Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

(2014) Jean-Marie Cornuet et al.   BIOINFORMATICS

Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

(2014) Sean Hoban et al.   Evolutionary Applications

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

(2014) Wesley A. Larson et al.   Evolutionary Applications

ABC inference of multi-population divergence with admixture from unphased population genomic data

(2014) John D. Robinson et al.   MOLECULAR ECOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations

(2014) Edson Sandoval-Castellanos et al.   PLoS One

An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone

(2013) J W Poelstra et al.   HEREDITY

Estimating genome-wide heterozygosity: effects of demographic history and marker type

(2013) J M Miller et al.   HEREDITY

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Likelihood-based inference of population history from low-coveragede novogenome assemblies

(2013) Jack Hearn et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation

(2012) Sen Li et al.   BMC GENETICS

Inferring the History of Population Size Change from Genome-Wide SNP Data

(2012) Christoph Theunert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent-Based Analysis Distinguishes between Allo- and Autopolyploid Origin in Shepherd's Purse (Capsella bursa-pastoris)

(2012) K. R. St. Onge et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Reliability of genetic bottleneck tests for detecting recent population declines

(2012) M. ZACHARIAH PEERY et al.   MOLECULAR ECOLOGY

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems

(2011) KATE R. ST. ONGE et al.   MOLECULAR ECOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

(2010) G. BERTORELLE et al.   MOLECULAR ECOLOGY

Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America

(2010) AARON B. A. SHAFER et al.   MOLECULAR ECOLOGY

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

(2009) Ferran Palero et al.   BMC EVOLUTIONARY BIOLOGY

Darwinian and demographic forces affecting human protein coding genes

(2009) R. Nielsen et al.   GENOME RESEARCH

Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data

(2009) T Guillemaud et al.   HEREDITY

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

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

Genetic signals of historic and recent migration between sub-populations of Atlantic walrus Odobenus rosmarus rosmarus west and east of Greenland

(2009) LW Andersen et al.   Endangered Species Research

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One