eSMC: a statistical model to infer admixture events from individual genomics data

[1]  X. Fang,et al.  Donkey genomes provide new insights into domestication and selection for coat color , 2020, Nature Communications.

[2]  O. François,et al.  Factor analysis of ancient population genomic samples , 2020, Nature Communications.

[3]  V. Savolainen,et al.  Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers , 2020, Philosophical Transactions of the Royal Society B.

[4]  J. Erdmann,et al.  Genomewide Association Study of Severe Covid-19 with Respiratory Failure , 2020, The New England journal of medicine.

[5]  L. Orlando,et al.  Animal domestication in the era of ancient genomics , 2020, Nature Reviews Genetics.

[6]  Vladimir Ulyantsev,et al.  GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data , 2020, GigaScience.

[7]  Joseph Willson There and back again — ancient genes reveal early migrations , 2020, Nature reviews genetics.

[8]  M. Price Africans, too, carry Neanderthal genetic legacy. , 2020, Science.

[9]  J. Akey,et al.  Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals , 2020, Cell.

[10]  Niklas Mather,et al.  A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data , 2019, Ecology and evolution.

[11]  G. Dreyfuss,et al.  U1 snRNP regulates cancer cell migration and invasion , 2019, bioRxiv.

[12]  Andrew B. Conley,et al.  Admixture-enabled selection for rapid adaptive evolution in the Americas , 2019, Genome Biology.

[13]  C. Viroli,et al.  Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees , 2019, Scientific Reports.

[14]  F. Bonhomme,et al.  The contribution of ancient admixture to reproductive isolation between European sea bass lineages , 2019, bioRxiv.

[15]  Arne Ludwig,et al.  Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series , 2019, Cell.

[16]  Yun S. Song,et al.  Inference of complex population histories using whole-genome sequences from multiple populations , 2015, Proceedings of the National Academy of Sciences.

[17]  Hui Xiang,et al.  Decrease of gene expression diversity during domestication of animals and plants , 2019, BMC Evolutionary Biology.

[18]  B. Guldbrandtsen,et al.  Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes , 2018, Genetics Selection Evolution.

[19]  Kirk E. Lohmueller,et al.  Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms , 2018, Annual Review of Ecology, Evolution, and Systematics.

[20]  Alexandra Jamieson,et al.  Paleogenomics of Animal Domestication , 2018 .

[21]  Jun Yu,et al.  Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat , 2018, GigaScience.

[22]  Jonathan Terhorst,et al.  Inference of population history using coalescent HMMs: review and outlook. , 2018, Current opinion in genetics & development.

[23]  D. Wittenburg,et al.  On Estimation of Genome Composition in Genetically Admixed Individuals Using Constrained Genomic Regression , 2018, Front. Genet..

[24]  G. Renaud,et al.  Improved de novo genomic assembly for the domestic donkey , 2018, Science Advances.

[25]  P. De Clercq,et al.  Population admixture can enhance establishment success of the introduced biological control agent Cryptolaemus montrouzieri , 2018, BMC Evolutionary Biology.

[26]  P. Taberlet,et al.  Convergent genomic signatures of domestication in sheep and goats , 2018, Nature Communications.

[27]  H. Caswell,et al.  Occupancy time in sets of states for demographic models , 2018, Theoretical population biology.

[28]  J. Tung,et al.  The contribution of admixture to primate evolution. , 2017, Current opinion in genetics & development.

[29]  J. Kelso,et al.  The Contribution of Neanderthals to Phenotypic Variation in Modern Humans , 2017, American journal of human genetics.

[30]  C. Thomas Inheritors of the Earth: How Nature Is Thriving in an Age of Extinction , 2017 .

[31]  M. M. Hansen,et al.  PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data , 2017, Molecular ecology resources.

[32]  Patrick T. McGrath,et al.  Genome-wide protein phylogenies for four African cichlid species , 2017, bioRxiv.

[33]  J. Kidd,et al.  Modeling Human Population Separation History Using Physically Phased Genomes , 2014, Genetics.

[34]  H. Ellegren,et al.  PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers , 2016, Molecular ecology.

[35]  Y. Teo,et al.  Estimating time to the most recent common ancestor (TMRCA): comparison and application of eight methods , 2015, European Journal of Human Genetics.

[36]  M. Zeder Core questions in domestication research , 2015, Proceedings of the National Academy of Sciences.

[37]  R. Durbin,et al.  Inferring human population size and separation history from multiple genome sequences , 2014, Nature Genetics.

[38]  M. Goddard,et al.  Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors , 2013, Molecular biology and evolution.

[39]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[40]  Jake K. Byrnes,et al.  PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations , 2012, Human biology.

[41]  R. Durbin,et al.  Inference of Human Population History From Whole Genome Sequence of A Single Individual , 2011, Nature.

[42]  S. Ho,et al.  Skyline‐plot methods for estimating demographic history from nucleotide sequences , 2011, Molecular ecology resources.

[43]  Ryan D. Hernandez,et al.  Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data , 2009, PLoS genetics.

[44]  A. Grant,et al.  Life History Evolution , 2002, Heredity.

[45]  P. Starkey,et al.  Regional and world trends in donkey populations by , 2000 .