Navigating the temporal continuum of effective population size

DILS: Demographic Inferences with Linked Selection by using ABC

(2021) Christelle Fraïsse et al.   Molecular Ecology Resources

Examining Natural History through the Lens of Palaeogenomics

(2021) Kieren J. Mitchell et al.   TRENDS IN ECOLOGY & EVOLUTION

The impact of purifying and background selection on the inference of population history: problems and prospects

(2021) Parul Johri et al.   MOLECULAR BIOLOGY AND EVOLUTION

The inflated significance of neutral genetic diversity in conservation genetics

(2021) João C. Teixeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Demographic inference

(2021) Nina Marchi et al.   CURRENT BIOLOGY

Inferring number of populations and changes in connectivity under the n-island model

(2021) Armando Arredondo et al.   HEREDITY

Automatic inference of demographic parameters using generative adversarial networks

(2021) Zhanpeng Wang et al.   Molecular Ecology Resources

Limits and Convergence properties of the Sequentially Markovian Coalescent

(2021) Thibaut Sellinger et al.   Molecular Ecology Resources

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

Towards population-scale long-read sequencing

(2021) Wouter De Coster et al.   NATURE REVIEWS GENETICS

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

(2021) Joana I. Meier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the landscape of recombination using deep learning

(2020) Jeffrey R Adrion et al.   MOLECULAR BIOLOGY AND EVOLUTION

Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

(2020) Parul Johri et al.   GENETICS

Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

(2020) Menno J. Jong et al.   MOLECULAR ECOLOGY

The evolutionary history of extinct and living lions

(2020) Marc de Manuel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Roe deer on ice: Selection despite limited effective population size through the Pleistocene

(2020) Alana Alexander et al.   MOLECULAR ECOLOGY

Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation

(2020) Théophile Sanchez et al.   Molecular Ecology Resources

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

(2020) Claire R. Peart et al.   Nature Ecology & Evolution

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

(2020) Quentin Rougemont et al.   PLoS Genetics

Population genomics for wildlife conservation and management

(2020) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

(2020) Liisa Loog   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression

(2020) Christopher C. Kyriazis et al.   Evolution Letters

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

(2019) Shaohong Feng et al.   CURRENT BIOLOGY

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions

(2019) Andrew M. Sackman et al.   GENETICS

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

(2019) Nils Ryman et al.   MOLECULAR ECOLOGY

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

(2019) Jacqueline A. Robinson et al.   Science Advances

Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance

(2019) Daniel E. Ruzzante et al.   Methods in Ecology and Evolution

Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian Devils

(2019) Austin H Patton et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring whole-genome histories in large population datasets

(2019) Jerome Kelleher et al.   NATURE GENETICS

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Beyond multiregional and simple out-of-Africa models of human evolution

(2019) Eleanor M. L. Scerri et al.   Nature Ecology & Evolution

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

(2019) Zachary A. Szpiech et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inference of recombination maps from a single pair of genomes and its application to ancient samples

(2019) Gustavo V. Barroso et al.   PLoS Genetics

The Genomic Impact of European Colonization of the Americas

(2019) Linda Ongaro et al.   CURRENT BIOLOGY

Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time

(2019) Lindsey E. Fenderson et al.   MOLECULAR ECOLOGY

Using Haplotype Information for Conservation Genomics

(2019) Maeva Leitwein et al.   TRENDS IN ECOLOGY & EVOLUTION

Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes

(2018) Simona Grusea et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The Neutral Theory in Light of Natural Selection

(2018) Andrew D Kern et al.   MOLECULAR BIOLOGY AND EVOLUTION

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

(2018) Eleanor M.L. Scerri et al.   TRENDS IN ECOLOGY & EVOLUTION

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

Ancestry-specific recent effective population size in the Americas

(2018) Sharon R. Browning et al.   PLoS Genetics

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

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

(2018) Annabel C. Beichman et al.   Annual Review of Ecology Evolution and Systematics

Inference of population history using coalescent HMMs: review and outlook

(2018) Jeffrey P Spence et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

(2018) Fanny Pouyet et al.   eLife

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

(2018) Tom van der Valk et al.   CURRENT BIOLOGY

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

(2018) Jeffrey D. Jensen et al.   EVOLUTION

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

(2018) Florianne Marandel et al.   FISH AND FISHERIES

The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

(2018) Willy Rodríguez et al.   HEREDITY

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

(2018) Lex Flagel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

(2017) Clément Rougeux et al.   Genome Biology and Evolution

The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

(2017) Lounès Chikhi et al.   HEREDITY

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Climate change and human colonization triggered habitat loss and fragmentation in Madagascar

(2017) Jordi Salmona et al.   MOLECULAR ECOLOGY

Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories

(2017) Annabel C. Beichman et al.   G3-Genes Genomes Genetics

Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

(2016) A. Jonas et al.   GENETICS

Prediction and estimation of effective population size

(2016) J Wang et al.   HEREDITY

Effective population size in ecology and evolution

(2016) M Husemann et al.   HEREDITY

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

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

(2016) R K Waples et al.   HEREDITY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Divergence history of the Carpathian and smooth newts modelled in space and time

(2016) P. Zieliński et al.   MOLECULAR ECOLOGY

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

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

Effective sizes and time to migration–drift equilibrium in geographically subdivided populations

(2016) O. Hössjer et al.   THEORETICAL POPULATION BIOLOGY

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

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

Deep Learning for Population Genetic Inference

(2016) Sara Sheehan et al.   PLoS Computational Biology

A Genomic Map of the Effects of Linked Selection in Drosophila

(2016) Eyal Elyashiv et al.   PLoS Genetics

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

(2016) Simon Boitard et al.   PLoS Genetics

Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

(2015) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2015) Kimberly J. Gilbert et al.   EVOLUTION

Estimating Effective Population Size from Temporally Spaced Samples with a Novel, Efficient Maximum-Likelihood Algorithm

(2015) T.-Y. J. Hui et al.   GENETICS

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk et al.   MOLECULAR ECOLOGY

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Methods and models for unravelling human evolutionary history

(2015) Joshua G. Schraiber et al.   NATURE REVIEWS GENETICS

Causes of natural variation in fitness: Evidence from studies ofDrosophilapopulations

(2015) Brian Charlesworth   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum

(2015) Jonathan Terhorst et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metapopulation inbreeding dynamics, effective size and subpopulation differentiation—A general analytical approach for diploid organisms

(2015) Ola Hössjer et al.   THEORETICAL POPULATION BIOLOGY

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

(2015) Mario Barbato et al.   Frontiers in Genetics

Habitat fragmentation and its lasting impact on Earth's ecosystems

(2015) N. M. Haddad et al.   Science Advances

Temporal Stability of Genetic Variability and Differentiation in the Three-Spined Stickleback (Gasterosteus aculeatus)

(2015) Jacquelin DeFaveri et al.   PLoS One

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

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

(2014) Robin S. Waples et al.   GENETICS

A new general analytical approach for modeling patterns of genetic differentiation and effective size of subdivided populations over time

(2014) Ola Hössjer et al.   MATHEMATICAL BIOSCIENCES

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

(2013) Iona M. MacLeod et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

(2013) Simon Gravel et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History

(2012) Pier Francesco Palamara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

(2011) MATTHEW P. HARE et al.   CONSERVATION BIOLOGY

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

(2011) Robin S. Waples et al.   GENETICS

Inbreeding effective population size and parentage analysis without parents

(2011) ROBIN S. WAPLES et al.   Molecular Ecology Resources

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

High-Resolution Detection of Identity by Descent in Unrelated Individuals

(2010) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

(2010) Daniel Wegmann et al.   BMC BIOINFORMATICS

A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors

(2010) I. M. MacLEOD et al.   Genetics Research

Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size

(2010) ROBIN S. WAPLES   Molecular Ecology Resources

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

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

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

(2009) T. Stadler et al.   GENETICS

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) JINLIANG WANG   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts

(2008) Lorenz Hauser et al.   FISH AND FISHERIES

Extensions of the Coalescent Effective Population Size

(2008) J. Wakeley et al.   GENETICS

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

COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation

(2007) DAVID A. TALLMON et al.   Molecular Ecology Resources