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Girard EB, Didaskalou EA, Pratama AMA, Rattner C, Morard R, Renema W. Quantitative assessment of reef foraminifera community from metabarcoding data. Mol Ecol Resour 2024:e14000. [PMID: 39041197 DOI: 10.1111/1755-0998.14000] [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: 12/08/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
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Affiliation(s)
- Elsa B Girard
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Andi M A Pratama
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia
| | | | | | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
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2
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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 PMCID: PMC11265005 DOI: 10.1186/s13071-024-06388-1] [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: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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3
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Cabodevilla X, Ortiz-Santaliestra ME, Fernández-Tizón M, Zurdo J, Madeira MJ, Giralt D, Sardà-Palomera F, Fernández-Benéitez MJ, Mougeot F. Dietary DNA metabarcoding reveals a trophic niche partitioning among sympatric Iberian sandgrouses and bustards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172989. [PMID: 38714259 DOI: 10.1016/j.scitotenv.2024.172989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
The study of trophic niche partitioning is of great importance for understanding community structure and species coexistence, particularly if these are threatened. Here DNA metabarcoding was used to assess the diet of four threatened steppe bird species (two bustards and two sandgrouses), with the aim of better understanding their dietary requirements, trophic interactions, and potential threats. The results showed seasonal and interspecific differences in their plant diet, with greater importance of cultivated plants during autumn and winter (around 50 % of their diet) than spring. Plants of the genus Convolvulus and of the family Brassicaceae were frequently consumed by all species. In spring, poppies (Papaver spp.) were a considerable part of their diet, and could be used as a source of carotenoids or for their anti-parasitic properties. Furthermore, results evidenced a trophic niche partitioning among species, with a marked segregation between bustard species and, to a lesser extent, between sandgrouse species. Diet similarity was generally higher between species from different orders that occur in mixed-species flocks (bustard - sandgrouse) than between species of the same order. This partitioning was probably related to a stratification in habitat use rather than to specialisation and might prevent competition to some extent. However, the homogenization of trophic resources resulting from agricultural intensification could pose an important threat, particularly during autumn, when weeds are scarcer and the most abundant trophic resource are sown seeds, which are often treated with pesticides.
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Affiliation(s)
- Xabier Cabodevilla
- Conservation Biology Group, Landscape Dynamics and Biodiversity Program, Forest Science and Technology Centre of Catalonia (CTFC), Solsona, Spain; Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain.
| | - Manuel E Ortiz-Santaliestra
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Mario Fernández-Tizón
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Julia Zurdo
- Terrestrial Ecology Group (TEG-UAM), Department of Ecology, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Madrid, Spain
| | - María J Madeira
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Alava, Spain
| | - David Giralt
- Conservation Biology Group, Landscape Dynamics and Biodiversity Program, Forest Science and Technology Centre of Catalonia (CTFC), Solsona, Spain
| | - Francesc Sardà-Palomera
- Conservation Biology Group, Landscape Dynamics and Biodiversity Program, Forest Science and Technology Centre of Catalonia (CTFC), Solsona, Spain
| | - María J Fernández-Benéitez
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain
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4
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [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: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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5
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Owens LA, Thurber MI, Goldberg TL. CRISPR-Cas9-mediated host signal reduction for 18S metabarcoding of host-associated eukaryotes. Mol Ecol Resour 2024:e13980. [PMID: 38804043 DOI: 10.1111/1755-0998.13980] [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: 12/09/2023] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Metabarcoding-based methods for identification of host-associated eukaryotes have the potential to revolutionize parasitology and microbial ecology, yet significant technical challenges remain. In particular, highly abundant host reads can mask the presence of less-abundant target organisms, especially for sample types rich in host DNA (e.g., blood and tissues). Here, we present a new CRISPR-Cas9-mediated approach designed to reduce host signal by selective amplicon digestion, thus enriching clinical samples for eukaryotic endosymbiont sequences during metabarcoding. Our method achieves a nearly 76% increased efficiency in host signal reduction compared with no treatment and a nearly 60% increased efficiency in host signal reduction compared with the most commonly used published method. Furthermore, the application of our method to clinical samples allows for the detection of parasite infections that would otherwise have been missed.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Flo S, Vader A, Præbel K. Brute force prey metabarcoding to explore the diets of small invertebrates. Ecol Evol 2024; 14:e11369. [PMID: 38711484 PMCID: PMC11070772 DOI: 10.1002/ece3.11369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator-prey studies of small-sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole-body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. After processing and curating raw data from two sequencing runs of varying depths (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15,900 and ~120,000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations, and copepod species, greater sequencing depth led to better separation of clusters. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that is impractical to dissect or unknown to science.
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Affiliation(s)
- Snorre Flo
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
- Faculty of Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
| | - Anna Vader
- Department of Arctic BiologyThe University Centre in SvalbardLongyearbyen, SvalbardNorway
| | - Kim Præbel
- The Norwegian College of Fishery Science (NFH)UiT The Arctic University of NorwayTromsøNorway
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesElverumNorway
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7
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Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [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: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
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Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
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8
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Mas-Carrió E, Churski M, Kuijper D, Fumagalli L. Niche overlap across landscape variability in summer between two large herbivores using eDNA metabarcoding. PLoS One 2024; 19:e0279672. [PMID: 38349911 PMCID: PMC10863879 DOI: 10.1371/journal.pone.0279672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
Understanding the relationship between a species feeding strategy and its environment (trophic ecology) is critical to assess environmental requirements and improve management policies. However, measuring trophic interactions remains challenging. Among the available methods, quantifying the plant composition of a species' diet indicates how species use their environment and their associated niche overlap. Nevertheless, most studies focusing on herbivore trophic ecology ignore the influence that landscape variability may have. Here, we explored how landscape variability influences diet composition through niche overlap. We used eDNA metabarcoding to quantify the diet composition of two large herbivores of the Bialowieza Forest, red deer (Cervus elaphus) and European bison (Bison bonasus) to investigate how increasing habitat quality (i.e. higher abundance of deciduous forage species) and predation risk (i.e. density of wolf in the area) influence their diet composition and niche partitioning. Our findings indicate diet composition is non-homogeneous across the landscape, both within and between species. Red deer showed greater diet variability and lower niche overlap within species compared to bison. We detected a reduction of niche overlap for red deer with increasing predation risk, leading to more dissimilar diets, suggesting their feeding behaviour is affected by wolf presence. This correlation was not found for bison, which are rarely predated by wolf. Higher habitat quality was associated with higher niche overlap only within bison, probably due to their suboptimal feeding strategy as browsers. These results show the importance of integrating environment-induced diet variation in studies aimed at determining the landscape usage or niche overlap of a species.
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Affiliation(s)
- Eduard Mas-Carrió
- Department of Ecology and Evolution, Laboratory for Conservation Biology, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Marcin Churski
- Mammal Research institute, Polish Academy of Sciences, Białowieża, Poland
| | - Dries Kuijper
- Mammal Research institute, Polish Academy of Sciences, Białowieża, Poland
| | - Luca Fumagalli
- Department of Ecology and Evolution, Laboratory for Conservation Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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9
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Velarde-Garcéz DA, Mata VA, Beja P, da Silva LP. DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler. Mol Ecol 2024; 33:e17245. [PMID: 38124452 DOI: 10.1111/mec.17245] [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: 06/12/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.
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Affiliation(s)
- Daniel A Velarde-Garcéz
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Luis P da Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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10
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Owens LA, Friant S, Martorelli Di Genova B, Knoll LJ, Contreras M, Noya-Alarcon O, Dominguez-Bello MG, Goldberg TL. VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages. Nat Commun 2024; 15:402. [PMID: 38195557 PMCID: PMC10776621 DOI: 10.1038/s41467-023-44521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sagan Friant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, VT, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Centro Amazónico de Investigación y Control de Enfermedades Tropicales-CAICET, Puerto Ayacucho, Amazonas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University-New Brunswick, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
- Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
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Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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12
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Lue CH, Abram PK, Hrcek J, Buffington ML, Staniczenko PPA. Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research. Mol Ecol 2023; 32:6461-6473. [PMID: 36040418 DOI: 10.1111/mec.16677] [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: 03/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio-economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.
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Affiliation(s)
- Chia-Hua Lue
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
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13
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Aihartza J, Vallejo N, Aldasoro M, García-Mudarra JL, Goiti U, Nogueras J, Ibáñez C. Aerospace-foraging bats eat seasonably across varying habitats. Sci Rep 2023; 13:19576. [PMID: 37950015 PMCID: PMC10638376 DOI: 10.1038/s41598-023-46939-7] [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: 05/23/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Recent research has confirmed the efficiency of insectivorous bats as pest suppressors, underlining the ecological services they offer in agroecosystems. Therefore, some efforts try to enhance bat foraging in agricultural landscapes by acting upon environmental factors favouring them. In this study, we monitored a Miniopterus schreibersii colony, in the southern Iberian Peninsula. We intensively sampled their faeces and analysed them by metabarcoding to describe how the bent-winged bat diet would change with time, and to test whether their most-consumed prey would seasonally depend on different landscapes or habitats. Our results confirm that M. schreibersii are selective opportunist predators of moths, dipterans, mayflies, and other fluttering insects, shifting their diet to temporary peaks of prey availability in their foraging range, including both pest and non-pest insects. Supporting our hypothesis, throughout the year, M. schreibersii consume insects linked to diverse open habitats, including wetlands, grassland, diverse croplands, and woodland. The importance of each prey habitat varies seasonally, depending on their insect phenology, making bats indirectly dependent on a diverse landscape as their primary prey source. Bats' predation upon pest insects is quantitatively high, consuming around 1610 kg in 5 months, of which 1467 kg correspond to ten species. So, their suppression effect may be relevant, mainly in patchy heterogeneous landscapes, where bats' foraging may concentrate in successive outbursts of pests, affecting different crops or woodlands. Our results stress that to take advantage of the ecosystem services of bats or other generalist insectivores, keeping the environmental conditions they require to thrive, particularly a heterogeneous landscape within the colony's foraging area, is crucial.
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Affiliation(s)
- Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain.
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | - Miren Aldasoro
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | | | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | - Jesus Nogueras
- Estación Biológica de Doñana (CSIC), P.O. Box 1056, 41080, Sevilla, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), P.O. Box 1056, 41080, Sevilla, Spain
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14
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Fernández-Vizcaíno E, Mougeot F, Cabodevilla X, Fernández-Tizón M, Mateo R, Madeira MJ, Ortiz-Santaliestra ME. Diet and Spatial Ecology Influence Red-Legged Partridge Exposure to Pesticides Used as Seed Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:14861-14870. [PMID: 37747849 PMCID: PMC10569034 DOI: 10.1021/acs.est.3c03905] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Seed treatment with pesticides is an extended agricultural practice with a high risk to granivorous birds that consume those seeds. To characterize that risk, it is necessary to understand the ecological factors that determine the exposure chances of birds to treated seeds. We investigated how pesticide uptake by red-legged partridges was related to cultivated plant ingestion and to the use of recently sown fields. We analyzed pesticide residues in 144 fecal samples from 32 flocks and determined the plant diet composition using DNA metabarcoding. Habitat use was studied through the monitoring of 15 GPS-tagged partridges. We confirmed, through the analysis of seeds, that >80% of cereal fields from the area had seeds treated with triazole fungicides. Tebuconazole was detected in 16.6% of partridges' feces. During the sowing season, cultivated plants accounted for half of the plant diet, but no association was found between cultivated plant consumption and pesticide intake. GPS tracking revealed that tebuconazole was detected in feces when partridges had recently used sown fields, whereas nonexposed partridges showed no overlap with recently sown areas. Our results highlight the need to incorporate field ecology into the characterization of pesticide exposure to improve the efficacy of environmental risk assessment.
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Affiliation(s)
- Elena Fernández-Vizcaíno
- Instituto
de Investigación en Recursos Cinegéticos (IREC) CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13005, Spain
| | - François Mougeot
- Instituto
de Investigación en Recursos Cinegéticos (IREC) CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13005, Spain
| | - Xabier Cabodevilla
- Conservation
Biology Group, Landscape Dynamics and Biodiversity Program, Forest Science and Technology Centre of Catalonia
(CTFC), km 2, Solsona 25280, Spain
- Terrestrial
Ecology Group (TEG-UAM), Department of Ecology, Universidad Autónoma de Madrid, Calle Darwin 2, Madrid 28049, Spain
| | - Mario Fernández-Tizón
- Instituto
de Investigación en Recursos Cinegéticos (IREC) CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13005, Spain
| | - Rafael Mateo
- Instituto
de Investigación en Recursos Cinegéticos (IREC) CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13005, Spain
| | - María J. Madeira
- Department
of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Alava, Spain
| | - Manuel E. Ortiz-Santaliestra
- Instituto
de Investigación en Recursos Cinegéticos (IREC) CSIC-UCLM-JCCM, Ronda de Toledo 12, Ciudad Real 13005, Spain
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15
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Westerduin C, Suokas M, Petäjä T, Saarela U, Vainio S, Mutanen M. Exploring and validating observations of non-local species in eDNA samples. Ecol Evol 2023; 13:e10612. [PMID: 37841221 PMCID: PMC10576249 DOI: 10.1002/ece3.10612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
The development of DNA-based methods in recent decades has opened the door to numerous new lines of research in the biological sciences. While the speed and accuracy of DNA methodologies are clearly beneficial, the sensitivity of these methods has the adverse effect of increased susceptibility to false positives resulting from contamination in field or lab. Here, we present findings from a metabarcoding study on the diet of and food availability for five insectivorous birds, in which multiple lepidopteran species not known to occur locally were discovered. After describing the pattern of occurrences of these non-local species in the samples, we discuss various potential origins of these sequences. First, we assessed that the taxonomic assignments appeared reliable, and local occurrences of many of the species could be plausibly ruled out. Then, we looked into the possibilities of natural environmental contamination, judging it to be unlikely, albeit impossible to fully falsify. Finally, while dissimilar combinations of non-local species' occurrences across the samples did not initially suggest lab contamination, we found overlap with taxa and sequences handled in the same lab, which was undoubtedly not coincidental. Even so, not all exact sequences were accounted for in these locally conducted studies, nor was it clear if these and other sequences could remain detectable years later. Although the full explanation for the observations of non-local species remains inconclusive, these findings highlight the importance of critical examination of metabarcoding results, and showcase how species-level taxonomic assignments utilizing comprehensive reference libraries may be a tool in detecting potential contamination events, and false positives in general.
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Affiliation(s)
- Coen Westerduin
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
| | - Marko Suokas
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
| | - Tuukka Petäjä
- Department of Physics, Institute for Atmospheric and Earth System Research (INAR)University of HelsinkiHelsinkiFinland
| | - Ulla Saarela
- CRC, The Faculty of MedicineUniversity of OuluOuluFinland
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Seppo Vainio
- Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, Faculty of ScienceUniversity of OuluOuluFinland
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16
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Bilbao J, Pavloudi C, Blanco-Rayón E, Franco J, Madariaga I, Seoane S. Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106175. [PMID: 37717336 DOI: 10.1016/j.marenvres.2023.106175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
Phytoplankton monitoring is essential for the global understanding of aquatic ecosystems. The present research studies the phytoplankton community of the Urdaibai estuary, combining microscopy and eDNA metabarcoding for the first time in the area. The main aims were to describe the phytoplankton community composition in relation to the environmental conditions of the estuary, and to compare the two methods used. Diatoms Minutocellus polymorphus and Chaetoceros tenuissimus dominated the outer estuary, being replaced by Teleaulax acuta (cryptophyte), Kryptoperidinium foliaceum (dinoflagellate) and Cyclotella spp. (diatom) towards the inner area. This change was mainly prompted by salinity and nutrients. Metabarcoding revealed the presence of 223 species that were not observed by microscopy in previous studies in the estuary. However, several characteristic species (e.g., K. foliaceum) were only detected with microscopy. Additionally, microscopy covered the limitations of eDNA metabarcoding concerning quantification. Thus, to give a full insight, a combination of techniques is recommended.
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Affiliation(s)
- Jone Bilbao
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain.
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology, Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece; Department of Biological Sciences, The George Washington University, District of Columbia, USA
| | - Esther Blanco-Rayón
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
| | | | - Iosu Madariaga
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sergio Seoane
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
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17
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McColl-Gausden EF, Weeks AR, Coleman R, Song S, Tingley R. Using hierarchical models to compare the sensitivity of metabarcoding and qPCR for eDNA detection. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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18
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Drake LE, Cuff JP, Bedmar S, McDonald R, Symondson WOC, Chadwick EA. Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters ( Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains. Ecol Evol 2023; 13:e10038. [PMID: 37181211 PMCID: PMC10170393 DOI: 10.1002/ece3.10038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.
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Affiliation(s)
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- School of Natural and Environmental SciencesNewcastle UniversityNewcastleUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | - Sergio Bedmar
- School of BiosciencesCardiff UniversityCardiffUK
- Department of Conservation BiologyDoñana Biological Station (EBD‐CSIC)SevillaSpain
| | - Robbie McDonald
- Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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19
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Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Symondson WOC, Orozco-terWengel P. Herbivorous dietary selection shown by hawfinch ( Coccothraustes coccothraustes) within mixed woodland habitats. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230156. [PMID: 37181798 PMCID: PMC10170347 DOI: 10.1098/rsos.230156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.
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Affiliation(s)
- Ewan H. Stenhouse
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Will Kirby
- RSPB Centre for Conservation Science, The Lodge, Sandy SG19 2DL, UK
| | - Ian P. Vaughan
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
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20
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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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21
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Iwaszkiewicz-Eggebrecht E, Granqvist E, Buczek M, Prus M, Kudlicka J, Roslin T, Tack AJ, Andersson AF, Miraldo A, Ronquist F, Łukasik P. Optimizing insect metabarcoding using replicated mock communities. Methods Ecol Evol 2023; 14:1130-1146. [PMID: 37876735 PMCID: PMC10593422 DOI: 10.1111/2041-210x.14073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/20/2023] [Indexed: 10/26/2023]
Abstract
1: Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. 2: Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? 3: We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. 4: We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
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Affiliation(s)
| | - Emma Granqvist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Monika Prus
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jan Kudlicka
- Department of Data Science and Analytics, BI Norwegian Business School, NO-0442 Oslo, Norway
| | - Tomas Roslin
- Department of Ecology; Box 7044, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Ayco J.M. Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Andreia Miraldo
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Piotr Łukasik
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
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22
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Paula DP, Andow DA. DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents. NEOTROPICAL ENTOMOLOGY 2023; 52:302-332. [PMID: 36478343 DOI: 10.1007/s13744-022-01011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.
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23
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Li M, Lei T, Wang G, Zhang D, Liu H, Zhang Z. Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China. Ecol Evol 2023; 13:e10031. [PMID: 37091562 PMCID: PMC10121320 DOI: 10.1002/ece3.10031] [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: 07/26/2022] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/25/2023] Open
Abstract
Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.
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Affiliation(s)
- Min Li
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Ting Lei
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Guobin Wang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Danli Zhang
- College of Biological Science and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Huaxi Liu
- Department of Life SciencesNatural History MuseumLondonUK
| | - Zhiwei Zhang
- College of Forestry, Shanxi Agricultural UniversityJinzhongChina
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24
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Schneider J, Brun L, Taberlet P, Fumagalli L, van de Waal E. Molecular assessment of dietary variation in neighbouring primate groups. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project, Mawana Game Reserve Swart Mfolozi South Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes, CNRS Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva Lausanne University Hospital and University of Lausanne Lausanne Switzerland
| | - Erica van de Waal
- Inkawu Vervet Project, Mawana Game Reserve Swart Mfolozi South Africa
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
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25
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Molecular Identification of Asian Hornet Vespa velutina nigrithorax Prey from Larval Gut Contents: A Promising Method to Study the Diet of an Invasive Pest. Animals (Basel) 2023; 13:ani13030511. [PMID: 36766400 PMCID: PMC9913685 DOI: 10.3390/ani13030511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The Asian hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), is an invasive hornet that was accidentally introduced into Europe in 2004. It mainly preys on other invertebrates and arthropod species, and often targets honey bee (Apis mellifera) colonies. The introduction of these hornets may damage indigenous fauna and apiculture. Knowledge of V. velutina prey preference and the species composition of their diet is relatively limited. In this study, we assessed methodologies for the molecular identification of prey using dissected larvae from destroyed nests. Ten larval samples were taken from five nests in areas where the hornets had not yet established: two from the Channel Islands and three in the mainland UK. DNA was extracted from the gut contents and sequenced and analysed by metabarcoding with Oxford Nanopore Technologies' Flongle and MinION devices. Numerous taxa were detected in each larval sample with the species composition varying by individual and by nest. Between 15 and 26 species were found per nest, with wasps (Vespula spp.), spiders, honey bees and blow flies being the most abundant taxa. These results demonstrate that metabarcoding larval gut contents can be used to study the Asian hornet diet and give a first snapshot of the prey items captured by V. v. nigrithorax in the UK. This method could be used for future large-scale testing of the gut contents of hornet nests, in order to provide a greater insight into the foraging behaviour of this predator across Europe and elsewhere.
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26
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Pont D, Meulenbroek P, Bammer V, Dejean T, Erős T, Jean P, Lenhardt M, Nagel C, Pekarik L, Schabuss M, Stoeckle BC, Stoica E, Zornig H, Weigand A, Valentini A. Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR. Mol Ecol Resour 2023; 23:396-409. [PMID: 36151931 DOI: 10.1111/1755-0998.13715] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/21/2022] [Accepted: 09/15/2022] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.
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Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Meulenbroek
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
- WasserCluster Lunz -Biologische Station GmbH, Lunz am See, Austria
| | - Vincenz Bammer
- Bundesamt für Wasserwirtschaft, Institut für Gewässerökologie und Fischereiwirtschaft, Abteilung Gewässerökologie, Mondsee, Austria
| | | | - Tibor Erős
- Balaton Limnological Research Institute, Eötvös Lor'and Research Network (ELKH), Tihany, Hungary
| | | | - Mirjana Lenhardt
- Institute for Multidisciplinary Research, Institute for Biological Research "Siniša Stanković," National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Christoffer Nagel
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Ladislav Pekarik
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Bernhard C Stoeckle
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa,", Constanţa, Romania
| | - Horst Zornig
- PRO FISCH OG Ecological Consultants, Vienna, Austria
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27
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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28
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Tercel MPTG, Cuff JP. The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022). Mol Ecol 2022; 31:5653-5659. [PMID: 35778947 DOI: 10.1111/mec.16576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023]
Abstract
In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.
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Affiliation(s)
- Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Trinity, Jersey, Channel Islands
| | - Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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29
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Hoenig BD, Trevelline BK, Kautz A, Latta SC, Porter BA. Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird. Mol Ecol 2022; 31:5635-5648. [PMID: 36089910 DOI: 10.1111/mec.16688] [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: 12/29/2021] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022]
Abstract
While an increasing number of studies are adopting molecular and chemical methods for dietary characterization, these studies often employ only one of these laboratory-based techniques; this approach may yield an incomplete, or even biased, understanding of diet due to each method's inherent limitations. To explore the utility of coupling molecular and chemical techniques for dietary characterizations, we applied DNA metabarcoding alongside stable isotope analysis to characterize the dietary niche of breeding Louisiana waterthrush (Parkesia motacilla), a migratory songbird hypothesized to preferentially provision its offspring with pollution-intolerant, aquatic arthropod prey. While DNA metabarcoding was unable to determine if waterthrush provision aquatic and terrestrial prey in different abundances, we found that specific aquatic taxa were more likely to be detected in successive seasons than their terrestrial counterparts, thus supporting the aquatic specialization hypothesis. Our isotopic analysis added greater context to this hypothesis by concluding that breeding waterthrush provisioned Ephemeroptera and Plecoptera, two pollution-intolerant, aquatic orders, in higher quantities than other prey groups, and expanded their functional trophic niche when such prey were not abundantly provisioned. Finally, we found that the dietary characterizations from each approach were often uncorrelated, indicating that the results gleaned from a diet study can be particularly sensitive to the applied methodologies. Our findings contribute to a growing body of work indicating the importance of high-quality, aquatic habitats for both consumers and their pollution-intolerant prey, while also demonstrating how the application of multiple, laboratory-based techniques can provide insights not offered by either technique alone.
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Affiliation(s)
- Brandon D Hoenig
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Brian K Trevelline
- The Cornell Laboratory of Ornithology, Cornell University, Ithaca, New York, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Andrea Kautz
- Powdermill Nature Reserve, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA
| | | | - Brady A Porter
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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30
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Zizka VMA, Geiger MF, Hörren T, Kirse A, Noll NW, Schäffler L, Scherges AM, Sorg M. Repeated subsamples during
DNA
extraction reveal increased diversity estimates in
DNA
metabarcoding of Malaise traps. Ecol Evol 2022; 12:e9502. [PMCID: PMC9702565 DOI: 10.1002/ece3.9502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vera M. A. Zizka
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Matthias F. Geiger
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | | | - Ameli Kirse
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Niklas W. Noll
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Livia Schäffler
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Alice M. Scherges
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Martin Sorg
- Entomological Society Krefeld (EVK) Krefeld Germany
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31
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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32
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Brun L, Schneider J, Carrió EM, Dongre P, Taberlet P, Waal VD, Fumagalli L. Focal vs. fecal: Seasonal variation in the diet of wild vervet monkeys from observational and
DNA
metabarcoding data. Ecol Evol 2022; 12:e9358. [PMID: 36203642 PMCID: PMC9526031 DOI: 10.1002/ece3.9358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Eduard Mas Carrió
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Pooja Dongre
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes, CNRS Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - van de Waal
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva, Lausanne University Hospital and University of Lausanne Lausanne Switzerland
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33
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Bailey SA, Brydges T, Casas-Monroy O, Kydd J, Linley RD, Rozon RM, Darling JA. First evaluation of ballast water management systems on operational ships for minimizing introductions of nonindigenous zooplankton. MARINE POLLUTION BULLETIN 2022; 182:113947. [PMID: 35926436 PMCID: PMC10949186 DOI: 10.1016/j.marpolbul.2022.113947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/05/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Ballast water is a leading pathway for the global introduction of aquatic nonindigenous species. Most international ships are expected to install ballast water management systems (BWMS) by 2024 to treat ballast water before release. This study examines if ballast water discharges managed by BWMS are meeting standards for organisms ≥50 μm in minimum dimension (i.e., <10 organisms per m3; typically zooplankton). Representative samples of ballast water were collected from 29 ships (using 14 different BWMS) arriving to Canada during 2017-2018. Fourteen samples (48 %) had zooplankton concentrations clearly exceeding the standard (ranging from 18 to 3822 organisms per m3). Nonetheless, compared to earlier management strategies, BWMS appear to reduce the frequency of high-risk introduction events. BWMS filter mesh size was an important predictor of zooplankton concentration following treatment. Greater rates of compliance may be achieved as ship crews gain experience with operation and maintenance of BWMS.
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Affiliation(s)
- Sarah A Bailey
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada.
| | - Torben Brydges
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Oscar Casas-Monroy
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Jocelyn Kydd
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - R Dallas Linley
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - Robin M Rozon
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON L7S 1A1, Canada
| | - John A Darling
- Center for Environmental Measurement & Modeling, United States Environmental Protection Agency, Research Triangle Park, NC, USA
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34
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Cuff JP, Kitson JJN, Hemprich-Bennett D, Tercel MPTG, Browett SS, Evans DM. The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth? Mol Ecol Resour 2022; 23:41-51. [PMID: 36017818 PMCID: PMC10087656 DOI: 10.1111/1755-0998.13705] [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: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed 'the predator problem'. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multi-predator-taxon studies. We suggest that multi-primer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multi-taxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.
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Affiliation(s)
- Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James J N Kitson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde Rue, Trinity, Jersey, JE3 5BP, Channel Islands
| | - Samuel S Browett
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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35
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Fonseca ML, Ramírez-Pinzón MA, McNeil KN, Guevara M, Gómez-Gutiérrez LM, Harter K, Mongui A, Stevenson PR. Dietary preferences and feeding strategies of Colombian highland woolly monkeys. Sci Rep 2022; 12:14364. [PMID: 35999220 PMCID: PMC9399098 DOI: 10.1038/s41598-022-17655-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Primates are very selective in the foods they include in their diets with foraging strategies that respond to spatial and temporal changes in resource availability, distribution and quality. Colombian woolly monkeys (Lagothrix lagotricha lugens), one of the largest primate species in the Americas, feed mainly on fruits, but they also eat a high percentage of arthropods. This differs from closely related Atelid species that supplement their diet with leaves. In an 11 month study, we investigated the foraging strategies of this endemic monkey and assessed how resource availability affects dietary selection. Using behavioural, phenological, arthropod sampling and metabarcoding methods, we recorded respectively foraging time, forest productivity, arthropod availability in the forest and arthropod consumption. Scat samples and capturing canopy substrates (i.e. moss, bromeliads, aerial insects) were used for assigning arthropod taxonomy. The most important resource in the diet was fruits (54%), followed by arthropods (28%). Resource availability predicted feeding time for arthropods but not for fruits. Further, there was a positive relationship between feeding time on fruits and arthropods, suggesting that eating both resources during the same periods might work as an optimal strategy to maximize nutrient intake. Woolly monkeys preferred and avoided some fruit and arthropod items available in their home range, choosing a wide variety of arthropods. Geometrid moths (Lepidoptera) were the most important and consistent insects eaten over time. We found no differences in the type of arthropods adults and juveniles ate, but adults invested more time foraging for this resource, especially in moss. Although woolly monkeys are generalist foragers, they do not select their food items randomly or opportunistically.
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Affiliation(s)
- Manuel L Fonseca
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia. .,Comparative Zoology, Institut für Evolution und Ökologie (EvE), Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marcela A Ramírez-Pinzón
- Laboratorio de Zoología y Ecología Acuática (LAZOEA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Kaylie N McNeil
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Michelle Guevara
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Laura M Gómez-Gutiérrez
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Klaus Harter
- Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Alvaro Mongui
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Pablo R Stevenson
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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36
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Luo M, Ji Y, Warton D, Yu DW. Extracting abundance information from
DNA
‐based data. Mol Ecol Resour 2022; 23:174-189. [PMID: 35986714 PMCID: PMC10087802 DOI: 10.1111/1755-0998.13703] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.
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Affiliation(s)
- Mingjie Luo
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingYunnanChina
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
| | - David Warton
- School of Mathematics and StatisticsUNSW SydneySydneyNew South WalesAustralia
- Evolution and Ecology Research Centre, UNSW SydneySydneyNew South WalesAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingYunnanChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingYunnanChina
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwichNorfolkUK
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37
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Hua Z, Jiang C, Song S, Tian D, Chen Z, Jin Y, Zhao Y, Zhou J, Zhang Z, Huang L, Yuan Y. Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence. Mol Ecol Resour 2022; 23:106-117. [PMID: 35951477 DOI: 10.1111/1755-0998.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022]
Abstract
Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3,899 angiosperm plant species were calculated based on a chloroplast dataset with 4,356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.
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Affiliation(s)
- Zhongyi Hua
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Shuhui Song
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Dongmei Tian
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ziyuan Chen
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yan Jin
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Zhang Zhang
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
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38
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Paula DP, Timbó RV, Togawa RC, Vogler AP, Andow DA. Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads. Mol Ecol Resour 2022; 23:64-80. [DOI: 10.1111/1755-0998.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 06/11/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Débora P. Paula
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
| | - Renata V. Timbó
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro Brasília DF Brazil
| | | | - Alfried P. Vogler
- Imperial College London Ascot UK
- Department of Life Sciences Natural History Museum London UK
| | - David A. Andow
- Department of Entomology University of Minnesota St. Paul USA
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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40
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Basset Y, Hajibabaei M, Wright MTG, Castillo AM, Donoso DA, Segar ST, Souto-Vilarós D, Soliman DY, Roslin T, Smith MA, Lamarre GPA, De León LF, Decaëns T, Palacios-Vargas JG, Castaño-Meneses G, Scheffrahn RH, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez Silva JA, Cruz MM, Galván AA, Barrios H. Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Sci Rep 2022; 12:10762. [PMID: 35750774 PMCID: PMC9232565 DOI: 10.1038/s41598-022-14915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples from Barro Colorado Island, Panama. The fauna was extracted with Berlese-Tullgren funnels and then either sorted with traditional taxonomy and known, individual DNA barcodes ("traditional samples") or processed with metabarcoding ("metabarcoding samples"). We detected 49 ant, 37 springtail and 34 termite species with 3.46 million reads of the COI gene, at a mean sequence length of 233 bp. Traditional identification yielded 80, 111 and 15 species of ants, springtails and termites, respectively; 98%, 37% and 100% of these species had a Barcode Index Number (BIN) allowing for direct comparison with metabarcoding. Ants were best surveyed through traditional methods, termites were better detected by metabarcoding, and springtails were equally well detected by both techniques. Species richness was underestimated, and faunal composition was different in metabarcoding samples, mostly because 37% of ant species were not detected. The prevalence of species in metabarcoding samples increased with their abundance in traditional samples, and seasonal shifts in species prevalence and faunal composition were similar between traditional and metabarcoding samples. Probable false positive and negative species records were reasonably low (13-18% of common species). We conclude that metabarcoding of samples extracted with Berlese-Tullgren funnels appear suitable for the long-term monitoring of termites and springtails in tropical rainforests. For ants, metabarcoding schemes should be complemented by additional samples of alates from Malaise or light traps.
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Affiliation(s)
- Yves Basset
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama.
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Michael T G Wright
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Anakena M Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
| | - David A Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, TF10 8NB, Shropshire, UK
| | - Daniel Souto-Vilarós
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague, Czech Republic
| | - Dina Y Soliman
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Greg P A Lamarre
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA
| | - Thibaud Decaëns
- CEFE, University of Montpellier, CNRS, EPHE, IRD, University Paul Valéry, Montpellier 3, Montpellier, France
| | - José G Palacios-Vargas
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Gabriela Castaño-Meneses
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla 76230, Querétaro, Mexico
| | - Rudolf H Scheffrahn
- Fort Lauderdale Research & Education Center, 3205 College Avenue, Davie, FL, 33314, USA
| | - Marleny Rivera
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Filonila Perez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Ricardo Bobadilla
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Yacksecari Lopez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | | | - Maira Montejo Cruz
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Angela Arango Galván
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Héctor Barrios
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama
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Kaczmarek M, Entling MH, Hoffmann C. Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort. INSECTS 2022; 13:insects13060507. [PMID: 35735844 PMCID: PMC9224819 DOI: 10.3390/insects13060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.
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Affiliation(s)
- Marvin Kaczmarek
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
- Correspondence:
| | - Martin H. Entling
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
| | - Christoph Hoffmann
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
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Stapleton TE, Weinstein SB, Greenhalgh R, Dearing MD. Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal. Mol Ecol Resour 2022; 22:2573-2586. [PMID: 35579046 DOI: 10.1111/1755-0998.13643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
DNA metabarcoding is widely used to determine wild animal diets, however whether this technique provides accurate, quantitative measurements is still under debate. To test our ability to accurately estimate abundance of dietary items using metabarcoding, we fed wild caught desert woodrats (Neotoma lepida) diets comprised of constant amounts of juniper (Juniperus osteosperma, 15%) and varying amounts of creosote (Larrea tridentata, 1-60%), or cactus (Opuntia sp., 0-100%), and commercial chow (0-85%). Using metabarcoding, we compared the representation of items in the original diet samples to that in the fecal samples to test the sensitivity and accuracy of diet metabarcoding, the performance of different bioinformatic pipelines, and our ability to correct sequence counts. Metabarcoding, using standard trnL primers, detected creosote, juniper, and chow. Different pipelines for assigning taxonomy performed similarly. While creosote was detectable at dietary proportions as low as 1%, we failed to detect cactus in most samples, likely due to a primer mismatch. Creosote read counts increased as its proportion in the diet increased, and we could differentiate when creosote was a minor and major component of the diet. However, we found that estimates of juniper and creosote varied. Using previously suggested methods to correct these errors did not improve accuracy estimates of creosote, but did reduce error for juniper and chow. Our results indicate that metabarcoding can provide quantitative information on dietary composition, but may be limited. We suggest that researchers use caution in quantitatively interpreting diet metabarcoding results unless they first experimentally determine the extent of possible biases.
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43
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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44
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Couton M, Lévêque L, Daguin-Thiébaut C, Comtet T, Viard F. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. BIOFOULING 2022; 38:367-383. [PMID: 35575060 DOI: 10.1080/08927014.2022.2075739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.
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Affiliation(s)
- Marjorie Couton
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Laurent Lévêque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Thierry Comtet
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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45
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Paula DP, Barros SKA, Pitta RM, Barreto MR, Togawa RC, Andow DA. Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators. Gigascience 2022; 11:6554098. [PMID: 35333301 PMCID: PMC8952265 DOI: 10.1093/gigascience/giac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Background A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). Results In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43–71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46–273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. Conclusions Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70770-917, Brazil
| | | | | | | | | | - David A Andow
- Department of Entomology, University of Minnesota, MN, 55108, St. Paul, USA
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46
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Abstract
The identification of floral visitation by pollinators provides an opportunity to improve our understanding of the fine-scale ecological interactions between plants and pollinators, contributing to biodiversity conservation and promoting ecosystem health. In this review, we outline the various methods which can be used to identify floral visitation, including plant-focused and insect-focused methods. We reviewed the literature covering the ways in which DNA metabarcoding has been used to answer ecological questions relating to plant use by pollinators and discuss the findings of this research. We present detailed methodological considerations for each step of the metabarcoding workflow, from sampling through to amplification, and finally bioinformatic analysis. Detailed guidance is provided to researchers for utilisation of these techniques, emphasising the importance of standardisation of methods and improving the reliability of results. Future opportunities and directions of using molecular methods to analyse plant–pollinator interactions are then discussed.
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47
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Wu HY, Shaw PC. Strategies for molecular authentication of herbal products: from experimental design to data analysis. Chin Med 2022; 17:38. [PMID: 35317843 PMCID: PMC8939074 DOI: 10.1186/s13020-022-00590-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/02/2022] [Indexed: 12/22/2022] Open
Abstract
Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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48
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Groen K, Trimbos KB, Hein S, Blaauw AI, van Bodegom PM, Hahne J, Jacob J. Establishment of a fecal DNA quantification technique for rare and cryptic diet constituents in small mammals. Mol Ecol Resour 2022; 22:2220-2231. [PMID: 35297564 DOI: 10.1111/1755-0998.13609] [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: 08/26/2021] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
DNA-based approaches have highly improved the applicability of dietary studies aimed at investigating ecological processes. These studies have provided direct insights into, otherwise difficult to measure, interactions between species and trophic levels, food web structure and ecosystem functioning. However, despite these advances, DNA-based methods have been struggling to accurately quantify the whole breadth of diet constituents because of methodological biases, such as amplification bias and digestive processes. This study is, to our knowledge, the first diet study that used droplet digital PCR to quantify diet constituents. We manipulated the diet of wild caught wood mice (Apodemus sylvaticus) by feeding them with a known amount of small vegetable seeds (onion and carrot) and quantified the DNA traces of these diet constituents in fecal samples. The sensitivity of the technique combined with the control on the experimental design allowed mitigation of methodological bias. We were able to accurately determine DNA concentrations of small vegetable seeds in the diet of wood mice. Quantification of target DNA demonstrated significant differences in DNA content when one vs. five seeds were consumed. These differences remained significant when the age, sex, and other diet constituents of the mice were altered. Different DNA markers, targeting different parts of the chloroplast, influenced onion DNA detectability. However, all onion and carrot markers showed higher DNA content for higher seed numbers. Overall, the sensitive DNA based approach developed in this study allows for minimally-invasive quantification of small diet constituents in feces, which would otherwise be undetectable with traditional methods.
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Affiliation(s)
- Kevin Groen
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Krijn B Trimbos
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Susanne Hein
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI) Federal Research Institute for Cultivated Plants, Toppheideweg 88, 48161, Münster, Germany.,Present address: BASF SE, Agricultural Solutions - Global Ecotoxicology, Limburgerhof, Germany
| | - Astrid I Blaauw
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Joerg Hahne
- Bayer AG, Crop Science Division, Terrestrial Vertebrates, Monheim am Rhein, Germany
| | - Jens Jacob
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI) Federal Research Institute for Cultivated Plants, Toppheideweg 88, 48161, Münster, Germany
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49
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Koskinen JS, Abrego N, Vesterinen EJ, Schulz T, Roslin T, Nyman T. Imprints of latitude, host taxon, and decay stage on fungus‐associated arthropod communities. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Janne S. Koskinen
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
- Department of Agricultural Sciences University of Helsinki Finland
| | - Nerea Abrego
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Biological and Environmental Science University of Jyväskylä Finland
| | | | - Torsti Schulz
- Organismal and Evolutionary Biology Research Programme University of Helsinki Finland
| | - Tomas Roslin
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region Norwegian Institute of Bioeconomy Research Svanvik Norway
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50
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Lowe A, Jones L, Brennan G, Creer S, Vere N. Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by
DNA
metabarcoding. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abigail Lowe
- National Botanic Garden of Wales, Llanarthne UK
- Molecular Ecology and Evolution Group, School of Natural Sciences Bangor University Bangor UK
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne UK
| | | | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences Bangor University Bangor UK
| | - Natasha Vere
- Natural History Museum of Denmark University of Copenhagen Denmark
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