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Claver C, Rodríguez-Ezpeleta N, Irigoien X, Canals O. Global distribution patterns of siphonophores across horizontal and vertical oceanic gradients. OPEN RESEARCH EUROPE 2024; 4:177. [PMID: 39279823 PMCID: PMC11399771 DOI: 10.12688/openreseurope.18226.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/30/2024] [Indexed: 09/18/2024]
Abstract
Background Siphonophores are diverse, globally distributed hydrozoans that play a central role in marine trophic webs worldwide. However, they still constitute an understudied fraction of the open ocean gelatinous taxa, mainly due to challenges related to siphonophore sampling and identification, which have led to a general knowledge gap about their diversity, distribution and abundance. Methods Here, we provide a global overview of the oceanic vertical distribution of siphonophores using DNA metabarcoding data from 77 bulk mesozooplankton samples collected at four different depth ranges (0-200, 200-500, 500-1000, 1000-3000 m depth) along the Atlantic, Pacific, and Indian Oceans during the MALASPINA-2010 circumnavigation expedition. Results We detected a total of 44 siphonophore species (which represents about one quarter of the described siphonophore species) from which 26 corresponded to Calycophores, 14 to Physonectae and 2 to Cystonectae. Our results suggest wider horizontal and vertical distributions of siphonophore species than previously described, including novel records of some species in certain oceanic basins. Also, we provide insights into the intraspecific variation of widely distributed species. Finally, we show a vertical structuring of siphonophores along the water column; Calycophores (siphonophores without pneumatophores) dominated the epipelagic (from the surface to 200 m depth) and upper mesopelagic layers (from 200 to 500 m depth), while the proportion Physonectids (siphonophores with pneumatophore) notably increased below 500 meters and were dominant at bathypelagic depths (>1000 m depth). Conclusions Our results support that the siphonophore community composition is vertically structured. Also, we provide insights into the potential existence of genetic variations within certain species that dominate some ocean basins or depth ranges. To our knowledge, this is the first time that DNA metabarcoding data is retrieved to study siphonophore distribution patterns, and the study provides evidence of the potential of molecular techniques to study the distribution of gelatinous organisms often destroyed in net sampling.
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Affiliation(s)
- Cristina Claver
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
| | - Naiara Rodríguez-Ezpeleta
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
| | - Xabier Irigoien
- Education Research and Innovation Foundation, NEOM Base Camp, Building Number: 4758, Ocean Science and Solutions Applied Research Institute (OSSARI), NEOM, 49643, Saudi Arabia
| | - Oriol Canals
- Marine Research Division, Basque Research and Technology Alliance (BRTA), AZTI Foundation Sukarrieta, Sukarrieta, Vizcaya, 48395, Spain
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2
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Buzan E, Potočnik H, Pokorny B, Potušek S, Iacolina L, Gerič U, Urzi F, Kos I. Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps. Front Zool 2024; 21:9. [PMID: 38500207 PMCID: PMC10949697 DOI: 10.1186/s12983-024-00530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Boštjan Pokorny
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Urška Gerič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Felicita Urzi
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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3
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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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4
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Maccapan D, Careddu G, Calizza E, Sporta Caputi S, Rossi L, Costantini ML. Effects of Sea-Ice Persistence on the Diet of Adélie Penguin ( Pygoscelis adeliae) Chicks and the Trophic Differences between Chicks and Adults in the Ross Sea, Antarctica. BIOLOGY 2023; 12:biology12050708. [PMID: 37237522 DOI: 10.3390/biology12050708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
In Antarctica, prey availability for the mesopredator Adélie penguin, Pygoscelis adeliae, depends on sea-ice dynamics. By affecting cycles of sea-ice formation and melt, climate change could thus affect penguin diet and recruitment. In the light of climate change, this raises concerns about the fate of this dominant endemic species, which plays a key role in the Antarctic food web. However, few quantitative studies measuring the effects of sea-ice persistence on the diet of penguin chicks have yet been conducted. The purpose of this study was to fill this gap by comparing penguin diets across four penguin colonies in the Ross Sea and evaluating latitudinal and interannual variation linked to different sea-ice persistence. Diet was evaluated by analysing the δ13C and δ15N values of penguin guano, and sea-ice persistence by means of satellite images. Isotopic values indicate that penguins consumed more krill in colonies with longer sea-ice persistence. In these colonies, the δ13C values of chicks were lower and closer to the pelagic chain than those of adults, suggesting that the latter apparently catch prey inshore for self-feeding and offshore for their chicks. The results indicate that sea-ice persistence is among the principal factors that influence the spatiotemporal variability of the penguins' diet.
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Affiliation(s)
- Deborah Maccapan
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
| | - Giulio Careddu
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Edoardo Calizza
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Simona Sporta Caputi
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Loreto Rossi
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Maria Letizia Costantini
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Rome, Italy
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Carreiro AR, Ramos JA, Mata VA, Matos DM, dos Santos I, Araújo PM, Rodrigues I, Almeida NM, Militão T, Saldanha S, Paiva VH, Lopes RJ. High-throughput sequencing reveals prey diversity overlap between sympatric Sulids in the tropical Atlantic. FOOD WEBS 2022. [DOI: 10.1016/j.fooweb.2022.e00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lewis PJ, Lashko A, Chiaradia A, Allinson G, Shimeta J, Emmerson L. New and legacy persistent organic pollutants (POPs) in breeding seabirds from the East Antarctic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119734. [PMID: 35835279 DOI: 10.1016/j.envpol.2022.119734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Persistent organic pollutants (POPs) are pervasive and a significant threat to the environment worldwide. Yet, reports of POP levels in Antarctic seabirds based on blood are scarce, resulting in significant geographical gaps. Blood concentrations offer a snapshot of contamination within live populations, and have been used widely for Arctic and Northern Hemisphere seabird species but less so in Antarctica. This paper presents levels of legacy POPs (polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs)) and novel brominated flame retardants (NBFRs) in the blood of five Antarctic seabird species breeding within Prydz Bay, East Antarctica. Legacy PCBs and OCPs were detected in all species sampled, with Adélie penguins showing comparatively high ∑PCB levels (61.1 ± 87.6 ng/g wet weight (ww)) compared to the four species of flying seabirds except the snow petrel (22.5 ± 15.5 ng/g ww), highlighting that legacy POPs are still present within Antarctic wildlife despite decades-long bans. Both PBDEs and NBFRs were detected in trace levels for all species and hexabromobenzene (HBB) was quantified in cape petrels (0.3 ± 0.2 ng/g ww) and snow petrels (0.2 ± 0.1 ng/g ww), comparable to concentrations found in Arctic seabirds. These results fill a significant data gap within the Antarctic region for POPs studies, representing a crucial step forward assessing the fate and impact of legacy POPs contamination in the Antarctic environment.
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Affiliation(s)
- Phoebe J Lewis
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia.
| | - Anna Lashko
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, 7050, Australia
| | - Andre Chiaradia
- Conservation Department, Phillip Island Nature Parks, Victoria, 3925, Australia
| | - Graeme Allinson
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Jeff Shimeta
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Louise Emmerson
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, 7050, Australia
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7
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Nordstrom B, Mitchell N, Byrne M, Jarman S. A review of applications of environmental DNA for reptile conservation and management. Ecol Evol 2022; 12:e8995. [PMID: 35784065 PMCID: PMC9168342 DOI: 10.1002/ece3.8995] [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: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio-temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
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Affiliation(s)
- Bethany Nordstrom
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Nicola Mitchell
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Margaret Byrne
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
| | - Simon Jarman
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- UWA Oceans InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
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8
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Johnston NM, Murphy EJ, Atkinson A, Constable AJ, Cotté C, Cox M, Daly KL, Driscoll R, Flores H, Halfter S, Henschke N, Hill SL, Höfer J, Hunt BPV, Kawaguchi S, Lindsay D, Liszka C, Loeb V, Manno C, Meyer B, Pakhomov EA, Pinkerton MH, Reiss CS, Richerson K, Jr. WOS, Steinberg DK, Swadling KM, Tarling GA, Thorpe SE, Veytia D, Ward P, Weldrick CK, Yang G. Status, Change, and Futures of Zooplankton in the Southern Ocean. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.624692] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In the Southern Ocean, several zooplankton taxonomic groups, euphausiids, copepods, salps and pteropods, are notable because of their biomass and abundance and their roles in maintaining food webs and ecosystem structure and function, including the provision of globally important ecosystem services. These groups are consumers of microbes, primary and secondary producers, and are prey for fishes, cephalopods, seabirds, and marine mammals. In providing the link between microbes, primary production, and higher trophic levels these taxa influence energy flows, biological production and biomass, biogeochemical cycles, carbon flux and food web interactions thereby modulating the structure and functioning of ecosystems. Additionally, Antarctic krill (Euphausia superba) and various fish species are harvested by international fisheries. Global and local drivers of change are expected to affect the dynamics of key zooplankton species, which may have potentially profound and wide-ranging implications for Southern Ocean ecosystems and the services they provide. Here we assess the current understanding of the dominant metazoan zooplankton within the Southern Ocean, including Antarctic krill and other key euphausiid, copepod, salp and pteropod species. We provide a systematic overview of observed and potential future responses of these taxa to a changing Southern Ocean and the functional relationships by which drivers may impact them. To support future ecosystem assessments and conservation and management strategies, we also identify priorities for Southern Ocean zooplankton research.
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9
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Molecular dietary analysis of Adélie (Pygoscelis adeliae) and Gentoo (Pygoscelis papua) penguins breeding sympatrically on Antarctic Ardley Island using fecal DNA. Polar Biol 2022. [DOI: 10.1007/s00300-022-03051-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Tabassum N, Lee JH, Lee SR, Kim JU, Park H, Kim HW, Kim JH. Molecular Diet Analysis of Adélie Penguins ( Pygoscelis adeliae) in the Ross Sea Using Fecal DNA. BIOLOGY 2022; 11:biology11020182. [PMID: 35205051 PMCID: PMC8869225 DOI: 10.3390/biology11020182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary The diet of Adélie penguins, Pygoscelis adeliae, in the Ross Sea was studied applying quantitative polymerase chain reaction (qPCR) protocols to their feces. Two krill species (Euphausia superba and Euphausia crystallorophias) and notothenioid fish (mainly Pleuragramma antarctica and Pagothenia borchgrevinki) were among the most abundant components of the diet. The composition of the two krill species and notothenioid fish was found to be strongly related to the geographic characteristics of the Ross Sea. Abstract The diet of Adélie penguins, Pygoscelis adeliae, is a useful indicator in understanding the ecological conditions of their habitats. The diets of Adélie penguins were studied using metabarcoding and quantitative PCR (qPCR) analyses of fecal DNA from seven habitats along the Ross Sea region. Using metabarcoding analysis with dual universal primers (18Sv9 and miniFish), the overall diet composition and detailed information about piscine prey were clearly elucidated. It was found that two krill species (Euphausia superba and Euphausia crystallorophias) and notothenioid fish were the most abundant in the diets of Adélie penguins. Among the notothenioid prey, Pleuragramma antarctica (56.50%) and Pagothenia borchgrevinki (18.21%) were the two most abundant species. qPCR analysis showed a significant geographic difference in the composition of main prey. Penguins inhabiting outbound parts of the Ross Sea (Capes Adare (CA) and Duke of York Island (DY)) mainly preyed on E. superba, without any significant changes in prey composition. By contrast, those inhabiting the inbound parts of the Ross Sea (Edmonson Point (EP) and Inexpressible Island (II)) preyed on E. crystallorophias and notothenioid fish rather than E. superba. Compared with the outbound habitats, prey compositions for penguins inhabiting the inbound regions were significantly different year to year, which was presumably due to the food availability based on the annual environmental and meteorological conditions of the coastal region along with the inbound parts of the Ross Sea.
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Affiliation(s)
- Nazia Tabassum
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Korea; (N.T.); (S.-R.L.)
| | - Ji-Hyun Lee
- Department of Marine Biology, Pukyong National University, Busan 48516, Korea;
| | - Soo-Rin Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Korea; (N.T.); (S.-R.L.)
| | - Jong-U Kim
- Division of Life Science, Korea Polar Research Institute, Incheon 21990, Korea;
| | - Hyun Park
- Department of Biotechnology, Korea University, Seoul 02841, Korea;
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48516, Korea;
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Korea
- Correspondence: (H.-W.K.); (J.-H.K.)
| | - Jeong-Hoon Kim
- Division of Life Science, Korea Polar Research Institute, Incheon 21990, Korea;
- Correspondence: (H.-W.K.); (J.-H.K.)
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11
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Urban P, Praebel K, Bhat S, Dierking J, Wangensteen OS. DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic. Mol Ecol 2021; 31:1562-1576. [PMID: 34936153 DOI: 10.1111/mec.16332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly molecular approaches such as DNA-metabarcoding are used in studying trophic relations, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA-metabarcoding with universal primers for cytochrome c oxidase I (COI), to study the diet composition of the Northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40-60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on SCA. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underscores the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.
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Affiliation(s)
- Paulina Urban
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Kim Praebel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, Elverum, Norway
| | - Shripathi Bhat
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
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12
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Liu G, Zhang S, Zhao X, Li C, Gong M. Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis. Genes (Basel) 2021; 12:genes12121854. [PMID: 34946803 PMCID: PMC8701983 DOI: 10.3390/genes12121854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Shumiao Zhang
- Beijing Milu Ecological Research Center, Beijing 100076, China;
| | - Xinsheng Zhao
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Chao Li
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Minghao Gong
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
- Correspondence: ; Tel.: +86-010-62884159
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13
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Miller CV, Pittman M. The diet of early birds based on modern and fossil evidence and a new framework for its reconstruction. Biol Rev Camb Philos Soc 2021; 96:2058-2112. [PMID: 34240530 PMCID: PMC8519158 DOI: 10.1111/brv.12743] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022]
Abstract
Birds are some of the most diverse organisms on Earth, with species inhabiting a wide variety of niches across every major biome. As such, birds are vital to our understanding of modern ecosystems. Unfortunately, our understanding of the evolutionary history of modern ecosystems is hampered by knowledge gaps in the origin of modern bird diversity and ecosystem ecology. A crucial part of addressing these shortcomings is improving our understanding of the earliest birds, the non-avian avialans (i.e. non-crown birds), particularly of their diet. The diet of non-avian avialans has been a matter of debate, in large part because of the ambiguous qualitative approaches that have been used to reconstruct it. Here we review methods for determining diet in modern and fossil avians (i.e. crown birds) as well as non-avian theropods, and comment on their usefulness when applied to non-avian avialans. We use this to propose a set of comparable, quantitative approaches to ascertain fossil bird diet and on this basis provide a consensus of what we currently know about fossil bird diet. While no single approach can precisely predict diet in birds, each can exclude some diets and narrow the dietary possibilities. We recommend combining (i) dental microwear, (ii) landmark-based muscular reconstruction, (iii) stable isotope geochemistry, (iv) body mass estimations, (v) traditional and/or geometric morphometric analysis, (vi) lever modelling, and (vii) finite element analysis to reconstruct fossil bird diet accurately. Our review provides specific methodologies to implement each approach and discusses complications future researchers should keep in mind. We note that current forms of assessment of dental mesowear, skull traditional morphometrics, geometric morphometrics, and certain stable isotope systems have yet to be proven effective at discerning fossil bird diet. On this basis we report the current state of knowledge of non-avian avialan diet which remains very incomplete. The ancestral dietary condition in non-avian avialans remains unclear due to scarce data and contradictory evidence in Archaeopteryx. Among early non-avian pygostylians, Confuciusornis has finite element analysis and mechanical advantage evidence pointing to herbivory, whilst Sapeornis only has mechanical advantage evidence indicating granivory, agreeing with fossilised ingested material known for this taxon. The enantiornithine ornithothoracine Shenqiornis has mechanical advantage and pedal morphometric evidence pointing to carnivory. In the hongshanornithid ornithuromorph Hongshanornis only mechanical advantage evidence indicates granivory, but this agrees with evidence of gastrolith ingestion in this taxon. Mechanical advantage and ingested fish support carnivory in the songlingornithid ornithuromorph Yanornis. Due to the sparsity of robust dietary assignments, no clear trends in non-avian avialan dietary evolution have yet emerged. Dietary diversity seems to increase through time, but this is a preservational bias associated with a predominance of data from the Early Cretaceous Jehol Lagerstätte. With this new framework and our synthesis of the current knowledge of non-avian avialan diet, we expect dietary knowledge and evolutionary trends to become much clearer in the coming years, especially as fossils from other locations and climates are found. This will allow for a deeper and more robust understanding of the role birds played in Mesozoic ecosystems and how this developed into their pivotal role in modern ecosystems.
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Affiliation(s)
- Case Vincent Miller
- Vertebrate Palaeontology Laboratory, Research Division for Earth and Planetary ScienceThe University of Hong KongPokfulamHong Kong SARChina
| | - Michael Pittman
- Vertebrate Palaeontology Laboratory, Research Division for Earth and Planetary ScienceThe University of Hong KongPokfulamHong Kong SARChina
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14
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Di Bernardi C, Wikenros C, Hedmark E, Boitani L, Ciucci P, Sand H, Åkesson M. Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecol Evol 2021; 11:11739-11748. [PMID: 34522337 PMCID: PMC8427573 DOI: 10.1002/ece3.7918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.
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Affiliation(s)
- Cecilia Di Bernardi
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Camilla Wikenros
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Eva Hedmark
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Håkan Sand
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
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15
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Günther B, Fromentin JM, Metral L, Arnaud-Haond S. Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey. PeerJ 2021; 9:e11757. [PMID: 34447617 PMCID: PMC8366523 DOI: 10.7717/peerj.11757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.
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Affiliation(s)
- Babett Günther
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | | | - Luisa Metral
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
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16
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Bourret V, Gutiérrez López R, Melo M, Loiseau C. Metabarcoding options to study eukaryotic endoparasites of birds. Ecol Evol 2021; 11:10821-10833. [PMID: 34429884 PMCID: PMC8366860 DOI: 10.1002/ece3.7748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
There is growing interest in the study of avian endoparasite communities, and metabarcoding is a promising approach to complement more conventional or targeted methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme, with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this challenge by comparing different primer sets across 16 samples from 5 bird species. Samples consisted of blood, feces, and controlled mixes with known proportions of bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in combination with a custom blocking primer allowed detection of various plasmodiid parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two potentially pathogenic fungal groups. When tested on the controlled DNA mixes, these primers also increased the proportion of nematode DNA by over an order of magnitude. An 18S primer set, originally designed to exclude metazoan sequences, was the most effective at reducing the relative number of avian DNA sequences and was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not allow nematode detection and also failed to detect avian malaria parasites. This study shows that a 28S set including a blocking primer allows detection of several major and very diverse bird parasite clades, while reliable amplification of all major parasite groups may require a combination of markers. It helps clarify options for bird parasite metabarcoding, according to priorities in terms of the endoparasite clades and the ecological questions researchers wish to focus on.
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Affiliation(s)
- Vincent Bourret
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Rafael Gutiérrez López
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Martim Melo
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- MHNC‐UP – Natural History and Science Museum of the University of PortoPortoPortugal
- FitzPatrick Institute of African OrnithologyUniversity of Cape TownCape TownSouth Africa
| | - Claire Loiseau
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- CEFEUniversité de MontpellierCNRSMontpellierFrance
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17
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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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18
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Wing SR, Wing LC, O’Connell-Milne SA, Barr D, Stokes D, Genovese S, Leichter JJ. Penguins and Seals Transport Limiting Nutrients Between Offshore Pelagic and Coastal Regions of Antarctica Under Changing Sea Ice. Ecosystems 2020. [DOI: 10.1007/s10021-020-00578-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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da Silva LP, Mata VA, Lopes PB, Lopes RJ, Beja P. High-resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism. Ecol Evol 2020; 10:10364-10373. [PMID: 33072265 PMCID: PMC7548197 DOI: 10.1002/ece3.6687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 11/11/2022] Open
Abstract
Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary studies, which may be unable to detect subtle intraspecific differentiation in prey consumption. Here, we show the power of multi‐marker metabarcoding to address these issues, focusing on a slightly dimorphic generalist passerine, the black wheatear Oenanthe leucura. Using markers from four genomic regions (18S, 16S, COI, and trnL), we analyzed fecal droppings collected from 93 adult black wheatears during the breeding season. We found that sexes were rather similar in bill and body features, though males had a slightly thicker bill and longer wings and tail than females. Diet was dominated in both sexes by a very wide range of arthropod species and a few fleshy fruits, but the overall diet diversity was higher for males than females, and there was a much higher frequency of occurrence of ants in female (58%) than male (29%) diets. We hypothesize that the observed sexual differentiation was likely related to females foraging closer to their offspring on abundant prey, while males consumed a wider variety of prey while foraging more widely. Overall, our results suggest that dietary sexual differentiation in birds may be more widespread than recognized at present and that multi‐marker DNA metabarcoding is a particularly powerful tool to unveiling such differences.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Vanessa A Mata
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | | | - Ricardo J Lopes
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Pedro Beja
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal.,CIBIO-InBIO Research Center in Biodiversity and Genetic Resources Institute of Agronomy University of Lisbon Lisbon Portugal
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20
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Pilcher N, Gaw S, Eisert R, Horton TW, Gormley AM, Cole TL, Lyver PO. Latitudinal, sex and inter-specific differences in mercury and other trace metal concentrations in Adélie and Emperor penguins in the Ross Sea, Antarctica. MARINE POLLUTION BULLETIN 2020; 154:111047. [PMID: 32319892 DOI: 10.1016/j.marpolbul.2020.111047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
We sought to determine mercury (Hg) and other trace metal concentrations in Adélie (Pygoscelis adeliae) and emperor penguin (Aptenodytes forsteri) breast feathers from the Ross Sea, Antarctica, and relate those concentrations to the trophic position and the habitats in which each of these species forage. Adélie penguin feathers from the southern Ross Sea colonies were higher in Hg than those sampled further north in the Ross Sea, potentially due to greater exposure to local sources, such as volcanism. Female Adélie penguins had lower feather total Hg concentrations than males. This may reflect female penguin's capacity to eliminate Hg through the egg development and laying process, or the larger and/or older prey items that male birds can consume, reflected by their higher trophic position. Emperor penguins have higher Hg concentrations than Adélie penguins which is also partially explained by Adélie penguins feeding at lower trophic levels than emperor penguins.
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Affiliation(s)
- Natalie Pilcher
- School of Physical and Chemical Sciences, University of Canterbury, New Zealand
| | - Sally Gaw
- School of Physical and Chemical Sciences, University of Canterbury, New Zealand
| | - Regina Eisert
- Gateway Antarctica, Department of Geography, University of Canterbury, New Zealand
| | - Travis W Horton
- Department of Geology, University of Canterbury, New Zealand
| | - Andrew M Gormley
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln 7640, New Zealand
| | - Theresa L Cole
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Phil O'B Lyver
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln 7640, New Zealand.
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21
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Takahashi M, DiBattista JD, Jarman S, Newman SJ, Wakefield CB, Harvey ES, Bunce M. Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding. Sci Rep 2020; 10:4319. [PMID: 32152406 PMCID: PMC7062689 DOI: 10.1038/s41598-020-60779-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/17/2020] [Indexed: 01/23/2023] Open
Abstract
Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of these two lutjanids. Major prey taxa were comprised of teleosts and crustaceans for all groups except adult L. erythropterus, which instead consumed soft bodied invertebrates (e.g. tunicates, comb jellies and medusae) as well as teleosts, with crustaceans being notably absent. Diet composition was significantly different among life history stages and species, which may be associated with niche habitat partitioning or differences in mouth morphology within adult life stages. This study provides the first evidence of diet partitioning between cryptic juveniles of overlapping lutjanid species, thus providing new insights into the ecological interactions, habitat associations, and the specialised adaptations required for the coexistence of closely related species. This study has improved our understanding of the differential contributions of the juvenile and adult diets of these sympatric species within food webs. The diet partitioning reported in this study was only revealed by the taxonomic resolution provided by the DNA metabarcoding approach and highlights the potential utility of this method to refine the dietary components of reef fishes more generally.
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Affiliation(s)
- Miwa Takahashi
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia.
| | - Joseph D DiBattista
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Corey B Wakefield
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
- Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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22
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Cabezas MP, Lasso-Alcalá OM, Xavier R, Jowers MJ. First genetic record of the non-native muzzled blenny Omobranchus punctatus (Teleostei: Blenniidae) in the Atlantic Coast of Central and South America. JOURNAL OF FISH BIOLOGY 2020; 96:841-846. [PMID: 31995228 DOI: 10.1111/jfb.14268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/27/2020] [Indexed: 05/12/2023]
Abstract
In this study we sequenced two mitochondrial (COI and 16S rRNA) and one nuclear (18S rRNA) gene fragment of an introduced muzzled blenny (Omobranchus punctatus) specimen collected from the Orinoco Delta (Gulf of Paria estuary) in Venezuela. This is the first genetic data generated for this species' introduced range in Central and South America, suggesting an introduction from the Indian Ocean.
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Affiliation(s)
- M Pilar Cabezas
- Department of Biology, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas nº 7, Vairão, Portugal
| | - Oscar M Lasso-Alcalá
- Museo de Historia Natural La Salle, Fundación La Salle de Ciencias Naturales, Caracas, Venezuela
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas nº 7, Vairão, Portugal
| | - Michael J Jowers
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas nº 7, Vairão, Portugal
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23
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Gil V, Pinho CJ, Aguiar CAS, Jardim C, Rebelo R, Vasconcelos R. Questioning the proverb 'more haste, less speed': classic versus metabarcoding approaches for the diet study of a remote island endemic gecko. PeerJ 2020; 8:e8084. [PMID: 31915567 PMCID: PMC6942681 DOI: 10.7717/peerj.8084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Dietary studies can reveal valuable information on how species exploit their habitats and are of particular importance for insular endemics conservation as these species present higher risk of extinction. Reptiles are often neglected in island systems, principally the ones inhabiting remote areas, therefore little is known on their ecological networks. The Selvagens gecko Tarentola (boettgeri) bischoffi, endemic to the remote and integral reserve of Selvagens Archipelago, is classified as Vulnerable by the Portuguese Red Data Book. Little is known about this gecko’s ecology and dietary habits, but it is assumed to be exclusively insectivorous. The diet of the continental Tarentola species was already studied using classical methods. Only two studies have used next-generation sequencing (NGS) techniques for this genus thus far, and very few NGS studies have been employed for reptiles in general. Considering the lack of information on its diet and the conservation interest of the Selvagens gecko, we used morphological and DNA metabarcoding approaches to characterize its diet. The traditional method of morphological identification of prey remains in faecal pellets collected over a longer period was compared with metabarcoding of samples collected during rapid surveys. Molecular results revealed that this species is a generalist, feeding on invertebrate, plant and vertebrate items, whereas the morphological approaches were unable to detect the latter two. These results opened up new questions on the ecological role of the Selvagens gecko that deserves to be further explored, such as the possible predation on seabirds, plant services or trophic competition with the sympatric Madeira lizard Teira dugesii. Metabarcoding identified a greater diversity of dietary items at higher taxonomic resolution, but morphological identification enabled calculation of relative abundances and biomasses of ingested arthropods, and detected a dietary shift on invertebrate preys between seasons. Results of this study highlight the global applicability of rapid metabarcoding surveys for understudied taxa on remote islands that are difficult to access. We recommend using the metabarcoding approach, even if ‘speedy’ sampling only is possible, but we must highlight that disregarding long-term ecological data may lead to ‘hasty’ conclusion.
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Affiliation(s)
- Vanessa Gil
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Catarina J Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Carlos A S Aguiar
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Carolina Jardim
- Instituto das Florestas e Conservação da Natureza IP-RAM, Funchal, Madeira, Portugal
| | - Rui Rebelo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
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Young MJ, Dutoit L, Robertson F, van Heezik Y, Seddon PJ, Robertson BC. Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin. WILDLIFE RESEARCH 2020. [DOI: 10.1071/wr19246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin.
Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples.
Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2.
Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified.
Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species.
Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.
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Metabarcoding-based dietary analysis of hen harrier (Circus cyaneus) in Great Britain using buccal swabs from chicks. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01215-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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da Silva LP, Mata VA, Lopes PB, Pereira P, Jarman SN, Lopes RJ, Beja P. Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists. Mol Ecol Resour 2019; 19:1420-1432. [PMID: 31332947 PMCID: PMC6899665 DOI: 10.1111/1755-0998.13060] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 01/01/2023]
Abstract
The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxonomic resolution and biases. Here, we test the use of a mix of universal and specific markers, provide criteria to integrate multi‐marker metabarcoding data and a python script to implement such criteria and produce a single list of taxa ingested per sample. We then compare the results of dietary analysis based on morphological methods, single markers, and the proposed combination of multiple markers. The study was based on the analysis of 115 faeces from a small passerine, the Black Wheatears (Oenanthe leucura). Morphological analysis detected far fewer plant taxa (12) than either a universal 18S marker (57) or the plant trnL marker (124). This may partly reflect the detection of secondary ingestion by molecular methods. Morphological identification also detected far fewer taxa (23) than when using 18S (91) or the arthropod markers IN16STK (244) and ZBJ (231), though each method missed or underestimated some prey items. Integration of multi‐marker data provided far more detailed dietary information than any single marker and estimated higher frequencies of occurrence of all taxa. Overall, our results show the value of integrating data from multiple, taxonomically overlapping markers in an example dietary data set.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CEF, Center for Functional Ecology - Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Vanessa A Mata
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Paulo Pereira
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Simon N Jarman
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,School of Biological Sciences, University of Western Australia, Perth, WA, Australia.,Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, Australia
| | - Ricardo J Lopes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Pedro Beja
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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Pereira A, Xavier R, Perera A, Salvi D, Harris DJ. DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, which have been the main tool for identification of prey in dietary studies of lizards. In this study, we applied a metabarcoding approach based on COI and 16S rRNA amplicons to assess diet partitioning and feeding strategies in three syntopic lizards from Taza, Morocco: Scelarcis perspicillata chabanaudi, Scelarcis perspicillata pellegrini and Podarcis vaucheri. In order to avoid competition, these lizards are expected to consume different prey species because they occupy distinct trophic niches, use different foraging strategies and express different dorsal pigmentation patterns. Given the spotted pattern of S. p. chabanaudi, we hypothesize a sit-and-wait foraging strategy with a less diverse diet and a higher consumption of mobile prey relative to the striped S. p. pellegrini and P. vaucheri which, as potential active foragers, are expected to have a higher diet diversity. Previous diet assessments using microscopy on faecal remains seem to contradict these expectations. Our results show that, as expected, the diet of S. p. chabanaudi is less diverse than the diet of S. p. pellegrini. Regarding P. vaucheri, our dietary data are consistent with the hypothesis that this species behaves as an active forager, owing to its high niche overlap with S. p. pellegrini. Advantages and limitations of molecular barcoding compared with the microscopy approach to the analysis of lizard diets are discussed.
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Affiliation(s)
- Ana Pereira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Ana Perera
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Daniele Salvi
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, Coppito, L’Aquila, Italy
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
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28
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Bessey C, Jarman SN, Stat M, Rohner CA, Bunce M, Koziol A, Power M, Rambahiniarison JM, Ponzo A, Richardson AJ, Berry O. DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines. Ecol Evol 2019; 9:2459-2474. [PMID: 30891193 PMCID: PMC6405500 DOI: 10.1002/ece3.4858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022] Open
Abstract
Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivorous elasmobranchs that are frequently caught either directly or as bycatch in fisheries, which, combined with their conservative life history strategy, makes their populations susceptible to decline in intensely fished regions. Effective management of these iconic and vulnerable species requires an understanding of the diets that sustain them, which can be difficult to determine using conventional sampling methods. We use three DNA metabarcode assays to identify 44 distinct taxa from the stomachs (n = 101) of four sympatric Mobula ray species (Mobula birostris, Mobula tarapacana, Mobula japanica, and Mobula thurstoni) caught over 3 years (2013-2015) in a direct fishery off Bohol in the Philippines. The diversity and incidence of bony fishes observed in ray diets were unprecedented. Nevertheless, rays showed dietary overlap, with krill (Euphausia) dominating their diet. Our results provide a more detailed assessment of sympatric ray diets than was previously described and reveal the complexity that can exist in food webs at critical foraging habitats.
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Affiliation(s)
- Cindy Bessey
- Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research Organization, Oceans and AtmosphereCrawleyWestern AustraliaAustralia
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
- School of Plant Biology and the Oceans InstituteUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
| | - Simon N. Jarman
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
| | - Michael Stat
- Department of Biological SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | | | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Adam Koziol
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Matthew Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | | | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute PhilippinesBoholPhilippines
| | - Anthony J. Richardson
- Commonwealth Scientific and Industrial Research Organization, Oceans and AtmospheresBrisbaneQueenslandAustralia
- Centre for Applications in Natural Resource Mathematics, School of Mathematics and PhysicsUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Oceans Marine Research CentreCommonwealth Scientific and Industrial Research OrganizationCrawleyWestern AustraliaAustralia
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29
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Carroll EL, Gallego R, Sewell MA, Zeldis J, Ranjard L, Ross HA, Tooman LK, O'Rorke R, Newcomb RD, Constantine R. Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Sci Rep 2019; 9:281. [PMID: 30670720 PMCID: PMC6342929 DOI: 10.1038/s41598-018-36478-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/22/2018] [Indexed: 01/26/2023] Open
Abstract
To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde's whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde's whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde's whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde's whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.
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Affiliation(s)
- E L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - R Gallego
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - M A Sewell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - J Zeldis
- National Institute of Water and Atmospheric Research, Christchurch, New Zealand
| | - L Ranjard
- Research School of Biology, the Australian National University, Canberra, ACT, Australia
| | - H A Ross
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - L K Tooman
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R O'Rorke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - R D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The Institute for Plant & Food Research, Auckland, New Zealand
| | - R Constantine
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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30
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Maqsood I, Bukhari SM, Ejaz R, Kausar S, Abbas MN, Ali B, Ke R. Biostatistical Options for Quantitative Diet Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5-12. [PMID: 30520629 DOI: 10.1021/acs.jafc.8b05156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sufficient statistics knowledge is crucial for the correct design of a research plan. The elucidations of results are interpretive only if appropriate statistical methods are applied. Statistical strategies are a particular approach to demonstrate complicated information in broad and explicable conclusions. The emergence of biostatistical approaches for diet evaluation has improved the accuracy of diet estimation, and different methodologies of data integration promise to magnify our understanding of ecological communities. The present study aimed to compile multiple statistical methods used for diet analysis. More specifically, the significant analysis used in diet assessment, central expectations, and preferences related to each measure was conceptualized. In addition, the ability of each test to evaluate diversity, richness, differentiation, fluctuation, similarity, and quantification of multiple diet items was summarized. Moreover, different options were proposed for researchers to select the appropriate statistical tests. This study covers a framework, aim, and understanding of the statistical test methods of diet analysis.
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Affiliation(s)
- Iram Maqsood
- College of Wildlife Resources , Northeast Forestry University , Hexing Road 59 Street , Xiang Fang District, Harbin City 150040 , China
- Department of Zoology , Shaheed Benazir Bhutto Women University Peshawar , Peshawar 25000 , Pakistan
| | - Syed Moshin Bukhari
- College of Wildlife and Ecology , University of Veterinary and Animal Sciences , Lahore 54500 , Pakistan
| | - Rabea Ejaz
- Department of Zoology , Shaheed Benazir Bhutto Women University Peshawar , Peshawar 25000 , Pakistan
| | - Saima Kausar
- College of Life Sciences . Anhui Agricultural University , Hefei 230036 , China
| | | | - Bahar Ali
- College of Plant Sciences and Technology, Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory , Huazhong Agriculture University , Wuhan , Hubei 430070 , China
| | - Rong Ke
- College of Wildlife Resources , Northeast Forestry University , Hexing Road 59 Street , Xiang Fang District, Harbin City 150040 , China
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31
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Ando H. Genetic and ecological conservation issues for oceanic island birds, revealed by a combination of the latest molecular techniques and conventional field work. Ecol Res 2019. [DOI: 10.1111/1440-1703.1062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies Ibaraki Japan
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32
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Hays GC, Doyle TK, Houghton JD. A Paradigm Shift in the Trophic Importance of Jellyfish? Trends Ecol Evol 2018; 33:874-884. [DOI: 10.1016/j.tree.2018.09.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022]
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33
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Mansor MS, Abdullah NA, Abdullah Halim MR, Md. Nor S, Ramli R. Diet of tropical insectivorous birds in lowland Malaysian rainforest. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1534015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Mohammad Saiful Mansor
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nurul Ashikin Abdullah
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Shukor Md. Nor
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Rosli Ramli
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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34
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Ando H, Fujii C, Kawanabe M, Ao Y, Inoue T, Takenaka A. Evaluation of plant contamination in metabarcoding diet analysis of a herbivore. Sci Rep 2018; 8:15563. [PMID: 30349088 PMCID: PMC6197254 DOI: 10.1038/s41598-018-32845-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022] Open
Abstract
Fecal DNA metabarcoding is currently used in various fields of ecology to determine animal diets. Contamination of non-food DNA from complex field environments is a considerable challenge to the reliability of this method but has rarely been quantified. We evaluated plant DNA contamination by sequencing the chloroplast trnL P6 loop region from food-controlled geese feces. The average percentage of contaminant sequences per sample was 1.86%. According to the results of generalized linear models, the probability of contamination was highest in samples placed in wet soil. The proportion of contaminant sequences was lowest at the earliest sampling point and was slightly higher in samples placed in open conditions. Exclusion of rare OTUs (operational taxonomic units) was effective for obtaining reliable dietary data from the obtained sequences, and a 1% cutoff reduced the percentage of contaminated samples to less than 30%. However, appropriate interpretation of the barcoding results considering inevitable contamination is an important issue to address. We suggest the following procedures for fecal sampling and sequence data treatment to increase the reliability of DNA metabarcoding diet analyses: (i) Collect samples as soon as possible after deposition, (ii) avoid samples from deposits on wet soil, and (iii) exclude rare OTUs from diet composition estimations.
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Affiliation(s)
- Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
| | - Chieko Fujii
- Tama Zoological Park, 7-1-1 Hodokubo, Hino-shi, Tokyo, 191-0042, Japan
| | - Masataka Kawanabe
- Tama Zoological Park, 7-1-1 Hodokubo, Hino-shi, Tokyo, 191-0042, Japan
| | - Yoshimi Ao
- Tama Zoological Park, 7-1-1 Hodokubo, Hino-shi, Tokyo, 191-0042, Japan
| | - Tomomi Inoue
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Akio Takenaka
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
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Thalinger B, Oehm J, Zeisler C, Vorhauser J, Traugott M. Sex-specific prey partitioning in breeding piscivorous birds examined via a novel, noninvasive approach. Ecol Evol 2018; 8:8985-8998. [PMID: 30271560 PMCID: PMC6157673 DOI: 10.1002/ece3.4421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023] Open
Abstract
Piscivorous birds frequently display sex-specific differences in their hunting and feeding behavior, which lead to diverging impacts on prey populations. Cormorants (Phalacrocoracidae), for example, were previously studied to examine dietary differences between the sexes and males were found to consume larger fish in coastal areas during autumn and winter. However, information on prey partitioning during breeding and generally on sex-specific foraging in inland waters is missing. Here, we assess sex-specific prey choice of Great Cormorants (Phalacrocorax carbo) during two subsequent breeding seasons in the Central European Alpine foreland, an area characterized by numerous stagnant and flowing waters in close proximity to each other. We developed a unique, noninvasive approach and applied it to regurgitated pellets: molecular cormorant sexing combined with molecular fish identification and fish-length regression analysis performed on prey hard parts. Altogether, 364 pellets delivered information on both, bird sex, and consumed prey. The sexes differed significantly in their overall prey composition, even though Perca fluviatilis, Rutilus rutilus, and Coregonus spp. represented the main food source for both. Albeit prey composition did not indicate the use of different water bodies by the sexes, male diet was characterized by higher prey diversity within a pellet and the consumption of larger fish. The current findings show that female and male cormorants to some extent target the available prey spectrum at different levels. Finally, the comprehensive and noninvasive approach has great potential for application in studies of other piscivorous bird species.
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Affiliation(s)
| | - Johannes Oehm
- Institute of EcologyUniversity of InnsbruckInnsbruckAustria
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36
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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37
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Dong Z, Sun T. Combined effects of ocean acidification and temperature on planula larvae of the moon jellyfish Aurelia coerulea. MARINE ENVIRONMENTAL RESEARCH 2018; 139:144-150. [PMID: 29789135 DOI: 10.1016/j.marenvres.2018.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
Rapidly rising levels of atmospheric CO2 have caused two environmental stressors, ocean acidification and seawater temperature increases, which represent major abiotic threats to marine organisms. Here, we investigated for the first time the combined effects of ocean acidification and seawater temperature increases on the behavior, survival, and settlement of the planula larvae of Aurelia coerulea, which is considered a nuisance species around the world. Three pH levels (8.1, 7.7 and 7.3) and two temperature levels (24 °C and 27 °C) were used in the present study. There were no interactive effects of temperature and pH on the behavior, survival, and settlement of planula larvae of A. coerulea. We found that the swimming speed and mortality of the planula larvae of A. coerulea were significantly affected by temperature, and low pH significantly affected settlement. Planula larvae of A. coerulea from the elevated temperature treatment moved faster and showed higher mortality than those at the control temperature. The settlement rate of A. coerulea planulae was significantly higher at the pH level of 7.3 than at other pH levels. These results suggest that seawater temperature increase, rather than reduced pH, was the main stress factor affecting the survival of A. coerulea planulae. Overall, the planula larvae of the common jellyfish A. coerulea appeared to be resistant to ocean acidification, but may be negatively affected by future seawater temperature increases.
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Affiliation(s)
- Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, PR China.
| | - Tingting Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, PR China
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Schaafsma FL, Cherel Y, Flores H, van Franeker JA, Lea MA, Raymond B, van de Putte AP. Review: the energetic value of zooplankton and nekton species of the Southern Ocean. MARINE BIOLOGY 2018; 165:129. [PMID: 30100628 PMCID: PMC6061478 DOI: 10.1007/s00227-018-3386-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/05/2018] [Indexed: 06/02/2023]
Abstract
Understanding the energy flux through food webs is important for estimating the capacity of marine ecosystems to support stocks of living resources. The energy density of species involved in trophic energy transfer has been measured in a large number of small studies, scattered over a 40-year publication record. Here, we reviewed energy density records of Southern Ocean zooplankton, nekton and several benthic taxa, including previously unpublished data. Comparing measured taxa, energy densities were highest in myctophid fishes (ranging from 17.1 to 39.3 kJ g-1 DW), intermediate in crustaceans (7.1 to 25.3 kJ g-1 DW), squid (16.2 to 24.0 kJ g-1 DW) and other fish families (14.8 to 29.9 kJ g-1 DW), and lowest in jelly fish (10.8 to 18.0 kJ g-1 DW), polychaetes (9.2 to 14.2 kJ g-1 DW) and chaetognaths (5.0-11.7 kJ g-1 DW). Data reveals differences in energy density within and between species related to size, age and other life cycle parameters. Important taxa in Antarctic food webs, such as copepods, squid and small euphausiids, remain under-sampled. The variability in energy density of Electrona antarctica was likely regional rather than seasonal, although for many species with limited data it remains difficult to disentangle regional and seasonal variability. Models are provided to estimate energy density more quickly using a species' physical parameters. It will become increasingly important to close knowledge gaps to improve the ability of bioenergetic and food web models to predict changes in the capacity of Antarctic ecosystems to support marine life.
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Affiliation(s)
- Fokje L. Schaafsma
- Wageningen Marine Research, Ankerpark 27, 1781 AG Den Helder, The Netherlands
| | - Yves Cherel
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS et de l’Université de La Rochelle, 79360 Villiers-en-Bois, France
| | - Hauke Flores
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Am Handeshafen 12, 27570 Bremerhaven, Germany
| | | | - Mary-Anne Lea
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, TAS 7004 Australia
| | - Ben Raymond
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, TAS 7004 Australia
- Australian Antarctic Division, Department of the Environment and Energy, 203 Channel Highway, Kingston, TAS 7050 Australia
- Antarctic and Climate Ecosystems Cooperative Research Centre, University of Tasmania, Private Bag 80, Hobart, TAS 7001 Australia
| | - Anton P. van de Putte
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
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Xavier JC, Cherel Y, Medeiros R, Velez N, Dewar M, Ratcliffe N, Carreiro AR, Trathan PN. Conventional and molecular analysis of the diet of gentoo penguins: contributions to assess scats for non-invasive penguin diet monitoring. Polar Biol 2018. [DOI: 10.1007/s00300-018-2364-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Mol Ecol 2018; 28:391-406. [PMID: 29858539 PMCID: PMC6905394 DOI: 10.1111/mec.14734] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023]
Abstract
Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.
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Affiliation(s)
- Bruce E Deagle
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia
| | | | - Julie C McInnes
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia
| | - Laurence J Clarke
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Eero J Vesterinen
- Biodiversity Unit and Department of Biology, University of Turku, Turku, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
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41
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Komura T, Ando H, Horikoshi K, Suzuki H, Isagi Y. DNA barcoding reveals seasonal shifts in diet and consumption of deep-sea fishes in wedge-tailed shearwaters. PLoS One 2018; 13:e0195385. [PMID: 29630670 PMCID: PMC5891018 DOI: 10.1371/journal.pone.0195385] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
The foraging ecology of pelagic seabirds is difficult to characterize because of their large foraging areas. In the face of this difficulty, DNA metabarcoding may be a useful approach to analyze diet compositions and foraging behaviors. Using this approach, we investigated the diet composition and its seasonal variation of a common seabird species on the Ogasawara Islands, Japan: the wedge-tailed shearwater Ardenna pacifica. We collected fecal samples during the prebreeding (N = 73) and rearing (N = 96) periods. The diet composition of wedge-tailed shearwater was analyzed by Ion Torrent sequencing using two universal polymerase chain reaction primers for the 12S and 16S mitochondrial DNA regions that targeted vertebrates and mollusks, respectively. The results of a BLAST search of obtained sequences detected 31 and 1 vertebrate and mollusk taxa, respectively. The results of the diet composition analysis showed that wedge-tailed shearwaters frequently consumed deep-sea fishes throughout the sampling season, indicating the importance of these fishes as a stable food resource. However, there was a marked seasonal shift in diet, which may reflect seasonal changes in food resource availability and wedge-tailed shearwater foraging behavior. The collected data regarding the shearwater diet may be useful for in situ conservation efforts. Future research that combines DNA metabarcoding with other tools, such as data logging, may provide further insight into the foraging ecology of pelagic seabirds.
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Affiliation(s)
- Taketo Komura
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Kazuo Horikoshi
- Institute of Boninology, Nishi-machi, Chichijima, Ogasawara, Tokyo, Japan
| | - Hajime Suzuki
- Institute of Boninology, Nishi-machi, Chichijima, Ogasawara, Tokyo, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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42
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Lee T, Alemseged Y, Mitchell A. Dropping Hints: Estimating the diets of livestock in rangelands using DNA metabarcoding of faeces. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.22467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The introduction of domesticated animals into new environments can lead to considerable ecological disruption, and it can be difficult to predict their impact on the new ecosystem. In this study, we use faecal metabarcoding to characterize the diets of three ruminant taxa in the rangelands of south-western New South Wales, Australia. Our study organisms included goats (Capraaegagrushircus) and two breeds of sheep (Ovisaries): Merinos, which have been present in Australia for over two hundred years, and Dorpers, which were introduced in the 1990s. We used High-Throughput Sequencing methods to sequence therbcLand ITS2 genes of plants in the faecal samples, and identified the samples using the GenBank and BOLD online databases, as well as a reference collection of sequences from plants collected in the study area. We found that the diets of all three taxa were dominated by the family Malvaceae, and that the Dorper diet was more diverse than the Merino diet at both the family and the species level. We conclude that Dorpers, like Merinos, are potentially a threat to some vulnerable species in the rangelands of New South Wales.
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Spinelli ML, Franzosi C, Olguin Salinas H, Capitanio FL, Alder VA. Appendicularians and copepods from Scotia Bay (Laurie island, South Orkney, Antarctica): fluctuations in community structure and diversity in two contrasting, consecutive summers. Polar Biol 2017. [DOI: 10.1007/s00300-017-2227-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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McInnes JC, Alderman R, Lea MA, Raymond B, Deagle BE, Phillips RA, Stanworth A, Thompson DR, Catry P, Weimerskirch H, Suazo CG, Gras M, Jarman SN. High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding. Mol Ecol 2017; 26:4831-4845. [DOI: 10.1111/mec.14245] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/21/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Julie C. McInnes
- Institute for Marine and Antarctic Studies; University of Tasmania; Hobart Tas. Australia
- Australian Antarctic Division; Kingston Tas. Australia
| | - Rachael Alderman
- Department of Primary Industries, Parks, Water and Environment; Hobart Tas. Australia
| | - Mary-Anne Lea
- Institute for Marine and Antarctic Studies; University of Tasmania; Hobart Tas. Australia
| | - Ben Raymond
- Institute for Marine and Antarctic Studies; University of Tasmania; Hobart Tas. Australia
- Australian Antarctic Division; Kingston Tas. Australia
| | | | - Richard A. Phillips
- British Antarctic Survey; Natural Environment Research Council; Cambridge UK
| | | | - David R. Thompson
- National Institute for Water and Atmospheric Research; Hataitai Wellington New Zealand
| | - Paulo Catry
- Marine and Environmental Sciences Centre (MARE); ISPA-Instituto Universitário; Lisbon Portugal
| | - Henri Weimerskirch
- Centre d'Etudes Biologiques de Chizé; UMR 7372 CNRS/ULR; Villiers-en-Bois France
| | - Cristián G. Suazo
- Department of Animal Ecology and Systematics; Justus Liebig University Giessen; Giessen Germany
| | - Michaël Gras
- Directorate of Natural Resources; Fisheries of the Falkland Islands Government; Stanley Falkland Islands
| | - Simon N. Jarman
- CIBIO-InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
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Wallinger C, Staudacher K, Sint D, Thalinger B, Oehm J, Juen A, Traugott M. Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples. Ecol Evol 2017; 7:6382-6389. [PMID: 28861241 PMCID: PMC5574753 DOI: 10.1002/ece3.3197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/26/2017] [Indexed: 02/01/2023] Open
Abstract
Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next‐generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high‐quality DNA extraction procedures for obtaining the minute quantities of short‐fragmented food DNA. Automatic high‐throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole‐body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high‐throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor‐intensive, low‐throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost‐efficient and innovative methodology at low contamination risk also in trophic ecology.
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Affiliation(s)
- Corinna Wallinger
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Karin Staudacher
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Daniela Sint
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Bettina Thalinger
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Johannes Oehm
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Anita Juen
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Michael Traugott
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
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The diet of a nocturnal pelagic predator, the Bulwer's petrel, across the lunar cycle. Sci Rep 2017; 7:1384. [PMID: 28469170 PMCID: PMC5431196 DOI: 10.1038/s41598-017-01312-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/29/2017] [Indexed: 11/13/2022] Open
Abstract
The lunar cycle is believed to strongly influence the vertical distribution of many oceanic taxa, with implications for the foraging behaviour of nocturnal marine predators. Most studies to date testing lunar effects on foraging have focused on predator activity at-sea, with some birds and marine mammals demonstrating contrasting behavioural patterns, depending on the lunar-phase. However, to date no study has focused on how the lunar cycle might actually affect predator-prey interactions in the upper layers of the ocean. Here, we tested whether the diet of the predominantly nocturnal pelagic predator, the Bulwer’s petrel (Bulweria bulwerii) would change throughout the lunar cycle, using molecular analysis to augment detection and taxonomic resolution of prey collected from stomach-contents. We found no evidence of dietary shifts in species composition or diversity, with Bulwer’s petrel always consuming a wide range of mesopelagic species. Other co-variables potentially affecting light availability at-sea, such as percentage of cloud cover, did not confound our results. Moreover, many of the species found are thought not to reach the sea-surface. Our findings reveal that nocturnal predators are probably more specialized than previously assumed, irrespective of ambient-light, but also reveal deficiencies in our current understanding of species vertical distribution and predation-dynamics at-sea.
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47
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Chilvers BL. Comparison of New Zealand’s little blue penguins, Eudyptula minor, diving behaviour. Polar Biol 2017. [DOI: 10.1007/s00300-017-2112-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Oehm J, Thalinger B, Eisenkölbl S, Traugott M. Diet analysis in piscivorous birds: What can the addition of molecular tools offer? Ecol Evol 2017; 7:1984-1995. [PMID: 28331605 PMCID: PMC5355203 DOI: 10.1002/ece3.2790] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 11/21/2022] Open
Abstract
In trophic studies on piscivorous birds, it is vital to know which kind of dietary sample provides the information of interest and how the prey can be identified reliably and efficiently. Often, noninvasively obtained dietary samples such as regurgitated pellets, feces, and regurgitated fish samples are the preferred source of information. Fish prey has usually been identified via morphological analysis of undigested hard parts, but molecular approaches are being increasingly used for this purpose. What remains unknown, however, is which dietary sample type is best suited for molecular diet analysis and how the molecular results compare to those obtained by morphological analysis. Pellets, feces, and regurgitated fish samples of Great Cormorants (Phalacrocorax carbo sinensis) were examined for prey using both morphological hard part analysis and molecular prey identification. The sample types and methods were compared regarding number of species detected (overall and per sample) as well as the prey species composition and its variability among individual samples. Via molecular analysis, significantly higher numbers of prey species were detected in pellets, feces, and fish samples. Of the three sample types, pellets contained the most comprehensive trophic information and could be obtained with the lowest sampling effort. Contrastingly, dietary information obtained from feces was least informative and most variable. For all sample types, the molecular approach outperformed morphological hard part identification regarding the detectable prey spectrum and prey species composition. We recommend the use of pellets in combination with molecular prey identification to study the diet of piscivorous birds.
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Affiliation(s)
- Johannes Oehm
- Institute of Ecology University of Innsbruck Innsbruck Austria
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49
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Clarke LJ, Beard JM, Swadling KM, Deagle BE. Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecol Evol 2017; 7:873-883. [PMID: 28168024 PMCID: PMC5288259 DOI: 10.1002/ece3.2667] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
| | - Jason M Beard
- Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Kerrie M Swadling
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Bruce E Deagle
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
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50
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McInnes JC, Alderman R, Deagle BE, Lea M, Raymond B, Jarman SN. Optimised scat collection protocols for dietary
DNA
metabarcoding in vertebrates. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12677] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie C. McInnes
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Rachael Alderman
- Department of Primary Industries, Parks, Water and Environment 134 Macquarie Street Hobart TAS 7000 Australia
| | - Bruce E. Deagle
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Mary‐Anne Lea
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
| | - Ben Raymond
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 129 Hobart TAS 7001 Australia
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
| | - Simon N. Jarman
- Australian Antarctic Division 203 Channel Highway Kingston TAS 7050 Australia
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão 4485‐661 Portugal
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