1
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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2
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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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3
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Ji Y, Baker CCM, Popescu VD, Wang J, Wu C, Wang Z, Li Y, Wang L, Hua C, Yang Z, Yang C, Xu CCY, Diana A, Wen Q, Pierce NE, Yu DW. Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nat Commun 2022; 13:1555. [PMID: 35322033 PMCID: PMC8943135 DOI: 10.1038/s41467-022-28778-8] [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: 02/13/2020] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas. Invertebrate-derived eDNA (iDNA) is an emerging tool for taxonomic and spatial biodiversity monitoring. Here, the authors use metabarcoding of leech-derived iDNA to estimate vertebrate occupancy over an entire protected area, the Ailaoshan Nature Reserve, China.
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Affiliation(s)
- Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Christopher C M Baker
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA. .,US Army ERDC Cold Regions Research and Engineering Laboratory, 72 Lyme Road, Hanover, NH, 03755, USA.
| | - Viorel D Popescu
- Department of Biological Sciences and Sustainability Studies Theme, Ohio University, 107 Irvine Hall, Athens, OH, 45701, USA.,Center for Environmental Studies (CCMESI), University of Bucharest, 1 N. Balcescu Blvd., Bucharest, Romania
| | - Jiaxin Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Chunying Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Yuanheng Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China.,Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Lin Wang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Mengla, China
| | - Chaolang Hua
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Zhongxing Yang
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China
| | - Charles C Y Xu
- Redpath Museum and Department of Biology, McGill University, 859 Sherbrooke Street West, Montreal, PQ, H3A2K6, Canada
| | - Alex Diana
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Sibson Building, Canterbury, Kent, CT27FS, UK
| | - Qingzhong Wen
- Yunnan Forestry Survey and Planning Institute, 289 Renmin E Rd, 650028, Kunming, Yunnan, China
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, 650223, Kunming, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK.
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4
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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 2022; 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] [MESH Headings] [Grants] [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 GenomicsThe Globe InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen KDenmark
| | - Alejandro Oceguera‐Figueroa
- Laboratorio de HelmintologíaDepartamento de ZoologíaInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Sebastian Kvist
- Department of Natural HistoryRoyal Ontario MuseumTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe Globe InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen KDenmark
- University MuseumNTNUTrondheimNorway
| | - Kristine Bohmann
- Section for Evolutionary GenomicsThe Globe InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen KDenmark
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5
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Lu F, Shi M, Liu J, Kong W, Zhang Y, Shi L. Characterization of the complete mitochondrial genome of Haemadipsa tianmushana Song 1977 (Hirudiniformes, Haemadipsidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:103-105. [PMID: 35005228 PMCID: PMC8741244 DOI: 10.1080/23802359.2021.2008827] [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] [Indexed: 11/24/2022] Open
Abstract
The complete mitochondrial genome of Haemadipsa tianmushana Song 1977 from China has been determined and reported for the first time in this study. It was 14,625 bp in length and consisted of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 3 control regions. The nucleotide base content of the complete mitogenome for this species was 35.1% A, 10.5% C, 11.6% G, and 42.8% T. The tRNA genes were ranged from 57 bp (SerTCT) to 66 bp (GlnTTG) in length. The phylogenetic analyses indicated that Hirudinea is a mono-phyletic clade. And it includes Whitmania acranulata, Whitmania pigra, Whitmania laevis, Zeylanicobdella arugamensis, Ozobranchus jantseanus and Placobdella lamothei. In Hirudiniformes, H. tianmushana and three species of Haemopidae were obviously clustered into two independent branches. This result is consistent with a taxonomy that they all belong to the same suborder. This study adds to the genetic resources currently available for the species.
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Affiliation(s)
- Fuhua Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Research and Development of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Jiali Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weijun Kong
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yufeng Zhang
- Hebei Key Laboratory of Animal Diversity, Langfang Normal University, Langfang, China
| | - Linchun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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6
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7
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Clare EL, Economou CK, Bennett FJ, Dyer CE, Adams K, McRobie B, Drinkwater R, Littlefair JE. Measuring biodiversity from DNA in the air. Curr Biol 2021; 32:693-700.e5. [PMID: 34995488 DOI: 10.1016/j.cub.2021.11.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/05/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022]
Abstract
The crisis of declining biodiversity1 exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential to quantify the causes and consequences of global change. Environmental DNA2 has revolutionized aquatic ecology,3 permitting population monitoring4 and remote diversity assessments matching or outperforming conventional methods of community sampling.3-5 Despite this model, similar methods have not been widely adopted in terrestrial ecosystems. Here, we demonstrate that DNA from terrestrial animals can be filtered, amplified, and then sequenced from air samples collected in natural settings representing a powerful tool for terrestrial ecology. We collected air samples at a zoological park, where spatially confined non-native species allowed us to track DNA sources. We show that DNA can be collected from air and used to identify species and their ecological interactions. Air samples contained DNA from 25 species of mammals and birds, including 17 known terrestrial resident zoo species. We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom. Our data demonstrate that airborne eDNA concentrates around recently inhabited areas but disperses away from sources, suggesting an ecology to airborne eDNA and the potential for sampling at a distance. Our findings demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Frances J Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Caitlin E Dyer
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | | | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Joanne E Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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8
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Massey AL, Bronzoni RVDM, da Silva DJF, Allen JM, de Lázari PR, Dos Santos-Filho M, Canale GR, Bernardo CSS, Peres CA, Levi T. Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers. Mol Ecol Resour 2021; 22:962-977. [PMID: 34601818 DOI: 10.1111/1755-0998.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or faeces. Here, we used metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) collected from 39 forested sites in the southern Amazon to profile gamma and alpha diversity. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance; and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. In total, we collected and analysed 1759 carrion flies, 48,686 sandflies, and 4776 mosquitos. Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.
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Affiliation(s)
- Aimee L Massey
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | | | - Jennifer M Allen
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Patrick Ricardo de Lázari
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Manoel Dos Santos-Filho
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Carlos Augusto Peres
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Instituto Juruá, Manaus, Brazil
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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9
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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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10
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Clare EL, Economou CK, Faulkes CG, Gilbert JD, Bennett F, Drinkwater R, Littlefair JE. eDNAir: proof of concept that animal DNA can be collected from air sampling. PeerJ 2021; 9:e11030. [PMID: 33850648 PMCID: PMC8019316 DOI: 10.7717/peerj.11030] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - James D Gilbert
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Frances Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joanne E Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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11
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Fahmy M, Williams KM, Tessler M, Weiskopf SR, Hekkala E, Siddall ME. Multilocus Metabarcoding of Terrestrial Leech Bloodmeal iDNA Increases Species Richness Uncovered in Surveys of Vertebrate Host Biodiversity. J Parasitol 2020; 106:843-853. [DOI: 10.1645/19-189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Mai Fahmy
- Department of Biological Sciences, Fordham University, Bronx, New York 10458
| | - Kalani M. Williams
- Department of Biological Sciences, Fordham University, Bronx, New York 10458
| | - Michael Tessler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024
| | - Sarah R. Weiskopf
- United States Geological Survey, National Climate Adaptation Science Center, 12201 Sunrise Valley Drive, MS 516, Reston, Virginia 20192
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, Bronx, New York 10458
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12
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Drinkwater R, Jucker T, Potter JHT, Swinfield T, Coomes DA, Slade EM, Gilbert MTP, Lewis OT, Bernard H, Struebig MJ, Clare EL, Rossiter SJ. Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats. Mol Ecol 2020; 30:3299-3312. [PMID: 33171014 PMCID: PMC8359290 DOI: 10.1111/mec.15724] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 12/29/2022]
Abstract
The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land‐use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood‐feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human‐modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tommaso Jucker
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Swinfield
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - David A Coomes
- Department of Plant Sciences, Forest and Ecology Conservation Group, University of Cambridge, Cambridge, UK
| | - Eleanor M Slade
- Department of Zoology, University of Oxford, Oxford, UK.,Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore
| | - M Thomas P Gilbert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology (DICE), School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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13
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GenBank's reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proc Natl Acad Sci U S A 2020; 117:32211-32212. [PMID: 33234565 DOI: 10.1073/pnas.2007421117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Williams KM, Barkdull M, Fahmy M, Hekkala E, Siddall ME, Kvist S. Caught red handed: iDNA points to wild source for CITES-protected contraband leeches. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01419-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Morishima K, Nakano T, Aizawa M. Sika deer presence affects the host-parasite interface of a Japanese land leech. Ecol Evol 2020; 10:6030-6038. [PMID: 32607210 PMCID: PMC7319141 DOI: 10.1002/ece3.6344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Since the 1990s, increasing populations of a blood feeding land leech (Haemadipsa japonica) have become a serious issue in several Japanese prefectures, and it may be caused by the increases in sika deer (Cervus nippon) populations seen over the last quarter of the century. Therefore, this study aimed to reveal the host animal species of H. japonica using iDNA (vertebrate DNA isolated from invertebrates) and to test the hypothesis that the increasingly widespread distribution of sika deer results in increased H. japonica populations through changes to the host-parasite interface. We amplified mitochondrial DNA 16S ribosome RNA fragments from iDNA isolated from the blood clots of H. japonica collected across Japan. We identified 17 host animal species, including four orders of Mammalia (Carnivora, Artiodactyla, Rodentia, and Lagomorpha) and two orders of Amphibia (Caudata and Anura). The sika deer was the dominant host species of H. japonica. Additionally, the host animal species composition of H. japonica differed according to the presence or absence of sika deer. In the sites where sika deer were not found, Anura (frog) species were the most commonly identified hosts of H. japonica. These results suggest that the increases in H. japonica populations might have occurred via a change in host preference to sika deer. This change might be driven by the increases in sika deer populations and subsequent increase in the frequency that H. japonica uses the sika deer as easy prey, as well as by sika deer providing more reproductive energy per blood meal than blood meal from frog species. The present study suggests that a more widespread distribution of sika deer resulted in an increase in H. japonica through a change in the host-parasite interface. Therefore, management that focuses on decreasing sika deer populations would likely be an effective method for the reduction of H. japonica populations.
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Affiliation(s)
- Kaori Morishima
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and TechnologyUtsunomiyaJapan
| | - Takafumi Nakano
- Department of ZoologyGraduate School of ScienceKyoto UniversityKyotoJapan
| | - Mineaki Aizawa
- Department of Forest ScienceSchool of AgricultureUtsunomiya UniversityUtsunomiyaJapan
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16
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Hanya G, Morishima K, Koide T, Otani Y, Hongo S, Honda T, Okamura H, Higo Y, Hattori M, Kondo Y, Kurihara Y, Jin S, Otake A, Shiroisihi I, Takakuwa T, Yamamoto H, Suzuki H, Kajimura H, Hayakawa T, Suzuki‐Hashido N, Nakano T. Host selection of hematophagous leeches (
Haemadipsa japonica
): Implications for iDNA studies. Ecol Res 2019. [DOI: 10.1111/1440-1703.12059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Goro Hanya
- Primate Research Institute Kyoto University Inuyama Japan
| | - Kaori Morishima
- United Graduate School of Agricultural Science Tokyo University of Agriculture and Technology Utsunomiya Japan
| | | | - Yosuke Otani
- Center for the Study of Co* Design Osaka University Toyonaka Japan
| | - Shun Hongo
- The Center for African Area Studies Kyoto University Kyoto Japan
| | - Takeaki Honda
- Primate Research Institute Kyoto University Inuyama Japan
| | - Hiroki Okamura
- Primate Research Institute Kyoto University Inuyama Japan
| | - Yuma Higo
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Masamichi Hattori
- Graduate School of Natural Science and Technology Gifu University Gifu Japan
| | - Yuki Kondo
- Graduate School of Education Gifu University Gifu Japan
- Graduate School of Science Osaka City University Osaka Japan
| | - Yosuke Kurihara
- Primate Research Institute Kyoto University Inuyama Japan
- Center for Education and Research in Field Sciences, Faculty of Agriculture Shizuoka University Hamamatsu Japan
| | - Sakura Jin
- Faculty of Agriculture Iwate University Morioka Japan
| | - Aji Otake
- Faculty of Agriculture Iwate University Morioka Japan
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | | | - Tomomi Takakuwa
- Faculty of Agriculture Tokyo University of Agriculture and Technology Fuchu Japan
| | | | - Hanami Suzuki
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Hisashi Kajimura
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Takashi Hayakawa
- Primate Research Institute Kyoto University Inuyama Japan
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
- Japan Monkey Centre Inuyama Japan
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17
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Fahmy M, Ravelomanantsoa NAF, Youssef S, Hekkala E, Siddall M. Biological inventory of Ranomafana National Park tetrapods using leech-derived iDNA. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1305-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Drinkwater R, Schnell IB, Bohmann K, Bernard H, Veron G, Clare E, Gilbert MTP, Rossiter SJ. Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo. Mol Ecol Resour 2019; 19:105-117. [PMID: 30225935 PMCID: PMC7379310 DOI: 10.1111/1755-0998.12943] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 01/09/2023]
Abstract
The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.
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Affiliation(s)
- Rosie Drinkwater
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | | | - Kristine Bohmann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwich, NorfolkUK
| | - Henry Bernard
- Institute for Tropical Biology and ConservationUniversiti Malaysia Sabah, Jalan UMSKota KinabaluSabahMalaysia
| | - Géraldine Veron
- Institut Systématique Evolution Biodiversité (ISYEB)Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEParis CedexFrance
| | - Elizabeth Clare
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - M. Thomas P. Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- NTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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19
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Clare EL, Fazekas AJ, Ivanova NV, Floyd RM, Hebert PDN, Adams AM, Nagel J, Girton R, Newmaster SG, Fenton MB. Approaches to integrating genetic data into ecological networks. Mol Ecol 2018; 28:503-519. [PMID: 30427082 DOI: 10.1111/mec.14941] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Aron J Fazekas
- The Arboretum, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Robin M Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Amanda M Adams
- Department of Biology, Texas A&M University, College Station, Texas
| | - Juliet Nagel
- Center for Environmental Science, University of Maryland, Frostburg, Maryland
| | - Rebecca Girton
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - M Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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