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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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2
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Newton JP, Nevill P, Bateman PW, Campbell MA, Allentoft ME. Spider webs capture environmental DNA from terrestrial vertebrates. iScience 2024; 27:108904. [PMID: 38533454 PMCID: PMC10964257 DOI: 10.1016/j.isci.2024.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 03/28/2024] Open
Abstract
Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.
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Affiliation(s)
- Joshua P. Newton
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Philip W. Bateman
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Matthew A. Campbell
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Morten E. Allentoft
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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3
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Zhang W, Lin L, Ding Y, Zhang F, Zhang J. Comparative Mitogenomics of Jumping Spiders with First Complete Mitochondrial Genomes of Euophryini (Araneae: Salticidae). INSECTS 2023; 14:517. [PMID: 37367333 DOI: 10.3390/insects14060517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
Salticidae is the most species-rich family of spiders with diverse morphology, ecology and behavior. However, the characteristics of the mitogenomes within this group are poorly understood with relatively few well-characterized complete mitochondrial genomes. In this study, we provide completely annotated mitogenomes for Corythalia opima and Parabathippus shelfordi, which represent the first complete mitogenomes of the tribe Euophryini of Salticidae. The features and characteristics of the mitochondrial genomes are elucidated for Salticidae by thoroughly comparing the known well-characterized mitogenomes. The gene rearrangement between trnL2 and trnN was found in two jumping spider species, Corythalia opima and Heliophanus lineiventris Simon, 1868. Additionally, the rearrangement of nad1 to between trnE and trnF found in Asemonea sichuanensis Song & Chai, 1992 is the first protein-coding gene rearrangement in Salticidae, which may have an important phylogenetic implication for the family. Tandem repeats of various copy numbers and lengths were discovered in three jumping spider species. The codon usage analyses showed that the evolution of codon usage bias in salticid mitogenomes was affected by both selection and mutational pressure, but selection may have played a more important role. The phylogenetic analyses provided insight into the taxonomy of Colopsus longipalpis (Żabka, 1985). The data presented in this study will improve our understanding of the evolution of mitochondrial genomes within Salticidae.
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Affiliation(s)
- Wenqiang Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Long Lin
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yuhui Ding
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Feng Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China
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Gregorič M, Kutnjak D, Bačnik K, Gostinčar C, Pecman A, Ravnikar M, Kuntner M. Spider webs as eDNA samplers: biodiversity assessment across the tree of life. Mol Ecol Resour 2022; 22:2534-2545. [PMID: 35510791 DOI: 10.1111/1755-0998.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi, and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.
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Affiliation(s)
- Matjaž Gregorič
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Wine Research Centre, University of Nova Gorica, Vipavska 13, 5000, Nova Gorica, Slovenia
| | - Matjaž Kuntner
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia.,Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington DC, 20560-0105, USA.,Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei, 430062, China
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5
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Xu CCY, Ramsay C, Cowan M, Dehghani M, Lasko P, Barrett RDH. Transgenes of genetically modified animals detected non-invasively via environmental DNA. PLoS One 2021; 16:e0249439. [PMID: 34437552 PMCID: PMC8389434 DOI: 10.1371/journal.pone.0249439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82–234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus ternetzi). With rapidly growing accessibility of genome-editing technologies such as CRISPR, the prevalence and diversity of GM animals will increase dramatically. GM animals have already been released into the wild with more releases planned in the future. eDNA methods have the potential to address the critical need for sensitive, accurate, and cost-effective detection and monitoring of GM animals and their transgenes in nature.
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Affiliation(s)
- Charles C. Y. Xu
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Claire Ramsay
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, Quebec, Canada
| | | | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Rowan D. H. Barrett
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
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6
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Woodell JD, Neiman M, Levri EP. Matching a snail's pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail. Biol Invasions 2021; 23:3263-3274. [PMID: 34093071 PMCID: PMC8166578 DOI: 10.1007/s10530-021-02576-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 05/13/2021] [Indexed: 12/27/2022]
Abstract
Early detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Here, we focus on whether eDNA techniques can be successfully applied to detect new invasions by the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS). It is an opportune time to apply eDNA-based detection in P. antipodarum, which is currently expanding its invasive range across eastern North America. We collected water samples from eight sites in central Pennsylvania that prior evidence indicated were not yet invaded by the NZMS but were part of the same watershed as other previously documented invaded sites. We found evidence for NZMS invasion at five of the eight sites, with subsequent physical confirmation of mud snails at one of these sites. This study is the first example of successful application of eDNA to detect a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.
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Affiliation(s)
- James D. Woodell
- Department of Biology & Department of Gender, Women’s, and Sexuality Studies, University of Iowa, 129 E Jefferson Street, Iowa City, IA 52242 USA
| | - Maurine Neiman
- Department of Biology & Department of Gender, Women’s, and Sexuality Studies, University of Iowa, 129 E Jefferson Street, Iowa City, IA 52242 USA
| | - Edward P. Levri
- Division of Mathematics and Natural Sciences, Penn State - Altoona, 3000 Ivyside Park, Altoona, PA 16601 USA
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7
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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8
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Huerlimann R, Cooper MK, Edmunds RC, Villacorta‐Rath C, Le Port A, Robson HLA, Strugnell JM, Burrows D, Jerry DR. Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists. Anim Conserv 2020. [DOI: 10.1111/acv.12583] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R. Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - M. K. Cooper
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - R. C. Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - C. Villacorta‐Rath
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - A. Le Port
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - H. L. A. Robson
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - J. M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - D. Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - D. R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Tropical Futures Institute James Cook University Singapore Singapore
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9
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Zemanova MA. Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Miriam A. Zemanova
- M. A. Zemanova (https://orcid.org/0000-0002-5002-3388) ✉ , Dept of Philosophy, Univ. of Basel, Steinengraben 5, CH-4051 Basel, Switzerland
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10
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Srivathsan A, Nagarajan N, Meier R. Boosting natural history research via metagenomic clean-up of crowdsourced feces. PLoS Biol 2019; 17:e3000517. [PMID: 31697678 PMCID: PMC6863569 DOI: 10.1371/journal.pbio.3000517] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research—a major source of information on noncharismatic species—is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are “crowdsourced” during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a “metagenomic clean-up” on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace’s favorite collecting sites. Natural history research is in crisis and non-charismatic species are increasingly ignored; this Community Page article argues and demonstrates that shotgun sequencing of serendipitously obtained faecal samples could reverse this trend for 1000 mammal species within 10 years.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
- School of Medicine, National University of Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- * E-mail:
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11
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Lyke MM, Di Fiore A, Fierer N, Madden AA, Lambert JE. Metagenomic analyses reveal previously unrecognized variation in the diets of sympatric Old World monkey species. PLoS One 2019; 14:e0218245. [PMID: 31242204 PMCID: PMC6594596 DOI: 10.1371/journal.pone.0218245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 05/29/2019] [Indexed: 11/18/2022] Open
Abstract
Insectivory, or the consumption of insects and other arthropods, is a significant yet cryptic component of omnivorous primate diets. Here, we used high-throughput DNA sequencing to identify arthropods from fecal DNA and assess variation in insectivory by closely-related sympatric primates. We identified arthropod prey taxa and tested the hypothesis that variation in insectivory facilitates niche differentiation and coexistence among closely-related species with high dietary overlap. We collected 233 fecal samples from redtail (Cercopithecus ascanius; n = 118) and blue monkeys (C. mitis; n = 115) and used a CO1 metabarcoding approach to identify arthropod DNA in each fecal sample. Arthropod DNA was detected in 99% of samples (N = 223 samples), and a total of 68 families (15 orders) were identified. Redtails consumed arthropods from 54 families, of which 12 (21.8%) were absent from blue monkey samples. Blue monkeys consumed arthropods from 56 families, of which 14 (24.6%) were absent from redtail samples. For both species, >97% of taxa present belonged to four orders (Araneae, Diptera, Hymenoptera, Lepidoptera). Redtail samples contained more Lepidoptera taxa (p<0.05), while blue monkey samples contained more Araneae (p<0.05). Blue monkeys consumed a greater diversity of arthropod taxa than redtail monkeys (p<0.05); however, the average number of arthropod families present per fecal sample was greater in the redtail monkey samples (p<0.05). These results indicate that while overlap exists in the arthropod portion of their diets, 20-25% of taxa consumed are unique to each group. Our findings suggest that variation in arthropod intake may help decrease dietary niche overlap and hence facilitate coexistence of closely-related primate species.
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Affiliation(s)
- Martha M. Lyke
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, United States of America
- * E-mail:
| | - Anthony Di Fiore
- Department of Anthropology, University of Texas, Austin, TX, United States of America
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, United States of America
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Joanna E. Lambert
- Department of Environmental Studies, University of Colorado, Boulder, CO, United States of America
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12
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Corse E, Tougard C, Archambaud‐Suard G, Agnèse J, Messu Mandeng FD, Bilong Bilong CF, Duneau D, Zinger L, Chappaz R, Xu CC, Meglécz E, Dubut V. One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies. Ecol Evol 2019; 9:4603-4620. [PMID: 31031930 PMCID: PMC6476781 DOI: 10.1002/ece3.5063] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one-locus-several-primer-sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.
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Affiliation(s)
- Emmanuel Corse
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
- Agence de Recherche pour la Biodiversité à la Réunion (ARBRE)Saint‐Leu, La RéunionFrance
| | | | | | | | - Françoise D. Messu Mandeng
- Laboratory of Parasitology and Ecology, Departement of Animal Biology and PhysiologyUniversity of Yaoundé IYaoundéCameroon
| | - Charles F. Bilong Bilong
- Laboratory of Parasitology and Ecology, Departement of Animal Biology and PhysiologyUniversity of Yaoundé IYaoundéCameroon
| | - David Duneau
- Université Toulouse 3 Paul SabatierCNRS, ENSFEA, EDB (Laboratoire Évolution & Diversité Biologique)ToulouseFrance
| | - Lucie Zinger
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERMPSL Research UniversityParisFrance
| | - Rémi Chappaz
- Irstea, Aix Marseille Univ, RECOVERAix‐en‐ProvenceFrance
| | - Charles C.Y. Xu
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQuebecCanada
| | - Emese Meglécz
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
| | - Vincent Dubut
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
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13
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Thomsen PF, Sigsgaard EE. Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. Ecol Evol 2019; 9:1665-1679. [PMID: 30847063 PMCID: PMC6392377 DOI: 10.1002/ece3.4809] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/05/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022] Open
Abstract
Terrestrial arthropods comprise the most species-rich communities on Earth, and grassland flowers provide resources for hundreds of thousands of arthropod species. Diverse grassland ecosystems worldwide are threatened by various types of environmental change, which has led to decline in arthropod diversity. At the same time, monitoring grassland arthropod diversity is time-consuming and strictly dependent on declining taxonomic expertise. Environmental DNA (eDNA) metabarcoding of complex samples has demonstrated that information on species compositions can be efficiently and non-invasively obtained. Here, we test the potential of wild flowers as a novel source of arthropod eDNA. We performed eDNA metabarcoding of flowers from several different plant species using two sets of generic primers, targeting the mitochondrial genes 16S rRNA and COI. Our results show that terrestrial arthropod species leave traces of DNA on the flowers that they interact with. We obtained eDNA from at least 135 arthropod species in 67 families and 14 orders, together representing diverse ecological groups including pollinators, parasitoids, gall inducers, predators, and phytophagous species. Arthropod communities clustered together according to plant species. Our data also indicate that this experiment was not exhaustive, and that an even higher arthropod richness could be obtained using this eDNA approach. Overall, our results demonstrate that it is possible to obtain information on diverse communities of insects and other terrestrial arthropods from eDNA metabarcoding of wild flowers. This novel source of eDNA represents a vast potential for addressing fundamental research questions in ecology, obtaining data on cryptic and unknown species of plant-associated arthropods, as well as applied research on pest management or conservation of endangered species such as wild pollinators.
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Littlefair JE, Zander A, Sena Costa C, Clare EL. DNA
metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient. Mol Ecol 2018; 28:281-292. [DOI: 10.1111/mec.14832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 07/03/2018] [Accepted: 07/28/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne E. Littlefair
- Department of Biology McGill University Montréal Québec Canada
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Axel Zander
- Department of Biology Unit of Ecology and Evolution University of Fribourg Fribourg Switzerland
| | - Clara Sena Costa
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences Queen Mary University of London London UK
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15
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Zhou Z, Zhang S, Cao Y, Marelli B, Xia X, Tao TH. Engineering the Future of Silk Materials through Advanced Manufacturing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706983. [PMID: 29956397 DOI: 10.1002/adma.201706983] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/19/2018] [Indexed: 05/05/2023]
Abstract
Silk is a natural fiber renowned for its outstanding mechanical properties that have enabled the manufacturing of ultralight and ultrastrong textiles. Recent advances in silk processing and manufacturing have underpinned a re-interpretation of silk from textiles to technological materials. Here, it is argued that silk materials-optimized by selective pressure to work in the environment at the biotic-abiotic interface-can be harnessed by human micro- and nanomanufacturing technology to impart new functionalities and opportunities. A critical overview of recent progress in silk technology is presented with emphasis on high-tech applications enabled by recent innovations in multilevel modifications, multiscale manufacturing, and multimodal characterization of silk materials. These advances have enabled successful demonstrations of silk materials across several disciplines, including tissue engineering, drug delivery, implantable medical devices, and biodissolvable/degradable devices.
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Affiliation(s)
- Zhitao Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
- School of Graduate Study, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaoqing Zhang
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Yunteng Cao
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
| | - Benedetto Marelli
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
| | - Xiaoxia Xia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tiger H Tao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
- School of Graduate Study, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
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16
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Macías-Hernández N, Athey K, Tonzo V, Wangensteen OS, Arnedo M, Harwood JD. Molecular gut content analysis of different spider body parts. PLoS One 2018; 13:e0196589. [PMID: 29847544 PMCID: PMC5976152 DOI: 10.1371/journal.pone.0196589] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
Molecular gut-content analysis has revolutionized the study of food webs and feeding interactions, allowing the detection of prey DNA within the gut of many organisms. However, successful prey detection is a challenging procedure in which many factors affect every step, starting from the DNA extraction process. Spiders are liquid feeders with branched gut diverticula extending into their legs and throughout the prosoma, thus digestion takes places in different parts of the body and simple gut dissection is not possible. In this study, we investigated differences in prey detectability in DNA extracts from different parts of the spider´s body: legs, prosoma and opisthosoma, using prey-specific PCR and metabarcoding approaches. We performed feeding trials with the woodlouse hunter spider Dysdera verneaui Simon, 1883 (Dysderidae) to estimate the time at which prey DNA is detectable within the predator after feeding. Although we found that all parts of the spider body are suitable for gut-content analysis when using prey-specific PCR approach, results based on metabarcoding suggested the opisthosoma is optimal for detection of predation in spiders because it contained the highest concentration of prey DNA for longer post feeding periods. Other spiders may show different results compared to D. verneaui, but given similarities in the physiology and digestion in different families, it is reasonable to assume this to be common across species and this approach having broad utility across spiders.
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Affiliation(s)
- Nuria Macías-Hernández
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Kacie Athey
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Vanina Tonzo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Miquel Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - James D. Harwood
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
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17
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Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 589] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
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Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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18
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Fang WY, Wang ZL, Li C, Yang XQ, Yu XP. The complete mitogenome of a jumping spider Carrhotus xanthogramma (Araneae: Salticidae) and comparative analysis in four salticid mitogenomes. Genetica 2016; 144:699-709. [DOI: 10.1007/s10709-016-9936-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/31/2016] [Indexed: 11/27/2022]
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19
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Littlefair JE, Clare EL. Barcoding the food chain: from Sanger to high-throughput sequencing. Genome 2016; 59:946-958. [DOI: 10.1139/gen-2016-0028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
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Affiliation(s)
- Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
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20
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Krehenwinkel H, Kennedy S, Pekár S, Gillespie RG. A cost‐efficient and simple protocol to enrich prey
DNA
from extractions of predatory arthropods for large‐scale gut content analysis by Illumina sequencing. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12647] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Susan Kennedy
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Stano Pekár
- Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 2 Brno 61137 Czech Republic
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and Management University of California Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
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21
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