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Boyi JO, Heße E, Rohner S, Säurich J, Siebert U, Gilles A, Lehnert K. Deciphering Eurasian otter (
Lutra lutra
L.) and seal (
Phoca vitulina
L.;
Halichoerus grypus
F.) diet: metabarcoding tailored for fresh and saltwater fish species. Mol Ecol 2022; 31:5089-5106. [DOI: 10.1111/mec.16635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Joy Ometere Boyi
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Eileen Heße
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Simon Rohner
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Josefin Säurich
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation Hannover Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Anita Gilles
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
| | - Kristina Lehnert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation Büsum Germany
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McLennan EA, Wise P, Lee AV, Grueber CE, Belov K, Hogg CJ. DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem. Ecol Evol 2022; 12:e8936. [PMID: 35600680 PMCID: PMC9120209 DOI: 10.1002/ece3.8936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species' native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species' native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short-tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.
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Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Phil Wise
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Andrew V. Lee
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Catherine E. Grueber
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Katherine Belov
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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Kim J, Lee WY, Park S. Trophic relations based on fecal DNA in tundra terrestrial food webs near Kongsfjorden, Svalbard, Norway. Polar Biol 2022. [DOI: 10.1007/s00300-022-03022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Boukhdoud L, Saliba C, Parker LD, McInerney NR, Kahale R, Saliba I, Maldonado JE, Kharrat MBD. Using DNA metabarcoding to decipher the diet plant component of mammals from the Eastern Mediterranean region. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.70107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Longevity of species populations depends largely on interactions among animals and plants in an ecosystem. Predation and seed dispersal are among the most important interactions necessary for species conservation and persistence, and diet analysis is a prerequisite tool to evaluate these interactions. Understanding these processes is crucial for identifying conservation targets and for executing efficient reforestation and ecological restoration. In this study, we applied a scat DNA metabarcoding technique using the P6-loop of the trnL (UAA) chloroplastic marker to describe the seasonal plant diet composition of 15 mammal species from a highly biodiverse Lebanese forest in the Eastern Mediterranean. We also recovered plant seeds, when present, from the scats for identification. The mammal species belong to 10 families from 5 different orders. More than 133 plant species from 54 plant families were detected and identified. Species from the Rosaceae, Poaceae, Apiaceae, Fabaceae, Fagaceae and Berberidaceae families were consumed by the majority of the mammals and should be taken into consideration in future reforestation and conservation projects. Our results showed that the DNA metabarcoding approach provides a promising method for tracking the dietary plant components of a wide diversity of mammals, yielding key insights into plant-animal interactions inside Lebanon’s forests.
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Massey AL, Roffler GH, Vermeul T, Allen JM, Levi T. Comparison of mechanical sorting and DNA metabarcoding for diet analysis with fresh and degraded wolf scats. Ecosphere 2021. [DOI: 10.1002/ecs2.3557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Aimee L. Massey
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Gretchen H. Roffler
- Alaska Department of Fish and Game Division of Wildlife Conservation P.O. Box 110024 Juneau Alaska99811USA
| | - Tessa Vermeul
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
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6
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van Zinnicq Bergmann MPM, Postaire BD, Gastrich K, Heithaus MR, Hoopes LA, Lyons K, Papastamatiou YP, Schneider EVC, Strickland BA, Talwar BS, Chapman DD, Bakker J. Elucidating shark diets with DNA metabarcoding from cloacal swabs. Mol Ecol Resour 2021; 21:1056-1067. [PMID: 33527665 DOI: 10.1111/1755-0998.13315] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high-resolution diet reconstruction tools are currently under-developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free-ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high-resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems.
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Affiliation(s)
- Maurits P M van Zinnicq Bergmann
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Bimini Biological Field Station Foundation, Bimini, The Bahamas
| | - Bautisse D Postaire
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Kirk Gastrich
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Michael R Heithaus
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | | | | | - Yannis P Papastamatiou
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Eric V C Schneider
- Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Bradley A Strickland
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Brendan S Talwar
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Demian D Chapman
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Judith Bakker
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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Traugott M, Thalinger B, Wallinger C, Sint D. Fish as predators and prey: DNA-based assessment of their role in food webs. JOURNAL OF FISH BIOLOGY 2021; 98:367-382. [PMID: 32441321 PMCID: PMC7891366 DOI: 10.1111/jfb.14400] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.
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Affiliation(s)
- Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Bettina Thalinger
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
- Centre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Corinna Wallinger
- Institute of Interdisciplinary Mountain Research, Austrian Academy of ScienceInnsbruckAustria
| | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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Bonin M, Dussault C, Taillon J, Lecomte N, Côté SD. Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers. Ecol Evol 2020; 10:6664-6676. [PMID: 32724540 PMCID: PMC7381590 DOI: 10.1002/ece3.6397] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.We used stable isotopes, morphological, and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.
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Affiliation(s)
- Michaël Bonin
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
| | - Christian Dussault
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Direction de l’expertise sur la faune terrestre, l’herpétofaune et l’avifauneMinistère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Joëlle Taillon
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Direction de l’expertise sur la faune terrestre, l’herpétofaune et l’avifauneMinistère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Nicolas Lecomte
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Chaire de recherche du Canada en écologie polaire et boréaleUniversité de MonctonMonctonNBCanada
| | - Steeve D. Côté
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
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