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  • Articles  (8)
  • Physics  (8)
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  • Articles  (8)
  • 1
    Publication Date: 2011-07-22
    Description: Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value 〈 10(-245)). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154982/" 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/PMC3154982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinch, Anjali G -- Tandon, Arti -- Patterson, Nick -- Song, Yunli -- Rohland, Nadin -- Palmer, Cameron D -- Chen, Gary K -- Wang, Kai -- Buxbaum, Sarah G -- Akylbekova, Ermeg L -- Aldrich, Melinda C -- Ambrosone, Christine B -- Amos, Christopher -- Bandera, Elisa V -- Berndt, Sonja I -- Bernstein, Leslie -- Blot, William J -- Bock, Cathryn H -- Boerwinkle, Eric -- Cai, Qiuyin -- Caporaso, Neil -- Casey, Graham -- Cupples, L Adrienne -- Deming, Sandra L -- Diver, W Ryan -- Divers, Jasmin -- Fornage, Myriam -- Gillanders, Elizabeth M -- Glessner, Joseph -- Harris, Curtis C -- Hu, Jennifer J -- Ingles, Sue A -- Isaacs, William -- John, Esther M -- Kao, W H Linda -- Keating, Brendan -- Kittles, Rick A -- Kolonel, Laurence N -- Larkin, Emma -- Le Marchand, Loic -- McNeill, Lorna H -- Millikan, Robert C -- Murphy, Adam -- Musani, Solomon -- Neslund-Dudas, Christine -- Nyante, Sarah -- Papanicolaou, George J -- Press, Michael F -- Psaty, Bruce M -- Reiner, Alex P -- Rich, Stephen S -- Rodriguez-Gil, Jorge L -- Rotter, Jerome I -- Rybicki, Benjamin A -- Schwartz, Ann G -- Signorello, Lisa B -- Spitz, Margaret -- Strom, Sara S -- Thun, Michael J -- Tucker, Margaret A -- Wang, Zhaoming -- Wiencke, John K -- Witte, John S -- Wrensch, Margaret -- Wu, Xifeng -- Yamamura, Yuko -- Zanetti, Krista A -- Zheng, Wei -- Ziegler, Regina G -- Zhu, Xiaofeng -- Redline, Susan -- Hirschhorn, Joel N -- Henderson, Brian E -- Taylor, Herman A Jr -- Price, Alkes L -- Hakonarson, Hakon -- Chanock, Stephen J -- Haiman, Christopher A -- Wilson, James G -- Reich, David -- Myers, Simon R -- 090532/Wellcome Trust/United Kingdom -- CA060691/CA/NCI NIH HHS/ -- CA092447/CA/NCI NIH HHS/ -- CA100374/CA/NCI NIH HHS/ -- CA100598/CA/NCI NIH HHS/ -- CA1116460/CA/NCI NIH HHS/ -- CA1116460S1/CA/NCI NIH HHS/ -- CA121197/CA/NCI NIH HHS/ -- CA121197S2/CA/NCI NIH HHS/ -- CA127219/CA/NCI NIH HHS/ -- CA1326792/CA/NCI NIH HHS/ -- CA140388/CA/NCI NIH HHS/ -- CA141716/CA/NCI NIH HHS/ -- CA148085/CA/NCI NIH HHS/ -- CA148127/CA/NCI NIH HHS/ -- CA22453/CA/NCI NIH HHS/ -- CA54281/CA/NCI NIH HHS/ -- CA55769/CA/NCI NIH HHS/ -- CA58223/CA/NCI NIH HHS/ -- CA63464/CA/NCI NIH HHS/ -- CA68485/CA/NCI NIH HHS/ -- CA68578/CA/NCI NIH HHS/ -- CA77305/CA/NCI NIH HHS/ -- CA87895/CA/NCI NIH HHS/ -- CA88164/CA/NCI NIH HHS/ -- ES007784/ES/NIEHS NIH HHS/ -- ES011126/ES/NIEHS NIH HHS/ -- ES06717/ES/NIEHS NIH HHS/ -- ES10126/ES/NIEHS NIH HHS/ -- GM08016/GM/NIGMS NIH HHS/ -- GM091332/GM/NIGMS NIH HHS/ -- HD33175/HD/NICHD NIH HHS/ -- HG004726/HG/NHGRI NIH HHS/ -- HHSN268200960009C/PHS HHS/ -- HL084107/HL/NHLBI NIH HHS/ -- N01-HC-65226/HC/NHLBI NIH HHS/ -- P30 ES010126/ES/NIEHS NIH HHS/ -- R01 CA052689/CA/NCI NIH HHS/ -- R01 CA092447/CA/NCI NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- R01 HL084107-04/HL/NHLBI NIH HHS/ -- R01-CA73629/CA/NCI NIH HHS/ -- U01 HG004168/HG/NHGRI NIH HHS/ -- U01 HG004168-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 Jul 20;476(7359):170-5. doi: 10.1038/nature10336.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21775986" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western/ethnology ; African Americans/*genetics ; Alleles ; Amino Acid Motifs ; Base Sequence ; Chromosome Mapping ; Crossing Over, Genetic/*genetics ; Europe/ethnology ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Genetics, Population ; Genome, Human/*genetics ; Genomics ; Haplotypes/genetics ; Histone-Lysine N-Methyltransferase/chemistry/genetics/metabolism ; Humans ; Male ; Molecular Sequence Data ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Probability
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2013-03-22
    Description: Recent upward revision of the 1872 Owens Valley earthquake from M w  7.4–7.5 to 7.7–7.9 implies either additional unrecognized rupture length or anomalously strong ground motions associated with this event. We investigate the first possibility through paleoseismic trenching south of the mapped surface rupture in the Haiwee area, where historical accounts suggest significant surface deformation following the earthquake. Trenching focused on a prominent north-striking scarp, herein termed the Sage Flat fault, expressed in Pleistocene alluvial fans east of Haiwee Reservoir. Surficial mapping and ground-based Light Detection and Ranging (lidar) surveying suggest that this fault accommodates east-down normal motion, and possibly a comparable amount of dextral slip. Trenching and luminescence dating brackets the timing of the most recent surface-rupturing earthquake between ~25.7 and 30.1 ka, and provides evidence for an earlier event predating this time. In combination with scarp profiling, these dates also suggest a maximum rate of normal, dip-slip fault motion up to ~0.1 mm/yr over this period. Although we discovered no evidence for recent surface rupture on the Sage Flat fault, a series of subvertical fractures and fissures cut across young trench stratigraphy, consistent with secondary deformation associated with seismic shaking. As such, we suggest that possible ground disturbance in the Haiwee area during the 1872 event primarily reflected ground shaking or liquefaction-related deformation rather than triggered slip. In addition, we infer a structural and kinematic connection between the Owens Valley fault and oblique-dextral faults north of Lower Cactus Flat in the northwestern Coso Range, rather than a west-step into northern or western Rose Valley. Consideration of these structures in the total extent of the Owens Valley fault suggests a length of 140 km, of which at least 113 km ruptured during the 1872 event. Online Material: Procedural details and expanded results from the OSL sample analyses, as well as high-resolution paleoseismic trench logs.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 1998-03-01
    Print ISSN: 0024-3590
    Electronic ISSN: 1939-5590
    Topics: Biology , Geosciences , Physics
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  • 4
    Publication Date: 1998-01-01
    Print ISSN: 0024-3590
    Electronic ISSN: 1939-5590
    Topics: Biology , Geosciences , Physics
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  • 5
    Publication Date: 2018-11-05
    Description: Characterizing the hazard associated with Quaternary-active faults in the forearc crust of the northern Cascadia subduction zone has proven challenging due to historically low rates of seismicity, late Quaternary glacial scouring, and dense vegetation that often obscures fault-related geomorphic features. We couple lidar topography with paleoseismic trenching across the Leech River Fault on southern Vancouver Island to produce the first detailed surface rupture history of an onland forearc fault in British Columbia, Canada. The results indicate that this fault produced three surface-rupturing earthquakes in the last ∼9 kyr and is therefore capable of producing large (Mw〉6) earthquakes in the future. We provide new constraints on the fault's length (∼130 km) and Holocene slip rate (≥0.2–0.3 mm/year) that, together with the earthquake ages, should be incorporated into new seismic hazard assessments and building code practices relevant to urban centers in southwestern British Columbia (Canada) and northwestern Washington State (United States). ©2018. American Geophysical Union. All Rights Reserved.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2016-06-01
    Description: The 1872 Owens Valley earthquake is the third largest known historical earthquake in California. Relatively sparse field data and a complex rupture trace, however, inhibited attempts to fully resolve the slip distribution and reconcile the total moment release. We present a new, comprehensive record of surface slip based on lidar and field investigation, documenting 162 new measurements of laterally and vertically displaced landforms for 1872 and prehistoric Owens Valley earthquakes. Our lidar analysis uses a newly developed analytical tool to measure fault slip based on cross-correlation of sublinear topographic features and to produce a uniquely shaped probability density function (PDF) for each measurement. Stacking PDFs along strike to form cumulative offset probability distribution plots (COPDs) highlights common values corresponding to single and multiple-event displacements. Lateral offsets for 1872 vary systematically from ∼1.0 to 6.0 m and average 3.3 ± 1.1 m (2σ). Vertical offsets are predominantly east-down between ∼0.1 and 2.4 m, with a mean of 0.8 ± 0.5 m. The average lateral-to-vertical ratio compiled at specific sites is ∼6:1. Summing displacements across subparallel, overlapping rupture traces implies a maximum of 7–11 m and net average of 4.4 ± 1.5 m, corresponding to a geologic Mw ∼7.5 for the 1872 event. We attribute progressively higher-offset lateral COPD peaks at 7.1 ± 2.0 m, 12.8 ± 1.5 m, and 16.6 ± 1.4 m to three earlier large surface ruptures. Evaluating cumulative displacements in context with previously dated landforms in Owens Valley suggests relatively modest rates of fault slip, averaging between ∼0.6 and 1.6 mm/yr (1σ) over the late Quaternary. © 2016. American Geophysical Union. All Rights Reserved.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 7
    Publication Date: 2013-03-21
    Description: Recent upward revision of the 1872 Owens Valley earthquake from M (sub w) 7.4-7.5 to 7.7-7.9 implies either additional unrecognized rupture length or anomalously strong ground motions associated with this event. We investigate the first possibility through paleoseismic trenching south of the mapped surface rupture in the Haiwee area, where historical accounts suggest significant surface deformation following the earthquake. Trenching focused on a prominent north-striking scarp, herein termed the Sage Flat fault, expressed in Pleistocene alluvial fans east of Haiwee Reservoir. Surficial mapping and ground-based Light Detection and Ranging (lidar) surveying suggest that this fault accommodates east-down normal motion, and possibly a comparable amount of dextral slip. Trenching and luminescence dating brackets the timing of the most recent surface-rupturing earthquake between approximately 25.7 and 30.1 ka, and provides evidence for an earlier event predating this time. In combination with scarp profiling, these dates also suggest a maximum rate of normal, dip-slip fault motion up to approximately 0.1 mm/yr over this period. Although we discovered no evidence for recent surface rupture on the Sage Flat fault, a series of subvertical fractures and fissures cut across young trench stratigraphy, consistent with secondary deformation associated with seismic shaking. As such, we suggest that possible ground disturbance in the Haiwee area during the 1872 event primarily reflected ground shaking or liquefaction-related deformation rather than triggered slip. In addition, we infer a structural and kinematic connection between the Owens Valley fault and oblique-dextral faults north of Lower Cactus Flat in the northwestern Coso Range, rather than a west-step into northern or western Rose Valley. Consideration of these structures in the total extent of the Owens Valley fault suggests a length of 140 km, of which at least 113 km ruptured during the 1872 event. Online Material: Procedural details and expanded results from the OSL sample analyses, as well as high-resolution paleoseismic trench logs.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 8
    Publication Date: 2009-09-01
    Print ISSN: 0006-291X
    Electronic ISSN: 1090-2104
    Topics: Biology , Chemistry and Pharmacology , Physics
    Published by Elsevier
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