Ancient admixture from an extinct ape lineage into bonobos

[1]  Martin Kuhlwilm,et al.  Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions , 2019, Genome biology and evolution.

[2]  T. Marquès-Bonet,et al.  Direct estimation of mutations in great apes reconciles phylogenetic dating , 2019, Nature Ecology & Evolution.

[3]  Yun S. Song,et al.  Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans , 2017, bioRxiv.

[4]  R. Durbin,et al.  Detecting archaic introgression using an unadmixed outgroup , 2018, PLoS genetics.

[5]  S. Tishkoff,et al.  Phylogeny Estimation by Integration over Isolation with Migration Models , 2018, Molecular biology and evolution.

[6]  Martin Kuhlwilm,et al.  Genetic differences between humans and other hominins contribute to the “human condition” , 2018, bioRxiv.

[7]  Martin Kuhlwilm,et al.  Selection in the Introgressed Regions of the Chimpanzee Genome , 2018, Genome biology and evolution.

[8]  Kevin E. Langergraber,et al.  The impact of endogenous content, replicates and pooling on genome capture from faecal samples , 2017, Molecular ecology resources.

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

[10]  E. Eichler,et al.  A high-coverage Neandertal genome from Vindija Cave in Croatia , 2017, Science.

[11]  Pavlos Pavlidis,et al.  Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation , 2017, Molecular biology and evolution.

[12]  Fernando Racimo,et al.  Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals , 2017, Nature Communications.

[13]  Tetsuya Sakamaki,et al.  The mitochondrial ancestor of bonobos and the origin of their major haplogroups , 2017, PloS one.

[14]  Helen E. Parkinson,et al.  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) , 2016, Nucleic Acids Res..

[15]  Syed Haider,et al.  A bedr way of genomic interval processing , 2016, Source Code for Biology and Medicine.

[16]  Martin Kuhlwilm,et al.  Evolution and demography of the great apes. , 2016, Current opinion in genetics & development.

[17]  A. Andrés,et al.  Natural Selection in the Great Apes , 2016, Molecular biology and evolution.

[18]  Kevin E. Langergraber,et al.  Chimpanzee genomic diversity reveals ancient admixture with bonobos , 2016, Science.

[19]  Fernando Racimo,et al.  Signatures of Archaic Adaptive Introgression in Present-Day Human Populations , 2016, bioRxiv.

[20]  D. Reich,et al.  The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans , 2016, Current Biology.

[21]  Jonathan Scott Friedlaender,et al.  Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals , 2016, Science.

[22]  August E. Woerner,et al.  Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies , 2016, Genome research.

[23]  Ilan Gronau,et al.  Ancient gene flow from early modern humans into Eastern Neanderthals , 2016, Nature.

[24]  A. Andrés,et al.  Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors , 2016, American journal of human genetics.

[25]  G. Coop,et al.  The Strength of Selection against Neanderthal Introgression , 2015, bioRxiv.

[26]  Jerome Kelleher,et al.  Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes , 2015, bioRxiv.

[27]  T. Furuichi,et al.  How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations , 2015, Evolutionary anthropology.

[28]  Swapan Mallick,et al.  An early modern human from Romania with a recent Neanderthal ancestor , 2015, Nature.

[29]  August E. Woerner,et al.  Extreme selective sweeps independently targeted the X chromosomes of the great apes , 2015, Proceedings of the National Academy of Sciences.

[30]  August E. Woerner,et al.  The Time-Scale of Recombination Rate Evolution in Great Apes , 2015, bioRxiv.

[31]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[32]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

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

[34]  M. Lercher,et al.  PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R , 2014, Molecular biology and evolution.

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

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

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

[38]  Matthew D. Rasmussen,et al.  Genome-Wide Inference of Ancestral Recombination Graphs , 2013, PLoS genetics.

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

[40]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[41]  Arcadi Navarro,et al.  Great ape genetic diversity and population history , 2013, Nature.

[42]  Tetsuya Sakamaki,et al.  Genetic Structure of Wild Bonobo Populations: Diversity of Mitochondrial DNA and Geographical Distribution , 2013, PloS one.

[43]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[44]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[45]  S. Steinberg,et al.  Rate of de novo mutations and the importance of father’s age to disease risk , 2012, Nature.

[46]  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.

[47]  S. Tishkoff,et al.  Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers , 2012, Cell.

[48]  Sergey Koren,et al.  The bonobo genome compared with the chimpanzee and human genomes , 2012, Nature.

[49]  Jacques Simpore,et al.  Hemoglobins S and C Interfere with Actin Remodeling in Plasmodium falciparum–Infected Erythrocytes , 2011, Science.

[50]  Thibaut Jombart,et al.  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data , 2011, Bioinform..

[51]  S. Bergmann,et al.  The evolution of gene expression levels in mammalian organs , 2011, Nature.

[52]  August E. Woerner,et al.  Genetic evidence for archaic admixture in Africa , 2011, Proceedings of the National Academy of Sciences.

[53]  Katalin Csill'ery,et al.  abc: an R package for approximate Bayesian computation (ABC) , 2011, 1106.2793.

[54]  S. Wood.  Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models , 2011 .

[55]  Klaus Peter Schliep,et al.  phangorn: phylogenetic analysis in R , 2010, Bioinform..

[56]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

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

[58]  J. Hey.  The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. , 2010, Molecular biology and evolution.

[59]  Emmanuel Paradis,et al.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[60]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[61]  Kirk E Lohmueller,et al.  Detecting ancient admixture and estimating demographic parameters in multiple human populations. , 2009, Molecular biology and evolution.

[62]  Robert Gentleman,et al.  rtracklayer: an R package for interfacing with genome browsers , 2009, Bioinform..

[63]  E. Birney,et al.  Genome-wide nucleotide-level mammalian ancestor reconstruction. , 2008, Genome research.

[64]  T. Furuichi.  Social interactions and the life history of femalePan paniscus in Wamba, Zaire , 1989, International Journal of Primatology.

[65]  Vincent Plagnol,et al.  Possible Ancestral Structure in Human Populations , 2006, PLoS genetics.

[66]  M. Piccinni.  T cells in normal pregnancy and recurrent pregnancy loss. , 2006, Reproductive biomedicine online.

[67]  N. Jablonski,et al.  First fossil chimpanzee , 2005, Nature.

[68]  Jody Hey,et al.  Divergence population genetics of chimpanzees. , 2004, Molecular biology and evolution.

[69]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[70]  S. Young.  Zoo and Wild Animal Medicine, 5th edn. Fowler ME, Miller RE. Saunders, Elselvier Science, Port Melbourne , 2004 .

[71]  Jo A Myers Thompson.  A model of the biogeographical journey from Proto-pan to Pan paniscus , 2003, Primates; journal of primatology.

[72]  Adoum H. Mahamat,et al.  A new hominid from the Upper Miocene of Chad, Central Africa , 2002, Nature.

[73]  Richard R. Hudson,et al.  Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..

[74]  J. D. Capra,et al.  Identification of centerin: a novel human germinal center B cell‐restricted serpin , 2000, European journal of immunology.

[75]  K. Suzuki,et al.  A novel glycosylphosphatidyl inositol-anchored protein on human leukocytes: a possible role for regulation of neutrophil adherence and migration. , 1999, Journal of immunology.

[76]  R. Nagel,et al.  An alanine-to-threonine substitution in protein 4.2 cDNA is associated with a Japanese form of hereditary hemolytic anemia (protein 4.2NIPPON) , 1992 .

[77]  R. Nagel,et al.  An alanine-to-threonine substitution in protein 4.2 cDNA is associated with a Japanese form of hereditary hemolytic anemia (protein 4.2NIPPON). , 1992, Blood.