman, and S. M. Sogard. 2004. Maternal age as a determinant of larval growth and survival in a marine fish, Sebastes melanops. Ecology 85:1258-1264. (Pubitemid 39188082)
4. Caballero, A. 1994. Developments in the prediction of effective population size. Heredity 73:657-679.
5. Charlesworth, B. 1980. Evolution in age-structured populations. Cambridge University Press, Cambridge, UK.
6. Charnov, E. L. 1982. The theory of sex allocation. Princeton University Press, Princeton, New Jersey, USA.
7. Cochran, M. E., and S. Ellner. 1992. Simple methods for calculating age-based life history parameters for stagestructured populations. Ecological Monographs 62:345-364. (Pubitemid 23396195)
8. Crow, J. F., and C. Denniston. 1988. Inbreeding and variance effective population numbers. Evolution 42:482-495.
9. Crow, J. F., and M. Kimura. 1970. An introduction to population genetics theory. Harper and Row, New York, New York, USA.
10. Crow, J. F., and N. E. Morton. 1955. Measurement of gene frequency drift in small populations. Evolution 9:202-214.
11. Engen, S., R. Lande, and B.-E. Sæther. 2005. Effective size of a fluctuating age-structured population. Genetics 170:941-954. (Pubitemid 40980693)
12. Engen, S., R. Lande, B.-E. Sæther, and P. Gienapp. 2010. Estimating the ratio of effective to actual size of an agestructured population from individual demographic data. Journal of Evolutionary Biology 23:1148-1158.
13. Engen, S., T. H. Ringsby, B.-E. Sæther, R. Lande, H. Jensen, M. Lillegard, and H. Ellegren. 2007. Effective size of fluctuating populations with two sexes and overlapping generations. Evolution 61:1885-1973.
14. Felsenstein, J. 1971. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 68:581-597.
15. Hard, J. J., L. S. Mills, and J. M. Peek. 2006. Genetic implications of reduced survival of male red deer (Cervus elaphus) under harvest. Wildlife Biology 12:427-441. (Pubitemid 46033191)
16. Harris, R. B., and F. W. Allendorf. 1989. Genetically effective population size of large mammals: an assessment of estimators. Conservation Biology 3:181-191. (Pubitemid 20422290)
17. Hill, W. G. 1972. Effective size of population with overlapping generations. Theoretical Population Biology 3:278-289.
18. Hill, W. G. 1979. A note on effective population size with overlapping generations. Genetics 92:317-322.
19. Johnson, D. L. 1977. Inbreeding in populations with overlapping generations. Genetics 87:581-591. (Pubitemid 8245292)
20. Jones, A. G., C. M. Small, K. A. Paczolt, and N. L. Ratterman. 2010. A practical guide to methods of parentage analysis. Molecular Ecology Resources 10:6-30.
21. Jorde, P. E., and N. Ryman. 1995. Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 139:1077-1090.
22. Jørgensen, C., at el. 2007. Managing evolving fish stocks. Science 318:1247-1248.
23. Kimura, M., and J. F. Crow. 1963. The measurement of effective population number. Evolution 17:279-288.
24. Lee, A. M., S. Engen, and B.-E. Sæther. 2011. The influence of persistent individual differences and age at maturity on effective population size. Proceedings of the Royal Society of London B, in press. [doi: 10.1098/rsbp.2011.0283]
25. Nei, M., and M. Murata. 1966. Effective population size when fertility is inherited. Genetical Research 8:257-260.
26. Nomura, T. 2008. Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evolutionary Applications 1:462-474.
27. Nunney, L. 1991. The influence of age structure and fecundity on effective population size. Proceedings of the Royal Society B 246:71-76. (Pubitemid 23400177)
28. Nunney, L. 1993. The influence of mating system and overlapping generations on effective population size. Evolution 47:1329-1341. (Pubitemid 2078213)
29. Nunney, L. 1996. The influence of variation in female fecundity on effective population size. Biological Journal of the Linnaean Society 59:411-425. (Pubitemid 27028063)
30. Nunney, L. 2002. The effective size of annual plant populations: The interaction of a seed bank with fluctuating population size in maintaining genetic variation. American Naturalist 160:195-204. (Pubitemid 34805518)
31. Palstra, F., M. F. O'Connell, and D. E. Ruzzante. 2009. Age structure, changing demography and effective population size in Atlantic salmon (Salmo salar). Genetics 182:1233-1249.
32. Richard, M., J. LeComte, M. de Fraipont, and J. Clobert. 2005. Age-specific mating strategies and reproductive senescence. Molecular Ecology 14:3147-3155.
33. Ryman, N., R. Bachus, C. Reuterwall, and M. H. Smith. 1981. Effective population size, generation interval, and potential loss of genetic variability in game species under different hunting regimes. Oikos 36:257-266.
34. Tallmon, D. A., A. Koyuk, G. Luikart, and M. A. Beaumont. 2008. ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Molecular Ecology Resources 8:299-301. (Pubitemid 351224892)
35. Vitalis, R., S. Glémin, and I. Olivieri. 2004. When genes go to sleep: The population genetic consequences of seed dormancy and monocarpic perenniality. American Naturalist 163:295-311. (Pubitemid 38335224)
36. Wang, J. 2009. A new method for estimating effective population size from a single sample of multilocus genotypes. Molecular Ecology 18:2148-2164.
37. Waples, R. S. 1990. Conservation genetics of Pacific salmon. II. Effective population size and the rate of loss of genetic variability. Journal of Heredity 81:267-276.
38. Waples, R. S. 2002a. Evaluating the effect of stage-specific survivorship on the Ne/N ratio. Molecular Ecology 11:1029-1037. (Pubitemid 34635173)
39. Waples, R. S. 2002b. The effective size of fluctuating salmon populations. Genetics 161:783-791. (Pubitemid 34705417)
40. Waples, R. S. 2006. Seed banks, salmon, and sleeping genes: Effective population size in semelparous, age-structured species with fluctuating abundance. American Naturalist 167:118-135. (Pubitemid 43039431)
41. Waples, R. S. 2010. Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Molecular Ecology Resources 10:785-796.
42. Waples, R. S., and C. Do. 2008. LDNE: A program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources 8:753-756. (Pubitemid 351989517)
43. Waples, R. S., and R. K. Waples. 2011. Inbreeding effective population size and parentage analysis without parents. Molecular Ecology Resources 11(Supplement 1):162-171.
44. Waples, R. S., and M. Yokota. 2007. Temporal estimates of effective population size in species with overlapping generations. Genetics 175:219-233. (Pubitemid 46168567)
45. Warner, R. R. 1975. The adaptive significance of sequential hermaphroditism in animals. American Naturalist 109:61-82.
46. Wright, S. 1938. Size of population and breeding structure in relation to evolution. Science 87:430-431.
47. Zhdanova, O. L., and A. I. Pudovkin. 2008. NbHetEx: A program to estimate the effective number of breeders. Journal of Heredity 99:694-695.