NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

Molecular Ecology Resources

Volumn 14, Issue 1, 2014, Pages 209-214

  Do, C ^a   Waples, R S ^b   Peel, D ^c   Macbeth, G M ^d   Tillett, B J ^e   Ovenden, J R ^f  

^a NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^b NATIONAL MARINE FISHERIES SERVICE   (United States)

^c CSIRO   (Australia)

^d DEPARTMENT OF AGRICULTURE AND FISHERIES   (Australia)

^e UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^f UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Heterozygote excess; Linkage disequilibrium; Molecular coancestry; Plan I and II temporal sampling

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENE LINKAGE DISEQUILIBRIUM; HETEROZYGOTE-EXCESS; METHODOLOGY; MOLECULAR COANCESTRY; PLAN I AND II TEMPORAL SAMPLING; POPULATION DENSITY;

HETEROZYGOTE-EXCESS; LINKAGE DISEQUILIBRIUM; MOLECULAR COANCESTRY; PLAN I AND II TEMPORAL SAMPLING;

COMPUTATIONAL BIOLOGY; POPULATION DENSITY; SOFTWARE;

EID: 84890151430     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12157     Document Type: Article

References (20)

1. Balloux F (2001) EASYPOP (version 1.7): a computer program for population genetics simulations. Journal of Heredity, 92, 301-302.
2. Charlesworth B (2009) Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10, 195-205.
3. Jorde PE, Ryman N (2007) Unbiased estimator for genetic drift and effective population size. Genetics, 177, 927-935.
4. Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics, 11, 255-373.
5. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
6. Nei M, Tajima F (1981) Genetic drift and estimation of effective population size. Genetics, 1981, 625-640.
7. Nomura T (2008) Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evolutionary Applications, 1, 462-474.
8. Ovenden J, 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.
9. Palstra FP, Fraser DJ (2012) Effective/census population size ratio estimation: a compendium and appraisal. Ecology and Evolution, 2, 2357-2365.
10. Peel D, Waples RS, Macbeth GM, Do C, Ovenden JR (2013) Accounting for missing data in the estimation of contemporary genetic effective population size (Ne). Molecular Ecology Resources, 13, 243-253.
11. Pollak E (1983) A new method for estimating the effective population size from allele frequency changes. Genetics, 104, 531-548.
12. Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution, 22, 25-33.
13. Wang JL (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research Cambridge, 78, 243-257.
14. Wang JL (2009) A new method for estimating effective population sizes from a single sample of multilocus genotypes. Molecular Ecology, 18, 2148-2164.
15. Waples RS (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, 121, 379-391.
16. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14, 3335-3352.
17. Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753-756.
18. Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications, 3, 244-262.
19. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
20. Zhdanova O, Pudovkin AI (2008) Nb_HetEx: a program to estimate the effective number of breeders. Journal of Heredity, 99, 694-695.