1
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Mechai S, Bilodeau G, Lung O, Roy M, Steeves R, Gagne N, Baird D, Lapen DR, Ludwig A, Ogden NH. Mosquito Identification From Bulk Samples Using DNA Metabarcoding: a Protocol to Support Mosquito-Borne Disease Surveillance in Canada. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1686-1700. [PMID: 33822118 DOI: 10.1093/jme/tjab046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Approximately 80 species of mosquitoes (Diptera: Culicidae) have been documented in Canada. Exotic species such as Aedes albopictus (Skuse) (Diptera: Culicidae) are becoming established. Recently occurring endemic mosquito-borne diseases (MBD) in Canada including West-Nile virus (WNV) and Eastern Equine Encephalitis (EEE) are having significant public health impacts. Here we explore the use of DNA metabarcoding to identify mosquitoes from CDC light-trap collections from two locations in eastern Canada. Two primer pairs (BF2-BR2 and F230) were used to amplify regions of the cytochrome c oxidase subunit I (CO1) gene. High throughput sequencing was conducted using an Illumina MiSeq platform and GenBank-based species identification was applied using a QIIME 1.9 bioinformatics pipeline. From a site in southeastern Ontario, Canada, 26 CDC light trap collections of 72 to >300 individual mosquitoes were used to explore the capacity of DNA metabarcoding to identify and quantify captured mosquitoes. The DNA metabarcoding method identified 33 species overall while 24 species were identified by key. Using replicates from each trap, the dried biomass needed to identify the majority of species was determined to be 76 mg (equivalent to approximately 72 mosquitoes), and at least two replicates from the dried biomass would be needed to reliably detect the majority of species in collections of 144-215 mosquitoes and three replicates would be advised for collections with >215 mosquitoes. This study supports the use of DNA metabarcoding as a mosquito surveillance tool in Canada which can help identify the emergence of new mosquito-borne disease potential threats.
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Affiliation(s)
- S Mechai
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Québec, Canada
| | - G Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - O Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - M Roy
- Aquatic Animal Health Section, Fisheries & Oceans Canada, Moncton, New Brunswick, Canada
| | - R Steeves
- Aquatic Animal Health Section, Fisheries & Oceans Canada, Moncton, New Brunswick, Canada
| | - N Gagne
- Aquatic Animal Health Section, Fisheries & Oceans Canada, Moncton, New Brunswick, Canada
| | - D Baird
- Environment and Climate Change Canada, Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - D R Lapen
- Ottawa Research Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - A Ludwig
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Québec, Canada
| | - N H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Québec, Canada
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2
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Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Li J, Zhang D, Su X, Shih C, Sun Y, Wilson JJ, Zhou X, Zhang A. Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10072-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Pedro PM, Amorim J, Rojas MVR, Sá IL, Galardo AKR, Santos Neto NF, Pires de Carvalho D, Nabas Ribeiro KA, Razzolini MTP, Sallum MAM. Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers. PeerJ 2020; 8:e9057. [PMID: 32607275 PMCID: PMC7315618 DOI: 10.7717/peerj.9057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/03/2020] [Indexed: 11/24/2022] Open
Abstract
A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.
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Affiliation(s)
- Pedro M Pedro
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil.,Biomonitoring and Sustainability, IPE-Institute for Ecological Research, Nazaré Paulista, SP, Brazil
| | - Jandui Amorim
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Martha V R Rojas
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ivy Luizi Sá
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Allan Kardec Ribeiro Galardo
- IEPA-Instituto de Pesquisas Cientificas e Tecnológicas do Estado do Amapá, Macapá, AP, Brazil.,FUNDUNESP-Fundação para o Desenvolvimento da UNESP, São Paulo, SP, Brazil
| | - Noel Fernandes Santos Neto
- IEPA-Instituto de Pesquisas Cientificas e Tecnológicas do Estado do Amapá, Macapá, AP, Brazil.,FUNDUNESP-Fundação para o Desenvolvimento da UNESP, São Paulo, SP, Brazil
| | | | | | - Maria Tereza Pepe Razzolini
- Departamento de Saúde Ambiental, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
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4
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Kelly RP, Shelton AO, Gallego R. Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies. Sci Rep 2019; 9:12133. [PMID: 31431641 PMCID: PMC6702206 DOI: 10.1038/s41598-019-48546-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/05/2019] [Indexed: 11/08/2022] Open
Abstract
As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species' true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.
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Affiliation(s)
- Ryan P Kelly
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA.
| | - Andrew Olaf Shelton
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, Washington, USA
| | - Ramón Gallego
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, Washington, USA
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5
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Matesanz S, Pescador DS, Pías B, Sánchez AM, Chacón‐Labella J, Illuminati A, Cruz M, López‐Angulo J, Marí‐Mena N, Vizcaíno A, Escudero A. Estimating belowground plant abundance with DNA metabarcoding. Mol Ecol Resour 2019; 19:1265-1277. [DOI: 10.1111/1755-0998.13049] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 06/01/2019] [Accepted: 06/12/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Silvia Matesanz
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - David S. Pescador
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Beatriz Pías
- Departamento de Biodiversidad Ecología y Evolución Universidad Complutense de Madrid Madrid Spain
| | - Ana M. Sánchez
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Julia Chacón‐Labella
- Departamento de Medio Ambiente Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain
| | - Angela Illuminati
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Marcelino Cruz
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Jesús López‐Angulo
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | | | | | - Adrián Escudero
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
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6
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Doña J, Serrano D, Mironov S, Montesinos-Navarro A, Jovani R. Unexpected bird-feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario. Mol Ecol 2019; 28:379-390. [PMID: 30536745 DOI: 10.1111/mec.14968] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/16/2018] [Indexed: 12/24/2022]
Abstract
The high relevance of host-switching for the diversification of highly host-specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host-switching dynamics at an ecological scale. Here, we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird-feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird-mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host-specific symbionts. Thus, host-switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - David Serrano
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Sergey Mironov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Embankment 1, Saint Petersburg, Russia
| | - Alicia Montesinos-Navarro
- Centro de Investigaciones sobre Desertificación (CSIC-UV-GV), Carretera Moncada-Náquera, Valencia, Spain
| | - Roger Jovani
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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7
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Lee CK, Glare TR. Biases in the metabarcoding of plant pathogens using rust fungi as a model system. Microbiologyopen 2018; 8:e00780. [PMID: 30585441 PMCID: PMC6612544 DOI: 10.1002/mbo3.780] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species.
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Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRAUniversité Bourgogne, Université Bourgogne Franche‐ComtéDijonFrance,Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyNew Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Charles K. Lee
- Waikato DNA Sequencing Facility, School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Travis R. Glare
- Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
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8
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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9
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Vizcaíno A, Doña J, Vierna J, Marí-Mena N, Esteban R, Mironov S, Urien C, Serrano D, Jovani R. Enabling large-scale feather mite studies: an Illumina DNA metabarcoding pipeline. EXPERIMENTAL & APPLIED ACAROLOGY 2018; 76:81-97. [PMID: 30178174 DOI: 10.1007/s10493-018-0288-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
Feather mites are among the most common and diverse ectosymbionts of birds, yet basic questions such as the nature of their relationship remain largely unanswered. One reason for feather mites being understudied is that their morphological identification is often virtually impossible when using female or young individuals. Even for adult male specimens this task is tedious and requires advanced taxonomic expertise, thus hampering large-scale studies. In addition, molecular-based methods are challenging because the low DNA amounts usually obtained from these tiny mites do not reach the levels required for high-throughput sequencing. This work aims to overcome these issues by using a DNA metabarcoding approach to accurately identify and quantify the feather mite species present in a sample. DNA metabarcoding is a widely used molecular technique that takes advantage of high-throughput sequencing methodologies to assign the taxonomic identity to all the organisms present in a complex sample (i.e., a sample made up of multiple specimens that are hard or impossible to individualise). We present a high-throughput method for feather mite identification using a fragment of the COI gene as marker and Illumina Miseq technology. We tested this method by performing two experiments plus a field test over a total of 11,861 individual mites (5360 of which were also morphologically identified). In the first experiment, we tested the probability of detecting a single feather mite in a heterogeneous pool of non-conspecific individuals. In the second experiment, we made 2 × 2 combinations of species and studied the relationship between the proportion of individuals of a given species in a sample and the proportion of sequences retrieved to test whether DNA metabarcoding can reliably quantify the relative abundance of mites in a sample. Here we also tested the efficacy of degenerate primers (i.e., a mixture of similar primers that differ in one or several bases that are designed to increase the chance of annealing) and investigated the relationship between the number of mismatches and PCR success. Finally, we applied our DNA metabarcoding pipeline to a total of 6501 unidentified and unsorted feather mite individuals sampled from 380 European passerine birds belonging to 10 bird species (field test). Our results show that this proposed pipeline is suitable for correct identification and quantitative estimation of the relative abundance of feather mite species in complex samples, especially when dealing with a moderate number (> 30) of individuals per sample.
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Affiliation(s)
- Antón Vizcaíno
- AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain
| | - Jorge Doña
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n, 41092, Seville, Spain
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816S. Oak St., Champaign, IL, 61820, USA
| | - Joaquín Vierna
- AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain
| | - Neus Marí-Mena
- AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain
| | - Rocío Esteban
- AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain
| | - Sergey Mironov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Embankment 1, Saint Petersburg, Russia
| | - Charlotte Urien
- AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain
| | - David Serrano
- Department of Conservation Biology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n, 41092, Seville, Spain
| | - Roger Jovani
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n, 41092, Seville, Spain.
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10
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Balasingham KD, Walter RP, Mandrak NE, Heath DD. Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries. Mol Ecol 2017; 27:112-127. [PMID: 29087006 DOI: 10.1111/mec.14395] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 10/03/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023]
Abstract
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom-designed group-specific primer set and next-generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.
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Affiliation(s)
- Katherine D Balasingham
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryan P Walter
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.,Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | - Nicholas E Mandrak
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Daniel D Heath
- Department of Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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11
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Kappel K, Haase I, Käppel C, Sotelo CG, Schröder U. Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments. Food Chem 2017; 234:212-219. [DOI: 10.1016/j.foodchem.2017.04.178] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
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12
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Vierna J, Doña J, Vizcaíno A, Serrano D, Jovani R. PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results. Genome 2017; 60:868-873. [PMID: 28753409 DOI: 10.1139/gen-2017-0081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform. Libraries were prepared with 40, 45, 50, 55, and 60 PCR cycles from four individuals belonging to four species of four genera of cephalopods. We found no relationship between the number of PCR cycles and the number of mutations despite using a nonproofreading polymerase. Moreover, even when using a high number of PCR cycles, the resulting number of mutations was low enough not to be an issue in the context of high-throughput DNA barcoding (but may still remain an issue in DNA metabarcoding due to chimera formation). We conclude that the common practice of increasing the number of PCR cycles should not negatively impact the outcome of a high-throughput DNA barcoding study in terms of the occurrence of point mutations.
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Affiliation(s)
- J Vierna
- a AllGenetics & Biology SL. Edificio CICA, Campus de Elviña s/n. E-15008 A Coruña, Spain
| | - J Doña
- b Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n. E-41092 Sevilla, Spain
| | - A Vizcaíno
- a AllGenetics & Biology SL. Edificio CICA, Campus de Elviña s/n. E-15008 A Coruña, Spain
| | - D Serrano
- c Department of Conservation Biology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n. E-41092 Sevilla, Spain
| | - R Jovani
- b Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio s/n. E-41092 Sevilla, Spain
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13
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Wilkinson MJ, Szabo C, Ford CS, Yarom Y, Croxford AE, Camp A, Gooding P. Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants. Sci Rep 2017; 7:46040. [PMID: 28401958 PMCID: PMC5388885 DOI: 10.1038/srep46040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/08/2017] [Indexed: 01/08/2023] Open
Abstract
We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that 'false' species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.
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Affiliation(s)
- Mike J. Wilkinson
- Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK
| | - Claudia Szabo
- School of Computer Science, The University of Adelaide, SA 5005, Australia
| | - Caroline S. Ford
- Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK
| | - Yuval Yarom
- School of Computer Science, The University of Adelaide, SA 5005, Australia
| | - Adam E. Croxford
- School of Agriculture, Food and Wine, Waite Campus, The University of Adelaide, SA 5064, Australia
| | - Amanda Camp
- School of Animal & Veterinary Sciences, Roseworthy Campus, The University of Adelaide, SA 5371, Australia
| | - Paul Gooding
- Australian Genome Research Facility, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
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14
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Saitoh S, Aoyama H, Fujii S, Sunagawa H, Nagahama H, Akutsu M, Shinzato N, Kaneko N, Nakamori T. A quantitative protocol for DNA metabarcoding of springtails (Collembola). Genome 2017; 59:705-23. [PMID: 27611697 DOI: 10.1139/gen-2015-0228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.
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Affiliation(s)
- Seikoh Saitoh
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Hiroaki Aoyama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Saori Fujii
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Haruki Sunagawa
- c Okinawa Prefectural Agricultural Research Center, 820 Makabe, Itoman 901-0336, Japan
| | - Hideki Nagahama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Masako Akutsu
- d Department of Electrical Engineering and Computer Science, School of Industrial and Welfare Engineering, Tokai University, Toroku 9-1-1, Higashi-ku, Kumamoto 862-8652, Japan
| | - Naoya Shinzato
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Nobuhiro Kaneko
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Taizo Nakamori
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
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15
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da Silva JM, Willows-Munro S. A review of over a decade of DNA barcoding in South Africa: a faunal perspective. AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1151377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Doña J, Moreno-García M, Criscione CD, Serrano D, Jovani R. Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system. Ecol Evol 2016; 5:5801-9. [PMID: 26811755 PMCID: PMC4717341 DOI: 10.1002/ece3.1842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/15/2023] Open
Abstract
Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host‐symbiont systems. Here, we studied mtDNA variation in a host‐symbiont non‐model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star‐like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avda. Americo Vespucio s/n Sevilla Spain
| | - Marina Moreno-García
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avda. Americo Vespucio s/n Sevilla Spain
| | - Charles D Criscione
- Department of Biology Texas A&M University 3258 TAMU College Station Texas 77843
| | - David Serrano
- Department of Conservation Biology Estación Biológica de Doñana (CSIC) Avda Americo Vespucio s/n Sevilla Spain
| | - Roger Jovani
- Department of Evolutionary Ecology Estación Biológica de Doñana (CSIC) Avda. Americo Vespucio s/n Sevilla Spain
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