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Saranholi BH, França FM, Vogler AP, Barlow J, Vaz de Mello FZ, Maldaner ME, Carvalho E, Gestich CC, Howes B, Banks-Leite C, Galetti PM. Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics. Mol Ecol Resour 2024; 24:e13961. [PMID: 38646932 DOI: 10.1111/1755-0998.13961] [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: 10/31/2023] [Revised: 03/16/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.
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Affiliation(s)
- Bruno H Saranholi
- Department of Life Sciences, Imperial College London, Ascot, UK
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Filipe M França
- School of Biological Sciences, University of Bristol, Bristol, UK
- Graduate Program in Ecology, Biological Sciences Institute, Federal University of Pará, Belém, Pará, Brazil
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Fernando Z Vaz de Mello
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Instituto de Biociências, Cuiabá, MT, Brazil
| | - Maria E Maldaner
- Programa de Pós-Graduação Em Ecologia e Conservação da Biodiversidade (PPGECB), Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Edrielly Carvalho
- Programa de Pós-Graduação Em Entomologia, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Benjamin Howes
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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2
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Pedersen KM, von Beeren C, Oggioni A, Blüthgen N. Mammal dung-dung beetle trophic networks: an improved method based on gut-content DNA. PeerJ 2024; 12:e16627. [PMID: 38500531 PMCID: PMC10946388 DOI: 10.7717/peerj.16627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 11/16/2023] [Indexed: 03/20/2024] Open
Abstract
Background Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding. Methods First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity. Results We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung-dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2': Ecuador = 0.49; Germany = 0.41). Conclusion We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung-dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.
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Affiliation(s)
- Karen M. Pedersen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | | | - Arianna Oggioni
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Nico Blüthgen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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Almeida CE, Máximo MM, Pires-Silva D, Takiya DM, Valença-Barbosa C, Viana MC, Reigada C, Iñiguez AM, Harry M, Folly-Ramos E. From molecules to ecosystems: Insights into a network of interactions for a Chagas disease outbreak using Triatoma brasiliensis as natural samplers. Acta Trop 2024; 251:107107. [PMID: 38190930 DOI: 10.1016/j.actatropica.2023.107107] [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: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Exploring the dynamics of disease transmission involves an understanding of complex interactions within the eco-epidemiologic framework. In the context of Chagas disease (CD), elements are mainly represented by the interactions among the pathogen, insect vector, host, humans and the environment. We performed quantitative and qualitative analyses on a dataset derived from 98 Triatoma brasiliensis infected by trypanosomatids, which were linked to a CD outbreak in the semi-arid region of northeastern Brazil. We extracted invertebrate-derived DNA (iDNA) from these insects, comprising 18 populations around the outbreak area, each indicative of various strata of anthropogenic influence. Food source (FS) diversity, representing potential parasite reservoirs, was determined through mitochondrial gene (cyt b) sequencing of vertebrates, and parasite genotyping was accessed using fluorescent amplified fragment barcodes (FFLB) of trypanosomatids. We also assessed the residents' awareness of breeding sites for CD vectors in the inspected houses. The quantification of Trypanosoma cruzi was estimated via real-time PCR and is denominated here as the average parasite load (PL) per insect (T. cruzi/intestinal unit). We aimed to address vector-parasite-host-environment interactions that were discussed based on their significance among the components. Notably, among the significant interactions, we observed that the PL in the insects was significantly influenced by FS. Infected insects that fed on the classic reservoir, Didelphis albiventris, and Galea spixii exhibited higher PLs, compared to those that fed on Kerodon rupestris (p < 0.04)-a primary host. While D. albiventris is already recognized as a synanthropic species, we propose that G. spixii may also be undergoing a synanthropic process. Conversely, domestic cats are frequently identified as FS in infected insects from the sylvatic environment, suggesting a possible change in their behavior towards a wild state. Therefore, we propose that neglected anthropogenic actions have facilitated the reciprocal (sylvatic-peridomestic) circulation of T. cruzi-especially noted for TcI because it was predominant in insects found in peridomestic environments. Residents are often unaware of the existence of insect breeding grounds near their homes, particularly when it involves the storage of materials without planning for use, such as piles of tiles, bricks and wood. Although indirect inferences about the interaction among vector-parasite-host-environment are still incipient, we highlight the potential use of vectors as natural samplers of biological and ecological components in transmitting the disease.
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Affiliation(s)
- Carlos E Almeida
- Universidade Federal da Paraíba (UFPB), Campus IV, Rio Tinto, Brasil; Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil.
| | - Milena M Máximo
- Universidade Federal da Paraíba (UFPB), Campus IV, Rio Tinto, Brasil
| | | | - Daniela M Takiya
- Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil
| | | | - Maria C Viana
- Universidade de Campinas (UNICAMP), Campinas, Brasil; Instituto Nacional de Câncer, Rio de Janeiro, Brasil
| | | | | | - Myriam Harry
- Université Paris-Saclay, CNRS, IRD, UMR EGCE, Evolution, Génomes, Comportement et Ecologie, IDEEV, Gif-sur-Yvette, France
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Frolov AV, Akhmetova LA, Vishnevskaya MS, Kiriukhin BA, Montreuil O, Lopes F, Tarasov SI. Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar. Zookeys 2023; 1181:29-39. [PMID: 37810459 PMCID: PMC10556875 DOI: 10.3897/zookeys.1181.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurusfissicollis (Fairmaire), H.giganteus (Harold), Nanosagaboides (Boucomont), and Epilissussplendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔-¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bostaurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.
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Affiliation(s)
- Andrey V. Frolov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, RussiaZoological Institute, Russian Academy of SciencesSaint PetersburgRussia
| | - Lilia A. Akhmetova
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, RussiaZoological Institute, Russian Academy of SciencesSaint PetersburgRussia
| | - Maria S. Vishnevskaya
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, RussiaZoological Institute, Russian Academy of SciencesSaint PetersburgRussia
- Department of Entomology, Saint Petersburg State University, Saint Petersburg, RussiaSaint Petersburg State UniversitySaint PetersburgRussia
| | - Bogdan A. Kiriukhin
- AquaBioSafe Laboratory, University of Tyumen, Tyumen, RussiaUniversity of TyumenTyumenRussia
| | - Olivier Montreuil
- National Museum of Natural History, Paris, FranceNational Museum of Natural HistoryParisFrance
| | - Fernando Lopes
- Finnish Museum of Natural History, University of Helsinki, Helsinki, FinlandUniversity of HelsinkiHelsinkiFinland
| | - Sergei I. Tarasov
- Finnish Museum of Natural History, University of Helsinki, Helsinki, FinlandUniversity of HelsinkiHelsinkiFinland
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5
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Liu H, Wang D, Zhang C, Pu T, Xiong L, Wei F, Hu Y. Development of short-target primers for species identification in biological studies of Carnivora. Ecol Evol 2023; 13:e10135. [PMID: 37250442 PMCID: PMC10212699 DOI: 10.1002/ece3.10135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.
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Affiliation(s)
- Huiwen Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dan Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | | | - Lijuan Xiong
- School of Life SciencesGuizhou Normal UniversityGuiyangChina
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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6
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Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
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Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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7
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Mugnai F, Costantini F, Chenuil A, Leduc M, Gutiérrez Ortega JM, Meglécz E. Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies. PeerJ 2023; 11:e14616. [PMID: 36643652 PMCID: PMC9835706 DOI: 10.7717/peerj.14616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments. Methods We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency. Results The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).
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Affiliation(s)
- Francesco Mugnai
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy
| | - Federica Costantini
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | | | | | - Emese Meglécz
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
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8
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Tosa MI, Lesmeister DB, Allen JM, Levi T. Multi‐locus
DNA
metabarcoding reveals seasonality of foraging ecology of western spotted skunks in the Pacific Northwest. Ecosphere 2023. [DOI: 10.1002/ecs2.4386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Pacific Northwest Research Station U.S. Department of Agriculture Forest Service Corvallis Oregon USA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
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9
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Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia. Nat Commun 2022; 13:3290. [PMID: 35672313 PMCID: PMC9174194 DOI: 10.1038/s41467-022-30842-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
Assessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within the same locality. However, remote disturbances may also affect local biodiversity. Here, we used environmental DNA metabarcoding to evaluate the relationships between vertebrate biodiversity (fish and mammals) and disturbance intensity in two Amazonian rivers. Measurements of anthropic disturbance -here forest cover losses- were made from the immediate vicinity of the biodiversity sampling sites to up to 90 km upstream. The findings suggest that anthropization had a spatially extended impact on biodiversity. Forest cover losses of <11% in areas up to 30 km upstream from the biodiversity sampling sites were linked to reductions of >22% in taxonomic and functional richness of both terrestrial and aquatic fauna. This underscores the vulnerability of Amazonian biodiversity even to low anthropization levels. The similar responses of aquatic and terrestrial fauna to remote disturbances indicate the need for cross-ecosystem conservation plans that consider the spatially extended effects of anthropization. It is unclear how far the impact of deforestation can spread. Here the authors analyse freshwater eDNA data along two rivers in the Amazon forest, and find that low levels of deforestation are linked to substantial reductions of fish and mammalian diversity downstream.
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10
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McLennan EA, Wise P, Lee AV, Grueber CE, Belov K, Hogg CJ. DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem. Ecol Evol 2022; 12:e8936. [PMID: 35600680 PMCID: PMC9120209 DOI: 10.1002/ece3.8936] [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: 11/10/2021] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species’ native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species’ native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short‐tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.
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Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Phil Wise
- Save the Tasmanian Devil Program NRE Hobart Tasmania Australia
| | - Andrew V. Lee
- Save the Tasmanian Devil Program NRE Hobart Tasmania Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Katherine Belov
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
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11
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Durso AM, Kieran TJ, Glenn TC, Mullin SJ. Comparison of Three Methods for Measuring Dietary Composition of Plains Hog-nosed Snakes. HERPETOLOGICA 2022. [DOI: 10.1655/herpetologica-d-21-00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andrew M. Durso
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Stephen J. Mullin
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
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12
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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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13
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Kocher A, Cornuault J, Gantier JC, Manzi S, Chavy A, Girod R, Dusfour I, Forget PM, Ginouves M, Prévot G, Guégan JF, Bañuls AL, de Thoisy B, Murienne J. Biodiversity and vector-borne diseases: host dilution and vector amplification occur simultaneously for Amazonian leishmaniases. Mol Ecol 2022; 32:1817-1831. [PMID: 35000240 DOI: 10.1111/mec.16341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022]
Abstract
Changes in biodiversity may impact infectious disease transmission through multiple mechanisms. We explored the impact of biodiversity changes on the transmission of Amazonian leishmaniases, a group of wild zoonoses transmitted by phlebotomine sand flies (Psychodidae), which represent an important health burden in a region where biodiversity is both rich and threatened. Using molecular analyses of sand fly pools and blood-fed dipterans, we characterized the disease system in forest sites in French Guiana undergoing different levels of human-induced disturbance. We show that the prevalence of Leishmania parasites in sand flies correlates positively with the relative abundance of mammal species known as Leishmania reservoirs. In addition, Leishmania reservoirs tend to dominate in less diverse mammal communities, in accordance with the dilution effect hypothesis. This results in a negative relationship between Leishmania prevalence and mammal diversity. On the other hand, higher mammal diversity is associated with higher sand fly density, possibly because more diverse mammal communities harbor higher biomass and more abundant feeding resources for sand flies, although more research is needed to identify the factors that shape sand fly communities. As a consequence of these antagonistic effects, decreased mammal diversity comes with an increase of parasite prevalence in sand flies, but has no detectable impact on the density of infected sand flies. These results represent additional evidence that biodiversity changes may simultaneously dilute and amplify vector-borne disease transmission through different mechanisms that need to be better understood before drawing generalities on the biodiversity-disease relationship.
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Affiliation(s)
- Arthur Kocher
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France.,MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.,Institut Pasteur de la Guyane, Cayenne, France.,Transmission, Infection, Diversification & Evolution Group, Max-Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Josselin Cornuault
- Real Jardín Botánico CSIC, Plaza Murillo 2, 28014, Madrid, Spain.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jean-Charles Gantier
- Laboratoire des Identifications Fongiques et Entomo-parasitologiques, Mennecy, France
| | - Sophie Manzi
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France
| | - Agathe Chavy
- Institut Pasteur de la Guyane, Cayenne, France.,TBIP, Université de Guyane, 97300, Cayenne, France
| | | | | | - Pierre-Michel Forget
- Muséum National d'Histoire Naturelle, UMR-7179 MECADEV (Mécanismes Adaptatifs et Evolution), MNHN-CNRS, Brunoy, France
| | - Marine Ginouves
- TBIP, Université de Guyane, 97300, Cayenne, France.,Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR9017-CIIL Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Ghislaine Prévot
- TBIP, Université de Guyane, 97300, Cayenne, France.,Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR9017-CIIL Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Jean-François Guégan
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.,INRAE, Cirad, Université de Montpellier, UMR ASTRE, Montpellier, France
| | | | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, France.,Association Kwata, Cayenne, French Guiana
| | - Jérôme Murienne
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France
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14
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Carvalho CS, de Oliveira ME, Rodriguez-Castro KG, Saranholi BH, Galetti PM. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Mol Ecol Resour 2021; 22:1262-1273. [PMID: 34724330 DOI: 10.1111/1755-0998.13543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been increasingly recognized as powerful tools for biodiversity assessment and conservation management. However, eDNA/iDNA efficiency for vertebrate diversity assessment remains uncertain, and comparisons to conventional methods are still rare. Through a meta-analysis of previously published vertebrate diversity surveys, we compared the efficiency of eDNA/iDNA against conventional methods across several types of samplers, vertebrate groups, and locations (tropical vs. temperate zones). We also assess eDNA/iDNA efficiency to estimate relative abundance or biomass over different molecular methods (qPCR and metabarcoding) and type of experiment (in the laboratory or in the field). We showed that for water sampler, fish as a target species, and studies achieved in temperate zones, eDNA presents lower risk of not detecting a species or a site with a target species than conventional methods. These results show that eDNA is an efficient tool to assess fish diversity. Moreover, eDNA data presents positive correlation with fish abundance or biomass. However, such correlation was higher in laboratory experiments than in the field. For the other samplers, vertebrate groups, and in tropical zones we were not able to draw general conclusion, highlighting the urgency of conducting more comparative studies.
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Affiliation(s)
- Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | - Karen Giselle Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Facultad de Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Department of Life Sciences, Imperial College London, London, UK
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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15
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Coutant O, Richard-Hansen C, de Thoisy B, Decotte JB, Valentini A, Dejean T, Vigouroux R, Murienne J, Brosse S. Amazonian mammal monitoring using aquatic environmental DNA. Mol Ecol Resour 2021; 21:1875-1888. [PMID: 33787010 DOI: 10.1111/1755-0998.13393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
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Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | | | | | | | | | - Tony Dejean
- VIGILIFE, Le Bourget-du-Lac, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, HYDRECO, Kourou Cedex, French Guiana
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
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16
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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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17
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Sales NG, Kaizer MDC, Coscia I, Perkins JC, Highlands A, Boubli JP, Magnusson WE, Da Silva MNF, Benvenuto C, Mcdevitt AD. Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil. Mamm Rev 2020. [DOI: 10.1111/mam.12183] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Naiara Guimarães Sales
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Mariane da Cruz Kaizer
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Ilaria Coscia
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Joseph C. Perkins
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Andrew Highlands
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Jean P. Boubli
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - William E. Magnusson
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Amazonas Brazil
| | | | - Chiara Benvenuto
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
| | - Allan D. Mcdevitt
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford SalfordM5 4WTUK
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18
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19
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Murienne J, Cantera I, Cerdan A, Cilleros K, Decotte JB, Dejean T, Vigouroux R, Brosse S. Aquatic eDNA for monitoring French Guiana biodiversity. Biodivers Data J 2019; 7:e37518. [PMID: 31592221 PMCID: PMC6751219 DOI: 10.3897/bdj.7.e37518] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 02/04/2023] Open
Abstract
Background Environmental DNA [eDNA] metabarcoding has recently emerged as a non-destructive alternative to traditional sampling for characterising species assemblages. New information We here provide a consistent dataset synthetising all eDNA sampling sites in French Guiana to date. Field collections have been initiated in 2014 and have continued until 2019. This dataset is however a work in progress and will be updated after each collecting campaign. We also provide a taxon by site matrix for fishes presence / absence as inferred from eDNA. Our aim is to allow a transparent communication to the stakeholders and provide the foundation for a monitoring programme based on eDNA. The lastest version of the dataset is publicly and freely accessible through the CEBA geoportal (http://vmcebagn-dev.ird.fr) or through the French Guiana geographic portal (https://www.geoguyane.fr).
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Affiliation(s)
- Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, France Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD Toulouse France
| | - Isabel Cantera
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, France Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD Toulouse France
| | - Axel Cerdan
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, France Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD Toulouse France
| | - Kévin Cilleros
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, France Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD Toulouse France
| | - Jean-Baptiste Decotte
- VigiLIFE 17, rue du Lac Saint-André Savoie Technolac - BP 10366, Le Bourget du Lac, France VigiLIFE 17, rue du Lac Saint-André Savoie Technolac - BP 10366 Le Bourget du Lac France
| | - Tony Dejean
- SPYGEN, 17 rue du Lac Saint-André Savoie Technolac - BP 274, Le Bourget du Lac, France SPYGEN, 17 rue du Lac Saint-André Savoie Technolac - BP 274 Le Bourget du Lac France
| | - Régis Vigouroux
- HYDRECO, Laboratoire Environnement de Petit Saut, B.P 823, F-97388, Kourou, French Guyana HYDRECO, Laboratoire Environnement de Petit Saut, B.P 823, F-97388 Kourou French Guyana
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, France Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD Toulouse France
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20
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Ritter CD, Häggqvist S, Karlsson D, Sääksjärvi IE, Muasya AM, Nilsson RH, Antonelli A. Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding. Genome 2019; 62:147-159. [DOI: 10.1139/gen-2018-0096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.
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Affiliation(s)
- Camila D. Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83 D-45141 Essen, Germany
| | - Sibylle Häggqvist
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 104 05 Stockholm, Sweden
| | - Dave Karlsson
- Station Linné, Skogsby 161, 386 94 Färjestaden, Sweden
| | | | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch 7701, RSA
| | - R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-41319 Göteborg, Sweden
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21
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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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22
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Egeter B, Peixoto S, Brito JC, Jarman S, Puppo P, Velo-Antón G. Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA. Genome 2018; 61:807-814. [DOI: 10.1139/gen-2018-0071] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.
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Affiliation(s)
- Bastian Egeter
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Sara Peixoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - José C. Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, Molecular and Life Sciences, Curtin University, WA, 6102, Australia
- Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, 6009, Australia
| | - Pamela Puppo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
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23
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Bylemans J, Gleeson DM, Hardy CM, Furlan E. Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). Ecol Evol 2018; 8:8697-8712. [PMID: 30271538 PMCID: PMC6157654 DOI: 10.1002/ece3.4387] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/21/2023] Open
Abstract
High-throughput sequencing of environmental DNA (i.e., eDNA metabarcoding) has become an increasingly popular method for monitoring aquatic biodiversity. At present, such analyses require target-specific primers to amplify DNA barcodes from co-occurring species, and this initial amplification can introduce biases. Understanding the performance of different primers is thus recommended prior to undertaking any metabarcoding initiative. While multiple software programs are available to evaluate metabarcoding primers, all programs have their own strengths and weaknesses. Therefore, a robust in silico workflow for the evaluation of metabarcoding primers will benefit from the use of multiple programs. Furthermore, geographic differences in species biodiversity are likely to influence the performance of metabarcoding primers and further complicate the evaluation process. Here, an in silico workflow is presented that can be used to evaluate the performance of metabarcoding primers on an ecoregion scale. This workflow was used to evaluate the performance of published and newly developed eDNA metabarcoding primers for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). To validate the in silico workflow, a subset of the primers, including one newly designed primer pair, were used in metabarcoding analyses of an artificial DNA community and eDNA samples. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers and can reveal important trade-offs that need to be considered when selecting the most suitable primer. Additionally, a new primer pair was described and validated that allows for more robust taxonomic assignments and is less influenced by primer biases compared to commonly used fish metabarcoding primers.
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Affiliation(s)
- Jonas Bylemans
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
- Invasive Animals Cooperative Research CentreUniversity of CanberraCanberraACTAustralia
| | - Dianne M. Gleeson
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
- Invasive Animals Cooperative Research CentreUniversity of CanberraCanberraACTAustralia
| | - Christopher M. Hardy
- Invasive Animals Cooperative Research CentreUniversity of CanberraCanberraACTAustralia
- CSIRO Land and WaterCanberraACTAustralia
| | - Elise Furlan
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
- Invasive Animals Cooperative Research CentreUniversity of CanberraCanberraACTAustralia
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High-throughput sequencing of kDNA amplicons for the analysis of Leishmania minicircles and identification of Neotropical species. Parasitology 2017; 145:585-594. [PMID: 29144208 DOI: 10.1017/s0031182017002013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Leishmania kinetoplast DNA contains thousands of small circular molecules referred to as kinetoplast DNA (kDNA) minicercles. kDNA minicircles are the preferred targets for sensitive Leishmania detection, because they are present in high copy number and contain conserved sequence blocks in which polymerase chain reaction (PCR) primers can be designed. On the other hand, the heterogenic nature of minicircle networks has hampered the use of this peculiar genomic region for strain typing. The characterization of Leishmania minicirculomes used to require isolation and cloning steps prior to sequencing. Here, we show that high-throughput sequencing of single minicircle PCR products allows bypassing these laborious laboratory tasks. The 120 bp long minicircle conserved region was amplified by PCR from 18 Leishmania strains representative of the major species complexes found in the Neotropics. High-throughput sequencing of PCR products enabled recovering significant numbers of distinct minicircle sequences from each strain, reflecting minicircle class diversity. Minicircle sequence analysis revealed patterns that are congruent with current hypothesis of Leishmania relationships. Then, we show that a barcoding-like approach based on minicircle sequence comparisons may allow reliable identifications of Leishmania spp. This work opens up promising perspectives for the study of kDNA minicercles and a variety of applications in Leishmania research.
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25
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Kocher A, de Thoisy B, Catzeflis F, Valière S, Bañuls AL, Murienne J. iDNA screening: Disease vectors as vertebrate samplers. Mol Ecol 2017; 26:6478-6486. [PMID: 28926155 DOI: 10.1111/mec.14362] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/28/2017] [Accepted: 09/12/2017] [Indexed: 01/13/2023]
Abstract
In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology.
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Affiliation(s)
- Arthur Kocher
- CNRS, Université Toulouse III Paul Sabatier, ENFA;, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France.,IRD 224, CNRS 5290, Université de Montpellier, UMR MIVEGEC, Montpellier, France
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana.,Association Kwata, Cayenne, French Guiana
| | - François Catzeflis
- Institut des Sciences de l'Evolution, Case Courrier 064, CNRS UMR-5554, Université Montpellier-2, Montpellier, France
| | - Sophie Valière
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Anne-Laure Bañuls
- IRD 224, CNRS 5290, Université de Montpellier, UMR MIVEGEC, Montpellier, France
| | - Jérôme Murienne
- CNRS, Université Toulouse III Paul Sabatier, ENFA;, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
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