1
|
Plowright RK, Ahmed AN, Coulson T, Crowther TW, Ejotre I, Faust CL, Frick WF, Hudson PJ, Kingston T, Nameer PO, O'Mara MT, Peel AJ, Possingham H, Razgour O, Reeder DM, Ruiz-Aravena M, Simmons NB, Srinivas PN, Tabor GM, Tanshi I, Thompson IG, Vanak AT, Vora NM, Willison CE, Keeley ATH. Ecological countermeasures to prevent pathogen spillover and subsequent pandemics. Nat Commun 2024; 15:2577. [PMID: 38531842 DOI: 10.1038/s41467-024-46151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
Substantial global attention is focused on how to reduce the risk of future pandemics. Reducing this risk requires investment in prevention, preparedness, and response. Although preparedness and response have received significant focus, prevention, especially the prevention of zoonotic spillover, remains largely absent from global conversations. This oversight is due in part to the lack of a clear definition of prevention and lack of guidance on how to achieve it. To address this gap, we elucidate the mechanisms linking environmental change and zoonotic spillover using spillover of viruses from bats as a case study. We identify ecological interventions that can disrupt these spillover mechanisms and propose policy frameworks for their implementation. Recognizing that pandemics originate in ecological systems, we advocate for integrating ecological approaches alongside biomedical approaches in a comprehensive and balanced pandemic prevention strategy.
Collapse
Affiliation(s)
- Raina K Plowright
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, 14853, USA.
| | - Aliyu N Ahmed
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Thomas W Crowther
- Department of Environmental Systems Science, ETH Zürich, Zürich, 8092, Switzerland
| | - Imran Ejotre
- Department of Biology, Muni University, P.O. Box 725, Arua, Uganda
| | - Christina L Faust
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Winifred F Frick
- Bat Conservation International, Austin, TX, 78746, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Peter J Hudson
- Centre for Infectious Disease Dynamics, Pennsylvania State University, State College, PA, 16801, USA
| | - Tigga Kingston
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409-3131, USA
| | - P O Nameer
- College of Climate Change and Environmental Science, Kerala Agricultural University, Kerala, 680 656, India
| | | | - Alison J Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, 4111, Australia
| | - Hugh Possingham
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Orly Razgour
- Biosciences, University of Exeter, Exeter, EX4 4PS, UK
| | - DeeAnn M Reeder
- Department of Biology, Bucknell University, Lewisburg, PA, 17937, USA
| | - Manuel Ruiz-Aravena
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, 14853, USA
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, 4111, Australia
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Starkville, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York City, NY, 10024, USA
| | | | - Gary M Tabor
- Center for Large Landscape Conservation, Bozeman, MT, 59771, USA
| | - Iroro Tanshi
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Small Mammal Conservation Organization, Benin City, 300251, Nigeria
- Department of Animal and Environmental Biology, University of Benin, Benin City, 300000, Nigeria
| | | | - Abi T Vanak
- Centre for Policy Design, Ashoka Trust for Research in Ecology and the Environment, Bengaluru, Karnataka, 560064, India
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Neil M Vora
- Conservation International, Arlington, VA, 22202, USA
| | - Charley E Willison
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, 14853, USA
| | | |
Collapse
|
2
|
Giannini NP, Cannell A, Amador LI, Simmons NB. Palaeoatmosphere facilitates a gliding transition to powered flight in the Eocene bat, Onychonycteris finneyi. Commun Biol 2024; 7:365. [PMID: 38532113 DOI: 10.1038/s42003-024-06032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The evolutionary transition to powered flight remains controversial in bats, the only flying mammals. We applied aerodynamic modeling to reconstruct flight in the oldest complete fossil bat, the archaic Onychonycteris finneyi from the early Eocene of North America. Results indicate that Onychonycteris was capable of both gliding and powered flight either in a standard normodense aerial medium or in the hyperdense atmosphere that we estimate for the Eocene from two independent palaeogeochemical proxies. Aerodynamic continuity across a morphological gradient is further demonstrated by modeled intermediate forms with increasing aspect ratio (AR) produced by digital elongation based on chiropteran developmental data. Here a gliding performance gradient emerged of decreasing sink rate with increasing AR that eventually allowed applying available muscle power to achieve level flight using flapping, which is greatly facilitated in hyperdense air. This gradient strongly supports a gliding (trees-down) transition to powered flight in bats.
Collapse
Affiliation(s)
- Norberto P Giannini
- Unidad Ejecutora Lillo, CONICET-Fundación Miguel Lillo, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina.
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY, USA.
| | - Alan Cannell
- ISIPU - Istituto Italiano di Paleontologia Umana, Rome, Italy
- Instituto de Estudos Avançados, Universidade de São Paulo, São Paulo, Brasil
| | - Lucila I Amador
- Unidad Ejecutora Lillo, CONICET-Fundación Miguel Lillo, Tucumán, Argentina
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY, USA
| |
Collapse
|
3
|
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Author Correction: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun 2024; 15:1777. [PMID: 38413559 PMCID: PMC10899600 DOI: 10.1038/s41467-024-44937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Affiliation(s)
- Wei E Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Biology, Menlo College, 1000 El Camino Real, Atherton, CA, 94027, USA
| | - Seungbyn Baek
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hai P Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Rachael Bradley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sarah L Fong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Alex Galazyuk
- Hearing Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lisa Noelle Cooper
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Martin Hemberg
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
| |
Collapse
|
4
|
Becker DJ, Dyer KE, Lock LR, Pladas SA, Sukhadia AA, Demory B, Batista JMN, Pineda M, Simmons NB, Adams AM, Frick WF, O’Mara MT, Volokhov DV. Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species. bioRxiv 2024:2024.02.08.577874. [PMID: 38370734 PMCID: PMC10871349 DOI: 10.1101/2024.02.08.577874] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Bacterial pathogens remain poorly characterized in bats, especially in North America. We describe novel (and in some cases panmictic) hemoplasmas (12.9% positivity) and bartonellae (16.7% positivity) across three colonies of Mexican free-tailed bats (Tadarida brasiliensis), a partially migratory species that can seasonally travel hundreds of kilometers. Molecular analyses identified three novel Candidatus hemoplasma species most similar to another novel Candidatus species in Neotropical molossid bats. We also detected novel hemoplasmas in sympatric cave myotis (Myotis velifer) and pallid bats (Antrozous pallidus), with sequences in the latter 96.5% related to C. Mycoplasma haemohominis. We identified eight Bartonella genotypes, including those in cave myotis, with 96.7% similarity to C. Bartonella mayotimonensis. We also detected Bartonella rochalimae in migratory Tadarida brasiliensis, representing the first report of this human pathogen in bats. The seasonality and diversity of these bacteria observed here suggest that additional longitudinal, genomic, and immunological studies in bats are warranted.
Collapse
Affiliation(s)
- Daniel J. Becker
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kristin E. Dyer
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Lauren R. Lock
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Shawn A. Pladas
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | | | - Bret Demory
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Juliana Maria Nunes Batista
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Micaela Pineda
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | | | - Winifred F. Frick
- Bat Conservation International, Austin, TX, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - M. Teague O’Mara
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
- Bat Conservation International, Austin, TX, USA
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| |
Collapse
|
5
|
DeAnglis IK, Andrews BR, Lock LR, Dyer KE, Yang A, Volokhov DV, Fenton MB, Simmons NB, Downs CJ, Becker DJ. Bat cellular immunity varies by year and dietary habit amidst land conversion. Conserv Physiol 2024; 12:coad102. [PMID: 38293641 PMCID: PMC10823333 DOI: 10.1093/conphys/coad102] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 10/11/2023] [Accepted: 11/28/2023] [Indexed: 02/01/2024]
Abstract
Monitoring the health of wildlife populations is essential in the face of increased agricultural expansion and forest fragmentation. Loss of habitat and habitat degradation can negatively affect an animal's physiological state, possibly resulting in immunosuppression and increased morbidity or mortality. We sought to determine how land conversion may differentially impact cellular immunity and infection risk in Neotropical bats species regularly infected with bloodborne pathogens, and to evaluate how effects may vary over time and by dietary habit. We studied common vampire bats (Desmodus rotundus), northern yellow-shouldered bats (Sturnira parvidens) and Mesoamerican mustached bats (Pteronotus mesoamericanus), representing the dietary habits of sanguivory, frugivory and insectivory respectively, in northern Belize. We compared estimated total white blood cell count, leukocyte differentials, neutrophil to lymphocyte ratio and infection status with two bloodborne bacterial pathogens (Bartonella spp. and hemoplasmas) of 118 bats captured in a broadleaf, secondary forest over three years (2017-2019). During this period, tree cover decreased by 14.5% while rangeland expanded by 14.3%, indicating increasing habitat loss and fragmentation. We found evidence for bat species-specific responses of cellular immunity between years, with neutrophil counts significantly decreasing in S. parvidens from 2017 to 2018, but marginally increasing in D. rotundus. However, the odds of infection with Bartonella spp. and hemoplasmas between 2017 and 2019 did not differ between bat species, contrary to our prediction that pathogen prevalence may increase with land conversion. We conclude that each bat species invested differently in cellular immunity in ways that changed over years of increasing habitat loss and fragmentation. We recommend further research on the interactions between land conversion, immunity and infection across dietary habits of Neotropical bats for informed management and conservation.
Collapse
Affiliation(s)
- Isabella K DeAnglis
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY, 13210, USA
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Benjamin R Andrews
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Lauren R Lock
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Kristin E Dyer
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Anni Yang
- Department of Geography and Environmental Sustainability, University of Oklahoma, 100 East Boyd St, Norman, OK, 73019, USA
| | - Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - M Brock Fenton
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 3K7, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA
| | - Cynthia J Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| |
Collapse
|
6
|
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun 2024; 15:12. [PMID: 38195585 PMCID: PMC10776631 DOI: 10.1038/s41467-023-44186-y] [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: 03/13/2023] [Accepted: 12/03/2023] [Indexed: 01/11/2024] Open
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancreases and identify key cell population, gene expression and regulatory differences associated with the Jamaican fruit bat that also relate to human disease, particularly diabetes. We find a decrease in loop of Henle and an increase in collecting duct cells, and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the Jamaican fruit bat kidney. The Jamaican fruit bat pancreas shows an increase in endocrine and a decrease in exocrine cells, and differences in genes and regulatory elements involved in insulin regulation. We also find that these frugivorous bats share several molecular characteristics with human diabetes. Combined, our work provides insights from a frugivorous mammal that could be leveraged for therapeutic purposes.
Collapse
Affiliation(s)
- Wei E Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Biology, Menlo College, 1000 El Camino Real, Atherton, CA, 94027, USA
| | - Seungbyn Baek
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hai P Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Rachael Bradley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sarah L Fong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Alex Galazyuk
- Hearing Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lisa Noelle Cooper
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Martin Hemberg
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
| |
Collapse
|
7
|
Vicente-Santos A, Lock LR, Allira M, Dyer KE, Dunsmore A, Tu W, Volokhov DV, Herrera C, Lei GS, Relich RF, Janech MG, Bland AM, Simmons NB, Becker DJ. Serum proteomics reveals a tolerant immune phenotype across multiple pathogen taxa in wild vampire bats. Front Immunol 2023; 14:1281732. [PMID: 38193073 PMCID: PMC10773587 DOI: 10.3389/fimmu.2023.1281732] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Bats carry many zoonotic pathogens without showing pronounced pathology, with a few exceptions. The underlying immune tolerance mechanisms in bats remain poorly understood, although information-rich omics tools hold promise for identifying a wide range of immune markers and their relationship with infection. To evaluate the generality of immune responses to infection, we assessed the differences and similarities in serum proteomes of wild vampire bats (Desmodus rotundus) across infection status with five taxonomically distinct pathogens: bacteria (Bartonella spp., hemoplasmas), protozoa (Trypanosoma cruzi), and DNA (herpesviruses) and RNA (alphacoronaviruses) viruses. From 19 bats sampled in 2019 in Belize, we evaluated the up- and downregulated immune responses of infected versus uninfected individuals for each pathogen. Using a high-quality genome annotation for vampire bats, we identified 586 serum proteins but found no evidence for differential abundance nor differences in composition between infected and uninfected bats. However, using receiver operating characteristic curves, we identified four to 48 candidate biomarkers of infection depending on the pathogen, including seven overlapping biomarkers (DSG2, PCBP1, MGAM, APOA4, DPEP1, GOT1, and IGFALS). Enrichment analysis of these proteins revealed that our viral pathogens, but not the bacteria or protozoa studied, were associated with upregulation of extracellular and cytoplasmatic secretory vesicles (indicative of viral replication) and downregulation of complement activation and coagulation cascades. Additionally, herpesvirus infection elicited a downregulation of leukocyte-mediated immunity and defense response but an upregulation of an inflammatory and humoral immune response. In contrast to our two viral infections, we found downregulation of lipid and cholesterol homeostasis and metabolism with Bartonella spp. infection, of platelet-dense and secretory granules with hemoplasma infection, and of blood coagulation pathways with T. cruzi infection. Despite the small sample size, our results suggest that vampire bats have a similar suite of immune mechanisms for viruses distinct from responses to the other pathogen taxa, and we identify potential biomarkers that can expand our understanding of pathogenesis of these infections in bats. By applying a proteomic approach to a multi-pathogen system in wild animals, our study provides a distinct framework that could be expanded across bat species to increase our understanding of how bats tolerate pathogens.
Collapse
Affiliation(s)
| | - Lauren R. Lock
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Meagan Allira
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Kristin E. Dyer
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| | - Annalise Dunsmore
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Weihong Tu
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Claudia Herrera
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, United States
| | - Guang-Sheng Lei
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Ryan F. Relich
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, SC, United States
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, SC, United States
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - Daniel J. Becker
- School of Biological Sciences, University of Oklahoma, Norman, OK, United States
| |
Collapse
|
8
|
Volokhov DV, Lock LR, Dyer KE, DeAnglis IK, Andrews BR, Simonis MC, Stockmaier S, Carter GG, Downs CJ, Fenton MB, Simmons NB, Becker DJ. Expanded diversity of novel hemoplasmas in rare and undersampled Neotropical bats. One Health 2023; 17:100633. [PMID: 37920218 PMCID: PMC10618802 DOI: 10.1016/j.onehlt.2023.100633] [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: 06/12/2023] [Revised: 08/19/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
Hemotropic mycoplasmas are emerging as a model system for studying bacterial pathogens in bats, but taxonomic coverage of sampled host species remains biased. We leveraged a long-term field study in Belize to uncover novel hemoplasma diversity in bats by analyzing 80 samples from 19 species, most of which are infrequently encountered. PCR targeting the partial 16S rRNA gene found 41% of bats positive for hemoplasmas. Phylogenetic analyses found two novel host shifts of hemoplasmas, four entirely new hemoplasma genotypes, and the first hemoplasma detections in four bat species. One of these novel hemoplasmas (from Neoeptesicus furinalis) shared 97.6% identity in the partial 16S rRNA gene to a human hemoplasma (Candidatus Mycoplasma haemohominis). Additional analysis of the partial 23S rRNA gene allowed us to also designate two novel hemoplasma species, in Myotis elegans and Phyllostomus discolor, with the proposed names Candidatus Mycoplasma haematomyotis sp. nov. and Candidatus Mycoplasma haematophyllostomi sp. nov., respectively. Our analyses show that additional hemoplasma diversity in bats can be uncovered by targeting rare or undersampled host species.
Collapse
Affiliation(s)
- Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lauren R. Lock
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kristin E. Dyer
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Isabella K. DeAnglis
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Benjamin R. Andrews
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Molly C. Simonis
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Sebastian Stockmaier
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Gerald G. Carter
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Cynthia J. Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Daniel J. Becker
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biol Evol 2023; 15:evad148. [PMID: 37728212 PMCID: PMC10510315 DOI: 10.1093/gbe/evad148] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Accepted: 08/03/2023] [Indexed: 09/21/2023] Open
Abstract
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.
Collapse
Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Oppenheim
- American Museum of Natural History, Institute for Comparative Genomics, New York, New York, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | |
Collapse
|
11
|
Goswami A, Noirault E, Coombs EJ, Clavel J, Fabre AC, Halliday TJD, Churchill M, Curtis A, Watanabe A, Simmons NB, Beatty BL, Geisler JH, Fox DL, Felice RN. Developmental origin underlies evolutionary rate variation across the placental skull. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220083. [PMID: 37183904 PMCID: PMC10184245 DOI: 10.1098/rstb.2022.0083] [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] [Indexed: 05/16/2023] Open
Abstract
The placental skull has evolved into myriad forms, from longirostrine whales to globular primates, and with a diverse array of appendages from antlers to tusks. This disparity has recently been studied from the perspective of the whole skull, but the skull is composed of numerous elements that have distinct developmental origins and varied functions. Here, we assess the evolution of the skull's major skeletal elements, decomposed into 17 individual regions. Using a high-dimensional morphometric approach for a dataset of 322 living and extinct eutherians (placental mammals and their stem relatives), we quantify patterns of variation and estimate phylogenetic, allometric and ecological signal across the skull. We further compare rates of evolution across ecological categories and ordinal-level clades and reconstruct rates of evolution along lineages and through time to assess whether developmental origin or function discriminate the evolutionary trajectories of individual cranial elements. Our results demonstrate distinct macroevolutionary patterns across cranial elements that reflect the ecological adaptations of major clades. Elements derived from neural crest show the fastest rates of evolution, but ecological signal is equally pronounced in bones derived from neural crest and paraxial mesoderm, suggesting that developmental origin may influence evolutionary tempo, but not capacity for specialisation. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
Collapse
Affiliation(s)
- Anjali Goswami
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Eve Noirault
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Ellen J Coombs
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Julien Clavel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622 Villeurbanne, France
| | - Anne-Claire Fabre
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Naturhistorisches Museum Bern, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Thomas J D Halliday
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Morgan Churchill
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
| | - Abigail Curtis
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Akinobu Watanabe
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Brian L Beatty
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Jonathan H Geisler
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - David L Fox
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryan N Felice
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| |
Collapse
|
12
|
Simmons NB, Ingala MR, Pieri M, Volkert TL, Singh LN, Philip P, Lindsey LL, Zhang N, Gray JL, O'Toole BP, Mai M, Teeling EC, Vernes SC. The genome sequence of Molossusnigricans (Chiroptera, Molossidae; Miller, 1902). Wellcome Open Res 2023; 8:198. [PMID: 37600588 PMCID: PMC10435916 DOI: 10.12688/wellcomeopenres.18724.1] [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] [Accepted: 02/06/2023] [Indexed: 08/22/2023] Open
Abstract
We present a genome assembly from an individual male Molossus nigricans (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.41 gigabases in span. The majority of the assembly is scaffolded into 24 chromosomal pseudomolecules, with the X sex chromosome assembled.
Collapse
Affiliation(s)
- Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY10024, USA
| | - Melissa R. Ingala
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ 07940, USA
| | - Myrtani Pieri
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | | | | | | | | | | | | | | | - Meike Mai
- School of Biology, The University of St Andrews, St Andrews, UK
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
| | - Sonja C. Vernes
- School of Biology, The University of St Andrews, St Andrews, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - the Bat Biology Foundation
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY10024, USA
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ 07940, USA
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- Paratus Sciences, New York NY, USA
- School of Biology, The University of St Andrews, St Andrews, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - the Bat1K Consortium
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY10024, USA
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ 07940, USA
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- Paratus Sciences, New York NY, USA
- School of Biology, The University of St Andrews, St Andrews, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| |
Collapse
|
13
|
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas. bioRxiv 2023:2023.02.12.528204. [PMID: 36824791 PMCID: PMC9949079 DOI: 10.1101/2023.02.12.528204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we used integrative single-cell sequencing on insectivorous and frugivorous bat kidneys and pancreases and identified key cell population, gene expression and regulatory element differences associated with frugivorous adaptation that also relate to human disease, particularly diabetes. We found an increase in collecting duct cells and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the frugivore kidney. In the frugivorous pancreas, we observed an increase in endocrine and a decrease in exocrine cells and differences in genes and regulatory elements involved in insulin regulation. Combined, our work provides novel insights into frugivorous adaptation that also could be leveraged for therapeutic purposes.
Collapse
|
14
|
Rietbergen TB, van den Hoek Ostende LW, Aase A, Jones MF, Medeiros ED, Simmons NB. The oldest known bat skeletons and their implications for Eocene chiropteran diversification. PLoS One 2023; 18:e0283505. [PMID: 37043445 PMCID: PMC10096270 DOI: 10.1371/journal.pone.0283505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/10/2023] [Indexed: 04/13/2023] Open
Abstract
The Fossil Lake deposits of the Green River Formation of Wyoming, a remarkable early Eocene Lagerstätte (51.98 ±0.35 Ma), have produced nearly 30 bat fossils over the last 50 years. However, diversity has thus far been limited to only two bat species. Here, we describe a new species of Icaronycteris based on two articulated skeletons discovered in the American Fossil Quarry northwest of Kemmerer, Wyoming. The relative stratigraphic position of these fossils indicates that they are the oldest bat skeletons recovered to date anywhere in the world. Phylogenetic analysis of Eocene fossil bats and living taxa places the new species within the family Icaronycteridae as sister to Icaronycteris index, and additionally indicates that the two Green River archaic bat families (Icaronycteridae and Onychonycteridae) form a clade distinct from known Old World lineages of archaic bats. Our analyses found no evidence that Icaronycteris? menui (France) nor I. sigei (India) belong to this clade; accordingly, we therefore remove them from Icaronycteridae. Taken in sum, our results indicate that Green River bats represent a separate chiropteran radiation of basal bats, and provide additional support for the hypothesis of a rapid radiation of bats on multiple continents during the early Eocene.
Collapse
Affiliation(s)
| | | | - Arvid Aase
- Fossil Butte National Monument, Kemmerer, Wyoming, United States of America
| | - Matthew F Jones
- Division of Vertebrate Paleontology, Department of Ecology and Evolutionary Biology, Natural History Museum and Biodiversity Institute, The University of Kansas Lawrence, Lawrence, Kansas, United States of America
| | - Edward D Medeiros
- Boreal Ecosystems and Agricultural Sciences, Grenfell Campus, Memorial University of Newfoundland, Corner Brook, Newfoundland, Canada
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, New York, United States of America
| |
Collapse
|
15
|
Garrett NR, Watkins J, Francis CM, Simmons NB, Ivanova N, Naaum A, Briscoe A, Drinkwater R, Clare EL. Out of thin air: surveying tropical bat roosts through air sampling of eDNA. PeerJ 2023; 11:e14772. [PMID: 37128209 PMCID: PMC10148639 DOI: 10.7717/peerj.14772] [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: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023] Open
Abstract
Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.
Collapse
Affiliation(s)
- Nina R. Garrett
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jonathan Watkins
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Charles M. Francis
- Canadian Wildlife Service, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | | | - Amanda Naaum
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Andrew Briscoe
- Nature Metrics Ltd., Surrey Research Park, Guildford, United Kingdom
| | - Rosie Drinkwater
- Palaeogenomics group, Department of Veterinary Sciences, Ludwig-Maximillian University Munich, Munich, Germany
| | | |
Collapse
|
16
|
Ch’ng L, Tsang SM, Ong ZA, Low DH, Wiantoro S, Smith IL, Simmons NB, Su YC, Lohman DJ, Smith GJ, Mendenhall IH. Co-circulation of alpha- and beta-coronaviruses in Pteropus vampyrus flying foxes from Indonesia. Transbound Emerg Dis 2022; 69:3917-3925. [PMID: 36382687 PMCID: PMC9898127 DOI: 10.1111/tbed.14762] [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: 05/19/2022] [Revised: 10/03/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Bats are important reservoirs for alpha- and beta-coronaviruses. Coronaviruses (CoV) have been detected in pteropodid bats from several Southeast Asian countries, but little is known about coronaviruses in the Indonesian archipelago in proportion to its mammalian biodiversity. In this study, we screened pooled faecal samples from the Indonesian colonies of Pteropus vampyrus with unbiased next-generation sequencing. Bat CoVs related to Rousettus leschenaultii CoV HKU9 and Eidolon helvum CoV were detected. The 121 faecal samples were further screened using a conventional hemi-nested pan-coronavirus PCR assay. Three positive samples were successfully sequenced, and phylogenetic reconstruction revealed the presence of alpha- and beta-coronaviruses. CoVs belonging to the subgenera Nobecovirus, Decacovirus and Pedacovirus were detected in a single P. vampyrus roost. This study expands current knowledge of coronavirus diversity in Indonesian flying foxes, highlighting the need for longitudinal surveillance of colonies as continuing urbanization and deforestation heighten the risk of spillover events.
Collapse
Affiliation(s)
- Lena Ch’ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Susan M. Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines
| | - Zoe A. Ong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H.W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, West Java 16911, Indonesia
| | - Ina L. Smith
- Health and Biosecurity, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, ACT 2601, Australia
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Yvonne C.F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David J. Lohman
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines
| | - Gavin J.D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore
| |
Collapse
|
17
|
Goswami A, Noirault E, Coombs EJ, Clavel J, Fabre AC, Halliday TJD, Churchill M, Curtis A, Watanabe A, Simmons NB, Beatty BL, Geisler JH, Fox DL, Felice RN. Attenuated evolution of mammals through the Cenozoic. Science 2022; 378:377-383. [DOI: 10.1126/science.abm7525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Cenozoic diversification of placental mammals is the archetypal adaptive radiation. Yet, discrepancies between molecular divergence estimates and the fossil record fuel ongoing debate around the timing, tempo, and drivers of this radiation. Analysis of a three-dimensional skull dataset for living and extinct placental mammals demonstrates that evolutionary rates peak early and attenuate quickly. This long-term decline in tempo is punctuated by bursts of innovation that decreased in amplitude over the past 66 million years. Social, precocial, aquatic, and herbivorous species evolve fastest, especially whales, elephants, sirenians, and extinct ungulates. Slow rates in rodents and bats indicate dissociation of taxonomic and morphological diversification. Frustratingly, highly similar ancestral shape estimates for placental mammal superorders suggest that their earliest representatives may continue to elude unequivocal identification.
Collapse
Affiliation(s)
- Anjali Goswami
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
| | - Eve Noirault
- Department of Life Sciences, Natural History Museum, London, UK
| | - Ellen J. Coombs
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Julien Clavel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Anne-Claire Fabre
- Department of Life Sciences, Natural History Museum, London, UK
- Naturhistorisches Museum Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas J. D. Halliday
- Department of Life Sciences, Natural History Museum, London, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Morgan Churchill
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Abigail Curtis
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Akinobu Watanabe
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Brian L. Beatty
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan H. Geisler
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David L. Fox
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ryan N. Felice
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, UK
| |
Collapse
|
18
|
Yohe LR, Fabbri M, Lee D, Davies KTJ, Yohe TP, Sánchez MKR, Rengifo EM, Hall RP, Mutumi G, Hedrick BP, Sadier A, Simmons NB, Sears KE, Dumont E, Rossiter SJ, Bhullar BAS, Dávalos LM. Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats. Evolution 2022; 76:2347-2360. [PMID: 35904467 DOI: 10.1111/evo.14591] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 01/22/2023]
Abstract
Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Deaprtment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA.,North Carolina Research Campus, Kannapolis, North Carolina, 28081, USA
| | - Matteo Fabbri
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Daniela Lee
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Harvard School of Medicine, Cambridge, Massachusetts, 02115, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | | | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, 20004, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13416-970, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, 15073, Peru
| | - Ronald P Hall
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Gregory Mutumi
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, New York, 10024, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Elizabeth Dumont
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06511, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Center for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794, USA
| |
Collapse
|
19
|
Speer KA, Teixeira TSM, Brown AM, Perkins SL, Dittmar K, Ingala MR, Wultsch C, Krampis K, Dick CW, Galen SC, Simmons NB, Clare EL. Cascading effects of habitat loss on ectoparasite-associated bacterial microbiomes. ISME Commun 2022; 2:67. [PMID: 37938296 PMCID: PMC9723575 DOI: 10.1038/s43705-022-00153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/04/2023]
Abstract
Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypothesized that evolution and ecology of an arthropod parasite will influence its microbiome more than broader environmental factors, but this hypothesis has not been extensively tested. To examine the influence of the broader environment on the parasite microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA to characterize the microbiome of 222 obligate ectoparasitic bat flies (Streblidae and Nycteribiidae) collected from 155 bats (representing six species) from ten habitat fragments in the Atlantic Forest of Brazil. Parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area, but not isolation, is associated with an increase in connectance and betweenness centrality of bacterial association networks driven by changes in the diversity of the parasite community. Controlling for the parasite community, bacterial network topology covaries with habitat patch area and exhibits parasite-species specific responses to environmental change. Taken together, habitat loss may have cascading consequences for communities of interacting macro- and microorgansims.
Collapse
Affiliation(s)
- Kelly A Speer
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, D.C, USA.
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C, USA.
| | | | - Alexis M Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Susan L Perkins
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
- Division of Science, City College of New York, New York, NY, USA
| | - Katharina Dittmar
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Melissa R Ingala
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
- Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Washington, D.C, USA
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, USA
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
- Bioinformatics and Computational Genomics Laboratory, Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Carl W Dick
- Department of Biology, Western Kentucky University, Bowling Green, KY, USA
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Spencer C Galen
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
- Biology Department, University of Scranton, Scranton, PA, USA
| | - Nancy B Simmons
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, GBR, UK
- Department of Biology, York University, Toronto, ON, Canada
| |
Collapse
|
20
|
Becker DJ, Albery GF, Sjodin AR, Poisot T, Bergner LM, Chen B, Cohen LE, Dallas TA, Eskew EA, Fagre AC, Farrell MJ, Guth S, Han BA, Simmons NB, Stock M, Teeling EC, Carlson CJ. Optimising predictive models to prioritise viral discovery in zoonotic reservoirs. Lancet Microbe 2022; 3:e625-e637. [PMID: 35036970 PMCID: PMC8747432 DOI: 10.1016/s2666-5247(21)00245-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Indexed: 01/03/2023]
Abstract
Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, and the drivers of model performance are consequently under-documented. Here, we use the bat hosts of betacoronaviruses as a case study for the data-driven process of comparing and validating predictive models of probable reservoir hosts. In early 2020, we generated an ensemble of eight statistical models that predicted host-virus associations and developed priority sampling recommendations for potential bat reservoirs of betacoronaviruses and bridge hosts for SARS-CoV-2. During a time frame of more than a year, we tracked the discovery of 47 new bat hosts of betacoronaviruses, validated the initial predictions, and dynamically updated our analytical pipeline. We found that ecological trait-based models performed well at predicting these novel hosts, whereas network methods consistently performed approximately as well or worse than expected at random. These findings illustrate the importance of ensemble modelling as a buffer against mixed-model quality and highlight the value of including host ecology in predictive models. Our revised models showed an improved performance compared with the initial ensemble, and predicted more than 400 bat species globally that could be undetected betacoronavirus hosts. We show, through systematic validation, that machine learning models can help to optimise wildlife sampling for undiscovered viruses and illustrates how such approaches are best implemented through a dynamic process of prediction, data collection, validation, and updating.
Collapse
Affiliation(s)
- Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Anna R Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Timothée Poisot
- Université de Montréal, Département de Sciences Biologiques, Montréal, QC, Canada
| | - Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Medical Research Centre, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad A Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
- Bat Health Foundation, Fort Collins, CO, USA
| | - Maxwell J Farrell
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sarah Guth
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Barbara A Han
- Cary Institute of Ecosystem Studies, Millbrook, NY, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Michiel Stock
- Research Unit Knowledge-based Systems, Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium
| | - Emma C Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | - Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| |
Collapse
|
21
|
Ferreira RL, Bernard E, da Cruz Júnior FW, Piló LB, Calux A, Souza-Silva M, Barlow J, Pompeu PS, Cardoso P, Mammola S, García AM, Jeffery WR, Shear W, Medellín RA, Wynne JJ, Borges PAV, Kamimura Y, Pipan T, Hajna NZ, Sendra A, Peck S, Onac BP, Culver DC, Hoch H, Flot JF, Stoch F, Pavlek M, Niemiller ML, Manchi S, Deharveng L, Fenolio D, Calaforra JM, Yager J, Griebler C, Nader FH, Humphreys WF, Hughes AC, Fenton B, Forti P, Sauro F, Veni G, Frumkin A, Gavish-Regev E, Fišer C, Trontelj P, Zagmajster M, Delic T, Galassi DMP, Vaccarelli I, Komnenov M, Gainett G, da Cunha Tavares V, Kováč Ľ, Miller AZ, Yoshizawa K, Di Lorenzo T, Moldovan OT, Sánchez-Fernández D, Moutaouakil S, Howarth F, Bilandžija H, Dražina T, Kuharić N, Butorac V, Lienhard C, Cooper SJB, Eme D, Strauss AM, Saccò M, Zhao Y, Williams P, Tian M, Tanalgo K, Woo KS, Barjakovic M, McCracken GF, Simmons NB, Racey PA, Ford D, Labegalini JA, Colzato N, Ramos Pereira MJ, Aguiar LMS, Moratelli R, Du Preez G, Pérez-González A, Reboleira ASPS, Gunn J, Mc Cartney A, Bobrowiec PED, Milko D, Kinuthia W, Fischer E, Meierhofer MB, Frick WF. Brazilian cave heritage under siege. Science 2022; 375:1238-1239. [PMID: 35298256 DOI: 10.1126/science.abo1973] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Rodrigo Lopes Ferreira
- Centro de Estudos em Biologia Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Lavras MG 37200-900, Brazil
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife PE 50670-901, Brazil
| | | | - Luis Beethoven Piló
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife PE 50670-901, Brazil
| | - Allan Calux
- Carstografica, Karst Applied Research Centre, Belo Horizonte, MG 31170-320, Brazil
| | - Marconi Souza-Silva
- Centro de Estudos em Biologia Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Lavras MG 37200-900, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Paulo S Pompeu
- Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History (Luomus), University of Helsinki, Helsinki, Finland
| | - Stefano Mammola
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History (Luomus), University of Helsinki, Helsinki, Finland.,Molecular Ecology Group, Water Research Institute, National Research Council (CNR-IRSA), Verbania Pallanza, Italy
| | - Alejandro Martínez García
- Molecular Ecology Group, Water Research Institute, National Research Council (CNR-IRSA), Verbania Pallanza, Italy
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD 20741, USA
| | - William Shear
- Hampden-Sydney College, Hampden-Sydney, VA 23901, USA
| | - Rodrigo A Medellín
- Instituto de Ecología, Universidad Nacional Autónoma de México, 04510 Ciudad Universitaria, Mexico
| | - J Judson Wynne
- Department of Biological Sciences and Center for Adaptive Western Landscapes, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paulo A V Borges
- Centre for Ecology, Evolution, and Environmental Changes/Azorean Biodiversity Group, Faculty of Agriculture and Environment, Universidade dos Açores, 9700-042 Angra do Heroísmo, Azores, Portugal
| | | | - Tanja Pipan
- Research Centre of the Slovenian Academy of Sciences and Arts, Karst Research Institute, SI-1000, Ljubljana, Slovenia
| | - Nadja Zupan Hajna
- Research Centre of the Slovenian Academy of Sciences and Arts, Karst Research Institute, SI-1000, Ljubljana, Slovenia.,Croatian Biospeleological Society, 10 000 Zagreb, Croatia
| | - Alberto Sendra
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri, Universitat de València, València, Spain
| | - Stewart Peck
- Carleton University, Ottawa, ON, K2C 0L3, Canada
| | - Bogdan P Onac
- School of Geosciences, University of South Florida, Tampa, FL 33620, USA
| | - David C Culver
- Department of Environmental Science, American University, Washington, DC 20016, USA
| | - Hannelore Hoch
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Humboldt-University, D-10115 Berlin, Germany
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB),2 1050 Brussels, Belgium
| | - Fabio Stoch
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | | | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Shelby Center for Science and Technology, Huntsville, AL 35899, USA
| | - Shirish Manchi
- Sàlim Ali Centre for Ornithology and Natural History, Coimbatore, 641108, Tamil Nadu, India.,Speleological Association of India, KNG Pudur, Coimbatore, 641025, Tamil Nadu, India
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, French National Center for Scientific Research (CNRS), Unité Mixte de Recherche 7205, Université Pierre et Marie Curie, Ecole Pratique des Hautes Études, Museum National d'Histoire Naturelle, Sorbonne Université, Paris, France.,International Union for Conservation of Nature Cave Invertebrate Specialist Group, 1196 Gland, Switzerland
| | - Danté Fenolio
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX 78212-3199, USA
| | - José-María Calaforra
- University of Almería, Water Resources & Environmental Geology, Carretera Sacramento s/n 04120 Almería, Spain
| | - Jill Yager
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20560, USA
| | - Christian Griebler
- Department of Functional & Evolutionary Ecology, Unit Limnology, University of Vienna, 1030 Wien, Austria
| | | | - William F Humphreys
- School of Biological Sciences, University of Western Australia, Perth WA 6009, Australia
| | - Alice C Hughes
- Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Brock Fenton
- Department of Biology, Western University, London, ON, Canada
| | - Paolo Forti
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Francesco Sauro
- Italian Institute of Speleology, University of Bologna, Bologna, Italy
| | - George Veni
- National Cave and Karst Research Institute, Carlsbad, NM 88220 USA.,International Union of Speleology, Postojna, 6230 Slovenia
| | - Amos Frumkin
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Efrat Gavish-Regev
- Arachnida & Other Terrestrial Arthropods, The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Cene Fišer
- SubBioLab, Department of Biology, Biotechnical Faculty, University of Ljubljana, SI1000 Ljubljana, Slovenia
| | - Peter Trontelj
- SubBioLab, Department of Biology, Biotechnical Faculty, University of Ljubljana, SI1000 Ljubljana, Slovenia
| | - Maja Zagmajster
- SubBioLab, Department of Biology, Biotechnical Faculty, University of Ljubljana, SI1000 Ljubljana, Slovenia
| | - Teo Delic
- SubBioLab, Department of Biology, Biotechnical Faculty, University of Ljubljana, SI1000 Ljubljana, Slovenia
| | - Diana M P Galassi
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Valeria da Cunha Tavares
- Instituto Tecnológico Vale, Belém, PA, Brazil.,Programa de Pós Graduação em Biologia/Zoologia, Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Ľubomír Kováč
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Košice, Slovakia
| | - Ana Z Miller
- Hercules Laboratory, University of Évora, 7000-809 Évora, Portugal; Instituto de Recursos Naturales y Agrobiología de Sevilla-Consejo Superior de Investigaciones Cientificas, 41012 Seville, Spain
| | - Kazunori Yoshizawa
- Systematic Entomology, School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tiziana Di Lorenzo
- Research Institute on Terrestrial Ecosystems of the National Research Council, 50019, Sesto Fiorentino, Firenze, Italy.,Emil Racovita Institute of Speleology, Romanian Academy, Cluj Napoca 400006, Romania
| | - Oana T Moldovan
- Emil Racovita Institute of Speleology, Romanian Academy, Cluj Napoca 400006, Romania
| | | | - Soumia Moutaouakil
- Museum of Natural History of Marrakech, Cadi Ayyad University, Marrakesh, Morocco
| | | | - Helena Bilandžija
- Ruđer Bošković Institute, 10000 Zagreb, Croatia.,Croatian Biospeleological Society, 10 000 Zagreb, Croatia
| | - Tvrtko Dražina
- Croatian Biospeleological Society, 10 000 Zagreb, Croatia
| | | | - Valerija Butorac
- Geography Department, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Charles Lienhard
- Arthropoda Department, Geneva Natural History Museum, Geneva, Switzerland
| | - Steve J B Cooper
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA 5000, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - David Eme
- RiverLY Research Unit, National Research Institute for Agriculture Food and Environment (INRAE), Villeurbanne, France
| | | | - Mattia Saccò
- Subterranean Research and Groundwater Ecology Group, Trace and Environmental DNA Lab, School of Molecular and Life Sciences, Curtin University, Perth, 6102 WA, Australia
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Paul Williams
- School of Environment, University of Auckland, Auckland 1142, New Zealand
| | - Mingyi Tian
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Krizler Tanalgo
- Ecology and Conservation Research Lab, Department of Biological Sciences, College of Science and Mathematics, University of Southern Mindanao, Kabacan 9407, North Cotabato, Philippines
| | - Kyung-Sik Woo
- Department of Geology, Kangwon National University, Chuncheon, Gangwondo 24341, Korea.,International Union for Conservation of Nature, World Commission on Protected Areas, Geoheritage Specialist Group, Seoul 06599, Korea
| | | | - Gary F McCracken
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Nancy B Simmons
- Department of Mammalogy, Richard Guilder Graduate School Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024 USA
| | - Paul A Racey
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Derek Ford
- International Union of Speleology, Postojna, 6230 Slovenia
| | | | | | - Maria João Ramos Pereira
- Bird and Mammal Evolution, Systematics and Ecology Lab, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ludmilla M S Aguiar
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil
| | - Ricardo Moratelli
- Área de Saúde Ambiental, Fiocruz Mata Atlântica, Fundação Oswaldo Cruz, Colônia Juliano Moreira, Taquara, Rio de Janeiro, RJ, 22713-375, Brazil
| | - Gerhard Du Preez
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Abel Pérez-González
- División de Aracnología, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', C1405DJR Buenos Aires, Argentina
| | - Ana Sofia P S Reboleira
- Centre for Ecology, Evolution, and Environmental Changes and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Natural History Museum of Denmark, University of Copenhagen, 2100 København Ø, Denmark
| | - John Gunn
- School of Geography, Earth, and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ann Mc Cartney
- Genome Informatics Section, National Human Genome Research Institute, National Institute of Health, Bethesda, MD 20894, USA
| | - Paulo E D Bobrowiec
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-graduação em Ecologia, Centro de Estudos da Biodiversidade Amazônica, Manaus, Brazil
| | - Dmitry Milko
- Entomology Department, Institute of Biology, Kyrgyz National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Wanja Kinuthia
- Eastern African Network of BioNET, International, National Museums of Kenya, Nairobi, Kenya
| | - Erich Fischer
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, Brazil
| | - Melissa B Meierhofer
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, 00100, Finland.,Department of Rangeland, Wildlife, and Fisheries Management, Texas A&M University, College Station, TX 77843, USA
| | - Winifred F Frick
- Bat Conservation International, Austin, TX 78746, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| |
Collapse
|
22
|
López-Aguirre C, Hand SJ, Simmons NB, Silcox MT. Untangling the ecological signal in the dental morphology in the bat superfamily Noctilionoidea. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09606-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
23
|
Murphy CT, Marx M, Martin WN, Jiang H, Lapseritis JM, French AN, Simmons NB, Moore MJ. Feeling for food: Can rostro-mental hair arrays sense hydrodynamic cues for foraging North Atlantic right whales? Anat Rec (Hoboken) 2022; 305:577-591. [PMID: 35122671 DOI: 10.1002/ar.24858] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/17/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
North Atlantic right whales (NARWs; Eubalaena glacialis) possess an arrangement of fine hairs on the rostrum and chin that may be used for hydrodynamic sensing during feeding. These hairs occur across mysticete species and are known to possess adequate innervation in the subdermal follicle to support their consideration as sensory hairs (vibrissae). However, the small size of the hair structure with respect to the enormous scale of the animal's body has caused doubts regarding their utility and prompted speculation that the hairs may be vestigial or minimally functional. Here we show that NARW hairs occur in abundance on the leading surface of the head in a unique and characteristic arrangement. We consider the sensory hairs in context of the fluid environment in which this species forages and argue that the size of the hair is scaled to the size of the animal's small planktonic prey, thus suggesting that the hairs play an important role in the sensory ecology of these animals.
Collapse
Affiliation(s)
- Christin T Murphy
- Naval Undersea Warfare Center, Division Newport, Newport, Rhode Island, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Marilyn Marx
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, USA
| | - William N Martin
- Naval Undersea Warfare Center, Division Newport, Newport, Rhode Island, USA
| | - Houshuo Jiang
- Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Joy M Lapseritis
- Naval Undersea Warfare Center, Division Newport, Newport, Rhode Island, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alison N French
- Naval Undersea Warfare Center, Division Newport, Newport, Rhode Island, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Michael J Moore
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| |
Collapse
|
24
|
Ingala MR, Simmons NB, Dunbar M, Wultsch C, Krampis K, Perkins SL. You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches. Anim Microbiome 2021; 3:82. [PMID: 34906258 PMCID: PMC8672517 DOI: 10.1186/s42523-021-00139-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 04/01/2021] [Accepted: 10/20/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts and their gut bacteria, fewer studies examine the potentially adaptive functional contributions of these microbes to the dietary habits of their hosts. In this study, we examined predicted metabolic pathways in the gut bacteria of more than 500 individual bats belonging to 60 species and compare the enrichment of these functions across hosts with distinct dietary ecologies. RESULTS We found that predicted microbiome functions were differentially enriched across hosts with different diets. Using a machine-learning approach, we also found that inferred microbiome functions could be used to predict specialized host diets with reasonable accuracy. We detected a relationship between both host phylogeny and diet with respect to microbiome functional repertoires. Because many predicted functions could potentially fill nutritional gaps for bats with specialized diets, we considered pathways discriminating dietary niches as traits of the host and fit them to comparative phylogenetic models of evolution. Our results suggest that some, but not all, predicted microbiome functions may evolve toward adaptive optima and thus be visible to the forces of natural selection operating on hosts over evolutionary time. CONCLUSIONS Our results suggest that bats with specialized diets may partially rely on their gut microbes to fulfill or augment critical nutritional pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. Our work adds to a growing body of literature suggesting that animal microbiomes are structured by a combination of ecological and evolutionary processes and sets the stage for future metagenomic and metabolic characterization of the bat microbiome to explore links between bacterial metabolism and host nutrition.
Collapse
Affiliation(s)
- Melissa R. Ingala
- Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC USA
- Department of Mammalogy, The American Museum of Natural History, New York, NY USA
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY USA
| | - Nancy B. Simmons
- Department of Mammalogy, The American Museum of Natural History, New York, NY USA
| | - Miranda Dunbar
- Department of Biological Sciences, Southern Connecticut State University, New Haven, CT USA
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, The American Museum of Natural History, New York, NY USA
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY USA
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, NY USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY USA
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY USA
| | - Susan L. Perkins
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY USA
- Sackler Institute for Comparative Genomics, The American Museum of Natural History, New York, NY USA
| |
Collapse
|
25
|
Van der Jeucht L, Groom Q, Agosti D, Phelps K, Reeder DM, Simmons NB. Using iNaturalist to monitor adherence to best practices in bat handling. Biodivers Data J 2021; 9:e68052. [PMID: 34690513 PMCID: PMC8484243 DOI: 10.3897/bdj.9.e68052] [Citation(s) in RCA: 3] [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: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Laura Van der Jeucht
- Free University of Brussels (VUB), Brussels, Belgium Free University of Brussels (VUB) Brussels Belgium
| | - Quentin Groom
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
| | | | - Kendra Phelps
- EcoHealth Alliance, New York, United States of America EcoHealth Alliance New York United States of America
| | - DeeAnn Marie Reeder
- Bucknell University, Lewisburg, United States of America Bucknell University Lewisburg United States of America
| | - Nancy B Simmons
- American Museum of Natural History, New York, United States of America American Museum of Natural History New York United States of America
| |
Collapse
|
26
|
Nesi N, Tsagkogeorga G, Tsang SM, Nicolas V, Lalis A, Scanlon AT, Riesle-Sbarbaro SA, Wiantoro S, Hitch AT, Juste J, Pinzari CA, Bonaccorso FJ, Todd CM, Lim BK, Simmons NB, McGowen MR, Rossiter SJ. Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae). Syst Biol 2021; 70:1077-1089. [PMID: 33693838 PMCID: PMC8513763 DOI: 10.1093/sysbio/syab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/27/2021] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].
Collapse
Affiliation(s)
- Nicolas Nesi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Susan M Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Zoology Section, National Museum of Natural History, Manila, Philippines
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Aude Lalis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Annette T Scanlon
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, Australia
| | - Silke A Riesle-Sbarbaro
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Alan T Hitch
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | | | | | - Christopher M Todd
- The Hawkesbury institute for the Environment, Western Sydney University, Australia
| | - Burton K Lim
- Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| |
Collapse
|
27
|
Upham NS, Poelen JH, Paul D, Groom QJ, Simmons NB, Vanhove MPM, Bertolino S, Reeder DM, Bastos-Silveira C, Sen A, Sterner B, Franz NM, Guidoti M, Penev L, Agosti D. Liberating host-virus knowledge from biological dark data. Lancet Planet Health 2021; 5:e746-e750. [PMID: 34562356 PMCID: PMC8457912 DOI: 10.1016/s2542-5196(21)00196-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/12/2020] [Revised: 06/20/2021] [Accepted: 07/06/2021] [Indexed: 05/18/2023]
Abstract
Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.
Collapse
Affiliation(s)
- Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Jorrit H Poelen
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA; Cheadle Center for Biodiversity and Ecological Restoration, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Deborah Paul
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Maarten P M Vanhove
- Zoology, Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sandro Bertolino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - DeeAnn M Reeder
- Department of Biology, Bucknell University, Lewisburg, PA, USA
| | | | - Atriya Sen
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA
| | - Beckett Sterner
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Nico M Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | | | | |
Collapse
|
28
|
Velazco PM, Voss RS, Fleck DW, Simmons NB. Mammalian Diversity and Matses Ethnomammalogy in Amazonian Peru Part 4: Bats. Bulletin of the American Museum of Natural History 2021. [DOI: 10.1206/0003-0090.451.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Paúl M. Velazco
- Department of Biology, Arcadia University, Glenside, PA; Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - David W. Fleck
- Division of Anthropology, American Museum of Natural History
| | - Nancy B. Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| |
Collapse
|
29
|
Sandoval-Herrera NI, Mastromonaco GF, Becker DJ, Simmons NB, Welch KC. Inter- and intra-specific variation in hair cortisol concentrations of Neotropical bats. Conserv Physiol 2021; 9:coab053. [PMID: 34267922 PMCID: PMC8278960 DOI: 10.1093/conphys/coab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/13/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Quantifying hair cortisol has become popular in wildlife ecology for its practical advantages for evaluating stress. Before hair cortisol levels can be reliably interpreted, however, it is key to first understand the intrinsic factors explaining intra- and inter-specific variation. Bats are an ecologically diverse group of mammals that allow studying such variation. Given that many bat species are threatened or have declining populations in parts of their range, minimally invasive tools for monitoring colony health and identifying cryptic stressors are needed to efficiently direct conservation efforts. Here we describe intra- and inter-specific sources of variation in hair cortisol levels in 18 Neotropical bat species from Belize and Mexico. We found that fecundity is an important ecological trait explaining inter-specific variation in bat hair cortisol. Other ecological variables such as colony size, roost durability and basal metabolic rate did not explain hair cortisol variation among species. At the individual level, females exhibited higher hair cortisol levels than males and the effect of body mass varied among species. Overall, our findings help validate and accurately apply hair cortisol as a monitoring tool in free-ranging bats.
Collapse
Affiliation(s)
- Natalia I Sandoval-Herrera
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Ontario, M1C 1A4, Canada
| | | | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024-5102, USA
| | - Kenneth C Welch
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Ontario, M1C 1A4, Canada
| |
Collapse
|
30
|
Cornelius Ruhs E, Becker DJ, Oakey SJ, Ogunsina O, Fenton MB, Simmons NB, Martin LB, Downs CJ. Body size affects immune cell proportions in birds and non-volant mammals, but not bats. J Exp Biol 2021; 224:269058. [PMID: 34104965 DOI: 10.1242/jeb.241109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/18/2020] [Accepted: 06/02/2021] [Indexed: 01/02/2023]
Abstract
Powered flight has evolved several times in vertebrates and constrains morphology and physiology in ways that likely have shaped how organisms cope with infections. Some of these constraints probably have impacts on aspects of immunology, such that larger fliers might prioritize risk reduction and safety. Addressing how the evolution of flight may have driven relationships between body size and immunity could be particularly informative for understanding the propensity of some taxa to harbor many virulent and sometimes zoonotic pathogens without showing clinical disease. Here, we used a comparative framework to quantify scaling relationships between body mass and the proportions of two types of white blood cells - lymphocytes and granulocytes (neutrophils/heterophils) - across 63 bat species, 400 bird species and 251 non-volant mammal species. By using phylogenetically informed statistical models on field-collected data from wild Neotropical bats and from captive bats, non-volant mammals and birds, we show that lymphocyte and neutrophil proportions do not vary systematically with body mass among bats. In contrast, larger birds and non-volant mammals have disproportionately higher granulocyte proportions than expected for their body size. Our inability to distinguish bat lymphocyte scaling from birds and bat granulocyte scaling from all other taxa suggests there may be other ecological explanations (i.e. not flight related) for the cell proportion scaling patterns. Future comparative studies of wild bats, birds and non-volant mammals of similar body mass should aim to further differentiate evolutionary effects and other aspects of life history on immune defense and its role in the tolerance of (zoonotic) infections.
Collapse
Affiliation(s)
- Emily Cornelius Ruhs
- Global Health and Infectious Disease Research, University of South Florida, Tampa, FL 33612, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Samantha J Oakey
- Global Health and Infectious Disease Research, University of South Florida, Tampa, FL 33612, USA
| | - Ololade Ogunsina
- Global Health and Infectious Disease Research, University of South Florida, Tampa, FL 33612, USA
| | - M Brock Fenton
- Department of Biology, Western University, London, ON, Canada, N6A 5B7
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024-5102, USA
| | - Lynn B Martin
- Global Health and Infectious Disease Research, University of South Florida, Tampa, FL 33612, USA
| | - Cynthia J Downs
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| |
Collapse
|
31
|
Groom Q, Adriaens T, Bertolino S, Phelps K, Poelen JH, Reeder DM, Richardson DM, Simmons NB, Upham N. Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms. Biodivers Data J 2021; 9:e65371. [PMID: 34168517 PMCID: PMC8219659 DOI: 10.3897/bdj.9.e65371] [Citation(s) in RCA: 2] [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: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 11/21/2022] Open
Abstract
Domestic and captive animals and cultivated plants should be recognised as integral components in contemporary ecosystems. They interact with wild organisms through such mechanisms as hybridization, predation, herbivory, competition and disease transmission and, in many cases, define ecosystem properties. Nevertheless, it is widespread practice for data on domestic, captive and cultivated organisms to be excluded from biodiversity repositories, such as natural history collections. Furthermore, there is a lack of integration of data collected about biodiversity in disciplines, such as agriculture, veterinary science, epidemiology and invasion science. Discipline-specific data are often intentionally excluded from integrative databases in order to maintain the “purity” of data on natural processes. Rather than being beneficial, we argue that this practise of data exclusivity greatly limits the utility of discipline-specific data for applications ranging from agricultural pest management to invasion biology, infectious disease prevention and community ecology. This problem can be resolved by data providers using standards to indicate whether the observed organism is of wild or domestic origin and by integrating their data with other biodiversity data (e.g. in the Global Biodiversity Information Facility). Doing so will enable efforts to integrate the full panorama of biodiversity knowledge across related disciplines to tackle pressing societal questions.
Collapse
Affiliation(s)
- Quentin Groom
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University Stellenbosch South Africa
| | - Tim Adriaens
- Research Inst. for Nature and Forest (INBO), Brussels, Belgium Research Inst. for Nature and Forest (INBO) Brussels Belgium
| | - Sandro Bertolino
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy Department of Life Sciences and Systems Biology, University of Turin Torino Italy
| | - Kendra Phelps
- EcoHealth Alliance, New York, United States of America EcoHealth Alliance New York United States of America
| | - Jorrit H Poelen
- Ronin Institute for Independent Scholarship, Montclair, United States of America Ronin Institute for Independent Scholarship Montclair United States of America
| | - DeeAnn Marie Reeder
- Bucknell University, Lewisburg, United States of America Bucknell University Lewisburg United States of America
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University Stellenbosch South Africa
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, United States of America Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History New York United States of America
| | - Nathan Upham
- Arizona State University, Tempe, United States of America Arizona State University Tempe United States of America
| |
Collapse
|
32
|
Ingala MR, Simmons NB, Wultsch C, Krampis K, Provost KL, Perkins SL. Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding. Ecol Evol 2021; 11:7474-7491. [PMID: 34188828 PMCID: PMC8216975 DOI: 10.1002/ece3.7579] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 01/19/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/30/2022] Open
Abstract
Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defined dietary guilds (e.g., insectivores, carnivores, and frugivores). Apart from these broad guilds, we lack detailed dietary information for many species and therefore have only a limited understanding of interaction networks linking bats and their diet items. In this study, we used DNA metabarcoding of plants, arthropods, and vertebrates to investigate the diets of 25 bat species from the tropical dry forests of Lamanai, Belize. Our results report some of the first detection of diet items for the focal bat taxa, adding rich and novel natural history information to the field of bat ecology. This study represents a comprehensive first effort to apply DNA metabarcoding to bat diets at Lamanai and provides a useful methodological framework for future studies testing hypotheses about coexistence and niche differentiation in the context of modern high-throughput molecular data.
Collapse
Affiliation(s)
- Melissa R. Ingala
- Division of MammalsDepartment of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Richard Gilder Graduate SchoolThe American Museum of Natural HistoryNew YorkNYUSA
- Department of Mammalogy, Division of Vertebrate ZoologyThe American Museum of Natural HistoryNew YorkNYUSA
- Division of Invertebrate ZoologyThe American Museum of Natural HistoryNew YorkNYUSA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate ZoologyThe American Museum of Natural HistoryNew YorkNYUSA
| | - Claudia Wultsch
- Sackler Institute for Comparative GenomicsThe American Museum of Natural HistoryNew YorkNYUSA
- Bioinformatics and Computational Genomics LaboratoryHunter CollegeCity University of New YorkNew YorkNYUSA
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics LaboratoryHunter CollegeCity University of New YorkNew YorkNYUSA
- Department of Biological SciencesHunter CollegeCity University of New YorkNew YorkNYUSA
- Institute of Computational BiomedicineWeill Cornell Medical CollegeNew YorkNYUSA
| | - Kaiya L. Provost
- Richard Gilder Graduate SchoolThe American Museum of Natural HistoryNew YorkNYUSA
- Department of OrnithologyThe American Museum of Natural HistoryNew YorkNYUSA
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
| | - Susan L. Perkins
- Division of Invertebrate ZoologyThe American Museum of Natural HistoryNew YorkNYUSA
- Sackler Institute for Comparative GenomicsThe American Museum of Natural HistoryNew YorkNYUSA
| |
Collapse
|
33
|
Neely BA, Becker DJ, Janech MG, Fenton MB, Simmons NB, Bland AM. Surveying the Vampire Bat ( Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res 2021; 20:2547-2559. [PMID: 33840197 PMCID: PMC9812275 DOI: 10.1021/acs.jproteome.0c00995] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.
Collapse
Affiliation(s)
- Benjamin A. Neely
- Chemical Sciences Division, National, Institute of Standards and Technology, Charleston, South, Carolina 29412, United States
| | - Daniel J. Becker
- Department of Biology, University of, Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael G. Janech
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
| | - M. Brock Fenton
- Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of, Vertebrate Zoology, American Museum of Natural History, New York 10024, United States
| | - Alison M. Bland
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States; Department of, Biology, College of Charleston, Charleston, South Carolina, 29424, United States
| |
Collapse
|
34
|
Morales AE, Fenton MB, Carstens BC, Simmons NB. Comment on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic exchange and hybridization appear common among the western long-eared bats from North America. Multiple sources of evidence indicate that lineages within this group are evolving independently, despite genetic exchange. However, evidence of gene flow raises questions about the species-level status of some lineages. C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279) proposed that Myotis evotis (H. Allen, 1864) (long-eared myotis) and Myotis keenii (Merriam, 1895) (Keen’s myotis) are one species, not two. This conclusion is based on analyses of cytochrome b and microsatellite data suggesting gene flow between these taxa. Microsatellites are not reliable markers for identifying species because homoplasy can be a major confounding factor, which appears to be true in this case. We reanalyzed the dataset of C.L. Lausen et al. (2019) and show that it is not reliable to distinguish between gene flow or homoplasy, and that these data do not support the conclusion that M. evotis and M. keenii represent a single species. Previous morphological and genomic studies indicate that these are separate species despite previous genetic exchange between them. Failing to recognize that gene flow can occur between independently evolving lineages is counterproductive for conservation because it can lead to neglect of important independent lineages, and likewise failing to use proper tools to delimit species is counterproductive to efforts to quantify biodiversity and design conservation strategies.
Collapse
Affiliation(s)
- Ariadna E. Morales
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| |
Collapse
|
35
|
Becker DJ, Speer KA, Korstian JM, Volokhov DV, Droke HF, Brown AM, Baijnauth CL, Padgett-Stewart T, Broders HG, Plowright RK, Rainwater TR, Fenton MB, Simmons NB, Chumchal MM. Disentangling interactions among mercury, immunity and infection in a Neotropical bat community. J Appl Ecol 2021; 58:879-889. [PMID: 33911313 PMCID: PMC8078557 DOI: 10.1111/1365-2664.13809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022]
Abstract
1. Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare. 2. We capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and bacterial pathogens. As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury-infection relationships. 3. Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for haemoplasmas and Bartonella spp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for haemoplasmas in Pteronotus mesoamericanus and Dermanura phaeotis. For Bartonella spp., mercury was associated with particularly low odds of infection in the genus Pteronotus but high odds in the subfamily Stenodermatinae. 4. Synthesis and application. Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e. anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest that contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales.
Collapse
Affiliation(s)
| | - Kelly A. Speer
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | | | - Dmitriy V. Volokhov
- Center for Biologies Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Hannah F. Droke
- Department of Global and Planetary Health, University of South Florida, Tampa, FL, USA
| | - Alexis M. Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Catherene L. Baijnauth
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Ticha Padgett-Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Hugh G. Broders
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Thomas R. Rainwater
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC, USA
- Tom Yawkey Wildlife Center, Georgetown, SC, USA
| | - M. Brock Fenton
- Department of Biology, Western University, London, ON, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | | |
Collapse
|
36
|
Tsang SM, Low DHW, Wiantoro S, Smith I, Jayakumar J, Simmons NB, Vijaykrishna D, Lohman DJ, Mendenhall IH. Detection of Tioman Virus in Pteropus vampyrus Near Flores, Indonesia. Viruses 2021; 13:v13040563. [PMID: 33810446 PMCID: PMC8067168 DOI: 10.3390/v13040563] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
Diverse paramyxoviruses have coevolved with their bat hosts, including fruit bats such as flying foxes (Chiroptera: Pteropodidae). Several of these viruses are zoonotic, but the diversity and distribution of Paramyxoviridae are poorly understood. We screened pooled feces samples from three Pteropus vampyrus colonies and assayed tissues, rectal swabs, and oral swabs from 95 individuals of 23 pteropodid species sampled at 17 sites across the Indonesian archipelago with a conventional paramyxovirus PCR; all tested negative. Samples from 43 individuals were screened with next generation sequencing (NGS), and a single Pteropus vampyrus collected near Flores had Tioman virus sequencing reads. Tioman virus is a bat-borne virus in the genus Pararubulavirus with prior evidence of spillover to humans. This work expands the known range of Tioman virus, and it is likely that this isolated colony likely has sustained intergenerational transmission over a long period.
Collapse
Affiliation(s)
- Susan M. Tsang
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA; (S.M.T.); (N.B.S.)
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines;
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; (D.H.W.L.); (J.J.)
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, West Java 16911, Indonesia;
| | - Ina Smith
- Health and Biosecurity, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, ACT 2601, Australia;
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; (D.H.W.L.); (J.J.)
| | - Nancy B. Simmons
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA; (S.M.T.); (N.B.S.)
| | - Dhanasekaran Vijaykrishna
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China;
| | - David J. Lohman
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines;
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; (D.H.W.L.); (J.J.)
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore
- Correspondence:
| |
Collapse
|
37
|
Simmons NB, Flanders J, Bakwo Fils EM, Parker G, Suter JD, Bamba S, Douno M, Keita MK, Morales AE, Frick WF. A New Dichromatic Species of Myotis (Chiroptera: Vespertilionidae) from the Nimba Mountains, Guinea. American Museum Novitates 2021. [DOI: 10.1206/3963.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Nancy B. Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, New York
| | - Jon Flanders
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, New York
| | - Eric Moïse Bakwo Fils
- Department of Biological Sciences, Faculty of Sciences, University of Maroua, Maroua, Cameroon
| | - Guy Parker
- Société des Mines de Fer de Guinée, Conakry, Guinea
| | | | - Seinan Bamba
- Société des Mines de Fer de Guinée, Conakry, Guinea
| | - Mory Douno
- Centre de Gestion de l'Environnement des Monts Nimba et Simandou/Ministère de l'Environnement, des Eaux et Forêts, Conakry, Guinea
| | | | - Ariadna E. Morales
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, New York
| | | |
Collapse
|
38
|
Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
Collapse
Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | |
Collapse
|
39
|
O'Toole B, Simmons NB, Hekkala E. Reconstructing the Genomic Diversity of a Widespread Sub-Saharan Bat (Pteropodidae: Eidolon helvum) Using Archival Museum Collections. Acta Chiropterologica 2020. [DOI: 10.3161/15081109acc2020.22.2.001] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Brian O'Toole
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| |
Collapse
|
40
|
Becker DJ, Broos A, Bergner LM, Meza DK, Simmons NB, Fenton MB, Altizer S, Streicker DG. Temporal patterns of vampire bat rabies and host connectivity in Belize. Transbound Emerg Dis 2020. [PMCID: PMC8246562 DOI: 10.1111/tbed.13754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Daniel J. Becker
- Odum School of Ecology University of Georgia Athens GA USA
- Center for the Ecology of Infectious Disease University of Georgia Athens GA USA
- Department of Biology Indiana University Bloomington IN USA
| | - Alice Broos
- MRC–University of Glasgow Centre for Virus Research Glasgow UK
| | - Laura M. Bergner
- MRC–University of Glasgow Centre for Virus Research Glasgow UK
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Diana K. Meza
- MRC–University of Glasgow Centre for Virus Research Glasgow UK
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Nancy B. Simmons
- Department of Mammalogy Division of Vertebrate Zoology American Museum of Natural History New York NY USA
| | | | - Sonia Altizer
- Odum School of Ecology University of Georgia Athens GA USA
- Center for the Ecology of Infectious Disease University of Georgia Athens GA USA
| | - Daniel G. Streicker
- Odum School of Ecology University of Georgia Athens GA USA
- MRC–University of Glasgow Centre for Virus Research Glasgow UK
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| |
Collapse
|
41
|
Cook JA, Arai S, Armién B, Bates J, Bonilla CAC, Cortez MBDS, Dunnum JL, Ferguson AW, Johnson KM, Khan FAA, Paul DL, Reeder DM, Revelez MA, Simmons NB, Thiers BM, Thompson CW, Upham NS, Vanhove MPM, Webala PW, Weksler M, Yanagihara R, Soltis PS. Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases. Bioscience 2020; 70:531-534. [PMID: 32665736 PMCID: PMC7340541 DOI: 10.1093/biosci/biaa064] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Blas Armién
- Departamento de Invetigación de Enfermedades Emergentes y Zoonóticas, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Republic of Panama
| | - John Bates
- Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, Illinois
| | - Carlos A Carrion Bonilla
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque, and with the Museo de Mastozoologia QCAZ, Universidad Catolica del Ecuador, Quito, Ecuador
| | - Maria Beatriz de Souza Cortez
- Florida Museum of Natural History, the UF Biodiversity Institute, and the Department of Biology, University of Florida, Gainesville
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque
| | - Adam W Ferguson
- Gantz Family Collections Center, The Field Museum of Natural History, Chicago, Ilinois
| | - Karl M Johnson
- Biology Department, University of New Mexico, Albuquerque
| | - Faisal Ali Anwarali Khan
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Jalan Datuk Mohammad Musa, Kota Samarahan, Sarawak, Malaysia
| | - Deborah L Paul
- iDigBio and iDigInfo, Florida State University, Tallahassee
| | - DeeAnn M Reeder
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania
| | | | - Nancy B Simmons
- Division of Vertebrate Zoology's Department of Mammalogy, American Museum of Natural History, New York, New York
| | - Barbara M Thiers
- William and Lynda Steere Herbarium, New York Botanical Garden, the Bronx, New York
| | - Cody W Thompson
- Department of Ecology and Evolutionary Biology and with the Museum of Zoology, University of Michigan, Ann Arbor
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe
| | - Maarten P M Vanhove
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Richard Yanagihara
- Pacific Center for Emerging Infectious Diseases Research, the John A. Burns School of Medicine, University of Hawaii, Manoa, Honolulu, Hawaii
| | - Pamela S Soltis
- Florida Museum of Natural History and with the UF Biodiversity Institute, University of Florida, Gainesville
| |
Collapse
|
42
|
Almeida FC, Simmons NB, Giannini NP. A Species-Level Phylogeny of Old World Fruit Bats with a New Higher-Level Classification of the Family Pteropodidae. American Museum Novitates 2020. [DOI: 10.1206/3950.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Francisca Cunha Almeida
- Instituto de Ecología, Genética y Evolución de Buenos Aires – CONICET, Buenos Aires, Argentina
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Norberto P. Giannini
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York
| |
Collapse
|
43
|
Becker DJ, Speer KA, Brown AM, Fenton MB, Washburne AD, Altizer S, Streicker DG, Plowright RK, Chizhikov VE, Simmons NB, Volokhov DV. Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community. Mol Ecol 2020; 29:1534-1549. [PMID: 32243630 PMCID: PMC8299350 DOI: 10.1111/mec.15422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 12/21/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022]
Abstract
Most emerging pathogens can infect multiple species, underlining the importance of understanding the ecological and evolutionary factors that allow some hosts to harbour greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is based primarily around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (order Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. Here were studied haemotropic Mycoplasma spp. (i.e., haemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were haemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Haemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported codivergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared haemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare-but detectable-bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts not only for viruses but also for bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and the epidemiological consequences of bacterial pathogens.
Collapse
Affiliation(s)
- Daniel J. Becker
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
| | - Kelly A. Speer
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of Invertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Alexis M. Brown
- Department of Ecology and EvolutionStony Brook UniversityStony BrookNYUSA
| | | | - Alex D. Washburne
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Sonia Altizer
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
| | - Daniel G. Streicker
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
- MRC–University of Glasgow Centre for Virus ResearchGlasgowUK
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Vladimir E. Chizhikov
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMDUSA
| | - Nancy B. Simmons
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of MammalogyDivision of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMDUSA
| |
Collapse
|
44
|
Tsang SM, Wiantoro S, Veluz MJ, Sugita N, Nguyen YL, Simmons NB, Lohman DJ. Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world's largest bats (Mammalia: Chiroptera). J Biogeogr 2020; 47:527-537. [PMID: 33041434 PMCID: PMC7546435 DOI: 10.1111/jbi.13750] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/04/2019] [Indexed: 05/25/2023]
Abstract
AIM Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. LOCATION Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands. TAXON Pteropus (Pteropodidae). METHODS To infer the biogeographic history of Pteropus, we sequenced up to 6169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognized Pteropus species and subspecies with 3 Acerodon outgroups using BEAST and subsequently estimated ancestral areas using models implemented in BioGeoBEARS. RESULTS Species-level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor with Acerodon; founder-event speciation out of Wallacea was a common inference. Pteropus species in Micronesia and the western Indian Ocean were also inferred to result from founder-event speciation. MAIN CONCLUSIONS Dispersal between regions of the IAA and the islands found therein fostered diversification of Pteropus throughout the IAA and beyond. Dispersal in Pteropus is far higher than in most other volant taxa studied to date, highlighting the importance of inter-island movement in the biogeographic history of this large clade of large bats.
Collapse
Affiliation(s)
- Susan M. Tsang
- Biology Department, City College, City University of New York, NY 10031, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, NY 10034, USA
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY 10024, USA
- Mammalogy Section, National Museum of Natural History, Manila 1000, Philippines
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences-LIPI, Bogor 16911, Indonesia
| | - Maria Josefa Veluz
- Mammalogy Section, National Museum of Natural History, Manila 1000, Philippines
| | - Norimasa Sugita
- Department of Zoology, National Museum of Nature and Science, Tokyo, Tsukuba, Ibaraki 305-0005, Japan
- National Institute for Environmental Studies, Tokyo, Tsukuba, Ibaraki 305-8506, Japan
| | - Y-Lan Nguyen
- Biology Department, City College, City University of New York, NY 10031, USA
- Macaulay Honors College, City University of New York, NY 10021, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY 10024, USA
| | - David J. Lohman
- Biology Department, City College, City University of New York, NY 10031, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, NY 10034, USA
- Entomology Section, National Museum of Natural History, Manila 1000, Philippines
| |
Collapse
|
45
|
Abstract
Diet is a key factor in determining and structuring animal diversity and adaptive radiations. The mammalian fossil record preserves phenotypic evidence of many dietary shifts, whereas genetic changes followed by dietary diversification in mammals remain largely unknown. To test whether living mammals preserve molecular evidence of dietary shifts, we examined the trehalase gene (Treh), which encodes an enzyme capable of digesting trehalose from insect blood, in bats and other mammals with diverse diets. Bats represent the largest dietary radiation among all mammalian orders, with independent origins of frugivory, nectarivory, carnivory, omnivory, and even sanguivory in an otherwise insectivorous clade. We found that Treh has been inactivated in unrelated bat lineages that independently radiated into noninsectivorous niches. Consistently, purifying selection has been markedly relaxed in noninsectivorous bats compared with their insectivorous relatives. Enzymatic assays of intestinal trehalase in bats suggest that trehalase activity tends to be lost or markedly reduced in noninsectivorous bats compared with their insectivorous relatives. Furthermore, our survey of Treh in 119 mammal species, which represent a deeper evolutionary timeframe, additionally identified a number of other independent losses of Treh in noninsectivorous species, recapitulating the evolutionary pattern that we found in bats. These results document a molecular record of dietary diversification in mammals, and suggest that such molecular signatures of dietary shifts would help us understand both historical and modern changes of animal diets.
Collapse
Affiliation(s)
- Hengwu Jiao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Huan-Wang Xie
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, NY
| | - Hui Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Huabin Zhao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Corresponding author: E-mail:
| |
Collapse
|
46
|
Affiliation(s)
- M. Brock Fenton
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Samira Mubareka
- Department of Microbiology and Division of Infectious Diseases, Sunnybrook Health Sciences Centre and Research Institute, 2075 Bayview Avenue, Room B1 03, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Susan M. Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Mammalogy Section, National Museum of the Philippines, 1000 Manila, Philippines
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Daniel J. Becker
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
47
|
Abstract
Bats are the only mammals capable of powered flight. One of the oldest bats known from a complete skeleton is Onychonycteris finneyi from the Early Eocene (Green River Formation, Wyoming, 52.5 Ma). Estimated to weigh approximately 40 g, Onychonycteris exhibits the most primitive combination of characters thus far known for bats. Here, we reconstructed the aerofoil of the two known specimens, calculated basic aerodynamic variables and compared them with those of extant bats and gliding mammals. Onychonycteris appears in the edges of the morphospace for bats, underscoring the primitive conformation of its flight apparatus. Low aerodynamic efficiency is inferred for this extinct species as compared to any extant bat. When we estimated aerofoil variables in a model of Onychonycteris excluding the handwing, it closely approached the morphospace of extant gliding mammals. Addition of a handwing to the model lacking this structure results in a 2.3-fold increase in aspect ratio and a 28% decrease in wing loading, thus greatly enhancing aerodynamics. In the context of these models, the rapid evolution of the chiropteran handwing via genetically mediated developmental changes appears to have been a key transformation in the hypothesized transition from gliding to flapping in early bats.
Collapse
Affiliation(s)
- Lucila I Amador
- 1 Unidad Ejecutora Lillo: Fundación Miguel Lillo - CONICET , CP 4000 San Miguel de Tucumán, Argentina
| | - Nancy B Simmons
- 2 Department of Mammalogy, American Museum of Natural History , New York, NY 10024, USA
| | - Norberto P Giannini
- 1 Unidad Ejecutora Lillo: Fundación Miguel Lillo - CONICET , CP 4000 San Miguel de Tucumán, Argentina.,2 Department of Mammalogy, American Museum of Natural History , New York, NY 10024, USA.,3 Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán , CP 4000 San Miguel de Tucumán, Argentina
| |
Collapse
|
48
|
Walker FM, Tobin A, Simmons NB, Sobek CJ, Sanchez DE, Chambers CL, Fofanov VY. A fecal sequel: Testing the limits of a genetic assay for bat species identification. PLoS One 2019; 14:e0224969. [PMID: 31725795 PMCID: PMC6855431 DOI: 10.1371/journal.pone.0224969] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/26/2019] [Indexed: 11/23/2022] Open
Abstract
DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.
Collapse
Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
| | - Abby Tobin
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carol L. Chambers
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Viacheslav Y. Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| |
Collapse
|
49
|
Yohe LR, Davies KTJ, Simmons NB, Sears KE, Dumont ER, Rossiter SJ, Dávalos LM. Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family. Mol Ecol Resour 2019; 20:140-153. [PMID: 31523924 DOI: 10.1111/1755-0998.13093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/20/2019] [Revised: 08/27/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for sequencing and downstream analyses. Focusing on the common vampire bat, Desmodus rotundus, we evaluated how different sequencing approaches performed in recovering the largest mammalian protein-coding multigene family: olfactory receptors (OR). Using the genome as a reference, we determined the proportion of intact protein-coding receptors recovered by: (a) amplicons from degenerate primers sequenced via Sanger technology, (b) RNA-Seq of the main olfactory epithelium, and (c) those genes captured with probes designed from transcriptomes of closely-related species. Our initial re-annotation of the high-quality vampire bat genome resulted in >400 intact OR genes, more than doubling the original estimate. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomic ORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all receptors in the genome. While some variation may be due to limitations of the study design (e.g., different individuals), variation among approaches was mostly caused by low coverage of some receptors rather than high rates of assembly error. Given this variability, we caution against using the counts of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Department of Geology and Geophysics, Yale University, Stony Brook, NY, USA
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
50
|
Faulkes CG, Elmore JS, Baines DA, Fenton B, Simmons NB, Clare EL. Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae). PeerJ 2019; 7:e7734. [PMID: 31579609 PMCID: PMC6754726 DOI: 10.7717/peerj.7734] [Citation(s) in RCA: 5] [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: 04/25/2019] [Accepted: 08/23/2019] [Indexed: 11/22/2022] Open
Abstract
Bats of the genus Sturnira (Family Phyllostomidae) are characterised by shoulder glands that are more developed in reproductively mature adult males. The glands produce a waxy secretion that accumulates on the fur around the gland, dyeing the fur a dark colour and giving off a pungent odour. These shoulder glands are thought to play a role in their reproductive behaviour. Using gas chromatography–mass spectrometry, we analysed solvent extracts of fur surrounding the shoulder gland in the northern-shouldered bat, Sturnira parvidens to (i) characterise the chemical composition of shoulder gland secretions for the first time, and (ii) look for differences in chemical composition among and between adult males, sub-adult/juvenile males and adult females. Fur solvent extracts were analysed as liquids and also further extracted using headspace solid-phase microextraction to identify volatile components in the odour itself. Odour fingerprint analysis using non-metric multidimensional scaling plots and multivariate analysis revealed clear and significant differences (P < 0.001) between adult males vs both juvenile males and adult females. The chemical components of the shoulder gland secretion included terpenes and phenolics, together with alcohols and esters, most likely derived from the frugivorous diet of the bat. Many of the compounds identified were found exclusively or in elevated quantities among adult (reproductive) males compared with adult females and non-reproductive (juvenile) males. This strongly suggests a specific role in male–female attraction although a function in male–male competition and/or species recognition is also possible.
Collapse
Affiliation(s)
- Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - J Stephen Elmore
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Brock Fenton
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nancy B Simmons
- Department of Mammalogy Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elizabeth L Clare
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|