Accounting for missing data in the estimation of contemporary genetic effective population size (Ne)

Molecular Ecology Resources

Volumn 13, Issue 2, 2013, Pages 243-253

  Peel, D ^a   Waples, R S ^b   Macbeth, G M ^b   Do, C ^c   Ovenden, J R ^b  

^a CSIRO   (Australia)

^b ALASKA FISHERIES SCIENCE CENTER   (United States)

^c NORTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

Effective population size; Linkage Disequilibrium; Missing data; Ne; Temporal method

Indexed keywords

ALLELE; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EPIDEMIOLOGY; GENE LINKAGE DISEQUILIBRIUM; GENOTYPE; POPULATION DENSITY; POPULATION GENETICS; REGRESSION ANALYSIS; STANDARD;

ALLELES; COMPUTER SIMULATION; GENETICS, POPULATION; GENOTYPE; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POPULATION DENSITY; REGRESSION ANALYSIS; SELECTION BIAS;

EID: 84873999147     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12049     Document Type: Article

References (24)

1. e from temporally spaced samples using a coalescent-based likelihood. Genetics, 170, 955-967.
2. Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genetical Research, 38, 209-216.
3. Jehle R, Arntzen, JW et al. (2001) The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus). Molecular Ecology, 10, 839-850.
4. Jorde PE, Ryman N (2007) Unbiased estimator for genetic drift and effective population size. Genetics, 177, 927-935.
5. Krimbas CB, Tsakas S (1971) The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide control - Selection of drift?. Evolution, 25, 454-460.
6. Leberg P (2005) Genetic approaches for estimating the effective size of populations. Journal of Wildlife Management, 69, 1385-1399.
7. Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based methods. Conservation Genetics, 11, 355-373.
8. Macbeth GM, Broderick D, Ovenden JR, Buckworth RC (2011) Likelihood-based genetic mark-recapture estimates when genotype samples are incomplete and contain typing errors. Theoretical Population Biology, 80, 185-196.
9. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of animals. Genetics, 89, 583-590.
10. Nei M, Tajima F (1981) Genetic drift and estimation of effective population size. Genetics, 98, 625-640.
11. Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish and Fisheries, 9, 450-461.
12. Nomura T (2008) Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evolutionary Applications, 1, 462-474.
13. Ovenden JR, Peel D, Street R et al. (2007) The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Molecular Ecology, 16, 127-138.
14. Pollak E (1983) A new method for estimating the effective population size from allele frequency changes. Genetics, 104, 531-548.
15. Tallmon DA, Koyuk A, Luikart G, Beaumont MA (2008) OneSamp: a program to estimate effective population size using approximate Bayesian computation. Molecular Ecology Resources, 8, 299-301.
16. Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research, 78, 243-257.
17. Wang J (2005) Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society, Series B: Biological Sciences, 360, 1395-1409.
18. Wang J (2009) A new method for estimating effective population size from a single sample of multilocus genotypes. Molecular Ecology, 18, 2148-2164.
19. Waples RS (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, 121, 379-391.
20. 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.
21. Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753-756.
22. Weir BS (1979) Inferences about linkage disequilibrium. Biometrics, 35, 235-254.
23. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
24. Zhdanova OL, Pudovkin AI (2008) Nb_HetEx: a program to estimate the effective number of breeders. Journal of Heredity, 99, 694-695.