作者：Xue, James R.; Mackay-Smith, Ava; Mouri, Kousuke; Garcia, Meilin Fernandez; Dong, Michael X.; Akers, Jared F.; Noble, Mark; Li, Xue; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Noonan, James P.; Capellini, Terence D.; Brennand, Kristen J.; Tewhey, Ryan; Sabeti, Pardis C.; Reilly, Steven K.; Zoonomia Consortium
作者单位：Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Harvard University; Yale University; Jackson Laboratory; Yale University; Uppsala University; University of Massachusetts System; University of Massachusetts Worcester; UMass Chan Medical School; University of Massachusetts System; UMass Chan Medical School; University of Massachusetts Worcester; Yale University; Yale University; Harvard University; University of Maine System; University of Maine Orono; Tufts University; Howard Hughes Medical Institute; Harvard University; Harvard T.H. Chan School of Public Health
摘要：Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rathe...
作者：Christmas, Matthew J.; Kaplow, Irene M.; Genereux, Diane P.; Dong, Michael X.; Hughes, Graham M.; Li, Xue; Sullivan, Patrick F.; Hindle, Allyson G.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Breit, Ana M.; Diekhans, Mark; Fanter, Cornelia; Foley, Nicole M.; Goodman, Daniel B.; Goodman, Linda; Keough, Kathleen C.; Kirilenko, Bogdan; Kowalczyk, Amanda; Lawless, Colleen; Lind, Abigail L.; Meadows, Jennifer R. S.; Moreira, Lucas R.; Redlich, Ruby W.; Ryan, Louise; Swofford, Ross; Valenzuela, Alejandro; Wagner, Franziska; Wallerman, Ola; Brown, Ashley R.; Damas, Joana; Fan, Kaili; Gatesy, John; Grimshaw, Jenna; Johnson, Jeremy; Kozyrev, Sergey V.; Lawler, Alyssa J.; Marinescu, Voichita D.; Morrill, Kathleen M.; Osmanski, Austin; Paulat, Nicole S.; Phan, BaDoi N.; Reilly, Steven K.; Schaeffer, Daniel E.; Steiner, Cynthia; Supple, Megan A.; Wilder, Aryn P.; Wirthlin, Morgan E.; Xue, James R.; Birren, Bruce W.; Gazal, Steven; Hubley, Robert M.; Koepfli, Klaus-Peter; Marques-Bonet, Tomas; Meyer, Wynn K.; Nweela, Martin; Sabeti, Pardis C.; Shapiro, Beth; Smit, Arian F. A.; Springer, Mark S.; Teeling, Emma C.; Weng, Zhiping; Hiller, Michael; Levesque, Danielle L.; Lewin, Harris A.; Murphy, William J.; Navarro, Arcadi; Paten, Benedict; Pollard, Katherine S.; Ray, David A.; Ruf, Irina; Ryder, Oliver A.; Pfenning, Andreas R.; Lindblad-Toh, Kerstin; Karlsson, Elinor K.
作者单位：Uppsala University; Carnegie Mellon University; Carnegie Mellon University; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; University College Dublin; University of Massachusetts System; UMass Chan Medical School; University of Massachusetts Worcester; University of Massachusetts System; UMass Chan Medical School; University of Massachusetts Worcester; Karolinska Institutet; Nevada System of Higher Education (NSHE); University of Nevada Las Vegas; University of California System; University of California Santa Cruz; University of Maine System; University of Maine Orono; Texas A&M University System; Texas A&M University College Station; University of California System; University of California San Francisco; University of California System; University of California San Francisco; University of California System; University of California San Francisco; The J David Gladstone Institutes; Goethe University Frankfurt; Leibniz Association; Senckenberg Gesellschaft fur Naturforschung (SGN); Carnegie Mellon University; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC-UPF - Institut de Biologia Evolutiva (IBE); Pompeu Fabra University; Leibniz Association; Senckenberg Gesellschaft fur Naturforschung (SGN); University of California System; University of California Davis; American Museum of Natural History (AMNH); Texas Tech University System; Texas Tech University; Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh; Yale University; University of California System; University of California Santa Cruz; Allen Institute for Brain Science; Harvard University; University of Southern California; Institute for Systems Biology (ISB); Smithsonian Institution; Smithsonian National Zoological Park & Conservation Biology Institute; ITMO University; Smithsonian Institution; Smithsonian National Zoological Park & Conservation Biology Institute; ICREA; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Consejo Superior de Investigaciones Cientificas (CSIC); CSIC-UPF - Institut de Biologia Evolutiva (IBE); Pompeu Fabra University; Autonomous University of Barcelona; Institut Catala de Paleontologia Miquel Crusafont (ICP); Lehigh University; University System of Ohio; Case Western Reserve University; Smithsonian Institution; Smithsonian National Museum of Natural History; Harvard University; Harvard School of Dental Medicine; Harvard University; Howard Hughes Medical Institute; University of California System; University of California Santa Cruz; Howard Hughes Medical Institute; University of California System; University of California Riverside; University of California System; University of California Davis; University of California System; University of California Davis; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Chan Zuckerberg Initiative (CZI); Leibniz Association; Senckenberg Gesellschaft fur Naturforschung (SGN); University of California System; University of California San Diego; University of Massachusetts System; UMass Chan Medical School; University of Massachusetts Worcester
摘要：Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (similar to 10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single...
作者：Wilder, Aryn P.; Supple, Megan A.; Subramanian, Ayshwarya; Mudide, Anish; Swofford, Ross; Serres-Armero, Aitor; Steiner, Cynthia; Koepfli, Klaus -Peter; Genereux, Diane P.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Marques-Bonet, Tomas; Fuentes, Violeta Munoz; Foley, Kathleen; Meyer, Wynn K.; Ryder, Oliver A.; Shapiro, Beth
作者单位：University of California System; University of California Santa Cruz; University of California System; University of California Santa Cruz; Howard Hughes Medical Institute; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Pompeu Fabra University; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC-UPF - Institut de Biologia Evolutiva (IBE); Smithsonian Institution; Smithsonian National Zoological Park & Conservation Biology Institute; Smithsonian Institution; Smithsonian National Zoological Park & Conservation Biology Institute; ITMO University; University of Massachusetts System; University of Massachusetts Worcester; Uppsala University; ICREA; Barcelona Institute of Science & Technology; Pompeu Fabra University; Centre de Regulacio Genomica (CRG); Institut Catala de Paleontologia Miquel Crusafont (ICP); Autonomous University of Barcelona; European Molecular Biology Laboratory (EMBL); European Bioinformatics Institute; University of Iowa; Lehigh University; University of California System; University of California San Diego
摘要：Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species wi...
作者：Kearney, Michael R.; Jusup, Marko
作者单位：University of Melbourne; Japan Fisheries Research & Education Agency (FRA)
摘要：The model used by White et al. (1) to explore life-history optimization of metabolic scaling has limited ability to capture observed combinations of growth and reproduction, including those of the domestic chicken. The analyses and interpretations may change substantially with realistic parameters. The model's biological and thermodynamic realism needs further exploration and justification before being applied to life-history optimization studies.
作者：McGuire, Amy L.; Lynch, Holly Fernandez; Grossman, Lewis A.; Cohen, I. Glenn
作者单位：Baylor College of Medicine; University of Pennsylvania; University of Pennsylvania; American University; Harvard University
