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Wolfe JM, Ballou L, Luque J, Watson-Zink VM, Ahyong ST, Barido-Sottani J, Chan TY, Chu KH, Crandall KA, Daniels SR, Felder DL, Mancke H, Martin JW, Ng PKL, Ortega-Hernández J, Palacios Theil E, Pentcheff ND, Robles R, Thoma BP, Tsang LM, Wetzer R, Windsor AM, Bracken-Grissom HD. Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments. Syst Biol 2023:syad066. [PMID: 37941464 DOI: 10.1093/sysbio/syad066] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Indexed: 11/10/2023] Open
Abstract
For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Lauren Ballou
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | | | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia
- School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Joëlle Barido-Sottani
- Institut de Biologie de l'École Normale Supérieure (IBENS), ENS, CNRS, INSERM, Université PSL (Paris Sciences & Lettres), Paris, France
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan, ROC
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Darryl L Felder
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Harrison Mancke
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Joel W Martin
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Emma Palacios Theil
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, ul. Banacha 12/16, 90237 Łódź, Poland
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Rafael Robles
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Campeche, San Francisco de Campeche, Campeche, México
| | - Brent P Thoma
- Department of Biology, Jackson State University, P.O. Box 18540, Jackson, MS 39217, USA
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Amanda M Windsor
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- United States Food and Drug Administration, Office of Regulatory Science, 5001 Campus Dr. College Park, MD 20740, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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2
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Stebbins TD, Wetzer R. Review and guide to the isopods (Crustacea, Isopoda) of littoral and sublittoral marine habitats in the Southern California Bight. Zookeys 2023; 1162:1-167. [PMID: 37235199 PMCID: PMC10206732 DOI: 10.3897/zookeys.1162.100390] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 05/28/2023] Open
Abstract
The isopod crustaceans reported from or expected to occur in littoral and sublittoral marine habitats of the Southern California Bight (SCB) in the northeastern Pacific Ocean are reviewed. A total of 190 species, representing 105 genera in 42 families and six suborders are covered. Approximately 84% of these isopods represent described species with the remaining 16% comprising well-documented "provisional" but undescribed species. Cymothoida and Asellota are the most diverse of the six suborders, accounting for ca. 36% and 29% of the species, respectively. Valvifera and Sphaeromatidea are the next most speciose suborders with between 13-15% of the species each, while the suborder Limnorioidea represents fewer than 2% of the SCB isopod fauna. Finally, the mostly terrestrial suborder Oniscidea accounts for ca. 5% of the species treated herein, each which occurs at or above the high tide mark in intertidal habitats. A key to the suborders and superfamilies is presented followed by nine keys to the SCB species within each of the resultant groups. Figures are provided for most species. Bathymetric range, geographic distribution, type locality, habitat, body size, and a comprehensive list of references are included for most species.
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Affiliation(s)
- Timothy D. Stebbins
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
- City of San Diego Marine Biology Laboratory (retired), Public Utilities Department, San Diego, California 92101, USACity of San Diego Marine Biology LaboratorySan DiegoUnited States of America
| | - Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
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3
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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4
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Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A 2022; 119:e2115635118. [PMID: 35042800 PMCID: PMC8795548 DOI: 10.1073/pnas.2115635118] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616;
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Erez Lieberman Aiden
- DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030
| | - Miguel L Allende
- Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile
- Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Miklós Bálint
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany
| | - Katharine B Barker
- Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Nicolette D Caperello
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Keith Carlson
- The Novim Group, University of California, Santa Barbara, CA 93106
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dalia A Conde
- Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425
- Department of Biology, University of Southern Denmark 5230 Odense M, Denmark
| | - Montserrat Corominas
- Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain
- Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain
| | - Keith A Crandall
- Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - ThankGod E Ebenezer
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Olivier Fedrigo
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Paul Flicek
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway
| | - Melissa M Goldstein
- Department of Health Policy and Management, George Washington University, Washington, DC 20052
| | - Jennifer Marshall Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA 94305
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Kevin J Hackett
- Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - David Haussler
- Genome Institute, University of California, Santa Cruz, CA 95060
- HHMI, Chevy Chase, MD 20815
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | | | - Axel Janke
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea
| | - W John Kress
- Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | | | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden
| | - Xin Liu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain
- Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Sophie Mazard
- Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonna A K Mazet
- One Health Institute, University of California Davis, CA 95616
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany
| | - Eugene W Myers
- Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Sadye Paez
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Hyun Park
- Division of Biotechnology, Korea University 02841 Seoul, Korea
| | - Gene E Robinson
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
- Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia
| | - H Bradley Shaffer
- La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Jacob S Sherkow
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia
- College of Science, King Saud University 11451 Riyadh, Saudi Arabia
| | | | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Xiaofeng Wei
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007
- Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Julia L Wilson
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Xun Xu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Huanming Yang
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark
- China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China
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5
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecol Appl 2021; 31:e02379. [PMID: 34013632 DOI: 10.5281/zenodo.4516670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/27/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California, 90089, USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California, 91009, USA
| | - Dannise V Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri, 65201, USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Melisa G Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, 90089, USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Teia M Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Tiara N Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Emma A Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Ana E Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Sarah K Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, 16911, Indonesia
| | - Miroslava N Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
- Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California, 90007, USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Michael N Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California, 95343, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California, 90095, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California, 95064, USA
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6
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Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Mejia MP, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecol Appl 2021; 31:e02379. [PMID: 34013632 PMCID: PMC9297316 DOI: 10.1002/eap.2379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/23/2020] [Accepted: 02/04/2021] [Indexed: 05/15/2023]
Abstract
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
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Affiliation(s)
- Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ariel Levi Simons
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, California 90089 USA
- Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Emily E. Curd
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Fabian D. Schneider
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91009 USA
| | - Dannise V. Ruiz-Ramos
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri 65201 USA
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Zack Gold
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Melisa G. Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 USA
| | - Sabrina Shirazi
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Teia M. Schweizer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523 USA
| | - Tiara N. Moore
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- School of Environmental and Forestry Sciences, University of Washington, Seattle, Washington 98195 USA
| | - Emma A. Fox
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Ana E. Garcia-Vedrenne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Sarah K. Helman
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Kelsi Rutledge
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Maura Palacios Mejia
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Onny Marwayana
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor 16911 Indonesia
| | - Miroslava N. Munguia Ramos
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
- Biological Sciences, University of Southern California, Los Angeles, California 90089 USA
| | - N. Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, California 90007 USA
| | - Emily Jane McTavish
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Michael N. Dawson
- Department of Life & Environmental Sciences, University of California-Merced, Merced, California 95343 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
- Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, California 95064 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, California 90095 USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, California 95064 USA
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7
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Wetzer R, Wall A, Bruce NL. Redescription of Gnorimosphaeroma oregonense (Dana, 1853) (Crustacea, Isopoda, Sphaeromatidae), designation of neotype, and 16S-rDNA molecular phylogeny of the north-eastern Pacific species. Zookeys 2021; 1037:23-56. [PMID: 34045916 PMCID: PMC8137637 DOI: 10.3897/zookeys.1037.63017] [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: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Gnorimosphaeroma oregonense (Dana, 1852) is revised, a male neotype is designated, photographed, and illustrated; the species occurs from Vancouver British Columbia to the central California coast. 16S-rDNA sequences (~650 bp) for all available ethanol preserved species of Gnorimosphaeroma were used to hypothesize their relationships. Our analyses revealed a sister taxon relationship between the fully marine G. oregonense and the brackish to freshwater species, G. noblei. The oyster associated and introduced G. rayi is sister to a previously not recognized or identified, but genetically distinct, Gnorimosphaeroma sp. collected at two sites in San Francisco Bay. Gnorimosphaeroma sp. is probably also a western Pacific species based on its genetic relationship to G. rayi. Photographic comparisons are offered for G. oregonense (marine), G. noblei (freshwater), G. rayi (introduced), G. sp. (presumably introduced), and G. insulare (San Nicolas Island). Records of the holdings at the Los Angeles County Museum of Natural History are summarized. Without material available north of Vancouver through Alaska, the range of G. oregonense could not be genetically verified. This review includes a diagnosis and description of the genus Gnorimosphaeroma Menzies, 1954.
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Affiliation(s)
- Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
| | - Adam Wall
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
| | - Niel L. Bruce
- Queensland Museum, Brisbane, AustraliaQueensland MuseumBrisbaneAustralia
- North-West University, Water Research Group, Unit for Environmental Sciences and Management, Private Bag C6001, Potchefstroom 2520, South AfricaNorth-West UniversityPotchefstroomSouth Africa
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8
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Gold Z, Wall AR, Curd EE, Kelly RP, Pentcheff ND, Ripma L, Barber PH, Wetzer R. eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.). CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01161-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Ellwood ER, Kimberly P, Guralnick R, Flemons P, Love K, Ellis S, Allen JM, Best JH, Carter R, Chagnoux S, Costello R, Denslow MW, Dunckel BA, Ferriter MM, Gilbert EE, Goforth C, Groom Q, Krimmel ER, LaFrance R, Martinec JL, Miller AN, Minnaert-Grote J, Nash T, Oboyski P, Paul DL, Pearson KD, Pentcheff ND, Roberts MA, Seltzer CE, Soltis PS, Stephens R, Sweeney PW, von Konrat M, Wall A, Wetzer R, Zimmerman C, Mast AR. Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar. Bioscience 2018; 68:112-124. [PMID: 29599548 PMCID: PMC5862351 DOI: 10.1093/biosci/bix143] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions—content now foundational to the growing WeDigBio event.
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Affiliation(s)
- Elizabeth R Ellwood
- La Brea Tar Pits & Museum, in Los Angeles, California, and was with the Department of Biological Science at Florida State University, in Tallahassee
| | - Paul Kimberly
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Robert Guralnick
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Kevin Love
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Shari Ellis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Julie M Allen
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Jason H Best
- Botanical Research Institute of Texas, in Fort Worth
| | - Richard Carter
- Biology Department at Valdosta State University, in Georgia
| | | | - Robert Costello
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Michael W Denslow
- Florida Museum of Natural History at the University of Florida, in Gainesville, and the Department of Biology at Appalachian State University, in Boone, North Carolina
| | - Betty A Dunckel
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Meghan M Ferriter
- Smithsonian Institution Transcription Center at the Smithsonian Institution Office of the Chief Information Officer, in Washington, DC
| | | | | | | | - Erica R Krimmel
- Department of Biology at The Chicago Academy of Sciences and the Peggy Notebaert Nature Museum, in Chicago, Illinois
| | - Raphael LaFrance
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Joann Lacey Martinec
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Andrew N Miller
- Illinois Natural History Survey at the University of Illinois Urbana-Champaign
| | | | | | - Peter Oboyski
- Essig Museum of Entomology at the University of California, in Berkeley
| | - Deborah L Paul
- Institute for Digital Information and Scientific Communication at Florida State University, in Tallahassee
| | - Katelin D Pearson
- Department of Biological Science at Florida State University, in Tallahassee
| | - N Dean Pentcheff
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Mari A Roberts
- William and Lynda Steere Herbarium at the New York Botanical Garden
| | | | - Pamela S Soltis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Patrick W Sweeney
- Yale Peabody Museum of Natural History at Yale University, in New Haven, Connecticut
| | - Matt von Konrat
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Adam Wall
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Regina Wetzer
- Research and Collections at the Natural History Museum of Los Angeles County
| | | | - Austin R Mast
- Department of Biological Science at Florida State University, in Tallahassee
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10
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Wetzer R, Mowery G. Redescription of Dynoides elegans (Boone, 1923) (Crustacea, Isopoda, Sphaeromatidae) from the north-eastern Pacific. Zookeys 2017:1-16. [PMID: 28228672 PMCID: PMC5299436 DOI: 10.3897/zookeys.646.10626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 09/26/2016] [Accepted: 01/04/2017] [Indexed: 11/29/2022] Open
Abstract
Dynoideselegans (Boone, 1923) from southern California is reviewed, redescribed, and figured. The original species description did not include figures, making it difficult to attribute individuals to the species. Dynoidessaldanai Carvacho and Haasmann, 1984 and Dynoidescrenulatus Carvacho & Haasman, 1984 from the Pacific Coast of Mexico and Dynoidesbrevicornis Kussakin & Malyutina, 1987, from Furugelm Island, Peter the Great Gulf in the Sea of Japan, appear morphologically more similar to each other than to western Pacific species. A large pleonal process is present in about half of the Dynoides species, but is absent in this north-eastern Pacific clade and the north-western Pacific Dynoidesbrevicornis and Dynoidesbrevispina. Dynoidesdentisinus Shen, 1929 possess a large pleonal spine. It is known from China, Japan, and Korea and is introduced in San Francisco Bay; it can be easily distinguished from Dynoideselegans by the presence of a pleonal process in the former. A key to the Pacific West Coast Dynoides is provided.
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Affiliation(s)
- Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007 USA; University of Southern California, Los Angeles, CA 90089 USA
| | - Gracie Mowery
- University of Southern California, Los Angeles, CA 90089 USA
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11
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Wall AR, Bruce NL, Wetzer R. Status of Exosphaeromaamplicauda (Stimpson, 1857), E.aphrodita (Boone, 1923) and description of three new species (Crustacea, Isopoda, Sphaeromatidae) from the north-eastern Pacific. Zookeys 2015:11-58. [PMID: 26019675 PMCID: PMC4443524 DOI: 10.3897/zookeys.504.8049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 06/06/2014] [Accepted: 02/11/2015] [Indexed: 11/12/2022] Open
Abstract
Exosphaeromaamplicauda (Stimpson, 1857) from the west coast of North America is reviewed and redescribed and revealed to be a group of closely related species. A neotype is designated and the species redescribed based on the neotype and topotypic specimens. Exosphaeromaamplicauda is known only from the coast of California, at Marin, Sonoma and San Mateo Counties. Exosphaeromaaphrodita (Boone, 1923), type locality La Jolla, California and previously considered nomen dubium is taken out of synonymy and re-validated. A further three species: Exosphaeromapaydenae sp. n., Exosphaeromarussellhansoni sp. n., and Exosphaeromapentcheffi sp. n. are described herein. Sphaeromaoctonctum Richardson, 1899 is placed into junior synonymy with Exosphaeromaamplicauda. A key to the Pacific West Coast Exosphaeroma is provided.
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Affiliation(s)
- Adam R Wall
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007 USA
| | - Niel L Bruce
- Museum of Tropical Queensland and School of Marine and Tropical Biology, James Cook University; 70-102 Flinders Street, Townsville, 4810 Australia ; Water Research Group (Ecology), Unit for Environmental Sciences and Management, North West University, Potchefstroom, 2520, South Africa
| | - Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007 USA
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12
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Abstract
Background Isopoda are the most diverse Crustacea. In order to encourage the study of isopod crustaceans and their use in biodiversity studies, systematics, ecology, physiology and more, one needs to know who the isopods are and where to find them. New information This is a short “how to” guide focusing on the free-living marine and freshwater isopods: where they live and how to collect and preserve them. The tools and techniques described here are simple, but invaluable in accessing the natural history of these remarkable creatures.
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Affiliation(s)
- Regina Wetzer
- Natural History Museum of Los Angeles County, Los Angeles, United States of America
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13
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Wall AR, Campo D, Wetzer R. Genetic utility of natural history museum specimens: endangered fairy shrimp (Branchiopoda, Anostraca). Zookeys 2014:1-14. [PMID: 25561827 PMCID: PMC4283361 DOI: 10.3897/zookeys.457.6822] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 09/13/2014] [Indexed: 11/13/2022] Open
Abstract
We examined the potential utility of museum specimens as a source for genetic analysis of fairy shrimp. Because of loss of their vernal pool habitat, some fairy shrimp (including Branchinectasandiegonensis and Branchinectalynchi) are listed as threatened or endangered in Southern California by the United States Fish and Wildlife Service. Management of those species requires extensive population genetics studies and the resolution of important genetic complexity (e.g. possible hybridization between endangered and non-endangered species). Regulations mandating deposition of specimens of listed species have resulted in thousands of specimens accessioned into the Natural History Museum of Los Angeles County that have been preserved in a variety of solutions. We subsampled those specimens, as well as other Anostraca with known collection and preservation histories, to test their potential for genetic analysis by attempting DNA extraction and amplification for mt16SrDNA. Fixation and preservation in not denatured ethanol had a far greater sequencing success rate than other (and unknown) fixatives and preservatives. To maximize scientific value we recommend field preservation in 95% not denatured ethanol (or, if pure ethanol is unavailable, high-proof drinking spirits, e.g. Everclear™, or 151 proof white rum), followed by storage in 95% not denatured ethanol.
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Affiliation(s)
- Adam R Wall
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007 USA
| | - Daniel Campo
- University of Southern California, Molecular and Computational Biology, Los Angeles, CA 90089 USA
| | - Regina Wetzer
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007 USA
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14
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Wetzer R, Pérez-Losada M, Bruce NL. Phylogenetic relationships of the family Sphaeromatidae Latreille, 1825 (Crustacea: Peracarida: Isopoda) within Sphaeromatidea based on 18S-rDNA molecular data. Zootaxa 2013; 3599:161-77. [PMID: 24614936 DOI: 10.11646/zootaxa.3599.2.3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Indexed: 11/04/2022]
Abstract
Based on 18S-rDNA sequences of 97 isopods including 18 Sphaeromatidea, we show Sphaeromatidae, Valvifera, Serolidae, and Ancinidae is a well supported clade. The within clade relationships of these taxa are not as definitively demonstrated because taxon sampling for some groups is still limited. In our analyses the Sphaeromatidae are shown to be unequivocally monophyletic. This is contrary to the morphology-based analysis by A. Brandt and G. Poore in 2003, which included only five Sphaeromatidae and found the family to be paraphyletic. The Ancinidae are also upheld, and the Valvifera is the sister taxon to Serolidae. Surprisingly Plakarthrium (Plakarthiidae) is nested within the Sphaeromatidae in most analyses. We point out short-comings in our sampling and suggest areas which would benefit from better sampling. We also review the long and convoluted nomenclatural history of the Sphaeromatidea, Sphaeromatoidea, and<br />Sphaeromatidae.
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Affiliation(s)
- Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA;
| | - Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal;
| | - Niel L Bruce
- Museum of Tropical Queensland and School of Marine and Tropical Biology, James Cook University; 70-102 Flinders Street, Townsville, 4810 Australia; Department of Zoology, University of Johannesburg, Auckland Park, 2006 South Africa;
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15
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Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010; 463:1079-83. [PMID: 20147900 DOI: 10.1038/nature08742] [Citation(s) in RCA: 609] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 12/10/2009] [Indexed: 11/09/2022]
Abstract
The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
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Affiliation(s)
- Jerome C Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
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Wetzer R, Martin JW, Trautwein SE. Phylogenetic relationships within the coral crab genus Carpilius (Brachyura, Xanthoidea, Carpiliidae) and of the Carpiliidae to other xanthoid crab families based on molecular sequence data. Mol Phylogenet Evol 2003; 27:410-21. [PMID: 12742746 DOI: 10.1016/s1055-7903(03)00021-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The coral crab genus Carpilius currently includes three widely distributed species that inhabit tropical coral reefs and adjacent waters. The relationship of Carpilius to other xanthoid crabs is unknown. Previously, carcinologists considered Carpilius to be allied with crabs of the family Xanthidae (e.g., Euryozius, Liagore, and Liomera), however, recent workers have considered it to be a monotypic genus within its own family, Carpiliidae. Mitochondrial 12S- and 16S-rDNA gene fragments confirm the monophyly and distinct status of the family Carpiliidae. Within the genus Carpilius, the Caribbean species C. corallinus is basal to the two Pacific species C. maculatus and C. convexus. The Pacific species are sister taxa, despite the greater morphological resemblance of C. corallinus to the Pacific C. convexus. The relationship of the Carpiliidae (Carpilius) to other xanthoid crabs is investigated, and results of a preliminary analysis of higher xanthoid relationships did not resolve the relationships of Carpiliidae, "Xanthidae," Menippidae, Trapeziidae, and Ocypodidae to one another. A Menippidae and Carpilius relationship could not be rejected, although a Liomera, Liagore, and Carpilius relationship was.
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Affiliation(s)
- Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USA.
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Abstract
Carefully collected molecular data and rigorous analyses are revolutionizing today’s phylogenetic studies. Although molecular data have been used to estimate various invertebrate phylogenies for more than a decade, this study is the first survey of different regions of mitochondrial DNA in isopod crustaceans assessing sequence divergence and hence the usefulness of these regions to infer phylogeny at different hierarchical levels. I evaluate three loci from the mitochondrial genome (two ribosomal RNAs (12S, 16S) and one protein-coding (COI)) for their appropriateness in inferring isopod phylogeny at the suborder level and below. The patterns are similar for all three loci with the most speciose suborders of isopods also having the most divergent mitochondrial nucleotide sequences. Recommendations for designing an order- or suborder-level molecular study in previously unstudied groups of Crustacea would include: (1) collecting a minimum of two-four species or genera thought to be most divergent, (2) sampling across the group of interest as equally as possible in terms of taxonomic representation and the distribution of species, (3) surveying several genes, and (4) carrying out preliminary alignments, checking data for nucleotide bias, transition/ transversion ratios, and saturation levels before committing to a large-scale sequencing effort.
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