Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

(2021) J. W. Thorne et al.   ANIMAL GENETICS

Genomic insights into population history and biological adaptation in Oceania

(2021) Jeremy Choin et al.   NATURE

Origin and population structure of Brazilian hair sheep breeds

(2021) T. P. Paim et al.   ANIMAL GENETICS

Phylogenomic assessment of the role of hybridization and introgression in trait evolution

(2021) Yaxuan Wang et al.   PLoS Genetics

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats

(2021) He Yu et al.   Science Advances

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

(2021) Ze-Hui Chen et al.   Communications Biology

Understanding the effects of the bovine POLLED variants

(2020) J. E. Aldersey et al.   ANIMAL GENETICS

The wild species genome ancestry of domestic chickens

(2020) Raman Akinyanju Lawal et al.   BMC BIOLOGY

Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

(2020) Eirini Skourtanioti et al.   CELL

Ancient hybridization with an unknown population facilitated high altitude adaptation of canids

(2020) Ming-Shan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Animal domestication in the era of ancient genomics

(2020) Laurent A. F. Frantz et al.   NATURE REVIEWS GENETICS

The origin of domestication genes in goats

(2020) Zhuqing Zheng et al.   Science Advances

The genetic diversity and phylogeography of Mexican domestic sheep

(2020) Edwina Campos et al.   SMALL RUMINANT RESEARCH

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

(2020) Xin Li et al.   Nature Communications

Paternal Origins and Migratory Episodes of Domestic Sheep

(2020) Juan Deng et al.   CURRENT BIOLOGY

Historical introgression from wild relatives enhanced climatic adaptation and resistance to pneumonia in sheep

(2020) Yin-Hong Cao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Triticum population sequencing provides insights into wheat adaptation

(2020) Yao Zhou et al.   NATURE GENETICS

The structural variation landscape in 492 Atlantic salmon genomes

(2020) Alicia C. Bertolotti et al.   Nature Communications

Mitochondrial DNA Variations in Colombian Creole Sheep Confirm an Iberian Origin and Shed Light on the Dynamics of Introduction Events of African Genotypes

(2020) Herman Alberto Revelo et al.   Animals

Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

(2020) Kunzhe Dong et al.   BMC GENOMICS

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

(2019) Lei Chen et al.   SCIENCE

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

(2019) Vasant Shinde et al.   CELL

The formation of human populations in South and Central Asia

(2019) Vagheesh M. Narasimhan et al.   SCIENCE

Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds

(2019) Jae-Yoon Kim et al.   Frontiers in Genetics

An Ancient Genome from the Indus Valley Civilization

(2019) Maanasa Raghavan et al.   CELL

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

(2019) M. Muñoz et al.   Scientific Reports

Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline

(2019) Jing Wu et al.   NATURE GENETICS

Genetic Diversity on the Sex Chromosomes

(2018) Melissa A Wilson Sayres   Genome Biology and Evolution

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

(2018) Aniek C. Bouwman et al.   NATURE GENETICS

The prehistoric peopling of Southeast Asia

(2018) Hugh McColl et al.   SCIENCE

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

(2018) Matthew R. Jones et al.   SCIENCE

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

(2018) Marina Naval-Sanchez et al.   Nature Communications

Convergent genomic signatures of domestication in sheep and goats

(2018) Florian J. Alberto et al.   Nature Communications

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization

(2018) Zhangyuan Pan et al.   GigaScience

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

(2018) Dong-Dong Wu et al.   Nature Ecology & Evolution

Comparative iTRAQ proteomics revealed proteins associated with horn development in yak

(2018) Mingna Li et al.   Proteome Science

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

(2018) Xiao-Ju Hu et al.   MOLECULAR BIOLOGY AND EVOLUTION

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations

(2017) Morgane Petit et al.   GENETICS

FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis

(2017) Ruslan Kalendar et al.   GENOMICS

Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing

(2017) Chugang Mei et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia

(2017) Yong-Xin Zhao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep

(2017) Julie Demars et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nomadic ecology shaped the highland geography of Asia’s Silk Roads

(2017) Michael D. Frachetti et al.   NATURE

Parallel palaeogenomic transects reveal complex genetic history of early European farmers

(2017) Mark Lipson et al.   NATURE

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

(2017) Ivica Medugorac et al.   NATURE GENETICS

Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep

(2017) Guang-Wei Ma et al.   PLoS One

Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

(2017) Gordon L. Spangler et al.   PLoS One

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations

(2017) Morgane Petit et al.   GENETICS

Genomic signatures of adaptive introgression from European mouflon into domestic sheep

(2017) Mario Barbato et al.   Scientific Reports

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments

(2016) Ji Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

Genomic insights into the origin of farming in the ancient Near East

(2016) Iosif Lazaridis et al.   NATURE

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Complex disease and phenotype mapping in the domestic dog

(2016) Jessica J. Hayward et al.   Nature Communications

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep

(2015) Feng-Hua Lv et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Genomic data as the “hitchhiker's guide” to cattle adaptation: tracking the milestones of past selection in the bovine genome

(2015) Yuri T. Utsunomiya et al.   Frontiers in Genetics

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

(2015) Mario Barbato et al.   Frontiers in Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Derived variants at six genes explain nearly half of size reduction in dog breeds

(2013) M. Rimbault et al.   GENOME RESEARCH

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

(2013) Mingzhou Li et al.   NATURE GENETICS

Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India

(2013) Sachin Singh et al.   PLoS One

Mitochondrial DNA Diversity of Modern, Ancient and Wild Sheep (Ovis gmelinii anatolica) from Turkey: New Insights on the Evolutionary History of Sheep

(2013) Sevgin Demirci et al.   PLoS One

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Molecular markers for genetic diversity and phylogeny research of Brazilian sheep breeds

(2012) Bruno do Amaral Crispim et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

VEGF induces proliferation of human hair follicle dermal papilla cells through VEGFR-2-mediated activation of ERK

(2012) Wei Li et al.   EXPERIMENTAL CELL RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

VEGF upregulates VEGF receptor-2 on human outer root sheath cells and stimulates proliferation through ERK pathway

(2012) Wei Li et al.   MOLECULAR BIOLOGY REPORTS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations

(2012) Michael P. Heaton et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Wildlife molecular forensics: Identification of the Sardinian mouflon using STR profiling and the Bayesian assignment test

(2011) Rita Lorenzini et al.   Forensic Science International-Genetics

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Rapid, global demographic expansions after the origins of agriculture

(2011) C. R. Gignoux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fundamental hair follicle biology and fine fibre production in animals

(2010) H. Galbraith   Animal

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

The Human Genetic History of South Asia

(2010) Partha P. Majumder   CURRENT BIOLOGY

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae)

(2009) Hamid Reza Rezaei et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Revealing the History of Sheep Domestication Using Retrovirus Integrations

(2009) B. Chessa et al.   SCIENCE

Runs of Homozygosity in European Populations

(2008) Ruth McQuillan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

(2008) K. De Preter et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact

(2008) M. A. Zeder   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Awassi sheep as a genetic resource and efforts for their genetic improvement—A review

(2008) S. Galal et al.   SMALL RUMINANT RESEARCH