How do SNP ascertainment schemes and population demographics affect inferences about population history?

A Genomic Approach for Distinguishing between Recent and Ancient Admixture as Applied to Cattle

(2014) Emily Jane McTavish et al.   JOURNAL OF HEREDITY

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

(2014) Luana Micallef et al.   PLoS One

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

Correcting Coalescent Analyses for Panel-Based SNP Ascertainment

(2013) J. R. McGill et al.   GENETICS

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

Characterizing Bias in Population Genetic Inferences from Low-Coverage Sequencing Data

(2013) Eunjung Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History

(2013) Rasmus Heller et al.   PLoS One

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

(2013) Nicolas Heslot et al.   PLoS One

New World cattle show ancestry from multiple independent domestication events

(2013) E. J. McTavish et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The Relationship Between FST and the Frequency of the Most Frequent Allele

(2012) M. Jakobsson et al.   GENETICS

Modern Taurine Cattle Descended from Small Number of Near-Eastern Founders

(2012) R. Bollongino et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1

(2012) Silvia Bonfiglio et al.   PLoS One

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

(2012) Chaolong Wang et al.   PLoS Genetics

Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

(2011) YONG WANG et al.   MOLECULAR ECOLOGY

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

(2011) PAUL A. HOHENLOHE et al.   Molecular Ecology Resources

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi et al.   GENETICS

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

(2010) Bridgett M. vonHoldt et al.   NATURE

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

Cattle demographic history modelled from autosomal sequence variation

(2010) C. Murray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae)

(2009) Sean MacEachern et al.   BMC GENOMICS

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

(2009) Sean MacEachern et al.   BMC GENOMICS

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

(2009) T. Stadler et al.   GENETICS

Genetic markers in the playground of multivariate analysis

(2009) T Jombart et al.   HEREDITY

Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts

(2009) AMANDA J. FINGER et al.   Molecular Ecology Resources

An agenda for personalized medicine

(2009) Pauline C. Ng et al.   NATURE

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome

(2009) Alessandro Achilli et al.   PLoS One

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

(2009) J. E. Decker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide patterns of population structure and admixture in West Africans and African Americans

(2009) K. Bryc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

(2008) S. Y.W Ho et al.   Biology Letters

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

(2008) Stephanie D McKay et al.   BMC GENETICS

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias

(2008) M. Brandstrom et al.   GENOME RESEARCH

A HapMap harvest of insights into the genetics of common disease

(2008) Teri A. Manolio et al.   JOURNAL OF CLINICAL INVESTIGATION

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

(2008) J. Z. Li et al.   SCIENCE

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources