Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution

Genetic methods are routinely used to estimate contemporary effective population size (Ne) in natural populations, but the vast majority of applications have used only the temporal (two‐sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single‐sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low‐frequency alleles upwardly bias , but a simple rule can reduce bias to

[1]  A. Pudovkin,et al.  Sampling properties of the heterozygote-excess estimator of the effective number of breeders , 2010, Conservation Genetics.

[2]  Jinliang Wang.  A new method for estimating effective population sizes from a single sample of multilocus genotypes , 2009, Molecular ecology.

[3]  James R. Faulkner,et al.  Modelling evolutionary processes in small populations: not as ideal as you think , 2009, Molecular ecology.

[4]  B. Charlesworth.  Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.

[5]  Song‐lin Chen,et al.  A new method for SNP discovery. , 2009, BioTechniques.

[6]  Bruce S. Weir,et al.  Correlation-Based Inference for Linkage Disequilibrium With Multiple Alleles , 2008, Genetics.

[7]  F. Palstra,et al.  Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? , 2008, Molecular ecology.

[8]  R. Waples,et al.  ldne: a program for estimating effective population size from data on linkage disequilibrium , 2008, Molecular ecology resources.

[9]  T. Nomura.  Estimation of effective number of breeders from molecular coancestry of single cohort sample , 2008, Evolutionary applications.

[10]  G. Luikart,et al.  COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation , 2008, Molecular ecology resources.

[11]  N. Ryman,et al.  Unbiased Estimator for Genetic Drift and Effective Population Size , 2007, Genetics.

[12]  L. Bernatchez,et al.  Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems , 2007, Molecular ecology.

[13]  Peter M Visscher,et al.  Recent human effective population size estimated from linkage disequilibrium. , 2007, Genome research.

[14]  A. Pudovkin,et al.  Small effective number of parents (Nb) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis , 2007 .

[15]  R. Waples,et al.  Temporal Estimates of Effective Population Size in Species With Overlapping Generations , 2007, Genetics.

[16]  R. Waples,et al.  A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci* , 2006, Conservation Genetics.

[17]  G. Luikart,et al.  Estimating effective population size from linkage disequilibrium: severe bias in small samples , 2006, Conservation Genetics.

[18]  R. Frankham.  Genetics and extinction , 2005 .

[19]  P. Leberg,et al.  GENETIC APPROACHES FOR ESTIMATING THE EFFECTIVE SIZE OF POPULATIONS , 2005 .

[20]  R. Waples.  Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? , 2005, Molecular ecology.

[21]  Jinlian Wang,et al.  Estimation of effective population sizes from data on genetic markers , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[22]  Franclois Balloux.  HETEROZYGOTE EXCESS IN SMALL POPULATIONS AND THE HETEROZYGOTE‐EXCESS EFFECTIVE POPULATION SIZE , 2004, Evolution; international journal of organic evolution.

[23]  Gordon Luikart,et al.  Comparative Evaluation of a New Effective Population Size Estimator Based on Approximate Bayesian Computation , 2004, Genetics.

[24]  G. Luikart,et al.  SNPs in ecology, evolution and conservation , 2004 .

[25]  R. Nielsen,et al.  Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. , 2003, Theoretical population biology.

[26]  L. Salter,et al.  Temporal-method estimates of Ne from highly polymorphic loci , 2001, Conservation Genetics.

[27]  J. Wang,et al.  A pseudo-likelihood method for estimating effective population size from temporally spaced samples. , 2001, Genetical research.

[28]  M. Xiong,et al.  The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. , 2001, American journal of human genetics.

[29]  F. Balloux.  EASYPOP (version 1.7): a computer program for population genetics simulations. , 2001, The Journal of heredity.

[30]  D. Couvet,et al.  Estimation of effective population size and migration rate from one- and two-locus identity measures. , 2001, Genetics.

[31]  G. Luikart,et al.  Using genetics to estimate the size of wild populations: many methods, much potential, uncertain utility , 1999 .

[32]  R. Waples.  Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species , 1998 .

[33]  A. Pudovkin,et al.  On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. , 1996, Genetics.

[34]  L. Nunney,et al.  Estimating the effective population size of conserved populations , 1994 .

[35]  R. Waples.  A generalized approach for estimating effective population size from temporal changes in allele frequency. , 1989, Genetics.

[36]  P. Hedrick,et al.  Gametic disequilibrium measures: proceed with caution. , 1987, Genetics.

[37]  R. Hudson,et al.  The sampling distribution of linkage disequilibrium under an infinite allele model without selection. , 1985, Genetics.

[38]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[39]  E. Pollak.  A new method for estimating the effective population size from allele frequency changes. , 1983, Genetics.

[40]  William G. Hill,et al.  Estimation of effective population size from data on linkage disequilibrium , 1981 .

[41]  M. Nei,et al.  Genetic drift and estimation of effective population size. , 1981, Genetics.

[42]  W. G. Hill,et al.  Effect of mating structure on variation in linkage disequilibrium. , 1980, Genetics.

[43]  B. Weir.  Inferences about linkage disequilibrium. , 1979, Biometrics.

[44]  C. Langley,et al.  Analysis of linkage disequilibria between allozyme loci in natural populations of Drosophila melanogaster. , 1978, Genetical research.

[45]  M. Nei,et al.  Estimation of average heterozygosity and genetic distance from a small number of individuals. , 1978, Genetics.

[46]  W. G. Hill,et al.  Estimation of linkage disequilibrium in randomly mating populations , 1974, Heredity.

[47]  M. Nei,et al.  Linkage disequilibrium in subdivided populations. , 1973, Genetics.

[48]  C. Krimbas,et al.  THE GENETICS OF DACUS OLEAE. V. CHANGES OF ESTERASE POLYMORPHISM IN A NATURAL POPULATION FOLLOWING INSECTICIDE CONTROL—SELECTION OR DRIFT? , 1971, Evolution; international journal of organic evolution.

[49]  REP. INT.,et al.  Genetic Methods for Estimating the Effective Size of Cetacean Populations , 2012 .

[50]  R. Fewster,et al.  Evaluation of the Linkage Disequilibrium Method for Estimating Effective Population Size , 2009 .

[51]  Gordon Luikart,et al.  Genetic monitoring as a promising tool for conservation and management. , 2007, Trends in ecology & evolution.