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Fleischer R, Jones C, Ledezma-Campos P, Czirják GÁ, Sommer S, Gillespie TR, Vicente-Santos A. Gut microbial shifts in vampire bats linked to immunity due to changed diet in human disturbed landscapes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167815. [PMID: 37852483 DOI: 10.1016/j.scitotenv.2023.167815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Anthropogenic land-use change alters wildlife habitats and modifies species composition, diversity, and contacts among wildlife, livestock, and humans. Such human-modified ecosystems have been associated with emerging infectious diseases, threatening human and animal health. However, human disturbance also creates new resources that some species can exploit. Common vampire bats (Desmodus rotundus) in Latin America constitute an important example, as their adaptation to human-modified habitats and livestock blood-feeding has implications for e.g., rabies transmission. Despite the well-known links between habitat degradation and disease emergence, few studies have explored how human-induced disturbance influences wildlife behavioural ecology and health, which can alter disease dynamics. To evaluate links among habitat disturbance, diet shifts, gut microbiota, and immunity, we quantified disturbance around roosting caves of common vampire bats in Costa Rica, measured their long-term diet preferences (livestock or wildlife blood) using stable isotopes of carbon and nitrogen, evaluated innate and adaptive immune markers, and characterized their gut microbiota. We observed that bats from roosting caves with more cattle farming nearby fed more on cattle blood. Moreover, gut microbial richness and the abundance of specific gut microbes differed according to feeding preferences. Interestingly, bats feeding primarily on wildlife blood harboured a higher abundance of the bacteria Edwardsiella sp., which tended to be associated with higher immunoglobulin G levels. Our results highlight how human land-use change may indirectly affect wildlife health and emerging infectious diseases through diet-induced shifts in microbiota, with implications for host immunity and potential consequences for susceptibility to pathogens.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.
| | - Christie Jones
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA; Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Thomas R Gillespie
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA; Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA
| | - Amanda Vicente-Santos
- Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA.
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2
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Júnior DST. High risk of bat bites in an indigenous village in Brazil: Warning of the re-emergence of rabies among the Maxakali People. Acta Trop 2024; 249:107073. [PMID: 37956818 DOI: 10.1016/j.actatropica.2023.107073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
Bat-mediated human rabies is a viral zoonotic disease that poses a serious threat to the public health of traditional peoples, especially indigenous populations that maintain primitive cultural and social habits, such as the Maxakali ethnic group, located in the southeastern region of Brazil. The sociocultural habit of this population led to the emergence between April and May 2022 of the viral spillover of rabies transmitted by bats, which decimated the lives of four children from this population who maintained contact with this animal as a recreational practice. Because the vampire bats Desmodus rotundus have exceptional ecology and social characteristics that can have important effects on the dynamics of viral dispersion in this indigenous population, I present the dynamics of contact between native children and the bat and the meaning of this relationship, which involves ritualistic and recreational significance. As important as knowing the reasons for this practice is discussing some intrinsic and extrinsic factors that imply risks that intensify the vulnerability of this population to the transmission of the rabies virus at any time. In view of this, I warn of the need to adopt efficient strategies to mitigate the risks of a new emergency in this region. Although emergency containment measures were carried out during the critical period of the outbreak, such animal and environmental control actions must become routine programmatic and structuring interventions. Essential for rabies surveillance in this population is to develop culturally adapted interethnic health education campaigns to guarantee the accessibility of the Maxakali indigenous people to the content taught, so that any attempt at domestication, captivity and recreational practices with bats of any species is discouraged, thus avoiding a possible re-emergence of this anthropozoonosis that has impacted not only the epidemiological scenario in this region, but throughout Brazil, and also throughout Latin America.
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Affiliation(s)
- Dilceu Silveira Tolentino Júnior
- Federal University of the Jequitinhonha and Mucuri Valleys, Postgraduate Program in Tecnhology, Environment and Society, Teófilo Otoni, Minas Gerais, Brazil.
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3
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Gao Y, Zhang X, Wang W, Xing Z, Xu L, Tian X. Qualitative identification of lonicerae japonicae flos in traditional chinese medicine using metabarcoding combined with specific mini-barcodes. Mol Biol Rep 2023; 50:8817-8825. [PMID: 37658933 DOI: 10.1007/s11033-023-08739-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Lonicerae japonicae flos, also known as Jinyinhua (JYH), is an important component of traditional Chinese patent medicine (TCPM) products. However, the potential for adulteration and substitution with low-quality materials highlights the need for a reliable and sensitive approach to identify the species composition of TCPM products for consumer safety. METHODS AND RESULTS We used universal ITS2 primers to amplify TCPMs containing JYH. However, the results were inconclusive, as only one operational taxonomic unit (OTU) was identified as Lonicera sp., which could not be identified at the species level. To confirm the species identification of Lonicera sp. in TCPM, we developed a short mini-barcode primer based on the psbA-trnH region, which, in combination with DNA metabarcoding technology, allowed for qualitative and quantitative analysis of artificially mixed samples. We applied the mini-barcode to distinguish TCPMs containing JYH and demonstrated its relatively accurate quantitative ability in identifying two Lonicera species. CONCLUSIONS Our study presents a method for qualitative and quantitative identification of JYH, providing a promising application of DNA metabarcoding technology in the quality control of TCPM products.
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Affiliation(s)
- Yuan Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Wenxiu Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Zhimei Xing
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Liuwei Xu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China.
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
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4
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Tang K, Wang Y, Wu M, Wang S, Fu C, Zhang Z, Fu Y. Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird. Curr Zool 2023; 69:501-513. [PMID: 37637316 PMCID: PMC10449430 DOI: 10.1093/cz/zoac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/02/2022] [Indexed: 08/29/2023] Open
Abstract
Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.
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Affiliation(s)
- Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Mengling Wu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Shufang Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Changkun Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yiqiang Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
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5
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Garwood TJ, Moore SA, Fountain-Jones NM, Larsen PA, Wolf TM. SPECIES IN THE FECES: DNA METABARCODING TO DETECT POTENTIAL GASTROPOD HOSTS OF PARELAPHOSTRONGYLUS TENUIS Consumed By Moose (Alces Alces). J Wildl Dis 2023; 59:640-650. [PMID: 37540143 DOI: 10.7589/jwd-d-22-00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/04/2023] [Indexed: 08/05/2023]
Abstract
Our understanding of wildlife multihost pathogen transmission systems is often incomplete due to the difficulty of observing contact between hosts. Understanding these interactions can be critical for preventing disease-induced wildlife declines. The proliferation of high-throughput sequencing technologies provides new opportunities to better explore these cryptic interactions. Parelaphostrongylus tenuis, a multihost parasite, is a leading cause of death in some moose (Alces alces) populations threatened by local extinction in the midwestern and northeastern US and southeastern Canada. Moose contract P. tenuis by consuming infected gastropod intermediate hosts, but little is known about which gastropod species moose consume. To gain more insight, we used a genetic metabarcoding approach on 258 georeferenced and temporally stratified moose fecal samples collected May-October 2017-20 from a declining population in the north-central US. We detected moose consumption of three species of gastropods across five positive samples. Two of these (Punctum minutissimum and Helisoma sp.) have been minimally investigated for the ability to host P. tenuis, while one (Zonitoides arboreus) is a well-documented host. Moose consumption of gastropods documented herein occurred in June and September. Our findings prove that moose consume gastropod species known to become infected by P. tenuis and demonstrate that fecal metabarcoding can provide novel insight on interactions between hosts of a multispecies pathogen transmission system. After determining and improving test sensitivity, these methods may also be extended to document important interactions in other multihost disease systems.
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Affiliation(s)
- Tyler J Garwood
- Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1988 Fitch Avenue, St. Paul, Minnesota 55108, USA
| | - Seth A Moore
- Department of Biology and Environment, Grand Portage Band of Lake Superior Chippewa, 27 Store Road, Grand Portage, Minnesota 55605, USA
| | - Nicholas M Fountain-Jones
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania 7001, Australia
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, Minnesota 55108, USA
| | - Tiffany M Wolf
- Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1988 Fitch Avenue, St. Paul, Minnesota 55108, USA
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6
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Riaz M, Warren D, Wittwer C, Cocchiararo B, Hundertmark I, Reiners TE, Klimpel S, Pfenninger M, Khaliq I, Nowak C. Using eDNA to understand predator-prey interactions influenced by invasive species. Oecologia 2023; 202:757-767. [PMID: 37594600 PMCID: PMC10474997 DOI: 10.1007/s00442-023-05434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany.
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany.
| | - Dan Warren
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Claudia Wittwer
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Inga Hundertmark
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Tobias Erik Reiners
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- Hessische Gesellschaft Für Ornithologie Und Naturschutz (HGON E. V.), Lindenstrasse 5, 61209, Echzell, Germany
| | - Sven Klimpel
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Straße 9, 60438, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Imran Khaliq
- Department of Education, Punjab, Pakistan
- Department of Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Überlandstrasse 133, 8600, Dübendorf, Switzerland
- Snow and Landscape Research (WSL), Swiss Federal Institute for Forest, Flüelastr. 11, 7260, Davos Dorf, Switzerland
| | - Carsten Nowak
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum, 63571, Frankfurt, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt Am Main, Germany
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7
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Serrana JM, Watanabe K. Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis. PLoS One 2023; 18:e0289056. [PMID: 37486933 PMCID: PMC10365294 DOI: 10.1371/journal.pone.0289056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
Metabarcoding is a molecular-based tool capable of large quantity high-throughput species identification from bulk samples that is a faster and more cost-effective alternative to conventional DNA-sequencing approaches. Still, further exploration and assessment of the laboratory and bioinformatics strategies are required to unlock the potential of metabarcoding-based inference of haplotype information. In this study, we assessed the inference of freshwater macroinvertebrate haplotypes from metabarcoding data in a mock sample. We also examined the influence of DNA template concentration and PCR cycle on detecting true and spurious haplotypes. We tested this strategy on a mock sample containing twenty individuals from four species with known haplotypes based on the 658-bp Folmer region of the mitochondrial cytochrome c oxidase gene. We recovered fourteen zero-radius operational taxonomic units (zOTUs) of 421-bp length, with twelve zOTUs having a 100% match with the Sanger haplotype sequences. High-quality reads relatively increased with increasing PCR cycles, and the relative abundance of each zOTU was consistent for each cycle. This suggests that increasing the PCR cycles from 24 to 64 did not affect the relative abundance of each zOTU. As metabarcoding becomes more established and laboratory protocols and bioinformatic pipelines are continuously being developed, our study demonstrated the method's ability to infer intraspecific variability while highlighting the challenges that must be addressed before its eventual application for population genetic studies.
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Affiliation(s)
- Joeselle M Serrana
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
- Faculty of Engineering, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
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8
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Brown N, Escobar LE. A review of the diet of the common vampire bat ( Desmodus rotundus) in the context of anthropogenic change. Mamm Biol 2023; 103:1-21. [PMID: 37363038 PMCID: PMC10258787 DOI: 10.1007/s42991-023-00358-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/30/2023] [Indexed: 06/28/2023]
Abstract
The common vampire bat (Desmodus rotundus) maintains a diverse, sanguivorous diet, utilizing a broad range of prey taxa. As anthropogenic change alters the distribution of this species, shifts in predator-prey interactions are expected. Understanding prey richness and patterns of prey selection is, thus, increasingly informative from ecological, epidemiological, and economic perspectives. We reviewed D. rotundus diet and assessed the geographical, taxonomical, and behavioral features to find 63 vertebrate species within 21 orders and 45 families constitute prey, including suitable host species in regions of invasion outside D. rotundus' range. Rodentia contained the largest number of species utilized by D. rotundus, though cattle were the most commonly reported prey source, likely linked to the high availability of livestock and visibility of bite wounds compared to wildlife. Additionally, there was tendency to predate upon species with diurnal activity and social behavior, potentially facilitating convenient and nocturnal predation. Our review highlights the dietary heterogeneity of D. rotundus across its distribution. We define D. rotundus as a generalist predator, or parasite, depending on the ecological definition of its symbiont roles in an ecosystem (i.e., lethal vs. non-lethal blood consumption). In view of the eminent role of D. rotundus in rabies virus transmission and its range expansion, an understanding of its ecology would benefit public health, wildlife management, and agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s42991-023-00358-3.
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Affiliation(s)
- Natalie Brown
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA USA
| | - Luis E. Escobar
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA USA
- Global Change Center, Virginia Tech, Blacksburg, VA USA
- Center for Emerging Zoonotic and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA USA
- Doctorado en Agrociencias, Facultad de Ciencias Agropecuarias, Universidad de La Salle, Carrera 7 No. 179-03, Bogotá, Colombia
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9
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Mendoza‐Sáenz VH, Saldaña‐Vázquez RA, Navarrete‐Gutiérrez D, Kraker‐Castañeda C, Ávila‐Flores R, Jiménez‐Ferrer G. Reducing conflict between the common vampire bat
Desmodus rotundus
and cattle ranching in Neotropical landscapes. Mamm Rev 2023. [DOI: 10.1111/mam.12313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Víctor Hugo Mendoza‐Sáenz
- Departamento de Conservación de la Biodiversidad El Colegio de la Frontera Sur (ECOSUR) Carretera Panamericana y Periférico Sur S/N, Barrio María Auxiliadora 29290 San Cristóbal de Las Casas Chiapas México
| | - Romeo A. Saldaña‐Vázquez
- Instituto de Investigaciones en Medio Ambiente Xabier Gorostiaga, S.J., Universidad Iberoamericana Puebla Boulevard del Niño Poblano No. 2901, Colonia Reserva Territorial Atlixcáyotl 72820 San Andrés Cholula, Puebla México
| | - Dario Navarrete‐Gutiérrez
- Grupo Académico Ecología, Paisaje y Sustentabilidad, Departamento Observación y Estudio de la Tierra, la Atmosfera y el Océano, El Colegio de La Frontera Sur (ECOSUR) Carretera Panamericana y Periférico Sur S/N, Barrio María Auxiliadora 29290 San Cristóbal de Las Casas Chiapas México
| | - Cristian Kraker‐Castañeda
- Departamento de Conservación de la Biodiversidad El Colegio de la Frontera Sur (ECOSUR) Carretera Panamericana y Periférico Sur S/N, Barrio María Auxiliadora 29290 San Cristóbal de Las Casas Chiapas México
- Unidad para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas (CECON) Universidad de San Carlos de Guatemala Avenida Reforma 0‐63, Zona 10 01010 Guatemala City Guatemala
| | - Rafael Ávila‐Flores
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco Carretera Villahermosa‐Cárdenas km 0.5 S/N, Entronque a Bosques de Saloya 86150 Villahermosa Tabasco México
| | - Guillermo Jiménez‐Ferrer
- Departamento de Agricultura, Sociedad y Ambiente El Colegio de la Frontera Sur (ECOSUR) Carretera Panamericana y Periférico Sur S/N, Barrio María Auxiliadora 29290 San Cristóbal de Las Casas Chiapas México
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10
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Pereira FMAM, Oliveira ARD, Soares-Neto LL, Munhoz L, Fernandes LS, Santos DOD, Carvalho TPD, Langoni H, Santos RL. Rabies in a Captive Lowland Tapir (Tapirus terrestris). J Comp Pathol 2022; 198:29-32. [PMID: 36116889 DOI: 10.1016/j.jcpa.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Rabies is a severe viral zoonosis of mammals and causes irreversible neurological damage. We describe the clinical presentation and anatomopathological lesions of rabies in a captive lowland tapir (Tapirus terrestris) in Bauru, São Paulo State, Brazil. The clinical course of the disease lasted 6 days and was characterized by progressive neurological deterioration and death. The main anatomopathological findings were non-suppurative encephalitis and presence of Negri bodies within neurons. Direct immunofluorescence and mouse inoculation tests were positive for rabies virus. This is the first report of rabies in a lowland tapir and highlights the importance of disease prevention under managed care and continuous control measures in urbanized environments.
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Affiliation(s)
| | - Ayisa R de Oliveira
- Departamento de Clínica e Cirurgia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Laura Munhoz
- Zoológico Municipal de Bauru, Bauru, São Paulo, Brazil
| | | | - Daniel O Dos Santos
- Departamento de Clínica e Cirurgia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thaynara P de Carvalho
- Departamento de Clínica e Cirurgia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Helio Langoni
- Departamento de Produção Animal e Medicina Veterinária Preventiva, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Renato L Santos
- Departamento de Clínica e Cirurgia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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11
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Meza DK, Mollentze N, Broos A, Tello C, Valderrama W, Recuenco S, Carrera JE, Shiva C, Falcon N, Viana M, Streicker DG. Ecological determinants of rabies virus dynamics in vampire bats and spillover to livestock. Proc Biol Sci 2022; 289:20220860. [PMID: 36069012 PMCID: PMC9449476 DOI: 10.1098/rspb.2022.0860] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
The pathogen transmission dynamics in bat reservoirs underpin efforts to reduce risks to human health and enhance bat conservation, but are notoriously challenging to resolve. For vampire bat rabies, the geographical scale of enzootic cycles, whether environmental factors modulate baseline risk, and how within-host processes affect population-level dynamics remain unresolved. We studied patterns of rabies exposure using an 11-year, spatially replicated sero-survey of 3709 Peruvian vampire bats and co-occurring outbreaks in livestock. Seroprevalence was correlated among nearby sites but fluctuated asynchronously at larger distances. A generalized additive mixed model confirmed spatially compartmentalized transmission cycles, but no effects of bat demography or environmental context on seroprevalence. Among 427 recaptured bats, we observed long-term survival following rabies exposure and antibody waning, supporting hypotheses that immunological mechanisms influence viral maintenance. Finally, seroprevalence in bats was only weakly correlated with outbreaks in livestock, reinforcing the challenge of spillover prediction even with extensive data. Together our results suggest that rabies maintenance requires transmission among multiple, nearby bat colonies which may be facilitated by waning of protective immunity. However, the likelihood of incursions and dynamics of transmission within bat colonies appear largely independent of bat ecology. The implications of these results for spillover anticipation and controlling transmission at the source are discussed.
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Affiliation(s)
- Diana K. Meza
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Nardus Mollentze
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Alice Broos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Carlos Tello
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
- Yunkawasi, Lima, Perú
| | - William Valderrama
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
- Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Sergio Recuenco
- Facultad de Medicina San Fernando, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Jorge E. Carrera
- Departamento de Mastozoología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Perú
- Programa de Conservación de Murciélagos de Perú, Perú
| | - Carlos Shiva
- Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Mafalda Viana
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Daniel G. Streicker
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
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12
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Lance RF, Guan X, Swift JF, Edwards CE, Lindsay DL, Britzke ER. Multifaceted DNA Metabarcoding of Guano to Uncover Multiple Classes of Ecological Data in Two Different Bat Communities. Evol Appl 2022; 15:1189-1200. [PMID: 35899252 PMCID: PMC9309442 DOI: 10.1111/eva.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022] Open
Abstract
DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next‐generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed‐species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White‐nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto‐ and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain.
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Affiliation(s)
- Richard F. Lance
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
| | - Xin Guan
- Bennett Aerospace 3909 Halls Ferry Road Vicksburg MS 39180 USA
- Moderna, Inc Cambridge MA USA
| | - Joel F. Swift
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110 USA
- Department of Biology St. Louis University St. Louis MO USA
| | - Christine E. Edwards
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110 USA
| | - Denise L. Lindsay
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
| | - Eric R. Britzke
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
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13
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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14
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Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K. A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.
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15
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Seroprevalence to Rabies Virus in Wildlife in Brazil. J Wildl Dis 2022; 58:431-435. [PMID: 35255127 DOI: 10.7589/jwd-d-21-00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 10/27/2021] [Indexed: 11/20/2022]
Abstract
Serum samples of 638 free-ranging wild mammals from São Paulo state, Brazil, were tested for neutralizing antibodies against rabies virus by the rapid fluorescent focus inhibition test. Overall seroprevalence was 1.7% among 24 species surveyed, with individuals of six species having positive results indicating exposure to rabies virus.
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16
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Littleford‐Colquhoun BL, Freeman PT, Sackett VI, Tulloss CV, McGarvey LM, Geremia C, Kartzinel TR. The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation. Mol Ecol 2022; 31:1615-1626. [PMID: 35043486 PMCID: PMC9303378 DOI: 10.1111/mec.16352] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 01/07/2022] [Indexed: 01/13/2023]
Abstract
Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data-or similar data such as environmental DNA, microbiomes, or pathobiomes-should be aware of drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.
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Affiliation(s)
- Bethan L. Littleford‐Colquhoun
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Patrick T. Freeman
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Violet I. Sackett
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Camille V. Tulloss
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Lauren M. McGarvey
- Yellowstone Center for Resources, Yellowstone National ParkMammoth Hot SpringsWyomingUSA
| | - Chris Geremia
- Yellowstone Center for Resources, Yellowstone National ParkMammoth Hot SpringsWyomingUSA
| | - Tyler R. Kartzinel
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
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17
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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18
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Drinkwater R, Williamson J, Clare EL, Chung AYC, Rossiter SJ, Slade E. Dung beetles as samplers of mammals in Malaysian Borneo-a test of high throughput metabarcoding of iDNA. PeerJ 2021; 9:e11897. [PMID: 34447624 PMCID: PMC8366524 DOI: 10.7717/peerj.11897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arthur Y C Chung
- Sabah Forestry Department, Forest Research Centre, Sandakan, Malaysia
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Eleanor Slade
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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19
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Lynggaard C, Oceguera-Figueroa A, Kvist S, Gilbert MTP, Bohmann K. The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation. Mol Ecol Resour 2021; 22:539-553. [PMID: 34402209 PMCID: PMC9292958 DOI: 10.1111/1755-0998.13486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/29/2021] [Accepted: 08/12/2021] [Indexed: 12/01/2022]
Abstract
Leeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate‐derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the Indo‐Pacific region and mainly leveraged the leech family Haemadipsidae, composed of bloodfeeding terrestrial leeches, while predatory, fluid/tissue‐feeding and aquatic bloodfeeding species have been largely disregarded. While there is some general knowledge regarding the taxonomic groups that leeches prefer to feed on, detailed taxonomic resolution is missing and, therefore, their potential use for monitoring animals is unknown. In this study, 116 leeches from 12 species (six families) and spanning the three feeding habits were collected in Mexico and Canada. We used DNA metabarcoding to investigate their diet and assess their potential use for biodiversity monitoring. We detected vertebrates from five orders including fish, turtles and birds in the diet of aquatic bloodfeeding leeches; eight invertebrate orders of annelids, arthropods and molluscs in leeches that feed on body fluids and tissues; and 10 orders of invertebrates belonging to Arthropoda and Annelida, as well as one vertebrate and one parasitic nematode, in predatory leeches. These results show the potential use of iDNA from aquatic bloodfeeding leeches for retrieving vertebrate taxa, and from predatory and fluid‐feeding leeches for invertebrates. Our study provides information about the dietary range of freshwater leeches and one terrestrial leech and contributes proof‐of‐concept for the use of these leeches for animal monitoring, expanding our knowledge of the use of iDNA from leech gut contents to North America.
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Affiliation(s)
- Christina Lynggaard
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen K, Denmark
| | - Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen K, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen K, Denmark
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20
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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21
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Abstract
Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
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22
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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: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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.
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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
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23
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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24
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Management of vampire bats and rabies: a precaution for rewilding projects in the Neotropics. Perspect Ecol Conserv 2021. [DOI: 10.1016/j.pecon.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Tang K, Xie F, Liu H, Pu Y, Chen D, Qin B, Fu C, Wang Q, Chen S, Guo K. DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew ( Anourosorex squamipes) with potential implications for evaluating crop impacts. Ecol Evol 2021; 11:376-389. [PMID: 33437436 PMCID: PMC7790647 DOI: 10.1002/ece3.7055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/11/2020] [Accepted: 10/25/2020] [Indexed: 01/02/2023] Open
Abstract
Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.
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Affiliation(s)
- Ke‐yi Tang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Fei Xie
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Hong‐yi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Ying‐ting Pu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Dan Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Bo‐xin Qin
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Chang‐kun Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Qiong Wang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Shun‐de Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Ke‐ji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland AdministrationChangshaChina
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26
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Lynggaard C, Yu DW, Oliveira G, Caldeira CF, Ramos SJ, Ellegaard MR, Gilbert MTP, Gastauer M, Bohmann K. DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.590976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human activities change natural landscapes, and in doing so endanger biodiversity and associated ecosystem services. To reduce the net impacts of these activities, such as mining, disturbed areas are rehabilitated and restored. During this process, monitoring is important to ensure that desired trajectories are maintained. In the Carajás region of the Brazilian Amazon, exploration for iron ores has transformed the original ecosystem; natural forest and a savanna formation with lateritic iron duricrust outcrops named canga. Here, native vegetation is logged and topsoil removed and deposited in waste piles along with mine waste. During rehabilitation, these waste piles are hydroseeded with non-native plant species to achieve rapid revegetation. Further, seeds of native canga and forest plant species are planted to point ecological succession towards natural ecosystems. In this study, we investigate diversity and composition of the arthropod community along a post-mining rehabilitation and restoration gradient, taking seasonality and primer bias into account. We use DNA metabarcoding of bulk arthropod samples collected in both the dry and rainy seasons from waste-pile benches at various stages of revegetation: non-revegetated exposed soils, initial stage with one-to-three-year-old stands, intermediate stage with four-to-five-year-old stands, and advanced stage with six-to-seven-year-old stands. We use samples from undisturbed cangas and forests as reference sites. In addition, we vegetation diversity and structure were measured to investigate relations between arthropod community and vegetation structure. Our results show that, over time, the arthropod community composition of the waste piles becomes more similar to the reference forests, but not to the reference cangas. Nevertheless, even the communities in the advanced-stage waste piles are different from the reference forests, and full restoration in these highly diverse ecosystems is not achieved, even after 6 to 7 years. Finally, our results show seasonal variation in arthropod communities and primer bias.
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27
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Havmøller RW, Jacobsen NS, Havmøller LW, Rovero F, Scharff N, Bohmann K. DNA metabarcoding reveals that African leopard diet varies between habitats. Afr J Ecol 2020. [DOI: 10.1111/aje.12817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rasmus Worsøe Havmøller
- Section for Evolutionary Genomics Globe Institute University of Copenhagen Copenhagen K Denmark
- Department of Anthropology University of California Davis CA USA
- Center for Macroecology, Evolution and Climate Globe Institute University of Copenhagen Copenhagen K Denmark
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Nis Sand Jacobsen
- National Institute of Aquatic Resources Technical University of Denmark Lyngby Denmark
| | - Linnea Worsøe Havmøller
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Francesco Rovero
- Department of Biology University of Florence Sesto Fiorentino Italy
- Section for Tropical Biodiversity MUSE‐Museo delle Scienze Trento Italy
| | - Nikolaj Scharff
- Natural History Museum of Denmark, Research and CollectionsUniversity of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute University of Copenhagen Copenhagen K Denmark
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28
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Jones PL, Divoll TJ, Dixon MM, Aparicio D, Cohen G, Mueller UG, Ryan MJ, Page RA. Sensory ecology of the frog-eating bat, Trachops cirrhosus, from DNA metabarcoding and behavior. Behav Ecol 2020. [DOI: 10.1093/beheco/araa100] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Metabarcoding of prey DNA from fecal samples can be used to design behavioral experiments to study the foraging behavior and sensory ecology of predators. The frog-eating bat, Trachops cirrhosus, eavesdrops on the mating calls of its anuran prey. We captured wild T. cirrhosus and identified prey remains in the bats’ fecal samples using DNA metabarcoding of two gene regions (CO1 and 16S). Bats were preying on frogs previously unknown in their diet, such as species in the genus Pristimantis, which occurred in 29% of T. cirrhosus samples. Twenty-three percent of samples also contained DNA of Anolis lizards. We additionally report apparently rare predation events on hummingbirds and heterospecific bats. We used results from metabarcoding to design acoustic and 3D model stimuli to present to bats in behavioral experiments. We show predatory responses by T. cirrhosus to the calls of the frog Pristimantis taeniatus and to the rustling sounds of anoles moving through leaf-litter, as well as attacks on a stuffed hummingbird and a plastic anole model. The combination of species-specific dietary information from metabarcoding analyses with behavioral responses to prey cues provides a unique window into the foraging ecology of predators that are difficult to observe in the wild.
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Affiliation(s)
| | - Timothy J Divoll
- Technology Solutions, SWCA Environmental Consultants, 15 Research Dr, Amherst, MA, USA
- Department of Biology, Center for Bat Research, Outreach, and Conservation, Indiana State University, Terre Haute, IN, USA
| | - M May Dixon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Dineilys Aparicio
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado Postal, Panamá
| | - Gregg Cohen
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado Postal, Panamá
| | - Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael J Ryan
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado Postal, Panamá
| | - Rachel A Page
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado Postal, Panamá
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29
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Benavides JA, Valderrama W, Recuenco S, Uieda W, Suzán G, Avila-Flores R, Velasco-Villa A, Almeida M, de Andrade FA, Molina-Flores B, Vigilato MAN, Pompei JCA, Tizzani P, Carrera JE, Ibanez D, Streicker DG. Defining New Pathways to Manage the Ongoing Emergence of Bat Rabies in Latin America. Viruses 2020; 12:v12091002. [PMID: 32911766 PMCID: PMC7551776 DOI: 10.3390/v12091002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Rabies transmitted by common vampire bats (Desmodus rotundus) has been known since the early 1900s but continues to expand geographically and in the range of species and environments affected. In this review, we present current knowledge of the epidemiology and management of rabies in D. rotundus and argue that it can be reasonably considered an emerging public health threat. We identify knowledge gaps related to the landscape determinants of the bat reservoir, reduction in bites on humans and livestock, and social barriers to prevention. We discuss how new technologies including autonomously-spreading vaccines and reproductive suppressants targeting bats might manage both rabies and undesirable growth of D. rotundus populations. Finally, we highlight widespread under-reporting of human and animal mortality and the scarcity of studies that quantify the efficacy of control measures such as bat culling. Collaborations between researchers and managers will be crucial to implement the next generation of rabies management in Latin America.
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Affiliation(s)
- Julio A. Benavides
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 8370146 Santiago, Chile
- Correspondence: (J.A.B.); (D.G.S.)
| | - William Valderrama
- Association for the Conservation and Development of Natural Resources ILLARIY, Lima 051, Peru;
- Departamento de Pediatría, Obstetricia y Ginecología y de Medicina Preventiva, Universidad Autónoma de Barcelona, 08007 Barcelona, Spain
| | - Sergio Recuenco
- Facultad de Medicina San Fernando, Universidad Nacional Mayor de San Marcos, Lima 15001, Peru;
| | - Wilson Uieda
- Departamento de Zoologia, Universidade Estadual Paulista Júlio de Mesquita Filho Campus de Botucatu, Botucatu 18618-970, Brazil;
| | - Gerardo Suzán
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México City 04510, Mexico;
| | - Rafael Avila-Flores
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa 86150, Mexico;
| | - Andres Velasco-Villa
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA 30329, USA;
| | - Marilene Almeida
- Centro de Controle de Zoonoses da Prefeitura do Município de São Paulo, São Paulo 02031-020, Brazil;
| | - Fernanda A.G. de Andrade
- Departamento de Biologia, Instituto Federal de Educação, Ciências e Tecnología do Pará, Tucuruí 68-455-695, Brazil;
| | - Baldomero Molina-Flores
- Pan-American Center for Foot-and-mouth Disease and Veterinary Public Health—Pan American Health Organization/World Health Organization (PANAFTOSA—PAHO/WHO), Rio de Janeiro 25045-002, Brazil; (B.M.-F.); (M.A.N.V.); (J.C.A.P.)
| | - Marco Antonio Natal Vigilato
- Pan-American Center for Foot-and-mouth Disease and Veterinary Public Health—Pan American Health Organization/World Health Organization (PANAFTOSA—PAHO/WHO), Rio de Janeiro 25045-002, Brazil; (B.M.-F.); (M.A.N.V.); (J.C.A.P.)
| | - Julio Cesar Augusto Pompei
- Pan-American Center for Foot-and-mouth Disease and Veterinary Public Health—Pan American Health Organization/World Health Organization (PANAFTOSA—PAHO/WHO), Rio de Janeiro 25045-002, Brazil; (B.M.-F.); (M.A.N.V.); (J.C.A.P.)
| | - Paolo Tizzani
- OIE-World Organisation for Animal Health, 75017 Paris, France;
| | - Jorge E. Carrera
- Departamento de Mastozoología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15072, Peru;
- Programa de Conservación de Murciélagos de Perú, Lima 15072, Peru
| | - Darcy Ibanez
- Director Regional de la Dirección Regional Sectorial Agraria, Gobierno Regional de Apurímac, Abancay 03001, Peru;
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Correspondence: (J.A.B.); (D.G.S.)
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30
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O'Rourke DR, Bokulich NA, Jusino MA, MacManes MD, Foster JT. A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses. Ecol Evol 2020; 10:9721-9739. [PMID: 33005342 PMCID: PMC7520210 DOI: 10.1002/ece3.6594] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 01/01/2023] Open
Abstract
Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results. We show that denoising methods have lower error rates compared to traditional clustering methods, although these differences are largely mitigated by removing low-abundance sequence variants. We also found that available reference datasets from GenBank and BOLD for the animal marker gene cytochrome oxidase I (COI) can be complementary, and we discuss methods to improve existing databases to include versioned releases. Taxonomic classification methods can dramatically affect results. For example, the commonly used Barcode of Life Database (BOLD) Classification API assigned fewer names to samples from order through species levels using both a mock community and bat guano samples compared to all other classifiers (vsearch-SINTAX and q2-feature-classifier's BLAST + LCA, VSEARCH + LCA, and Naive Bayes classifiers). The lack of consensus on bioinformatics best practices limits comparisons among studies and may introduce biases. Our work suggests that biological mock communities offer a useful standard to evaluate the myriad computational decisions impacting animal metabarcoding accuracy. Further, these comparisons highlight the need for continual evaluations as new tools are adopted to ensure that the inferences drawn reflect meaningful biology instead of digital artifacts.
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Affiliation(s)
- Devon R. O'Rourke
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
| | - Nicholas A. Bokulich
- Laboratory of Food Systems BiotechnologyInstitute of Food, Nutrition, and HealthETH ZurichZurichSwitzerland
| | - Michelle A. Jusino
- Biology DepartmentWilliam & MaryWilliamsburgVAUSA
- Center for Forest Mycology ResearchUSDA Forest ServiceNorthern Research StationMadisonUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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31
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Carøe C, Bohmann K. Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Mol Ecol Resour 2020; 20:1620-1631. [PMID: 32663358 DOI: 10.1111/1755-0998.13227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps: (a) T4 DNA polymerase blunt-ending in the end-repair step and (b) postligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a PCR-free metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and postligation PCR on the occurrence of tag-jumps and demonstrate that both blunt-ending and postligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
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Affiliation(s)
- Christian Carøe
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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32
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Tournayre O, Leuchtmann M, Filippi‐Codaccioni O, Trillat M, Piry S, Pontier D, Charbonnel N, Galan M. In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses. Ecol Evol 2020; 10:6310-6332. [PMID: 32724515 PMCID: PMC7381572 DOI: 10.1002/ece3.6362] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/20/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | | | - Ondine Filippi‐Codaccioni
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Marine Trillat
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Sylvain Piry
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Dominique Pontier
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Nathalie Charbonnel
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Maxime Galan
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
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33
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Benavides JA, Velasco-Villa A, Godino LC, Satheshkumar PS, Nino R, Rojas-Paniagua E, Shiva C, Falcon N, Streicker DG. Abortive vampire bat rabies infections in Peruvian peridomestic livestock. PLoS Negl Trop Dis 2020; 14:e0008194. [PMID: 32598388 PMCID: PMC7351222 DOI: 10.1371/journal.pntd.0008194] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 07/10/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
Rabies virus infections normally cause universally lethal encephalitis across mammals. However, 'abortive infections' which are resolved prior to the onset of lethal disease have been described in bats and a variety of non-reservoir species. Here, we surveyed rabies virus neutralizing antibody titers in 332 unvaccinated livestock of 5 species from a vampire bat rabies endemic region of southern Peru where livestock are the main food source for bats. We detected rabies virus neutralizing antibody titers in 11, 5 and 3.6% of cows, goats and sheep respectively and seropositive animals did not die from rabies within two years after sampling. Seroprevalence was correlated with the number of local livestock rabies mortalities reported one year prior but also one year after sample collection. This suggests that serological status of livestock can indicate the past and future levels of rabies risk to non-reservoir hosts. To our knowledge, this is the first report of anti-rabies antibodies among goats and sheep, suggesting widespread abortive infections among livestock in vampire bat rabies endemic areas. Future research should resolve the within-host biology underlying clearance of rabies infections. Cost-effectiveness analyses are also needed to evaluate whether serological monitoring of livestock can be a viable complement to current monitoring of vampire bat rabies risk based on animal mortalities alone.
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Affiliation(s)
- Julio A. Benavides
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Andres Velasco-Villa
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, NE, Atlanta, Georgia, United States of America
| | - Lauren C. Godino
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, NE, Atlanta, Georgia, United States of America
| | - Panayampalli Subbian Satheshkumar
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, NE, Atlanta, Georgia, United States of America
| | - Ruby Nino
- Colegio Médico Veterinario de Apurimac, Abancay, Peru
| | | | - Carlos Shiva
- Faculty of Veterinary Medicine and Zootechnics, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nestor Falcon
- Faculty of Veterinary Medicine and Zootechnics, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- MRC-University of Glasgow Centre for Virus Research, Sir Henry Wellcome Building, Glasgow, Scotland, United Kingdom
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34
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Botto Nuñez G, Becker DJ, Lawrence RL, Plowright RK. Synergistic Effects of Grassland Fragmentation and Temperature on Bovine Rabies Emergence. ECOHEALTH 2020; 17:203-216. [PMID: 32699950 PMCID: PMC7885335 DOI: 10.1007/s10393-020-01486-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
In 2007, common vampire bats were the source of the first outbreak of paralytic bovine rabies in Uruguay. The outbreak coincided in space and time with the fragmentation of native grasslands for monospecific forestry for wood and cellulose production. Using spatial analyses, we show that the increase in grassland fragmentation, together with the minimum temperature in the winter, accounts for the spatial pattern of outbreaks in the country. We propose that fragmentation may increase the connectivity of vampire bat colonies by promoting the sharing of feeding areas, while temperature modulates their home range plasticity. While a recent introduction of the virus from neighboring Brazil could have had an effect on outbreak occurrence, we show here that the distribution of rabies cases is unlikely to be explained by only an invasion process from Brazil. In accordance with previous modeling efforts, an increase in connectivity may promote spatial persistence of rabies virus within vampire bat populations. Our results suggest that land use planning might help to reduce grassland fragmentation and thus reduce risk of rabies transmission to livestock. This will be especially important in the context of climatic changes and increasing minimum temperatures in the winter.
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Affiliation(s)
- Germán Botto Nuñez
- Department of Microbiology and Immunology, Bozeman Disease Ecology Lab, Montana State University, 109 Lewis Hall, Bozeman, MT, 59717, USA.
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay.
- Programa para la Conservación de los Murciélagos de Uruguay, Museo Nacional de Historia Natural, Montevideo, 11000, Uruguay.
| | - Daniel J Becker
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Rick L Lawrence
- Spatial Sciences Center, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Raina K Plowright
- Department of Microbiology and Immunology, Bozeman Disease Ecology Lab, Montana State University, 109 Lewis Hall, Bozeman, MT, 59717, USA
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Cohen Y, Bar-David S, Nielsen M, Bohmann K, Korine C. An appetite for pests: Synanthropic insectivorous bats exploit cotton pest irruptions and consume various deleterious arthropods. Mol Ecol 2020; 29:1185-1198. [PMID: 32153071 DOI: 10.1111/mec.15393] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
Conservation biological control (CBC) seeks to minimize the deleterious effects of agricultural pests by enhancing the efficiency of natural enemies. Despite the documented potential of insectivorous bats to consume pests, many synanthropic bat species are still underappreciated as beneficial species. We investigated the diet of Kuhl's pipistrelle (Pipistrellus kuhlii), a common synanthropic insectivorous bat that forages in urban and agricultural areas, to determine whether it may function as a natural enemy in CBC. Faecal samples of P. kuhlii were collected throughout the cotton-growing season from five roost sites near cotton fields located in a Mediterranean agroecosystem, Israel, and analyzed using DNA metabarcoding. Additionally, data on estimated abundance of major cotton pests were collected. We found that the diet of P. kuhlii significantly varied according to sites and dates and comprised 27 species of agricultural pests that were found in 77.2% of the samples, including pests of key economic concern. The dominant prey was the widespread cotton pest, the pink bollworm, Pectinophora gossypiella, found in 31% of the samples and in all the roosts. Pink bollworm abundance was positively correlated with its occurrence in the bat diet. Furthermore, the bats' dietary breadth narrowed, while temporal dietary overlap increased, in relation to increasing frequencies of pink bollworms in the diet. This suggests that P. kuhlii exploits pink bollworm irruptions by opportunistic feeding. We suggest that synanthropic bats provide important pest suppression services, may function as CBC agents of cotton pests and potentially contribute to suppress additional deleterious arthropods found in their diet in high frequencies.
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Affiliation(s)
- Yuval Cohen
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Carmi Korine
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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37
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Rocha F, Ulloa-Stanojlovic FM, Rabaquim VCV, Fadil P, Pompei JC, Brandão PE, Dias RA. Relations between topography, feeding sites, and foraging behavior of the vampire bat, Desmodus rotundus. J Mammal 2019. [DOI: 10.1093/jmammal/gyz177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The vampire bat (Desmodus rotundus) plays a crucial role in the maintenance and transmission of the rabies virus to humans and livestock, impacting public health and economic production. Its importance lies not only in its capacity to transmit the virus but also in its ability to adapt to anthropic changes, as expressed in its wide geographic distribution in Latin America. Deforestation, livestock intensification, and other human activities have reduced the abundance of its wild prey but have also provided new and abundant shelter and foraging resources for the vampire bats. We used radiotelemetry to evaluate relations between topography, feeding site choice, and foraging behavior in southeastern Brazil, where three occupied D. rotundus roosts, out of 11 possible, were systematically monitored throughout a 1-year period once every 2 months. Sixty-two vampire bats were captured; biometric data were collected and 44 radiotransmitters were installed in adult individuals, producing telemetry data that were recorded in VHF receptors installed in the farms. Elevation of the roosts was related to the farms attacked by the vampire bats. Understanding the use of the environment and resources by vampire bats is critical to improving rabies control aiming at the reduction of disease impacts. From the perspective of the official veterinary service, telemetry would be ineffective as a rabies surveillance system due to the costs and limitations of the available technology. However, livestock rabies control measures would be greatly improved if ecological characteristics of the vampire bat were considered.
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Affiliation(s)
- Felipe Rocha
- Laboratory of Epidemiology and Biostatistics, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Francisco Miroslav Ulloa-Stanojlovic
- Laboratory of Epidemiology and Biostatistics, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Vanessa Cristina Victor Rabaquim
- Laboratory of Epidemiology and Biostatistics, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Paulo Fadil
- Coordenadoria de Defesa Agropecuária, Sao Paulo State Secretariat for Agriculture and Food Supply, Campinas, Brazil
| | - Júlio César Pompei
- Pan American Center of Foot-and-mouth Disease, Pan American Health Association, Rio de Janeiro, Brazil
| | - Paulo Eduardo Brandão
- Laboratory of Viral Zoonosis, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Ricardo Augusto Dias
- Laboratory of Epidemiology and Biostatistics, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
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Bergner LM, Orton RJ, Benavides JA, Becker DJ, Tello C, Biek R, Streicker DG. Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Mol Ecol 2019; 29:26-39. [PMID: 31561274 PMCID: PMC7004108 DOI: 10.1111/mec.15250] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023]
Abstract
Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.
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Affiliation(s)
- Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Julio A Benavides
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Departamento de Ecología, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Daniel J Becker
- Odum School of Ecology, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Department of Biology, Indiana University, Bloomington, IN, USA
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, Lima, Peru.,Yunkawasi, Lima, Peru
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Elbrecht V, Braukmann TW, Ivanova NV, Prosser SW, Hajibabaei M, Wright M, Zakharov EV, Hebert PD, Steinke D. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 2019; 7:e7745. [PMID: 31608170 PMCID: PMC6786254 DOI: 10.7717/peerj.7745] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/25/2019] [Indexed: 01/08/2023] Open
Abstract
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40-60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
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Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Michael Wright
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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40
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Assessment of seasonal variation of diet composition in rodents using DNA barcoding and Real-Time PCR. Sci Rep 2019; 9:14124. [PMID: 31575934 PMCID: PMC6773709 DOI: 10.1038/s41598-019-50676-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/10/2019] [Indexed: 02/08/2023] Open
Abstract
The study of animal diet and feeding behaviour is a fundamental tool for the illustration of the ecological role of species in the ecosystem. However, size and quality of food intake samples make it hard for researchers to describe the diet composition of many small species. In our study, we exploited genomic tools for the analysis of the diet composition of the Savi’s pine vole (Microtus savii) using DNA barcoding and qPCR techniques for the identification of ingested plant species retrieved from stomach contents. In contrast with previous studies, we found that, despite being a fossorial species, the Savi’s pine vole is a selective feeder that undergoes intense superficial activity in search for food. In addition, our study shows that with a a priori knowledge of the candidate plant species included in animal diet, qPCR is a powerful tool to assess presence/absence, frequency of occurrence and electivity of ingested species. We conclude that this approach offers new opportunities to implement the analysis of food selection in small animals, thereby revealing a detailed picture of plant-animal interactions.
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41
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Andriollo T, Gillet F, Michaux JR, Ruedi M. The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus. PLoS One 2019; 14:e0219135. [PMID: 31276547 PMCID: PMC6611578 DOI: 10.1371/journal.pone.0219135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/17/2019] [Indexed: 11/19/2022] Open
Abstract
Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- Section of Biology, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet, Geneva, Switzerland
| | - François Gillet
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- Comportement et Écologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique, Auzeville, Castanet-Tolosan Cedex, France
| | - Johan R. Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- CIRAD, Agirs Unit, TA C- 22/E- Campus international de Baillarguet, Montpellier Cedex, France
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- * E-mail:
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Zizka VMA, Elbrecht V, Macher J, Leese F. Assessing the influence of sample tagging and library preparation on DNA metabarcoding. Mol Ecol Resour 2019; 19:893-899. [DOI: 10.1111/1755-0998.13018] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/13/2019] [Accepted: 03/28/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Vera M. A. Zizka
- Aquatic Ecosystem Research, Faculty of Biology University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) Essen University of Duisburg‐Essen Essen Germany
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of Biology University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) Essen University of Duisburg‐Essen Essen Germany
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Titcomb GC, Jerde CL, Young HS. High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Bohmann K, Gopalakrishnan S, Nielsen M, Nielsen LDSB, Jones G, Streicker DG, Gilbert MTP. Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure. Mol Ecol Resour 2018; 18:1050-1063. [PMID: 29673092 PMCID: PMC6120510 DOI: 10.1111/1755-0998.12891] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/29/2022]
Abstract
Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large-scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large-scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure.
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Affiliation(s)
- Kristine Bohmann
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- School of Biological SciencesUniversity of East AngliaNorwichNorfolkUK
| | - Shyam Gopalakrishnan
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Martin Nielsen
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | | | - Gareth Jones
- School of Biological SciencesUniversity of BristolBristolUK
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative MedicineMRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- NTNU University MuseumTrondheimNorway
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