Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

(2017) Mikkel Schubert et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ancient genomic changes associated with domestication of the horse

(2017) Pablo Librado et al.   SCIENCE

Identification of genomic variants putatively targeted by selection during dog domestication

(2016) Alex Cagan et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions

(2016) Zhaohua Liu et al.   BMC GENOMICS

Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7

(2016) Peter A. Leegwater et al.   BMC GENOMICS

Experimental conditions improving in-solution target enrichment for ancient DNA

(2016) Diana I. Cruz-Dávalos et al.   Molecular Ecology Resources

Of horse metapodials debitage during the Upper Magdalenian in Europe: An overview of techniques, methods and operational sequences

(2016) Olivier Bignon-Lau et al.   QUATERNARY INTERNATIONAL

Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

(2016) Vinicius Henrique da Silva et al.   PLoS One

Bayesian Analysis of Radiocarbon Dates

(2016) Christopher Bronk Ramsey   RADIOCARBON

Variant in the RFWD3 gene associated with PATN1 , a modifier of leopard complex spotting

(2015) H. M. Holl et al.   ANIMAL GENETICS

A Genome-wide Scan for Selective Sweeps in Racing Horses

(2015) Sunjin Moon et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

(2015) Thorfinn Sand Korneliussen et al.   BIOINFORMATICS

Improving the estimation of genetic distances from Next-Generation Sequencing data

(2015) Filipe G. Vieira et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

(2015) Clio Der Sarkissian et al.   CURRENT BIOLOGY

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

(2015) Cristina Gamba et al.   Molecular Ecology Resources

Massive migration from the steppe was a source for Indo-European languages in Europe

(2015) Wolfgang Haak et al.   NATURE

Population genomics of Bronze Age Eurasia

(2015) Morten E. Allentoft et al.   NATURE

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses

(2015) Freyja Imsland et al.   NATURE GENETICS

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

(2015) Laurent A F Frantz et al.   NATURE GENETICS

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

(2015) Pablo Librado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies

(2015) Carrie J. Finno et al.   PLoS Genetics

Rewriting the Central European Early Bronze Age Chronology: Evidence from Large-Scale Radiocarbon Dating

(2015) Philipp W. Stockhammer et al.   PLoS One

A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses

(2015) Mirjam Frischknecht et al.   PLoS One

Haplotype diversity in the equinemyostatingene with focus on variants associated with race distance propensity and muscle fiber type proportions

(2014) Jessica L. Petersen et al.   ANIMAL GENETICS

The Evolution of Animal Domestication

(2014) Greger Larson et al.   Annual Review of Ecology Evolution and Systematics

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

(2014) Dong-Hyun Shin et al.   BMC GENOMICS

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication

(2014) Julia Metzger et al.   BMC GENOMICS

Next-generation sequencing reveals large connected networks of intra-host HCV variants

(2014) David S Campo et al.   BMC GENOMICS

The DMRT3 ‘Gait keeper’ mutation affects performance of Nordic and Standardbred trotters1

(2014) K. Jäderkvist et al.   JOURNAL OF ANIMAL SCIENCE

Genomic characterization of the Przewalski׳s horse inhabiting Mongolian steppe by whole genome re-sequencing

(2014) Kyoung-Tag Do et al.   Livestock Science

Shotgun microbial profiling of fossil remains

(2014) C. Der Sarkissian et al.   MOLECULAR ECOLOGY

Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

(2014) Chao Wang et al.   Molecular Ecology Resources

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

(2014) Morten Rasmussen et al.   NATURE

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses

(2014) Arne Ludwig et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

(2014) N. Rohland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Investigation of De Novo Unique Differentially Expressed Genes Related to Evolution in Exercise Response during Domestication in Thoroughbred Race Horses

(2014) Woncheoul Park et al.   PLoS One

Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

(2014) Beatriz Gutiérrez-Gil et al.   PLoS One

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

(2014) Michael J. Montague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

(2014) Mikkel Schubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel variants in theKITandPAX3genes in horses with white-spotted coat colour phenotypes

(2013) Regula Hauswirth et al.   ANIMAL GENETICS

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Detection of selective sweeps in cattle using genome-wide SNP data

(2013) Holly R Ramey et al.   BMC GENOMICS

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

(2013) Anna Esteve-Codina et al.   BMC GENOMICS

Peeling Back the Evolutionary Layers of Molecular Mechanisms Responsive to Exercise-Stress in the Skeletal Muscle of the Racing Horse

(2013) H. Kim et al.   DNA RESEARCH

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse

(2013) Rebecca R. Bellone et al.   PLoS One

A Nonsense Mutation in the IKBKG Gene in Mares with Incontinentia Pigmenti

(2013) Rachel E. Towers et al.   PLoS One

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice

(2012) Lisa S. Andersson et al.   NATURE

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

A Genome-Wide Association Study Reveals Loci Influencing Height and Other Conformation Traits in Horses

(2012) Heidi Signer-Hasler et al.   PLoS One

Four Loci Explain 83% of Size Variation in the Horse

(2012) Shokouh Makvandi-Nejad et al.   PLoS One

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication

(2012) A. Achilli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations in MITF and PAX3 Cause “Splashed White” and Other White Spotting Phenotypes in Horses

(2012) Regula Hauswirth et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

(2011) Sebastian Lippold et al.   BMC EVOLUTIONARY BIOLOGY

Fine-mapping and mutation analysis of TRPM1: a candidate gene for leopard complex (LP) spotting and congenital stationary night blindness in horses

(2011) R. R. Bellone et al.   Briefings in Functional Genomics

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

(2011) Hiroki Goto et al.   Genome Biology and Evolution

A missense mutation in the skeletal muscle chloride channel 1 (CLCN1) as candidate causal mutation for congenital myotonia in a New Forest pony

(2011) Inge D. Wijnberg et al.   NEUROMUSCULAR DISORDERS

GTG Mutation in the Start Codon of the Androgen Receptor Gene in a Family of Horses with 64,XY Disorder of Sex Development

(2011) T. Révay et al.   Sexual Development

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Congenital stationary night blindness is associated with the leopard complex in the miniature horse

(2011) Lynne S. Sandmeyer et al.   VETERINARY OPHTHALMOLOGY

Identification of a Mutation Associated with Fatal Foal Immunodeficiency Syndrome in the Fell and Dales Pony

(2011) Laura Y. Fox-Clipsham et al.   PLoS Genetics

Association analysis of candidate SNPs in TRPM1 with leopard complex spotting (LP ) and congenital stationary night blindness (CSNB) in horses

(2010) R. R. Bellone et al.   ANIMAL GENETICS

Genome-wide SNP association-based localization of a dwarfism gene in Friesian dwarf horses

(2010) N. Orr et al.   ANIMAL GENETICS

Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance

(2010) E. W. Hill et al.   ANIMAL GENETICS

Association of sequence variants in CKM (creatine kinase, muscle) and COX4I2 (cytochrome c oxidase, subunit 4, isoform 2) genes with racing performance in Thoroughbred horses

(2010) J. GU et al.   EQUINE VETERINARY JOURNAL

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Mapping of equine cerebellar abiotrophy to ECA2 and identification of a potential causative mutation affecting expression of MUTYH

(2010) Leah S. Brault et al.   GENOMICS

The complete mitochondrial genome and phylogenetic analysis of the Debao pony (Equus caballus)

(2010) Qinyang Jiang et al.   MOLECULAR BIOLOGY REPORTS

A Sequence Polymorphism in MSTN Predicts Sprinting Ability and Racing Stamina in Thoroughbred Horses

(2010) Emmeline W. Hill et al.   PLoS One

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Ancient DNA provides new insights into the history of south Siberian Kurgan people

(2009) Christine Keyser et al.   HUMAN GENETICS

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses

(2009) JAIME LIRA et al.   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

The Earliest Horse Harnessing and Milking

(2009) A. K. Outram et al.   SCIENCE

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses

(2008) Deborah Cook et al.   PLoS Genetics