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  • 1
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    Exonic transcription factor binding directs codon choice and affects protein evolution (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-18
    Description: Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967546/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967546/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stergachis, Andrew B -- Haugen, Eric -- Shafer, Anthony -- Fu, Wenqing -- Vernot, Benjamin -- Reynolds, Alex -- Raubitschek, Anthony -- Ziegler, Steven -- LeProust, Emily M -- Akey, Joshua M -- Stamatoyannopoulos, John A -- F30 DK095678/DK/NIDDK NIH HHS/ -- FDK095678A/PHS HHS/ -- T32 GM007266/GM/NIGMS NIH HHS/ -- U01ES01156/ES/NIEHS NIH HHS/ -- U54 HG004592/HG/NHGRI NIH HHS/ -- U54 HG007010/HG/NHGRI NIH HHS/ -- U54HG004592/HG/NHGRI NIH HHS/ -- U54HG007010/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1367-72. doi: 10.1126/science.1243490.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24337295" target="_blank"〉PubMed〈/a〉
    Keywords: Codon/*genetics ; DNA Footprinting ; Deoxyribonuclease I/chemistry ; *Evolution, Molecular ; *Exome ; *Exons ; *Genome, Human ; Humans ; Polymorphism, Single Nucleotide ; Transcription Factors/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Resurrecting surviving Neandertal lineages from modern human genomes (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-01-31
    Description: Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1 to 3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering more than 15 gigabases of introgressed sequence that spans ~20% of the Neandertal genome (false discovery rate = 5%). Analyses of surviving archaic lineages suggest that there were fitness costs to hybridization, admixture occurred both before and after divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups, even in the absence of fossilized remains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vernot, Benjamin -- Akey, Joshua M -- New York, N.Y. -- Science. 2014 Feb 28;343(6174):1017-21. doi: 10.1126/science.1245938. Epub 2014 Jan 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24476670" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Genetic Variation ; *Genome, Human ; Humans ; Hybridization, Genetic ; Indians, North American/genetics ; Neanderthals/*genetics ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    An expansive human regulatory lexicon encoded in transcription factor footprints (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-08
    Description: Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736582/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736582/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neph, Shane -- Vierstra, Jeff -- Stergachis, Andrew B -- Reynolds, Alex P -- Haugen, Eric -- Vernot, Benjamin -- Thurman, Robert E -- John, Sam -- Sandstrom, Richard -- Johnson, Audra K -- Maurano, Matthew T -- Humbert, Richard -- Rynes, Eric -- Wang, Hao -- Vong, Shinny -- Lee, Kristen -- Bates, Daniel -- Diegel, Morgan -- Roach, Vaughn -- Dunn, Douglas -- Neri, Jun -- Schafer, Anthony -- Hansen, R Scott -- Kutyavin, Tanya -- Giste, Erika -- Weaver, Molly -- Canfield, Theresa -- Sabo, Peter -- Zhang, Miaohua -- Balasundaram, Gayathri -- Byron, Rachel -- MacCoss, Michael J -- Akey, Joshua M -- Bender, M A -- Groudine, Mark -- Kaul, Rajinder -- Stamatoyannopoulos, John A -- F30 DK095678/DK/NIDDK NIH HHS/ -- HG004592/HG/NHGRI NIH HHS/ -- P30 CA015704/CA/NCI NIH HHS/ -- R37 DK044746/DK/NIDDK NIH HHS/ -- RC2 HG005654/HG/NHGRI NIH HHS/ -- RC2HG005654/HG/NHGRI NIH HHS/ -- U54 HG004592/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955618" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/*genetics ; *DNA Footprinting ; DNA Methylation ; DNA-Binding Proteins/metabolism ; Deoxyribonuclease I/metabolism ; *Encyclopedias as Topic ; Genome, Human/*genetics ; Genomic Imprinting ; Genomics ; Humans ; *Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Transcription Factors/*metabolism ; Transcription Initiation Site
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    The accessible chromatin landscape of the human genome (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-09-08
    Description: DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify approximately 2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect approximately 580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721348/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thurman, Robert E -- Rynes, Eric -- Humbert, Richard -- Vierstra, Jeff -- Maurano, Matthew T -- Haugen, Eric -- Sheffield, Nathan C -- Stergachis, Andrew B -- Wang, Hao -- Vernot, Benjamin -- Garg, Kavita -- John, Sam -- Sandstrom, Richard -- Bates, Daniel -- Boatman, Lisa -- Canfield, Theresa K -- Diegel, Morgan -- Dunn, Douglas -- Ebersol, Abigail K -- Frum, Tristan -- Giste, Erika -- Johnson, Audra K -- Johnson, Ericka M -- Kutyavin, Tanya -- Lajoie, Bryan -- Lee, Bum-Kyu -- Lee, Kristen -- London, Darin -- Lotakis, Dimitra -- Neph, Shane -- Neri, Fidencio -- Nguyen, Eric D -- Qu, Hongzhu -- Reynolds, Alex P -- Roach, Vaughn -- Safi, Alexias -- Sanchez, Minerva E -- Sanyal, Amartya -- Shafer, Anthony -- Simon, Jeremy M -- Song, Lingyun -- Vong, Shinny -- Weaver, Molly -- Yan, Yongqi -- Zhang, Zhancheng -- Zhang, Zhuzhu -- Lenhard, Boris -- Tewari, Muneesh -- Dorschner, Michael O -- Hansen, R Scott -- Navas, Patrick A -- Stamatoyannopoulos, George -- Iyer, Vishwanath R -- Lieb, Jason D -- Sunyaev, Shamil R -- Akey, Joshua M -- Sabo, Peter J -- Kaul, Rajinder -- Furey, Terrence S -- Dekker, Job -- Crawford, Gregory E -- Stamatoyannopoulos, John A -- F30 DK095678/DK/NIDDK NIH HHS/ -- GM076036/GM/NIGMS NIH HHS/ -- HG004563/HG/NHGRI NIH HHS/ -- HG004592/HG/NHGRI NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- MC_UP_1102/1/Medical Research Council/United Kingdom -- P30 CA016086/CA/NCI NIH HHS/ -- R01 GM076036/GM/NIGMS NIH HHS/ -- R01 HG003143/HG/NHGRI NIH HHS/ -- R01 MH084676/MH/NIMH NIH HHS/ -- R01MH084676/MH/NIMH NIH HHS/ -- U54 HG004563/HG/NHGRI NIH HHS/ -- U54 HG004592/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955617" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/*genetics/*metabolism ; DNA/*genetics ; DNA Footprinting ; DNA Methylation ; DNA-Binding Proteins/metabolism ; Deoxyribonuclease I/metabolism ; *Encyclopedias as Topic ; Evolution, Molecular ; Genome, Human/*genetics ; Genomics ; Humans ; *Molecular Sequence Annotation ; Mutation Rate ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Transcription Factors/metabolism ; Transcription Initiation Site ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-04-13
    Description: It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected beta-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350576/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350576/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Roak, Brian J -- Vives, Laura -- Girirajan, Santhosh -- Karakoc, Emre -- Krumm, Niklas -- Coe, Bradley P -- Levy, Roie -- Ko, Arthur -- Lee, Choli -- Smith, Joshua D -- Turner, Emily H -- Stanaway, Ian B -- Vernot, Benjamin -- Malig, Maika -- Baker, Carl -- Reilly, Beau -- Akey, Joshua M -- Borenstein, Elhanan -- Rieder, Mark J -- Nickerson, Deborah A -- Bernier, Raphael -- Shendure, Jay -- Eichler, Evan E -- HD065285/HD/NICHD NIH HHS/ -- HHSN273200800010C/PHS HHS/ -- HL 094976/HL/NHLBI NIH HHS/ -- HL 1029230/HL/NHLBI NIH HHS/ -- HL 102924/HL/NHLBI NIH HHS/ -- HL102926/HL/NHLBI NIH HHS/ -- R01 HD065285/HD/NICHD NIH HHS/ -- R01 HD065285-02/HD/NICHD NIH HHS/ -- R01 HL094976/HL/NHLBI NIH HHS/ -- RC2 HL102923/HL/NHLBI NIH HHS/ -- RC2 HL102926/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;485(7397):246-50. doi: 10.1038/nature10989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495309" target="_blank"〉PubMed〈/a〉
    Keywords: Autistic Disorder/*genetics ; DNA-Binding Proteins/genetics ; Exome/*genetics ; Exons/*genetics ; GPI-Linked Proteins/genetics ; Genetic Predisposition to Disease/genetics ; Humans ; Laminin/genetics ; NAV1.1 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins/genetics ; Parents ; Point Mutation/*genetics ; Protein Interaction Maps/*genetics ; Receptors, N-Methyl-D-Aspartate/genetics ; Reproducibility of Results ; Siblings ; Signal Transduction ; Sodium Channels/genetics ; Stochastic Processes ; Transcription Factors/genetics ; Tumor Suppressor Protein p53/metabolism ; beta Catenin/metabolism
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    The phenotypic legacy of admixture between modern humans and Neandertals (2016)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2016-02-26
    Description: Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)-derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use. Our results establish that archaic admixture influences disease risk in modern humans, provide hypotheses about the effects of hundreds of Neandertal haplotypes, and demonstrate the utility of EHR data in evolutionary analyses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simonti, Corinne N -- Vernot, Benjamin -- Bastarache, Lisa -- Bottinger, Erwin -- Carrell, David S -- Chisholm, Rex L -- Crosslin, David R -- Hebbring, Scott J -- Jarvik, Gail P -- Kullo, Iftikhar J -- Li, Rongling -- Pathak, Jyotishman -- Ritchie, Marylyn D -- Roden, Dan M -- Verma, Shefali S -- Tromp, Gerard -- Prato, Jeffrey D -- Bush, William S -- Akey, Joshua M -- Denny, Joshua C -- Capra, John A -- 1K22LM011938/LM/NLM NIH HHS/ -- 1R01GM114128/GM/NIGMS NIH HHS/ -- 5T32EY021453/EY/NEI NIH HHS/ -- R01GM110068/GM/NIGMS NIH HHS/ -- R01LM010685/LM/NLM NIH HHS/ -- U01HG004438/HG/NHGRI NIH HHS/ -- U01HG004608/HG/NHGRI NIH HHS/ -- U01HG004609/HG/NHGRI NIH HHS/ -- U01HG004610/HG/NHGRI NIH HHS/ -- U01HG006378/HG/NHGRI NIH HHS/ -- U01HG006379/HG/NHGRI NIH HHS/ -- U01HG006380/HG/NHGRI NIH HHS/ -- U01HG006382/HG/NHGRI NIH HHS/ -- U01HG006385/HG/NHGRI NIH HHS/ -- U01HG006388/HG/NHGRI NIH HHS/ -- U01HG006389/HG/NHGRI NIH HHS/ -- U01HG008657/HG/NHGRI NIH HHS/ -- U01HG04599/HG/NHGRI NIH HHS/ -- U01HG04603/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2016 Feb 12;351(6274):737-41. doi: 10.1126/science.aad2149.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. ; Department of Genome Sciences, University of Washington, Seattle, WA, USA. ; Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. ; Mount Sinai School of Medicine, New York, NY, USA. ; Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA. ; Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. ; Department of Genome Sciences, University of Washington, Seattle, WA, USA. Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA. ; Center for Human Genetics, Marshfield Clinic, Marshfield, WI, USA. ; Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA. ; Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. ; Division of Health Sciences Research, Mayo Clinic, Rochester, MN, USA. ; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA. ; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Medicine, Vanderbilt University, Nashville, TN, USA. Department of Pharmacology, Vanderbilt University, Nashville, TN, USA. ; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. ; Weis Center for Research, Geisinger Health System, Danville, PA, USA. Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Science, Stellenbosch University, Tygerberg, South Africa. ; Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA. ; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Medicine, Vanderbilt University, Nashville, TN, USA. ; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912863" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Depression/genetics ; Disease/*genetics ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Human ; Haplotypes ; Humans ; Keratosis, Actinic/genetics ; Neanderthals/*genetics ; Phenotype
    Print ISSN: 0036-8075
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  • 7
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    Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-03-19
    Description: Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vernot, Benjamin -- Tucci, Serena -- Kelso, Janet -- Schraiber, Joshua G -- Wolf, Aaron B -- Gittelman, Rachel M -- Dannemann, Michael -- Grote, Steffi -- McCoy, Rajiv C -- Norton, Heather -- Scheinfeldt, Laura B -- Merriwether, David A -- Koki, George -- Friedlaender, Jonathan S -- Wakefield, Jon -- Paabo, Svante -- Akey, Joshua M -- 5R01GM110068/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 8;352(6282):235-9. doi: 10.1126/science.aad9416. Epub 2016 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, Washington, USA. ; Department of Genome Sciences, University of Washington, Seattle, Washington, USA. Department of Life Sciences and Biotechnology, University of Ferrara, Italy. ; Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. ; Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA. ; Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA. ; Department of Anthropology, Binghamton University, Binghamton, NY, USA. ; Institute for Medical Research, Goroka, Eastern Highlands Province, Papua New Guinea. ; Department of Anthropology, Temple University, Philadelphia PA, USA. ; Department of Statistics, University of Washington, Seattle, Washington, USA. ; Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. paabo@eva.mpg.de akeyj@uw.edu. ; Department of Genome Sciences, University of Washington, Seattle, Washington, USA. paabo@eva.mpg.de akeyj@uw.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26989198" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA/*genetics ; Genetic Variation ; Genome, Human/*genetics ; Humans ; Melanesia ; Neanderthals/*genetics ; Oceanic Ancestry Group/*genetics ; Sequence Analysis, DNA
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  • 8
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    Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-08
    Description: Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. Results: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Availability: Our algorithms have been implemented in N otung , a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung . Contact: mstolzer@andrew.cmu.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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    Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-08-03
    Description: Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis , which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.
    Keywords: Evolution, Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    A high-coverage Neandertal genome from Vindija Cave in Croatia (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-03
    Description: To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
    Keywords: Anthropology, Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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