A potential bias in the temporal method for estimating Ne in admixed populations under natural selection

Molecular Ecology

Volumn 16, Issue 11, 2007, Pages 2261-2271

  Araki, Hitoshi ^a   Waples, Robin S ^b   Blouin, Michael S ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

Effective population size; Hatchery program; Migration; Natural selection; Steelhead; Temporal method

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EPIDEMIOLOGY; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC SELECTION; GENETICS; GENOTYPE; MALE; MONTE CARLO METHOD; POPULATION DENSITY; RAINBOW TROUT;

ANIMALS; BIAS (EPIDEMIOLOGY); COMPUTER SIMULATION; FEMALE; GENOTYPE; LINKAGE DISEQUILIBRIUM; MALE; MICROSATELLITE REPEATS; MODELS, GENETIC; MONTE CARLO METHOD; ONCORHYNCHUS MYKISS; POPULATION DENSITY; SELECTION (GENETICS);

ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 34250157763     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03307.x     Document Type: Article

References (37)

1. Araki H, Ardren WR, Olsen E, Cooper B, Blouin MS (2006) Reproductive success of captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River. Conservation Biology, 21, 181 190.
2. Araki H, Waples RS, Ardren WR, Cooper B, Blouin MS (2007) Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology, 16, 953 WR, Kapuscinski AR (2003) Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout. Molecular Ecology, 12, 35 49.
3. Bartley D, Bagley M, Gall G, Bentley M (1992) Use of linkage disequilibrium data to estimate effective size of hatchery and natural fish populations. Conservation Biology, 6, 365 375.
4. Berthier P, Beaumont MA, Cornuet JM, Luikart G (2002) Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics, 160, 741 751.
5. Bucci G, Vendramin GG, Lelli L, Vicario F (1997) Assessing the genetic divergence of Pinus leucodermis Ant. endangered populations: use of molecular markers for conservation purposes. Theoretical and Applied Genetics, 95, 1138 1146.
6. Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH (2006) Comparative population structure of Cynopterus fruit bats in peninsular Malaysia and southern Thailand. Molecular Ecology, 15, 29 47.
7. Charlesworth D, Charlesworth B, Morgan MT (1995) The pattern of neutral molecular variation under the background selection model. Genetics, 141, 1619 1632.
8. Crow JF, Kimura M (1970) An Introduction to Population Genetics Theory. Harper & Row, New York.
9. Duchesne P, Bernatchez L (2002) An analytical investigation of the dynamics of inbreeding in multi-generation supportive breeding. Conservation Genetics, 3, 45 58.
10. Fleming IA, Peterson E (2001) The ability of released hatchery salmonids to breed and contribute to the natural productivity of wild populations. Nordic Journal of Freshwater Research, 75, 71 98.
11. Goldringer I, Bataillon T (2004) On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection. Genetics, 168, 563 568.
12. Hedrick PW (2005) Genetics of Populations. Jones & Bartlett, Boston.
13. Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genetical Research, 38, 209 216.
14. Joron M, Brakefield PM (2003) Captivity masks inbreeding effects on male mating success in butterflies. Nature, 424, 191 194.
15. Krimbas CB, Tsakas S (1971) The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide control - selection or drift? Evolution, 25, 454 460.
16. McGinnity P, Prodohl P, Ferquson A et al. (2003) Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. Proceedings of the Royal Society of London. Series B, Biological Sciences, 270, 2443 2450.
17. Miller CR, Waits LP (2003) The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation. Proceedings of National Academy of Sciences, USA, 100, 4334 4339.
18. Mousseau TA, Sinervo B, Endler JA (2000) Adaptive Genetic Variation in the Wild. Oxford University Press, New York.
19. Nei M, Li WH (1973) Linkage disequilibrium in subdivided populations. Genetics, 75, 213 219.
20. Nei M, Tajima F (1981) Genetic drift and estimation of effective population size. Genetics, 98, 625 640.
21. Piggott MP, Banks SC, Taylor AC (2006) Population structure of brush-tailed rock-wallaby (Petrogale penicillata) colonies inferred from analysis of faecal DNA. Molecular Ecology, 15, 93 105.
22. Pollak E (1983) A new method for estimating the population size from allele frequency changes. Genetics, 104, 531 548.
23. Ryman N, Laikre L (1991) Effects of supportive breeding on the genetically effective population size. Conservation Biology, 5, 325 329.
24. Santiago E, Caballero A (1998) Effective size and polymorphism of linked neutral loci in populations under directional selection. Genetics, 149, 2105 2117.
25. Sinnock P (1975) The Wahlund effect for the two-locus model. American Naturalist, 109, 565 570.
26. Tallmon DA, Luikart G, Waples RS (2004) The alluring simplicity and complex reality of genetic rescue. Trends in Ecology & Evolution, 19, 489 496.
27. Turner TF, Salter LA, Gold JR (2001) Temporal-method estimates of Ne from highly polymorphic loci. Conservation Genetics, 2, 297 308.
28. Vitalis R, Couvet D (2001) estim 1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities. Molecular Ecology Notes, 1, 354 356.
29. Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetic Research, 78, 243 257.
30. Wang J, Ryman N (2001) Genetic effects of multiple generations of supportive breeding. Conservation Biology, 15, 1619 1631.
31. Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics, 163, 429 446.
32. Waples RS (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, 121, 379 391.
33. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14, 3335 3352.
34. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7, 167 184.
35. Waples RS, Do C (1994) Genetic risk associated with supplementation of Pacific salmonids: captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences, 51 (Suppl. 1 310 329.
36. Waples RS, Smouse PE (1990) Gametic disequilibrium analysis as a means of identifying mixtures of salmon populations. American Fisheries Society Symposium, 7, 439 458.
37. Weir BS (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Sunderland, Massachusetts.