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

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

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

Inference of complex population histories using whole-genome sequences from multiple populations

(2019) Matthias Steinrücken et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis )

(2018) Rory J. Craig et al.   MOLECULAR ECOLOGY

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

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

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

(2018) Florianne Marandel et al.   FISH AND FISHERIES

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

(2017) Marty Kardos et al.   GENETICS

Demographic history, selection and functional diversity of the canine genome

(2017) Elaine A. Ostrander et al.   NATURE REVIEWS GENETICS

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

(2017) Marty Kardos et al.   GENETICS

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

(2016) PingHsun Hsieh et al.   GENOME RESEARCH

Prediction and estimation of effective population size

(2016) J Wang 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

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

(2016) Jinliang Wang   MOLECULAR ECOLOGY

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

(2016) Jonathan Terhorst et al.   NATURE GENETICS

The Strength of Selection against Neanderthal Introgression

(2016) Ivan Juric 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

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC 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

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation

(2013) Nils Ryman et al.   Molecular Ecology Resources

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

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

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

Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

(2012) D. Serbezov et al.   GENETICS

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Robin S. Waples et al.   GENETICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

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

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