Animal domestication in the era of ancient genomics

Loss of function mutations in essential genes cause embryonic lethality in pigs

(2019) Martijn F. L. Derks et al.   PLoS Genetics

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

(2019) Antoine Fages et al.   CELL

Ancient pathogen genomics as an emerging tool for infectious disease research

(2019) Maria A. Spyrou et al.   NATURE REVIEWS GENETICS

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

(2019) Laurent A. F. Frantz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Evolution of Deleterious Mutations in Horses

(2019) Ludovic Orlando et al.   Genes

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

(2019) Gillian P. McHugo et al.   BMC BIOLOGY

The History of Farm Foxes Undermines the Animal Domestication Syndrome

(2019) Kathryn A. Lord et al.   TRENDS IN ECOLOGY & EVOLUTION

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

(2018) Amanda L. Pendleton et al.   BMC BIOLOGY

A re-evaluation of the domestication bottleneck from archaeogenomic evidence

(2018) Robin G Allaby et al.   Evolutionary Applications

137 ancient human genomes from across the Eurasian steppes

(2018) Peter de Barros Damgaard et al.   NATURE

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

(2018) Charleen Gaunitz et al.   SCIENCE

The evolutionary history of dogs in the Americas

(2018) Máire Ní Leathlobhair et al.   SCIENCE

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

(2018) Kevin G. Daly et al.   SCIENCE

Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull

(2018) Maiken Hemme Bro-Jørgensen et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Dogs accompanied humans during the Neolithic expansion into Europe

(2018) Morgane Ollivier et al.   Biology Letters

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

(2018) Choongwon Jeong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices

(2017) Liisa Loog et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient genomic changes associated with domestication of the horse

(2017) Pablo Librado et al.   SCIENCE

Ancient European dog genomes reveal continuity since the Early Neolithic

(2017) Laura R. Botigué et al.   Nature Communications

Improving ancient DNA genome assembly

(2017) Alexander Seitz et al.   PeerJ

The origin of ambling horses

(2016) Saskia Wutke et al.   CURRENT BIOLOGY

Bayesian Inference of Natural Selection from Allele Frequency Time Series

(2016) Joshua G. Schraiber et al.   GENETICS

NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

(2016) Carole Charlier et al.   GENOME RESEARCH

A wolf in dog's clothing: Initial dog domestication and Pleistocene wolf variation

(2016) Angela Perri   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Temporal and spatial dynamics of insular Rusa deer and wild pig populations in Komodo National Park

(2016) Achmad Ariefiandy et al.   JOURNAL OF MAMMALOGY

Combining bleach and mild predigestion improves ancient DNA recovery from bones

(2016) Sanne Boessenkool et al.   Molecular Ecology Resources

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

Genomic and archaeological evidence suggest a dual origin of domestic dogs

(2016) Laurent A. F. Frantz et al.   SCIENCE

The Evolution of Suidae

(2016) Laurent Frantz et al.   Annual Review of Animal Biosciences

Bayesian Inference of Natural Selection from Allele Frequency Time Series

(2016) Joshua G. Schraiber et al.   GENETICS

A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing

(2016) Niall J. O’Sullivan et al.   Scientific Reports

Out of southern East Asia: the natural history of domestic dogs across the world

(2015) Guo-Dong Wang et al.   CELL RESEARCH

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

(2015) Pontus Skoglund et al.   CURRENT BIOLOGY

Amazonia and the Anthropocene: What was the spatial extent and intensity of human landscape modification in the Amazon Basin at the end of prehistory?

(2015) Dolores R Piperno et al.   HOLOCENE

Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective

(2015) Anna-Sapfo Malaspinas   MOLECULAR ECOLOGY

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

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

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Genetic structure in village dogs reveals a Central Asian domestication origin

(2015) Laura M. Shannon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

(2015) Clare D. Marsden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

(2015) Mirte Bosse et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the late Paleolithic

(2015) Abby Grace Drake et al.   Scientific Reports

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

The Effect of a Mutation in the Thyroid Stimulating Hormone Receptor (TSHR) on Development, Behaviour and TH Levels in Domesticated Chickens

(2015) Anna-Carin Karlsson et al.   PLoS One

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergentSus scrofapopulations

(2014) Mirte Bosse et al.   MOLECULAR ECOLOGY

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing

(2014) M. D. Teasdale 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

Establishing the validity of domestication genes using DNA from ancient chickens

(2014) L. Girdland Flink et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating the roles of directed breeding and gene flow in animal domestication

(2014) F. B. Marshall 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

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

(2014) Mirte Bosse et al.   Nature Communications

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

Genome Sequencing Highlights the Dynamic Early History of Dogs

(2014) Adam H. Freedman et al.   PLoS Genetics

FPSAC: fast phylogenetic scaffolding of ancient contigs

(2013) Ashok Rajaraman et al.   BIOINFORMATICS

Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

(2013) Iona M. MacLeod et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

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

Used planet: A global history

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

The role of humans in facilitating and sustaining coat colour variation in domestic animals

(2013) Anna Linderholm et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A population genetics view of animal domestication

(2013) Greger Larson et al.   TRENDS IN GENETICS

Impact of wild boar (Sus scrofa) in its introduced and native range: a review

(2012) M. Noelia Barrios-Garcia et al.   BIOLOGICAL INVASIONS

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

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

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

Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

(2012) Claudio Ottoni 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

Four Loci Explain 83% of Size Variation in the Horse

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

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

(2012) V. Warmuth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking dog domestication by integrating genetics, archeology, and biogeography

(2012) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

(2012) Mirte Bosse et al.   PLoS Genetics

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

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

Conservation genetics of cattle, sheep, and goats

(2011) Pierre Taberlet et al.   COMPTES RENDUS BIOLOGIES

The origins of animal domestication and husbandry: A major change in the history of humanity and the biosphere

(2011) Jean-Denis Vigne   COMPTES RENDUS BIOLOGIES

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

The domestic dog: man's best friend in the genomic era

(2011) Adam R Boyko   GENOME BIOLOGY

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

(2010) P. Pavlidis et al.   GENETICS

Meta-analysis of zooarchaeological data from SW Asia and SE Europe provides insight into the origins and spread of animal husbandry

(2010) James Conolly et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

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

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin 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

THE SOAY SHEEP OF THE ISLAND OF HIRTA, ST. KILDA. A STUDY OF A FERAL POPULATION

(2010) J. MORTON BOYD et al.   PROCEEDINGS OF THE ZOOLOGICAL SOCIETY OF LONDON

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Canine Morphology: Hunting for Genes and Tracking Mutations

(2010) Abigail L. Shearin et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves

(2009) J.-F. Pang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago

(2009) J.-D. Vigne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coat Color Variation at the Beginning of Horse Domestication

(2009) A. Ludwig et al.   SCIENCE

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

The Earliest Horse Harnessing and Milking

(2009) A. K. Outram et al.   SCIENCE

The different levels of genetic diversity in sex chromosomes and autosomes

(2009) Hans Ellegren   TRENDS IN GENETICS

Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs

(2009) Meiying Fang et al.   PLoS Genetics

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

(2008) S. Naderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken

(2008) Jonas Eriksson et al.   PLoS Genetics

Are cattle, sheep, and goats endangered species?

(2007) P. TABERLET et al.   MOLECULAR ECOLOGY