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

[1]  A. Hobolth,et al.  Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach , 2009, Genetics.

[2]  Joshua M. Akey,et al.  Resurrecting Surviving Neandertal Lineages from Modern Human Genomes , 2014, Science.

[3]  L. Excoffier,et al.  Robust Demographic Inference from Genomic and SNP Data , 2013, PLoS genetics.

[4]  Yun S. Song,et al.  diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals , 2014, bioRxiv.

[5]  Swapan Mallick,et al.  The genomic landscape of Neanderthal ancestry in present-day humans. , 2016 .

[6]  D. Hartl,et al.  Population genetics of polymorphism and divergence. , 1992, Genetics.

[7]  P. Donnelly,et al.  Progress in population genetics and human evolution , 1997 .

[8]  Yun S. Song,et al.  Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data , 2014, bioRxiv.

[9]  Jacob A. Tennessen,et al.  Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes , 2012, Science.

[10]  R. Nielsen,et al.  Evidence for archaic adaptive introgression in humans , 2015, Nature Reviews Genetics.

[11]  Joshua S. Paul,et al.  An Accurate Sequentially Markov Conditional Sampling Distribution for the Coalescent With Recombination , 2011, Genetics.

[12]  Heng Li,et al.  Genome sequence of a 45,000-year-old modern human from western Siberia , 2014, Nature.

[13]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[14]  Kevin E. Langergraber,et al.  Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution , 2012, Proceedings of the National Academy of Sciences.

[15]  W. Miller,et al.  Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change , 2012, Proceedings of the National Academy of Sciences.

[16]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[17]  Philip L. F. Johnson,et al.  The complete genome sequence of a Neanderthal from the Altai Mountains , 2013 .

[18]  Joshua S. Paul,et al.  A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. , 2012, Theoretical population biology.

[19]  O. Delaneau,et al.  Supplementary Information for ‘ Improved whole chromosome phasing for disease and population genetic studies ’ , 2012 .

[20]  B. Browning,et al.  Haplotype phasing: existing methods and new developments , 2011, Nature Reviews Genetics.

[21]  Yun S. Song,et al.  Blockwise HMM computation for large-scale population genomic inference , 2012, Bioinform..

[22]  G. McVean,et al.  Approximating the coalescent with recombination , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[23]  J. Stewart,et al.  Human Evolution Out of Africa: The Role of Refugia and Climate Change , 2012, Science.

[24]  D. Reich,et al.  Genetic evidence for two founding populations of the Americas , 2015, Nature.

[25]  Asan,et al.  Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA , 2014, Nature.

[26]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[27]  R. Durbin,et al.  Inference of human population history from individual whole-genome sequences. , 2011, Nature.

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

[29]  M. Kimmel,et al.  New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. , 2003, Genetics.

[30]  J. Hein,et al.  Recombination as a point process along sequences. , 1999, Theoretical population biology.

[31]  S. Sampling theory for neutral alleles in a varying environment , 2003 .

[32]  Churchill,et al.  A Markov Chain Model of Coalescence with Recombination , 1997, Theoretical population biology.

[33]  Jonathan Terhorst,et al.  Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations , 2015, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

[34]  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.

[35]  Paul Marjoram,et al.  Fast "coalescent" simulation , 2006, BMC Genetics.

[36]  D. Reich,et al.  The landscape of Neandertal ancestry in present-day humans , 2014, Nature.

[37]  Russell B. Corbett-Detig,et al.  The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population , 2015, Genetics.

[38]  Mattias Jakobsson,et al.  Genomic evidence for the Pleistocene and recent population history of Native Americans , 2015, Science.

[39]  Asger Hobolth,et al.  Markovian approximation to the finite loci coalescent with recombination along multiple sequences. , 2014, Theoretical population biology.

[40]  Yun S. Song,et al.  Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach , 2013, Genetics.

[41]  Gil McVean,et al.  Stable recombination hotspots in birds , 2015, Science.

[42]  D. Halligan,et al.  Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family , 2013, Genetics.

[43]  Richard Durbin,et al.  Inferring human population size and separation history from multiple genome sequences , 2014 .

[44]  Yun S. Song,et al.  Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum , 2015, Proceedings of the National Academy of Sciences.

[45]  Paul R. Staab,et al.  scrm: efficiently simulating long sequences using the approximated coalescent with recombination , 2015, Bioinform..

[46]  Asger Hobolth,et al.  The SMC′ Is a Highly Accurate Approximation to the Ancestral Recombination Graph , 2015, Genetics.