Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review

Comparing estimates of census and effective population size in an endangered amphibian

(2023) G. C. Brooks et al.   ANIMAL CONSERVATION

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

(2023) Seyedeh Fatemeh Mousavi et al.   HEREDITY

The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection

(2022) Irene Novo et al.   PLoS Genetics

Genomic insights into the historical and contemporary demographics of the grey reef shark

(2022) Cameron A. J. Walsh et al.   HEREDITY

Patterns of genetic diversity of brown trout in a northern Spanish catchment linked to structural connectivity

(2022) Alexia María González-Ferreras et al.   AQUATIC SCIENCES

Big data in conservation genomics: boosting skills, hedging bets, and staying current in the field

(2021) Rena M Schweizer et al.   JOURNAL OF HEREDITY

Genomic inference of contemporary effective population size in a large island population of collared flycatchers ( Ficedula albicollis )

(2021) Krystyna Nadachowska‐Brzyska et al.   MOLECULAR ECOLOGY

Pseudoreplication in genomic‐scale data sets

(2021) Robin S. Waples et al.   Molecular Ecology Resources

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data

(2020) C. J. Battey et al.   GENETICS

Recent demographic history inferred by high-resolution analysis of linkage disequilibrium

(2020) Enrique Santiago et al.   MOLECULAR BIOLOGY AND EVOLUTION

AgeStrucNb: Software for Simulating and Detecting Changes in the Effective Number of Breeders (Nb)

(2020) Tiago Antao et al.   JOURNAL OF HEREDITY

Detecting population declines via monitoring the effective number of breeders ( N b )

(2020) Gordon Luikart et al.   Molecular Ecology Resources

The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus

(2020) Matthew L. Bootsma et al.   Evolutionary Applications

Do estimates of contemporary effective population size tell us what we want to know?

(2019) Nils Ryman et al.   MOLECULAR ECOLOGY

ngsLD: evaluating linkage disequilibrium using genotype likelihoods

(2019) Emma A Fox et al.   BIOINFORMATICS

Landscape, colonization and life history: Their effects on genetic diversity in four sympatric species inhabiting a dendritic system

(2019) Daniel E Ruzzante et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Null Alleles and FIS × FST Correlations

(2018) Robin S Waples   JOURNAL OF HEREDITY

A non-zero variance of Tajima’s estimator for two sequences even for infinitely many unlinked loci

(2018) Léandra King et al.   THEORETICAL POPULATION BIOLOGY

Robust estimates of a high N e / N ratio in a top marine predator, southern bluefin tuna

(2018) Robin S. Waples et al.   Science Advances

Estimating effective population size of large marine populations, is it feasible?

(2018) Florianne Marandel et al.   FISH AND FISHERIES

Purging putative siblings from population genetic data sets: a cautionary view

(2017) Robin S. Waples et al.   MOLECULAR ECOLOGY

A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci

(2016) C M Hollenbeck et al.   HEREDITY

Improved confidence intervals for the linkage disequilibrium method for estimating effective population size

(2016) A T Jones et al.   HEREDITY

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

(2016) R K Waples et al.   HEREDITY

Tiny estimates of theNe/Nratio in marine fishes: Are they real?

(2016) R. S. Waples   JOURNAL OF FISH BIOLOGY

A comparison of single-sample estimators of effective population sizes from genetic marker data

(2016) Jinliang Wang   MOLECULAR ECOLOGY

Effective number of breeders, effective population size and their relationship with census size in an iteroparous species,Salvelinus fontinalis

(2016) Daniel E. Ruzzante et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture

(2016) Mark V. Bravington et al.   Nature Communications

Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages

(2016) William Peterman et al.   PeerJ

Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case

(2015) María Saura et al.   BMC GENOMICS

Evaluating methods for estimating local effective population size with and without migration

(2015) Kimberly J. Gilbert et al.   EVOLUTION

Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Yellowstone grizzly bears

(2015) Pauline L. Kamath et al.   MOLECULAR ECOLOGY

Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

(2015) Andrew R. Whiteley et al.   MOLECULAR ECOLOGY

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

(2014) Robin S. Waples et al.   GENETICS

Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

(2014) Jon E. Hess et al.   Molecular Ecology Resources

Estimation of effective population size in continuously distributed populations: there goes the neighborhood

(2013) M C Neel et al.   HEREDITY

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

Estimating Effective Population Size from Linkage Disequilibrium between Unlinked Loci: Theory and Application to Fruit Fly Outbreak Populations

(2013) John A Sved et al.   PLoS One

Simple life-history traits explain key effective population size ratios across diverse taxa

(2013) R. S. Waples et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Linkage disequilibrium and effective population size when generations overlap

(2012) John D. Robinson et al.   Evolutionary Applications

Estimation of historical effective population size using linkage disequilibria with marker data

(2012) L.J. Corbin et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

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

(2012) D. Peel et al.   Molecular Ecology Resources

Effective/census population size ratio estimation: a compendium and appraisal

(2012) Friso P. Palstra et al.   Ecology and Evolution

Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration

(2011) Robin S. Waples et al.   GENETICS

Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

(2011) F P Palstra et al.   HEREDITY

Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

(2011) X. Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early detection of population fragmentation using linkage disequilibrium estimation of effective population size

(2010) Phillip R. England et al.   CONSERVATION GENETICS

Early detection of population declines: high power of genetic monitoring using effective population size estimators

(2010) Tiago Antao et al.   Evolutionary Applications

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

(2010) DAVID A. TALLMON et al.   Molecular Ecology Resources

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

(2009) Robin S. Waples et al.   Evolutionary Applications

A new method for estimating effective population sizes from a single sample of multilocus genotypes

(2009) JINLIANG WANG   MOLECULAR ECOLOGY

Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure

(2009) CAREN S. GOLDBERG et al.   Molecular Ecology Resources

Non-random error in genotype calling procedures: Implications for family-based and case-control genome-wide association studies

(2008) Richard J.L. Anney et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms

(2008) Xiaoyi Gao et al.   GENETIC EPIDEMIOLOGY

Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence?

(2008) FRISO P. PALSTRA et al.   MOLECULAR ECOLOGY

ldne: a program for estimating effective population size from data on linkage disequilibrium

(2008) ROBIN S. WAPLES et al.   Molecular Ecology Resources