Article
Agriculture, Dairy & Animal Science
Stephen J. O'Brien
ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 8, 2020
(2020)
Article
Evolutionary Biology
Irene Sacristan, Francisca Acuna, Emilio Aguilar, Sebastian Garcia, Maria Jose Lopez, Javier Cabello, Ezequiel Hidalgo-Hermoso, Jim Sanderson, Karen A. Terio, Vanessa Barrs, Julia Beatty, Warren E. Johnson, Javier Millan, Elie Poulin, Constanza Napolitano
Summary: The study reveals that human transformation of natural habitats can lead to increased pathogen transmission between animals, such as the interspecific transmission of feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) between guignas and domestic cats. The prevalence of FeLV and FIV in guignas and domestic cats was very similar, with guigna FeLV infection significantly associated with fragmented landscapes with resident domestic cats.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sovi, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio Mello, Samantha R. Friedrich, Peter Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O'Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis
Summary: The Vertebrate Genome Project and the international Genome 10K consortium have collaborated to generate high-quality genome assemblies for 16 species representing six major vertebrate lineages, leading to new biological discoveries. Long-read sequencing technologies are essential for maximizing genome quality, and addressing complex repeats and haplotype heterozygosity are crucial for reducing assembly errors and improving completeness of reference genomes. The lessons learned from this project have paved the way for the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all known vertebrate species.
Article
Zoology
Andres Mesas, Erika Cuellar-Soto, Karina Romero, Trinidad Zegers, Valeria Varas, Benito A. Gonzalez, Warren E. Johnson, Juan C. Marin
Summary: The guanaco population in the Bolivian Chaco is threatened by hunting and habitat degradation, and only 74 individuals were identified in the most recent census. The population shows moderate genetic diversity, but the estimated effective population size is low and indicates a continuing loss of allelic variation. Gene flow between Bolivian and Paraguayan guanaco Chaco populations should be assessed and integrated into conservation management plans.
STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT
(2023)
Article
Agriculture, Dairy & Animal Science
Andres Mesas, Ricardo Baldi, Benito A. Gonzalez, Virginia Burgi, Alexandra Chavez, Warren E. Johnson, Juan C. Marin
Summary: The study evaluates the diversity and genetic structure of endemic guanacos in central Argentina, which have been impacted by human activities such as livestock production and urbanization. It reveals high levels of genetic variation and latitudinal segregation of mitochondrial haplotypes, indicating at least two historical populations in the region. The results highlight the importance of conservation management plans to ensure the persistence of guanaco populations in the face of livestock activity and urbanization.
Article
Marine & Freshwater Biology
Siri Ofsthus Goksoyr, Jed Goldstone, Roger Lille-Langoy, Erik-Jan Lock, Pal A. Olsvik, Anders Goksoyr, Odd Andre Karlsen
Summary: The study revealed that the Atlantic cod possesses two VDR orthologous genes, which can be activated by vitamin D. Some polycyclic aromatic hydrocarbons can interact with VDRs, affecting their transcriptional activities and potentially altering the vitamin D signaling pathway, leading to adverse effects on the cardiac development and bone deformities in fish.
AQUATIC TOXICOLOGY
(2021)
Editorial Material
Multidisciplinary Sciences
Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklos Balint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O'Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mara K. N. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards
Summary: The Earth BioGenome Project (EBP) is a global international initiative that requires agreement and coordination on standards. To ensure rapid progress towards its goals, EBP has established five technical standards committees and made the current versions of the standards documents available on its website.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Nadja R. Brun, Matthew C. Salanga, Francisco X. Mora-Zamorano, David C. Lamb, Jared Goldstone, John J. Stegeman
Summary: Orphan cytochrome P450 enzyme CYP20A1 has been found to play an important role in brain function and early embryonic development in human and zebrafish. Zebrafish cyp20a1 mutants created using CRISPR/Cas9 technology exhibited significant behavioral differences from wild-type fish, showing characteristics such as anxiety and hyperactivity. This suggests that orphan CYP20A1 may have a neurophysiological role.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Nadja R. Brun, Jennifer M. Panlilio, Kun Zhang, Yanbin Zhao, Evgeny Ivashkin, John J. Stegeman, Jared Goldstone
Summary: The study demonstrates that early exposure to polychlorinated biphenyls affects neural development and behavior in zebrafish, leading to sensory deficits and disruption of dopaminergic and GABAergic signaling. PCB153-induced swelling of afferent sensory neurons and disruption of neurotransmitter signaling contribute to motor deficits in zebrafish. The findings suggest that non-dioxin-like PCBs may contribute to neurodevelopmental abnormalities in humans and exert selection pressures on vertebrate wildlife.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shaohong Feng, Ming Bai, Iker Rivas-Gonzalez, Cai Li, Shiping Liu, Yijie Tong, Haidong Yang, Guangji Chen, Duo Xie, Karen E. Sears, Lida M. Franco, Juan Diego Gaitan-Espitia, Roberto F. Nespolo, Warren E. Johnson, Huanming Yang, Parice A. Brandies, Carolyn J. Hogg, Katherine Belov, Marilyn B. Renfree, Kristofer M. Helgen, Jacobus J. Boomsma, Mikkel Heide Schierup, Guojie Zhang
Summary: Incomplete lineage sorting (ILS) can lead to incongruences between gene trees and species trees during rapid speciation events. Through phylogenomic analyses, it has been discovered that the South American monito del monte is the sister lineage of all Australian marsupials, despite a portion of its genome being more similar to the Diprotodontia. Conflicting phylogenetic signals across the whole genome are consistent with morphological variation among extant marsupials. Furthermore, hundreds of genes have been found to encode the same amino acids in non-sister species due to stochastic fixation during ILS. Functional experiments have provided evidence of how ILS directly contributes to hemiplasy in morphological traits established during rapid marsupial speciation approximately 60 million years ago.
Article
Biochemistry & Molecular Biology
Jorge L. Ramirez, Jonas Lescroart, Henrique Figueiro, Juan Pablo Torres-Florez, Priscilla M. S. Villela, Luiz L. Coutinho, Patricia D. Freitas, Warren E. Johnson, Agostinho Antunes, Pedro M. Galetti, Eduardo Eizirik
Summary: Using whole genome sequences, this study investigates the ecological differentiation among five species from the genus Leopardus, and explores their genomic features, comparative demographic history and positive selection. The results show that divergent ecological strategies are reflected in genomic features, and that the demographic history of these cats is influenced by climate fluctuations and habitat specialization, resulting in distinct evolutionary trajectories. Additionally, a gene involved in vertebrate retinal neurogenesis was found to be under positive selection in a specific species with nocturnal and arboreal specializations, indicating its importance in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Daniel E. Chavez, Ilan Gronau, Taylor Hains, Rebecca B. Dikow, Paul B. Frandsen, Henrique V. Figueiro, Fabricio S. Garcez, Ligia Tchaicka, Erio C. De Paula, Avio H. G. Rodrigues, Rodrigo S. P. Jorge, Edson S. Lima, Nucharin Songsasen, Warren E. Johnson, Eduardo Eizirik, Klaus-Peter Koepfli, Robert K. Wayne
Summary: Through genomic analysis of South American canid species, this study reveals their origin, interspecific hybridization, historical demographic, genetic diversity, and molecular basis of adaptations. The research found that South American canids originated from a single ancestor and radiated west of the Andes. Historical gene flow, distinct patterns of genomic diversity, and genetic variants associated with limb proportions, frugivory, and dental adaptations were observed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Multidisciplinary Sciences
Sadye Paez, Robert H. S. Kraus, Beth Shapiro, M. Thomas P. Gilbert, Erich D. Jarvis
Article
Multidisciplinary Sciences
Madeline G. Bursell, Rebecca B. Dikow, Henrique Figueiro, Olga Dudchenko, Joseph P. Flanagan, Erez Lieberman Aiden, Benoit Goossens, Senthilvel K. S. S. Nathan, Warren E. Johnson, Klaus-Peter Koepfli, Paul B. Frandsen
Summary: Populations of clouded leopards are declining, and understanding their patterns of genetic variation is crucial for conservation efforts. This study reveals that the divergence time between mainland and Sunda clouded leopards is earlier than previously estimated, and the Sunda clouded leopard has lower genetic diversity compared to the mainland clouded leopard.