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Blackburn DC, Boyer DM, Gray JA, Winchester J, Bates JM, Baumgart SL, Braker E, Coldren D, Conway KW, Rabosky AD, de la Sancha N, Dillman CB, Dunnum JL, Early CM, Frable BW, Gage MW, Hanken J, Maisano JA, Marks BD, Maslenikov KP, McCormack JE, Nagesan RS, Pandelis GG, Prestridge HL, Rabosky DL, Randall ZS, Robbins MB, Scheinberg LA, Spencer CL, Summers AP, Tapanila L, Thompson CW, Tornabene L, Watkins-Colwell GJ, Welton LJ, Stanley EL. Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network. Bioscience 2024; 74:169-186. [PMID: 38560620 PMCID: PMC10977868 DOI: 10.1093/biosci/biad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/08/2023] [Indexed: 04/04/2024] Open
Abstract
The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.
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Affiliation(s)
- David C Blackburn
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | - Doug M Boyer
- Duke University, Durham, North Carolina, United States
| | - Jaimi A Gray
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | - John M Bates
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Stephanie L Baumgart
- University of Chicago and University of Florida, Gainesville, Florida, United States
| | - Emily Braker
- University of Colorado, Boulder, Colorado, United States
| | - Daryl Coldren
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Kevin W Conway
- Texas A&M University, College Station, Texas, United States
| | | | - Noé de la Sancha
- Chicago State University DePaul University, Chicago, Illinois, United States
| | | | - Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Catherine M Early
- FLMNH Science Museum of Minnesota, St. Paul, Minnesota, United States
| | - Benjamin W Frable
- Scripps Institute of Oceanography, University of California, San Diego, San Diego, California, United States
| | - Matt W Gage
- Harvard University, Cambridge, Massachusetts, United States
| | - James Hanken
- Harvard University, Cambridge, Massachusetts, United States
| | | | - Ben D Marks
- Field Museum of Natural History, Chicago, Illinois, United States
| | | | | | | | | | | | | | - Zachary S Randall
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | | | - Carol L Spencer
- University of California, Berkeley, in Berkeley, California, United States
| | - Adam P Summers
- University of Washington, Seattle, Washington, United States
| | - Leif Tapanila
- Idaho State University, Pocatello, Idaho, United States
| | | | - Luke Tornabene
- University of Washington, Seattle, Washington, United States
| | | | - Luke J Welton
- University of Kansas, Lawrence, Kansas, United States
| | | | - Edward L Stanley
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
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2
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Ferrão M, Hanken J, Oda FH, Campião KM, Penhacek M, Anjos S, Rodrigues DJ. A new snouted treefrog (Anura, Hylidae, Scinax) from fluvial islands of the Juruena River, southern Brazilian Amazonia. PLoS One 2024; 19:e0292441. [PMID: 38295055 PMCID: PMC10830056 DOI: 10.1371/journal.pone.0292441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/19/2023] [Indexed: 02/02/2024] Open
Abstract
Southern Amazonia is one of the less-explored regions by anuran taxonomists. We describe a small new species of snouted treefrog, genus Scinax, from this region, from a fluvial archipelago in the Juruena River, state of Mato Grosso, Brazil. The description is based on external morphology of adults and tadpoles, advertisement call and molecular data. The species is phylogenetically related to other snouted treefrogs of the Scinax cruentomma species group and shows the most southeastern distribution in Amazonia among its close relatives. It is distinguished from congeners mainly by its larger adult body size and bilobate vocal sac that reaches the level of the pectoral fold, a reddish-brown horizontal stripe on the iris, dark melanophores or blotches on the vocal sac and the throat of females, and the uniformly brown posterior portion of the thigh. The advertisement call comprises one pulsed note emitted at regular intervals, with a duration of 189-227 ms, 30-35 pulses/note and a dominant frequency of 2,250-2,344 Hz. The type locality is suffering several environmental impacts, including illegal mining, overfishing, unsustainable agriculture, uncontrolled logging and degradation associated with the construction of new hydroelectric dams. Further study of the biology and regional distribution of the new species is required to propose mitigation measures needed for its conservation.
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Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Fabrício H. Oda
- Laboratório de Parasitologia Animal, Instituto de Biociências, Fundação Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação, Instituto de Biociências, Fundação Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Karla M. Campião
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marcos Penhacek
- Programa de Pós-Graduação em Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Samuel Anjos
- Programa de Pós-Graduação em Ciências Ambientais, Universidade Federal de Mato Grosso, Sinop, Mato Grosso, Brazil
| | - Domingo J. Rodrigues
- Programa de Pós-Graduação em Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Programa de Pós-Graduação em Ciências Ambientais, Universidade Federal de Mato Grosso, Sinop, Mato Grosso, Brazil
- Acervo Biológico da Amazônia Meridional, Universidade Federal de Mato Grosso, Sinop, Mato Grosso, Brazil
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3
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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4
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Nachman MW, Beckman EJ, Bowie RCK, Cicero C, Conroy CJ, Dudley R, Hayes TB, Koo MS, Lacey EA, Martin CH, McGuire JA, Patton JL, Spencer CL, Tarvin RD, Wake MH, Wang IJ, Achmadi A, Álvarez-Castañeda ST, Andersen MJ, Arroyave J, Austin CC, Barker FK, Barrow LN, Barrowclough GF, Bates J, Bauer AM, Bell KC, Bell RC, Bronson AW, Brown RM, Burbrink FT, Burns KJ, Cadena CD, Cannatella DC, Castoe TA, Chakrabarty P, Colella JP, Cook JA, Cracraft JL, Davis DR, Davis Rabosky AR, D’Elía G, Dumbacher JP, Dunnum JL, Edwards SV, Esselstyn JA, Faivovich J, Fjeldså J, Flores-Villela OA, Ford K, Fuchs J, Fujita MK, Good JM, Greenbaum E, Greene HW, Hackett S, Hamidy A, Hanken J, Haryoko T, Hawkins MTR, Heaney LR, Hillis DM, Hollingsworth BD, Hornsby AD, Hosner PA, Irham M, Jansa S, Jiménez RA, Joseph L, Kirchman JJ, LaDuc TJ, Leaché AD, Lessa EP, López-Fernández H, Mason NA, McCormack JE, McMahan CD, Moyle RG, Ojeda RA, Olson LE, Kin Onn C, Parenti LR, Parra-Olea G, Patterson BD, Pauly GB, Pavan SE, Peterson AT, Poe S, Rabosky DL, Raxworthy CJ, Reddy S, Rico-Guevara A, Riyanto A, Rocha LA, Ron SR, Rovito SM, Rowe KC, Rowley J, Ruane S, Salazar-Valenzuela D, Shultz AJ, Sidlauskas B, Sikes DS, Simmons NB, Stiassny MLJ, Streicher JW, Stuart BL, Summers AP, Tavera J, Teta P, Thompson CW, Timm RM, Torres-Carvajal O, Voelker G, Voss RS, Winker K, Witt C, Wommack EA, Zink RM. Specimen collection is essential for modern science. PLoS Biol 2023; 21:e3002318. [PMID: 37992027 PMCID: PMC10664955 DOI: 10.1371/journal.pbio.3002318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 11/24/2023] Open
Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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Affiliation(s)
- Michael W. Nachman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Chris J. Conroy
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Robert Dudley
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Tyrone B. Hayes
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Eileen A. Lacey
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Christopher H. Martin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carol L. Spencer
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Marvalee H. Wake
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Ian J. Wang
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Michael J. Andersen
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christopher C. Austin
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lisa N. Barrow
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | - John Bates
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Kayce C. Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Rayna C. Bell
- California Academy of Sciences, San Francisco, California, United States of America
| | - Allison W. Bronson
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - Rafe M. Brown
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Frank T. Burbrink
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | | | - David C. Cannatella
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jocelyn P. Colella
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joel L. Cracraft
- American Museum of Natural History, New York, New York, United States of America
| | - Drew R. Davis
- Natural History Museum and Dept. of Biology, Eastern New Mexico University, Portales, New Mexico, United States of America
| | | | - Guillermo D’Elía
- Instituto de Cs. Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - John P. Dumbacher
- California Academy of Sciences, San Francisco, California, United States of America
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Scott V. Edwards
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Julián Faivovich
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Kassandra Ford
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jérôme Fuchs
- ISYEB, Muséum national d’Histoire naturelle, Paris, France
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jeffrey M. Good
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Eli Greenbaum
- Biodiversity Collections and Dept. of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Harry W. Greene
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shannon Hackett
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Melissa TR Hawkins
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Lawrence R. Heaney
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - David M. Hillis
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Angela D. Hornsby
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Peter A. Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sharon Jansa
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Rosa Alicia Jiménez
- Escuela de Biología, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | | | - Travis J. LaDuc
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam D. Leaché
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Universidad de la República, Montevideo, Uruguay
| | - Hernán López-Fernández
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John E. McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Ricardo A. Ojeda
- CONICET, Centro de Ciencia y Técnica Mendoza, Mendoza, Argentina
| | - Link E. Olson
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | | | - Lynne R. Parenti
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Bruce D. Patterson
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Silvia E. Pavan
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - A Townsend Peterson
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Steven Poe
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daniel L. Rabosky
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Sushma Reddy
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | | | - Awal Riyanto
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Luiz A. Rocha
- California Academy of Sciences, San Francisco, California, United States of America
| | - Santiago R. Ron
- Museo de Zoología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Kevin C. Rowe
- Museums Victoria Research Institute, Melbourne, Australia
| | - Jodi Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Sara Ruane
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | | | - Allison J. Shultz
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Brian Sidlauskas
- Dept. of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Nancy B. Simmons
- American Museum of Natural History, New York, New York, United States of America
| | | | | | - Bryan L. Stuart
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
| | - Adam P. Summers
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
| | | | - Pablo Teta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Cody W. Thompson
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert M. Timm
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | | | - Gary Voelker
- Dept. Ecology and Conservation Biology, Texas A&M University, College Station, Texas, United States of America
| | - Robert S. Voss
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Christopher Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
| | - Robert M. Zink
- University of Nebraska State Museum, Lincoln, Nebraska, United States of America
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5
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Abstract
Modularity (segmentation), homology and heterochrony were essential concepts embraced by Gavin de Beer in his studies of the development and evolution of the vertebrate skull. While his pioneering contributions have stood the test of time, our understanding of the biological processes that underlie each concept has evolved. We assess de Beer's initial training as an experimental embryologist; his switch to comparative and descriptive studies of skulls, jaws and middle ear ossicles; and his later research on the mammalian skull, including his approach to head segmentation. The role of cells of neural crest and mesodermal origin in skull development, and developmental, palaeontological and molecular evidence for the origin of middle ear ossicles in the evolutionary transition from reptiles to mammals are used to illustrate our current understanding of modularity, homology and heterochrony. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Brian K Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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6
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Lewis ZR, Kerney R, Hanken J. Developmental basis of evolutionary lung loss in plethodontid salamanders. Sci Adv 2022; 8:eabo6108. [PMID: 35977024 PMCID: PMC9385146 DOI: 10.1126/sciadv.abo6108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
One or more members of four living amphibian clades have independently dispensed with pulmonary respiration and lack lungs, but little is known of the developmental basis of lung loss in any taxon. We use morphological, molecular, and experimental approaches to examine the Plethodontidae, a dominant family of salamanders, all of which are lungless as adults. We confirm an early anecdotal report that plethodontids complete early stages of lung morphogenesis: Transient embryonic lung primordia form but regress by apoptosis before hatching. Initiation of pulmonary development coincides with expression of the lung-specification gene Wnt2b in adjacent mesoderm, and the lung rudiment expresses pulmonary markers Nkx2.1 and Sox9. Lung developmental-genetic pathways are at least partially conserved despite the absence of functional adult lungs for at least 25 and possibly exceeding 60 million years. Adult lung loss appears associated with altered expression of signaling molecules that mediate later stages of tracheal and pulmonary development.
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Affiliation(s)
- Zachary R. Lewis
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, PA, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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7
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Ferrão M, Hanken J, Lima AP. A new nurse frog of the Allobates tapajos species complex (Anura: Aromobatidae) from the upper Madeira River, Brazilian Amazonia. PeerJ 2022; 10:e13751. [PMID: 35942125 PMCID: PMC9356586 DOI: 10.7717/peerj.13751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/28/2022] [Indexed: 01/17/2023] Open
Abstract
Cryptic diversity is extremely common in widespread Amazonian anurans, but especially in nurse frogs of the genus Allobates. There is an urgent need to formally describe the many distinct but unnamed species, both to enable studies of their basic biology but especially to facilitate conservation of threatened environments in which many are found. Here, we describe through integrative taxonomy a new species of the Allobates tapajos species complex from the upper Madeira River, southwestern Amazonia. Species delimitation analyses based on molecular data are congruent and delimit five candidate species in addition to A. tapajos sensu stricto. The new species is recovered as sister to A. tapajos clade F, a candidate species from Teles-Pires River, southeastern Amazonia. The new species differs from nominal congeners in adult and larval morphology and in male advertisement call. Egg deposition sites differ between east and west banks of the upper Madeira River, but there is no evidence of corresponding morphologic or bioacoustic differentiation. The new species appears to be restricted to riparian forests; its known geographic range falls entirely within the influence zone of reservoirs of two large dams, which underscores the urgent need of a conservation assessment through long-term monitoring. This region harbors the richest assemblage of Allobates reported for Brazilian Amazonia, with six nominal species and four additional candidate species awaiting formal description.
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Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Albertina P. Lima
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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8
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Ferrão M, de Souza RA, Colatreli OP, Hanken J, Lima AP. Hidden in the litter: cryptic diversity of the leaf-litter toad Rhinella castaneotica– proboscidea complex revealed through integrative taxonomy, with description of a new species from south-western Amazonia. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2039317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Romildo Augusto de Souza
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Olavo Pinhatti Colatreli
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Albertina Pimentel Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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9
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Ferrão M, Lima AP, Ron S, Santos SPD, Hanken J. New Species of Leaf-litter Toad of the Rhinella margaritifera Species Group (Anura: Bufonidae) from Amazonia. COPEIA 2020. [DOI: 10.1643/ch2020043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts; (MF) ; and (JH) . Send reprint requests to MF
| | - Albertina Pimentel Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil;
| | - Santiago Ron
- Museum of Zoology–QCAZ, Pontificia Universidad Católica del Ecuador, Quito, Ecuador; (SR) ; and (SPS)
| | - Sueny Paloma dos Santos
- Museum of Zoology–QCAZ, Pontificia Universidad Católica del Ecuador, Quito, Ecuador; (SR) ; and (SPS)
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts; (MF) ; and (JH) . Send reprint requests to MF
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10
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Souza JRD, Ferrão M, Hanken J, Lima AP. A new nurse frog (Anura: Allobates) from Brazilian Amazonia with a remarkably fast multi-noted advertisement call. PeerJ 2020; 8:e9979. [PMID: 33194373 PMCID: PMC7648453 DOI: 10.7717/peerj.9979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/27/2020] [Indexed: 11/25/2022] Open
Abstract
Nurse frogs (Aromobatidae: Allobates) are probably the most extensively studied genus by taxonomists in Brazilian Amazonia. The southwestern portion of Amazonia is the most species-rich: as many as seven species may occur in sympatry at a single locality. In this study, we describe a new species of nurse frog from this region. The description integrates data from larval and adult morphology, advertisement calls and DNA sequences. Allobates velocicantus sp. nov. is distinguished from other Allobates mainly by the absence of hourglass-shaped dark marks on the dorsum and dark transverse bars on the thigh; a throat that is white centrally and yellow marginally; basal webbing on toes II and III; finger I longer than finger II; and an advertisement call composed of 66–138 pulsed notes with a note duration of 5–13 ms, inter-note intervals of 10–18 ms and a dominant frequency of 5,512–6,158 Hz. Tadpoles of the new species have 3–4 short, rounded papillae on the anterior labium, 16–23 papillae on the posterior labium, and a labial keratodont row formula 2(2)/3(1). This is the fifth species of Allobates described from the state of Acre, southwestern Brazilian Amazonia.
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Affiliation(s)
- Jesus R D Souza
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.,Departamento de Áreas Protegidas e Biodiversidade, Secretaria de Meio Ambiente do Acre, Rio Branco, Acre, Brazil
| | - Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA.,Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Albertina P Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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11
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Ferrão M, Moravec J, Hanken J, Lima AP. A new species of Dendropsophus (Anura, Hylidae) from southwestern Amazonia with a green bilobate vocal sac. Zookeys 2020; 942:77-104. [PMID: 32612443 PMCID: PMC7316805 DOI: 10.3897/zookeys.942.51864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022] Open
Abstract
Recent studies have shown that species diversity of the South American frog genus Dendropsophus is significantly underestimated, especially in Amazonia. Herein, through integrative taxonomy a new species of Dendropsophus from the east bank of the upper Madeira River, Brazil is described. Based on molecular phylogenetic and morphological analyses, the new species is referred to the D. microcephalus species group, where it is differentiated from its congeners mainly by having a green bilobate vocal sac and an advertisement call comprising 1-4 monophasic notes emitted with a dominant frequency of 8,979-9,606 Hz. Based on intensive sampling conducted in the study area over the last ten years, the new species is restricted to the east bank of the upper Madeira River, although its geographic range is expected to include Bolivian forests close to the type locality.
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Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA Harvard University Cambridge United States of America.,Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Jiří Moravec
- Department of Zoology, National Museum, Prague, Czech Republic National Museum Prague Czech Republic
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA Harvard University Cambridge United States of America
| | - Albertina Pimentel Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
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12
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Maddin HC, Piekarski N, Reisz RR, Hanken J. Development and evolution of the tetrapod skull-neck boundary. Biol Rev Camb Philos Soc 2020; 95:573-591. [PMID: 31912655 PMCID: PMC7318664 DOI: 10.1111/brv.12578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 11/26/2022]
Abstract
The origin and evolution of the vertebrate skull have been topics of intense study for more than two centuries. Whereas early theories of skull origin, such as the influential vertebral theory, have been largely refuted with respect to the anterior (pre-otic) region of the skull, the posterior (post-otic) region is known to be derived from the anteriormost paraxial segments, i.e. the somites. Here we review the morphology and development of the occiput in both living and extinct tetrapods, taking into account revised knowledge of skull development by augmenting historical accounts with recent data. When occipital composition is evaluated relative to its position along the neural axis, and specifically to the hypoglossal nerve complex, much of the apparent interspecific variation in the location of the skull-neck boundary stabilizes in a phylogenetically informative way. Based on this criterion, three distinct conditions are identified in (i) frogs, (ii) salamanders and caecilians, and (iii) amniotes. The position of the posteriormost occipital segment relative to the hypoglossal nerve is key to understanding the evolution of the posterior limit of the skull. By using cranial foramina as osteological proxies of the hypoglossal nerve, a survey of fossil taxa reveals the amniote condition to be present at the base of Tetrapoda. This result challenges traditional theories of cranial evolution, which posit translocation of the occiput to a more posterior location in amniotes relative to lissamphibians (frogs, salamanders, caecilians), and instead supports the largely overlooked hypothesis that the reduced occiput in lissamphibians is secondarily derived. Recent advances in our understanding of the genetic basis of axial patterning and its regulation in amniotes support the hypothesis that the lissamphibian occipital form may have arisen as the product of a homeotic shift in segment fate from an amniote-like condition.
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Affiliation(s)
- Hillary C. Maddin
- Museum of Comparative ZoologyHarvard University, 26 Oxford StreetCambridgeMA02138U.S.A.
- Department of Earth SciencesCarleton University, 1125 Colonel By DriveOttawaOntarioK1S 5B6Canada
| | - Nadine Piekarski
- Museum of Comparative ZoologyHarvard University, 26 Oxford StreetCambridgeMA02138U.S.A.
| | - Robert R. Reisz
- Department of BiologyUniversity of Toronto Mississauga3359 Mississauga Road, MississaugaOntarioL5L 1C6Canada
| | - James Hanken
- Museum of Comparative ZoologyHarvard University, 26 Oxford StreetCambridgeMA02138U.S.A.
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13
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Parra Olea G, Garcia-Castillo MG, Rovito SM, Maisano JA, Hanken J, Wake DB. Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa. PeerJ 2020; 8:e8800. [PMID: 32518712 PMCID: PMC7258950 DOI: 10.7717/peerj.8800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/25/2020] [Indexed: 11/20/2022] Open
Abstract
The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico's amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has 18 described species including terrestrial, arboreal and cave-dwelling species. In previous molecular studies, the presence of multiple undescribed species was evident. We present a phylogenetic hypothesis based on mitochondrial data, which includes all described species and six undescribed taxa. Based on the morphological analyses and, when available, combined with molecular data, we describe five new species of the genus; Chiropterotriton casasi sp. nov., C. ceronorum sp. nov., C. melipona sp. nov., C. perotensis sp. nov. and C. totonacus sp. nov. In addition, we redescribe two others: Chiropterotriton chiropterus and C. orculus, and provide a comparable account of one additional sympatric congener. This increases the number of species in the genus to 23, which represent a considerable component of Mexican plethodontid richness.
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Affiliation(s)
- Gabriela Parra Olea
- Zoology, Instituto de Biología, Universidad Nacional Autonoma de México, Mexico city, México
| | - Mirna G Garcia-Castillo
- Zoology, Instituto de Biología, Universidad Nacional Autonoma de México, Mexico city, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sean M Rovito
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato, Guanajuato, México
| | - Jessica A Maisano
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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14
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Hanken J, Lewis Z. Developmental Basis and Consequences of a Key Innovation in Lungless Salamanders. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Cordeiro IR, Kabashima K, Ochi H, Munakata K, Nishimori C, Laslo M, Hanken J, Tanaka M. Environmental Oxygen Exposure Allows for the Evolution of Interdigital Cell Death in Limb Patterning. Dev Cell 2019; 50:155-166.e4. [PMID: 31204171 DOI: 10.1016/j.devcel.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/01/2019] [Accepted: 05/10/2019] [Indexed: 01/04/2023]
Abstract
Amphibians form fingers without webbing by differential growth between digital and interdigital regions. Amniotes, however, employ interdigital cell death (ICD), an additional mechanism that contributes to a greater variation of limb shapes. Here, we investigate the role of environmental oxygen in the evolution of ICD in tetrapods. While cell death is restricted to the limb margin in amphibians with aquatic tadpoles, Eleutherodactylus coqui, a frog with terrestrial-direct-developing eggs, has cell death in the interdigital region. Chicken requires sufficient oxygen and reactive oxygen species to induce cell death, with the oxygen tension profile itself being distinct between the limbs of chicken and Xenopus laevis frogs. Notably, increasing blood vessel density in X. laevis limbs, as well as incubating tadpoles under high oxygen levels, induces ICD. We propose that the oxygen available to terrestrial eggs was an ecological feature crucial for the evolution of ICD, made possible by conserved autopod-patterning mechanisms.
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Affiliation(s)
- Ingrid Rosenburg Cordeiro
- School of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kaori Kabashima
- School of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan
| | - Keijiro Munakata
- School of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Chika Nishimori
- School of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Mikiko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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16
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Laslo M, Denver RJ, Hanken J. Evolutionary Conservation of Thyroid Hormone Receptor and Deiodinase Expression Dynamics in ovo in a Direct-Developing Frog, Eleutherodactylus coqui. Front Endocrinol (Lausanne) 2019; 10:307. [PMID: 31178826 PMCID: PMC6542950 DOI: 10.3389/fendo.2019.00307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
Direct development is a reproductive mode in amphibians that has evolved independently from the ancestral biphasic life history in at least a dozen anuran lineages. Most direct-developing frogs, including the Puerto Rican coquí, Eleutherodactylus coqui, lack a free-living aquatic larva and instead hatch from terrestrial eggs as miniature adults. Their embryonic development includes the transient formation of many larval-specific features and the formation of adult-specific features that typically form postembryonically-during metamorphosis-in indirect-developing frogs. We found that pre-hatching developmental patterns of thyroid hormone receptors alpha (thra) and beta (thrb) and deiodinases type II (dio2) and type III (dio3) mRNAs in E. coqui limb and tail are conserved relative to those seen during metamorphosis in indirect-developing frogs. Additionally, thra, thrb, and dio2 mRNAs are expressed in the limb before formation of the embryonic thyroid gland. Liquid-chromatography mass-spectrometry revealed that maternally derived thyroid hormone is present throughout early embryogenesis, including stages of digit formation that occur prior to the increase in embryonically produced thyroid hormone. Eleutherodactylus coqui embryos take up much less 3,5,3'-triiodothyronine (T3) from the environment compared with X. tropicalis tadpoles. However, E. coqui tissue explants mount robust and direct gene expression responses to exogenous T3 similar to those seen in metamorphosing species. The presence of key components of the thyroid axis in the limb and the ability of limb tissue to respond to T3 suggest that thyroid hormone-mediated limb development may begin prior to thyroid gland formation. Thyroid hormone-dependent limb development and tail resorption characteristic of metamorphosis in indirect-developing anurans are evolutionarily conserved, but they occur instead in ovo in E. coqui.
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Affiliation(s)
- Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
- *Correspondence: Mara Laslo
| | - Robert J. Denver
- Departments of Molecular, Cellular and Developmental Biology, and Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
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17
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Lewis ZR, Dorantes JA, Hanken J. Expression of a novel surfactant protein gene is associated with sites of extrapulmonary respiration in a lungless salamander. Proc Biol Sci 2018; 285:rspb.2018.1589. [PMID: 30282653 PMCID: PMC6191699 DOI: 10.1098/rspb.2018.1589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/05/2018] [Indexed: 01/10/2023] Open
Abstract
Numerous physiological and morphological adaptations were achieved during the transition to lungless respiration that accompanied evolutionary lung loss in plethodontid salamanders, including those that enable efficient gas exchange across extrapulmonary tissue. However, the molecular basis of these adaptations is unknown. Here, we show that lungless salamanders express in the larval integument and the adult buccopharynx—principal sites of respiratory gas exchange in these species—a novel paralogue of the gene surfactant-associated protein C (SFTPC), which is a critical component of pulmonary surfactant expressed exclusively in the lung in other vertebrates. The paralogous gene appears to be found only in salamanders, but, similar to SFTPC, in lunged salamanders it is expressed only in the lung. This heterotopic gene expression, combined with predictions from structural modelling and respiratory tissue ultrastructure, suggests that lungless salamanders may produce pulmonary surfactant-like secretions outside the lungs and that the novel paralogue of SFTPC might facilitate extrapulmonary respiration in the absence of lungs. Heterotopic expression of the SFTPC paralogue may have contributed to the remarkable evolutionary radiation of lungless salamanders, which account for more than two thirds of urodele species alive today.
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Affiliation(s)
- Zachary R Lewis
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jorge A Dorantes
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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18
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Kerney RR, Hanken J, Blackburn DC. Cover Image: Volume 20, Issue 3‐4. Evol Dev 2018. [DOI: 10.1111/ede.12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Abstract
Direct-developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct-developing frogs, but little attention has been given to direct-developing salamanders. We use expression patterns of two genes, sox9 and col2a1, to assess skeletal patterning during embryonic limb development in the direct-developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior-to-posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial cartilages (radius/tibia) is not accelerated in relation to the postaxial cartilages, and there is no early differentiation of autopodial elements in relation to more proximal cartilages. Instead, digit II forms in continuity with the ulnar/fibular arch. This amniote-like connectivity to the first digit that forms may be a consequence of the embryonic formation of limbs in this direct-developing species. Additionally, and contrary to recent models of amphibian digit identity, there is no evidence of vestigial digits. This is the first account of gene expression in a plethodontid salamander and only the second published account of embryonic limb patterning in a direct-developing salamander species.
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Affiliation(s)
- Ryan R Kerney
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
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20
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Abstract
Nearly two thirds of the approximately 700 species of living salamanders are lungless. These species respire entirely through the skin and buccopharyngeal mucosa. Lung loss dramatically impacts the configuration of the circulatory system but the effects of evolutionary lung loss on cardiac morphology have long been controversial. For example, there is presumably little need for an atrial septum in lungless salamanders due to the absence of pulmonary veins and the presence of a single source of mixed blood flowing into the heart, but whether lungless salamanders possess an atrial septum and whether the sinoatrial aperture is located in the left or right atrium are unresolved; authors have stated opposing claims since the late 1800s. Here, we use micro-computed tomography (μ-CT) imaging, gross dissection and histological reconstruction to compare cardiac morphology among lungless plethodontid salamanders (Plethodontidae), salamanders with lungs, and the convergently lungless species Onychodactylus japonicus (Hynobiidae). Plethodontid salamanders have partial atrial septa and incomplete separation of the atrium into left and right halves. Partial septation is also seen in O. japonicus. Hence, lungless salamanders from two lineages convergently evolved similar morphology of the atrial septum. The partial septum in lungless salamanders can make it appear that the sinoatrial aperture is in the left atrium, but this interpretation is incorrect. Outgroup comparisons demonstrate that the aperture is located in a posterodorsal extension of the right atrium into the left side of the heart. Independent evolutionary losses of the atrial septum may have a similar developmental basis. In mammals, the lungs induce formation of the atrial septum by secreting morphogens to neighboring mesenchyme. We hypothesize that the lungs induce atrial septum development in amphibians in a similar fashion to mammals, and that atrial septum reduction in lungless salamanders is a direct result of lunglessness.
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Affiliation(s)
- Zachary R. Lewis
- Department of Organismic and Evolutionary Biology, and Museum of Comparative ZoologyHarvard UniversityCambridgeMAUSA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative ZoologyHarvard UniversityCambridgeMAUSA
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21
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Parra-Olea G, Rovito SM, García-París M, Maisano JA, Wake DB, Hanken J. Biology of tiny animals: three new species of minute salamanders (Plethodontidae: Thorius) from Oaxaca, Mexico. PeerJ 2016; 4:e2694. [PMID: 27896029 PMCID: PMC5119241 DOI: 10.7717/peerj.2694] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/16/2016] [Indexed: 11/20/2022] Open
Abstract
We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species, T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. Adult Thorius pinicola sp. nov., T. longicaudus sp. nov., and T. tlaxiacus sp. nov. are larger than T. minutissimus and possess elliptical rather than oval nostrils; T. pinicola and T. longicaudus also have longer tails. All three new species occur west of the range of T. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other named Thorius in Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribe T. minutissimus and a related species, T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiated Thorius that cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature. Thorius may be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.
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Affiliation(s)
- Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Sean M Rovito
- Unidad de Genómica Avanzada (Langebio), CINVESTAV , Irapuato, Guanajuato , Mexico
| | - Mario García-París
- Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC) , Madrid , Spain
| | - Jessica A Maisano
- Jackson School of Geosciences, University of Texas at Austin , Austin, Texas , United States
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California , Berkeley, California , United States
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University , Cambridge, Massachusetts , United States
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22
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Maddin HC, Piekarski N, Sefton EM, Hanken J. Homology of the cranial vault in birds: new insights based on embryonic fate-mapping and character analysis. R Soc Open Sci 2016; 3:160356. [PMID: 27853617 PMCID: PMC5108967 DOI: 10.1098/rsos.160356] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/12/2016] [Indexed: 05/24/2023]
Abstract
Bones of the cranial vault appear to be highly conserved among tetrapod vertebrates. Moreover, bones identified with the same name are assumed to be evolutionarily homologous. However, recent developmental studies reveal a key difference in the embryonic origin of cranial vault bones between representatives of two amniote lineages, mammals and birds, thereby challenging this view. In the mouse, the frontal is derived from cranial neural crest (CNC) but the parietal is derived from mesoderm, placing the CNC-mesoderm boundary at the suture between these bones. In the chicken, this boundary is located within the frontal. This difference and related data have led several recent authors to suggest that bones of the avian cranial vault are misidentified and should be renamed. To elucidate this apparent conflict, we fate-mapped CNC and mesoderm in axolotl to reveal the contributions of these two embryonic cell populations to the cranial vault in a urodele amphibian. The CNC-mesoderm boundary in axolotl is located between the frontal and parietal bones, as in the mouse but unlike the chicken. If, however, the avian frontal is regarded instead as a fused frontal and parietal (i.e. frontoparietal) and the parietal as a postparietal, then the cranial vault of birds becomes developmentally and topologically congruent with those of urodeles and mammals. This alternative hypothesis of cranial vault homology is also phylogenetically consistent with data from the tetrapod fossil record, where frontal, parietal and postparietal bones are present in stem lineages of all extant taxa, including birds. It further implies that a postparietal may be present in most non-avian archosaurs, but fused to the parietal or supraoccipital as in many extant mammals.
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Affiliation(s)
- Hillary C Maddin
- Museum of Comparative Zoology , Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Nadine Piekarski
- Museum of Comparative Zoology , Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Elizabeth M Sefton
- Museum of Comparative Zoology , Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - James Hanken
- Museum of Comparative Zoology , Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
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23
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Abstract
Vertebrate neck musculature spans the transition zone between head and trunk. The extent to which the cucullaris muscle is a cranial muscle allied with the gill levators of anamniotes or is instead a trunk muscle is an ongoing debate. Novel computed tomography datasets reveal broad conservation of the cucullaris in gnathostomes, including coelacanth and caecilian, two sarcopterygians previously thought to lack it. In chicken, lateral plate mesoderm (LPM) adjacent to occipital somites is a recently identified embryonic source of cervical musculature. We fate-map this mesoderm in the axolotl (Ambystoma mexicanum), which retains external gills, and demonstrate its contribution to posterior gill-levator muscles and the cucullaris. Accordingly, LPM adjacent to the occipital somites should be regarded as posterior cranial mesoderm. The axial position of the head-trunk border in axolotl is congruent between LPM and somitic mesoderm, unlike in chicken and possibly other amniotes.
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Affiliation(s)
- Elizabeth M Sefton
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
| | - Bhart-Anjan S Bhullar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States.,Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States.,Department of Geology and Geophysics, Yale University, New Haven, United States.,Yale Peabody Museum of Natural History, Yale University, New Haven, United States
| | - Zahra Mohaddes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
| | - James Hanken
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Museum of Comparative Zoology, Harvard University, Cambridge, United States
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24
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Senevirathne G, Thomas A, Kerney R, Hanken J, Biju SD, Meegaskumbura M. From Clinging to Digging: The Postembryonic Skeletal Ontogeny of the Indian Purple Frog, Nasikabatrachus sahyadrensis (Anura: Nasikabatrachidae). PLoS One 2016; 11:e0151114. [PMID: 27028113 PMCID: PMC4814056 DOI: 10.1371/journal.pone.0151114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
The Indian Purple frog, Nasikabatrachus sahyadrensis, occupies a basal phylogenetic position among neobatrachian anurans and has a very unusual life history. Tadpoles have a large ventral oral sucker, which they use to cling to rocks in torrents, whereas metamorphs possess adaptations for life underground. The developmental changes that underlie these shifts in habits and habitats, and especially the internal remodeling of the cranial and postcranial skeleton, are unknown. Using a nearly complete metamorphic series from free-living larva to metamorph, we describe the postembryonic skeletal ontogeny of this ancient and unique monotypic lineage. The torrent-dwelling larva possesses a dorsoventrally flattened body and a head with tiny dorsal eyes, robust lower and upper jaw cartilages, well-developed trabecular horns, and a definable gap between the trabecular horns and the tip of the snout. Unlike tadpoles of many other frogs, those of Nasikabatrachus retain larval mouthparts into late metamorphic stages. This unusual feature enables the larvae to maintain their clinging habit until near the end of metamorphosis. The subsequent ontogenetic shift from clinging to digging is correlated with rapid morphological changes and behavioral modifications. Metamorphs are equipped with a shortened tibiafibula and ossified prehallical elements, which likely facilitate initial digging using the hind limbs. Subsequently, the frogs may shift to headfirst burrowing by using the wedge-shaped skull, anteriorly positioned pectoral girdle, well-developed humeral crests and spatula-shaped forelimbs. The transition from an aquatic life in torrents to a terrestrial life underground entails dramatic changes in skeletal morphology and function that represent an extreme in metamorphic remodeling. Our analysis enhances the scope for detailed comparative studies across anurans, a group renowned for the diversity of its life history strategies.
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Affiliation(s)
- Gayani Senevirathne
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Ashish Thomas
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, United States of America
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - S. D. Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Madhava Meegaskumbura
- Department of Molecular Biology & Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
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25
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Meegaskumbura M, Senevirathne G, Biju SD, Garg S, Meegaskumbura S, Pethiyagoda R, Hanken J, Schneider CJ. Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madhava Meegaskumbura
- Department of Molecular Biology & Biotechnology; Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | - Gayani Senevirathne
- Department of Molecular Biology & Biotechnology; Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | - S. D. Biju
- Department of Environmental Studies; University of Delhi; Delhi 110 007 India
| | - Sonali Garg
- Department of Environmental Studies; University of Delhi; Delhi 110 007 India
| | - Suyama Meegaskumbura
- Department of Zoology Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | | | - James Hanken
- Museum of Comparative Zoology; Harvard University; Cambridge MA 02138 USA
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26
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McPhillips T, Song T, Kolisnik T, Aulenbach S, Belhajjame K, Bocinsky RK, Cao Y, Cheney J, Chirigati F, Dey S, Freire J, Jones C, Hanken J, Kintigh KW, Kohler TA, Koop D, Macklin JA, Missier P, Schildhauer M, Schwalm C, Wei Y, Bieda M, Ludäscher B. YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts. IJDC 2015. [DOI: 10.2218/ijdc.v10i1.370] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, and MATLAB), and to the high productivity many scientists experience when using these languages. YesWorkflow is a set of software tools that aim to provide such users of scripting languages with many of the benefits of scientific workflow systems. YesWorkflow requires neither the use of a workflow engine nor the overhead of adapting code to run effectively in such a system. Instead, YesWorkflow enables scientists to annotate existing scripts with special comments that reveal the computational modules and dataflows otherwise implicit in these scripts. YesWorkflow tools extract and analyze these comments, represent the scripts in terms of entities based on the typical scientific workflow model, and provide graphical renderings of this workflow-like view of the scripts. Future version of YesWorkflow will also allow the prospective provenance of the data products of these scripts to be queried in ways similar to those available to users of scientific workflow systems.
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27
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Sefton EM, Piekarski N, Hanken J. Dual embryonic origin and patterning of the pharyngeal skeleton in the axolotl (
Ambystoma mexicanum
). Evol Dev 2015; 17:175-84. [DOI: 10.1111/ede.12124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elizabeth M. Sefton
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard University26 Oxford StreetCambridgeMA02138USA
| | - Nadine Piekarski
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard University26 Oxford StreetCambridgeMA02138USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard University26 Oxford StreetCambridgeMA02138USA
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28
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Lewis Z, Hanken J. A salamander model for atrial septal defects and cardiopulmonary evolution. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.552.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zachary Lewis
- Dept. of Organismic and EvolutionaryBiology Harvard UniversityCambridgeMAUnited States
| | - James Hanken
- Dept. of Organismic and EvolutionaryBiology Harvard UniversityCambridgeMAUnited States
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29
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Jennings DH, Evans B, Hanken J. Development of neuroendocrine components of the thyroid axis in the direct-developing frog Eleutherodactylus coqui: formation of the median eminence and onset of pituitary TSH production. Gen Comp Endocrinol 2015; 214:62-7. [PMID: 25745815 DOI: 10.1016/j.ygcen.2015.01.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 01/21/2015] [Accepted: 01/24/2015] [Indexed: 11/26/2022]
Abstract
Direct-developing frogs lack, wholly or in part, a wide range of larval features found in metamorphosing species and form adult-specific features precociously, during embryogenesis. Most information on thyroid regulation of direct development relies on hormone manipulations; the ontogeny of many thyroid axis components has not been fully described. This analysis examines differentiation of the median eminence of the hypothalamus and production of thyroid-stimulating hormone (TSH) by the pituitary of the direct-developing frog Eleutherodactylus coqui. The median eminence is established two-thirds of the way through embryogenesis. Cells immunoreactive to human TSHβ antibodies are first detected during embryogenesis and quantitative changes in TSHβ-IR cells resemble those in metamorphosing amphibians. Formation of the median eminence of the hypothalamus and TSHβ production by the pituitary precede or coincide with morphological changes during embryogenesis that occur during metamorphosis in biphasic anurans. Thus, while the onset of neuroendocrine regulation has changed during the evolution of direct development, it is likely that these thyroid axis components still mediate the formation of adult features.
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Affiliation(s)
- David H Jennings
- Department of Environmental, Population and Organismic Biology, University of Colorado, Boulder, CO 80309, United States; Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, United States.
| | - Bryce Evans
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, United States
| | - James Hanken
- Department of Environmental, Population and Organismic Biology, University of Colorado, Boulder, CO 80309, United States
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30
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Maddin H, Piekarski N, Sefton E, Hanken J. Reevaluation of the homology of bones of the cranial vault in tetrapod vertebrates. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.867.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hillary Maddin
- Earth Sciences Carleton UniversityOttawaOntarioCanada
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMassachusettsUnited States
| | - Nadine Piekarski
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMassachusettsUnited States
| | - Elizabeth Sefton
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMassachusettsUnited States
| | - James Hanken
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMassachusettsUnited States
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31
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Sefton E, Hanken J. Embryonic Origin and Patterning of Cranial Muscle in the Mexican Axolotl (
Ambystoma mexicanum
). FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.872.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elizabeth Sefton
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMAUnited States
| | - James Hanken
- Organismic and Evolutionary Biology Harvard UniversityCambridgeMAUnited States
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32
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Song T, Köhler S, Ludäscher B, Hanken J, Kelly M, Lowery D, Macklin JA, Morris PJ, Morris RA. Towards Automated Design, Analysis and Optimization of Declarative Curation Workflows. IJDC 2014. [DOI: 10.2218/ijdc.v9i2.337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Data curation is increasingly important. Our previous work on a Kepler curation package has demonstrated advantages that come from automating data curation pipelines by using workflow systems. However, manually designed curation workflows can be error-prone and inefficient due to a lack of user understanding of the workflow system, misuse of actors, or human error. Correcting problematic workflows is often very time-consuming. A more proactive workflow system can help users avoid such pitfalls. For example, static analysis before execution can be used to detect the potential problems in a workflow and help the user to improve workflow design. In this paper, we propose a declarative workflow approach that supports semi-automated workflow design, analysis and optimization. We show how the workflow design engine helps users to construct data curation workflows, how the workflow analysis engine detects different design problems of workflows and how workflows can be optimized by exploiting parallelism.
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33
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Cook JA, Edwards SV, Lacey EA, Guralnick RP, Soltis PS, Soltis DE, Welch CK, Bell KC, Galbreath KE, Himes C, Allen JM, Heath TA, Carnaval AC, Cooper KL, Liu M, Hanken J, Ickert-Bond S. Natural History Collections as Emerging Resources for Innovative Education. Bioscience 2014. [DOI: 10.1093/biosci/biu096] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Abstract
Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.
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Affiliation(s)
- Robert A. Morris
- Harvard University Herbaria, Cambridge, Massachusetts, United States of America
- Computer Science Department, University of Massachusetts, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lei Dou
- UC Davis Genome Center, University of California, Davis, California, United States of America
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maureen Kelly
- Harvard University Herbaria, Cambridge, Massachusetts, United States of America
| | - David B. Lowery
- Harvard University Herbaria, Cambridge, Massachusetts, United States of America
- Computer Science Department, University of Massachusetts, Boston, Massachusetts, United States of America
| | - Bertram Ludäscher
- UC Davis Genome Center, University of California, Davis, California, United States of America
| | | | - Paul J. Morris
- Harvard University Herbaria, Cambridge, Massachusetts, United States of America
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
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35
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Abstract
Phenotypic variation is a prerequisite for evolution by natural selection, yet the processes that give rise to the novel morphologies upon which selection acts are poorly understood. We employed a chemical genetic screen to identify developmental changes capable of generating ecologically relevant morphological variation as observed among extant species. Specifically, we assayed for exogenously applied small molecules capable of transforming the ancestral larval foregut of the herbivorous Xenopus laevis to resemble the derived larval foregut of the carnivorous Lepidobatrachus laevis. Appropriately, the small molecules that demonstrate this capacity modulate conserved morphogenetic pathways involved in gut development, including downregulation of retinoic acid (RA) signaling. Identical manipulation of RA signaling in a species that is more closely related to Lepidobatrachus, Ceratophrys cranwelli, yielded even more similar transformations, corroborating the relevance of RA signaling variation in interspecific morphological change. Finally, we were able to recover the ancestral gut phenotype in Lepidobatrachus by performing a reverse chemical manipulation to upregulate RA signaling, providing strong evidence that modifications to this specific pathway promoted the emergence of a lineage-specific phenotypic novelty. Interestingly, our screen also revealed pathways that have not yet been implicated in early gut morphogenesis, such as thyroid hormone signaling. In general, the chemical genetic screen may be a valuable tool for identifying developmental mechanisms that underlie ecologically and evolutionarily relevant phenotypic variation.
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Affiliation(s)
- Stephanie Bloom
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606 USA
| | - Cris Ledon-Rettig
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606 USA
| | - Carlos Infante
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Anne Everly
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Nanette Nascone-Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606 USA
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36
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Rovito SM, Parra-Olea G, Hanken J, Bonett RM, Wake DB. Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae:Thorius). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12083] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Gabriela Parra-Olea
- Departamento de Zoología; Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153, CP 04510, Ciudad Universitaria; México; D.F.; México
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology; Harvard University; 26 Oxford St.; Cambridge; MA; 02138; USA
| | - Ronald M. Bonett
- Department of Biological Science; University of Tulsa; 800 S Tucker Drive; Tulsa; OK; 74104; USA
| | - David B. Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology; University of California; Berkeley; CA; 94720-3160; USA
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Nascone‐Yoder N, Bloom S, Ledon‐Rettig C, Infante C, Hanken J. Developmental origins of novel gut morphology in frogs. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.446.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nanette Nascone‐Yoder
- Molecular Biomedical SciencesNorth Carolina State UniversityCollege of Veterinary MedicineRaleighNC
| | - Stephanie Bloom
- Molecular Biomedical SciencesNorth Carolina State UniversityCollege of Veterinary MedicineRaleighNC
| | - Cristina Ledon‐Rettig
- Molecular Biomedical SciencesNorth Carolina State UniversityCollege of Veterinary MedicineRaleighNC
| | | | - James Hanken
- Museum of Comparative ZoologyHarvard UniversityCambridgeMA
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Hanken J, Piekarski N. Embryonic origin of the skull: Has the pattern of neural crest derivation changed during vertebrate evolution? FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.315.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- James Hanken
- Museum of Comparative ZoologyHarvard UniversityCambridgeMA
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Abstract
The vertebrate limb demonstrates remarkable similarity in basic organization across phylogenetically disparate groups. To gain further insight into how this morphological similarity is maintained in different developmental contexts, we explored the molecular anatomy of size-reduced embryos of the Puerto Rican coquí frog, Eleutherodactylus coqui. This animal demonstrates direct development, a life-history strategy marked by rapid progression from egg to adult and absence of a free-living, aquatic larva. Nonetheless, coquí exhibits a basal anuran limb structure, with four toes on the forelimb and five toes on the hind limb. We investigated the extent to which coquí limb bud development conforms to the model of limb development derived from amniote studies. Toward this end, we characterized dynamic patterns of expression for 13 critical patterning genes across three principle stages of limb development. As expected, most genes demonstrate expression patterns that are essentially unchanged compared to amniote species. For example, we identified an EcFgf8-expression domain within the apical ectodermal ridge (AER). This expression pattern defines a putatively functional AER signaling domain, despite the absence of a morphological ridge in coquí embryos. However, two genes, EcMeis2 and EcAlx4, demonstrate altered domains of expression, which imply a potential shift in gene function between coquí frogs and amniote model systems. Unexpectedly, several genes thought to be critical for limb patterning in other systems, including EcFgf4, EcWnt3a, EcWnt7a, and EcGremlin, demonstrated no evident expression pattern in the limb at the three stages we analyzed. The absence of EcFgf4 and EcWnt3a expression during limb patterning is perhaps not surprising, given that neither gene is critical for proper limb development in the mouse, based on knockout and expression analyses. In contrast, absence of EcWnt7a and EcGremlin is surprising, given that expression of these molecules appears to be absolutely essential in all other model systems so far examined. Although this analysis substantiates the existence of a core set of ancient limb-patterning molecules, which likely mediate identical functions across highly diverse vertebrate forms, it also reveals remarkable evolutionary flexibility in the genetic control of a conserved morphological pattern across evolutionary time.
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Affiliation(s)
- Joshua B Gross
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Whited JL, Tsai SL, Beier KT, White JN, Piekarski N, Hanken J, Cepko CL, Tabin CJ. Pseudotyped retroviruses for infecting axolotl in vivo and in vitro. Development 2013; 140:1137-46. [PMID: 23344705 DOI: 10.1242/dev.087734] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Axolotls are poised to become the premiere model system for studying vertebrate appendage regeneration. However, very few molecular tools exist for studying crucial cell lineage relationships over regeneration or for robust and sustained misexpression of genetic elements to test their function. Furthermore, targeting specific cell types will be necessary to understand how regeneration of the diverse tissues within the limb is accomplished. We report that pseudotyped, replication-incompetent retroviruses can be used in axolotls to permanently express markers or genetic elements for functional study. These viruses, when modified by changing their coat protein, can infect axolotl cells only when they have been experimentally manipulated to express the receptor for that coat protein, thus allowing for the possibility of targeting specific cell types. Using viral vectors, we have found that progenitor populations for many different cell types within the blastema are present at all stages of limb regeneration, although their relative proportions change with time.
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Affiliation(s)
- Jessica L Whited
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Wu Y, Wang Y, Jiang K, Hanken J. Significance of pre-Quaternary climate change for montane species diversity: insights from Asian salamanders (Salamandridae: Pachytriton). Mol Phylogenet Evol 2012; 66:380-90. [PMID: 23110935 DOI: 10.1016/j.ympev.2012.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 01/20/2023]
Abstract
Despite extensive focus on the genetic legacy of Pleistocene glaciation, impacts of earlier climatic change on biodiversity are poorly understood. Because amphibians are highly sensitive to variations in precipitation and temperature, we use a genus of Chinese montane salamanders (Salamandridae: Pachytriton) to study paleoclimatic change in East Asia, which experienced intensification of its monsoon circulation in the late Miocene associated with subsequent Pliocene warming. Using both nuclear and mitochondrial DNA sequences, we reconstruct the species tree under a coalescent model and demonstrate that all major lineages originated before the Quaternary. Initial speciation within the genus occurred after the summer monsoon entered a stage of substantial intensification. Heavy summer precipitation established temporary water connectivity through overflows between adjacent stream systems, which may facilitate geographic range expansion by aquatic species such as Pachytriton. Species were formed in allopatry likely through vicariant isolation during or after range expansion. To evaluate the influence of Pliocene warming on these cold-adapted salamanders, we construct a novel temperature buffer-zone model, which suggests widespread physiological stress or even extinction during the warming period. A significant deceleration of species accumulation rate is consistent with Pliocene range contraction, which affected P. granulosus and P. archospotus the most because they lack large temperature buffer zones. In contrast, demographic growth occurred in species for which refugia persist. The buffer-zone model reveals the Huangshan Mountain as a potential climatic refugium, which is similar to that found for other East Asian organisms. Our approach can incorporate future climatic data to evaluate the potential impact of ongoing global warming on montane species (particularly amphibians) and to predict possible population declines.
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Affiliation(s)
- Yunke Wu
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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Affiliation(s)
- M K Richardson
- Dept of Anatomy and Developmental Biology, St George's Hospital Medical School, Cranmer Terrace, London, UK SW17 0RE
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Zimkus BM, Lawson L, Loader SP, Hanken J. Terrestrialization, miniaturization and rates of diversification in African puddle frogs (Anura: Phrynobatrachidae). PLoS One 2012; 7:e35118. [PMID: 22509392 PMCID: PMC3325629 DOI: 10.1371/journal.pone.0035118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 03/13/2012] [Indexed: 11/29/2022] Open
Abstract
Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible "key innovations" that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the "key innovations" hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity.
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Affiliation(s)
- Breda M Zimkus
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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Piekarski N, Hanken J. Neural crest derivation of the bony skull of the Mexican axolotl. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.457.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wheeler QD, Knapp S, Stevenson DW, Stevenson J, Blum SD, Boom BM, Borisy GG, Buizer JL, De Carvalho MR, Cibrian A, Donoghue MJ, Doyle V, Gerson EM, Graham CH, Graves P, Graves SJ, Guralnick RP, Hamilton AL, Hanken J, Law W, Lipscomb DL, Lovejoy TE, Miller H, Miller JS, Naeem S, Novacek MJ, Page LM, Platnick NI, Porter-Morgan H, Raven PH, Solis MA, Valdecasas AG, Van Der Leeuw S, Vasco A, Vermeulen N, Vogel J, Walls RL, Wilson EO, Woolley JB. Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.665095] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ziermann JM, Infante C, Hanken J, Olsson L. Morphology of the cranial skeleton and musculature in the obligate carnivorous tadpole ofLepidobatrachus laevis(Anura: Ceratophryidae). ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2011.00525.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Kerney RR, Blackburn DC, Müller H, Hanken J. DO LARVAL TRAITS RE-EVOLVE? EVIDENCE FROM THE EMBRYOGENESIS OF A DIRECT-DEVELOPING SALAMANDER, PLETHODON CINEREUS. Evolution 2011; 66:252-62. [DOI: 10.1111/j.1558-5646.2011.01426.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Piekarski N, Hanken J. The embryonic origin of the axolotl skull (Ambystoma mexicanum). Dev Biol 2011. [DOI: 10.1016/j.ydbio.2011.05.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sefton E, Piekarski N, Hanken J. How somitic cells migrate into the axolotl limb bud and vertebrate appendicular muscle evolution. Dev Biol 2011. [DOI: 10.1016/j.ydbio.2011.05.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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