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

Jaatha: a fast composite-likelihood approach to estimate demographic parameters

(2011) LISHA NADUVILEZHATH et al.   MOLECULAR ECOLOGY

Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon

(2011) L. W. SEEB et al.   Molecular Ecology Resources

Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod,Gadus morhua

(2011) IAN R. BRADBURY et al.   Molecular Ecology Resources

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

(2011) S. J. HELYAR et al.   Molecular Ecology Resources

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds1

(2010) P. Uimari et al.   JOURNAL OF ANIMAL SCIENCE

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

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

Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes

(2010) A. M. LEWANDOWSKA-SABAT et al.   MOLECULAR ECOLOGY

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

(2010) Bridgett M. vonHoldt et al.   NATURE

Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data

(2010) M. Moragues et al.   THEORETICAL AND APPLIED GENETICS

Whole-Genome SNP Association in the Horse: Identification of a Deletion in Myosin Va Responsible for Lavender Foal Syndrome

(2010) Samantha A. Brooks et al.   PLoS Genetics

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data

(2009) J. Yin et al.   BIOINFORMATICS

Correcting for ascertainment bias in the inference of population structure

(2009) Gilles Guillot et al.   BIOINFORMATICS

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Composite likelihood estimation of demographic parameters

(2009) Daniel Garrigan   BMC GENETICS

Methods for Human Demographic Inference Using Haplotype Patterns From Genomewide Single-Nucleotide Polymorphism Data

(2009) K. E. Lohmueller et al.   GENETICS

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

(2009) Y. Wang et al.   GENETICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses

(2009) J. Hey   MOLECULAR BIOLOGY AND EVOLUTION

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

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

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

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE

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

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

Effects of Spatially Varying Selection on Nucleotide Diversity and Linkage Disequilibrium: Insights From Deer Mouse Globin Genes

(2008) J. F. Storz et al.   GENETICS

A Two-Stage Pruning Algorithm for Likelihood Computation for a Population Tree

(2008) A. RoyChoudhury et al.   GENETICS

Genotype, haplotype and copy-number variation in worldwide human populations

(2008) Mattias Jakobsson et al.   NATURE

Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays

(2008) Chao Tian et al.   PLoS One

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

(2008) J. Z. Li et al.   SCIENCE