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Harvey Sky N, Britnell J, Antwis R, Kartzinel T, Rubenstein D, Toye P, Karani B, Njeru R, Hinchcliffe D, Gaymer J, Mutisya S, Shultz S. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 2024; 7:333. [PMID: 38491117 PMCID: PMC10943211 DOI: 10.1038/s42003-024-05983-3] [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: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.
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Affiliation(s)
- Nick Harvey Sky
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK.
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK.
| | - Jake Britnell
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK
| | - Rachael Antwis
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WX, UK
| | - Tyler Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
- Institute at Brown for Environment and Society, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
| | - Daniel Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-2016, USA
| | - Phil Toye
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Benedict Karani
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Regina Njeru
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Danielle Hinchcliffe
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | | | | | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
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2
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Vanderpool DD, Wilcox TM, Young MK, Pilgrim KL, Schwartz MK. Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study. Ecol Evol 2024; 14:e11020. [PMID: 38371866 PMCID: PMC10870330 DOI: 10.1002/ece3.11020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non-destructive and suitable for the detection of endangered species where "no take" restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.
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Affiliation(s)
- Daniel D. Vanderpool
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Taylor M. Wilcox
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Young
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Kristine L. Pilgrim
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Schwartz
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
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3
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Gill BA, Wittemyer G, Cerling TE, Musili PM, Kartzinel TR. Foraging history of individual elephants using DNA metabarcoding. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230337. [PMID: 37416829 PMCID: PMC10320352 DOI: 10.1098/rsos.230337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Individual animals should adjust diets according to food availability. We used DNA metabarcoding to construct individual-level dietary timeseries for elephants from two family groups in Kenya varying in habitat use, social position and reproductive status. We detected at least 367 dietary plant taxa, with up to 137 unique plant sequences in one fecal sample. Results matched well-established trends: elephants tended to eat more grass when it rained and other plants when dry. Nested within these switches from 'grazing' to 'browsing' strategies, dietary DNA revealed seasonal shifts in food richness, composition and overlap between individuals. Elephants of both families converged on relatively cohesive diets in dry seasons but varied in their maintenance of cohesion during wet seasons. Dietary cohesion throughout the timeseries of the subdominant 'Artists' family was stronger and more consistently positive compared to the dominant 'Royals' family. The greater degree of individuality within the dominant family's timeseries could reflect more divergent nutritional requirements associated with calf dependency and/or priority access to preferred habitats. Whereas theory predicts that individuals should specialize on different foods under resource scarcity, our data suggest family bonds may promote cohesion and foster the emergence of diverse feeding cultures reflecting links between social behaviour and nutrition.
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Affiliation(s)
- Brian A. Gill
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
| | - George Wittemyer
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
- Save the Elephants, Nairobi, Kenya
| | - Thure E. Cerling
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Paul M. Musili
- Botany Department, East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Tyler R. Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
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4
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De Wolfe TJ, Wright ES. Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis. BMC Microbiol 2023; 23:107. [PMID: 37076812 PMCID: PMC10114302 DOI: 10.1186/s12866-023-02851-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles. RESULTS Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%). CONCLUSIONS Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.
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Affiliation(s)
- Travis J. De Wolfe
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
- Department of Pediatrics, BC Children’s Hospital Research Institute, University of British Columbia, 4480 Oak Street Rm. 208B, Vancouver, BC V6H 4E4 Canada
- Gut4Health, BC Children’s Hospital Research Institute, University of British Columbia, 950 West 28th Avenue Rm. 211, Vancouver, BC V5Z 4H4 Canada
| | - Erik S. Wright
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
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5
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Domestic Cattle in a National Park Restricting the Sika Deer Due to Diet Overlap. Animals (Basel) 2023; 13:ani13040561. [PMID: 36830347 PMCID: PMC9951756 DOI: 10.3390/ani13040561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Managers need to know the extent of the conflict between livestock and wild animals. Although many studies have reported the conflict between livestock and wild animals, few have checked the extent of the conflict. Cattle raising in the Northeast Tiger and Leopard National Park is considered one of the main driving forces behind the restricted distribution of sika deer. To understand whether foraging competition is contributing to avoidance patterns between sika deer and cattle, we investigated their feeding habits using DNA barcoding and high-throughput sequencing. Our study shows that although cattle are grazers in the traditional division of herbivores, their diet shifted to a predominance of dicotyledonous woody plants, and this diet shift resulted in a high degree of dietary overlap between sika deer and cattle. Moreover, compared to sika deer, cattle diets are more diverse at the species level with a wider ecological niche. Our results confirm that overlapping dietary niches and the superior competitive abilities of cattle contribute to the restricted distribution of the sika deer, which has critical implications for the conservation of their predators. Our study suggests that cattle grazing should be prohibited in the Park and effective measures should be taken for the benefit of sika deer.
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VTAM: A robust pipeline for validating metabarcoding data using controls. Comput Struct Biotechnol J 2023; 21:1151-1156. [PMID: 36789260 PMCID: PMC9918390 DOI: 10.1016/j.csbj.2023.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
To obtain accurate estimates for biodiversity and ecological studies, metabarcoding studies should be carefully designed to minimize both false positive (FP) and false negative (FN) occurrences. Internal controls (mock samples and negative controls), replicates, and overlapping markers allow controlling metabarcoding errors but current metabarcoding software packages do not explicitly integrate these additional experimental data to optimize filtering. We have developed the metabarcoding analysis software VTAM, which uses explicitly these elements of the experimental design to find optimal parameter settings that minimize FP and FN occurrences. VTAM showed similar sensitivity, but a higher precision compared to two other pipelines using three datasets and two different markers (COI, 16S). The stringent filtering procedure implemented in VTAM aims to produce robust metabarcoding data to obtain accurate ecological estimates and represents an important step towards a non-arbitrary and standardized validation of metabarcoding data for conducting ecological studies. VTAM is implemented in Python and available from: https://github.com/aitgon/vtam. The VTAM benchmark code is available from: https://github.com/aitgon/vtam_benchmark.
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7
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Rieseberg L, Warschefsky E, Ortiz-Barrientos D, Kane NC, Thresher K, Sibbett B. Editorial 2023. Mol Ecol 2023; 32:1-25. [PMID: 36573261 DOI: 10.1111/mec.16815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022]
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8
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Tercel MPTG, Cuff JP. The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022). Mol Ecol 2022; 31:5653-5659. [PMID: 35778947 DOI: 10.1111/mec.16576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023]
Abstract
In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.
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Affiliation(s)
- Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Trinity, Jersey, Channel Islands
| | - Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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9
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Villsen K, Corse E, Meglécz E, Archambaud‐Suard G, Vignes H, Ereskovsky AV, Chappaz R, Dubut V. DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish. Mol Ecol 2022; 31:5889-5908. [PMID: 36125278 PMCID: PMC9828795 DOI: 10.1111/mec.16698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.
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Affiliation(s)
- Kurt Villsen
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | - Emmanuel Corse
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,Centre Universitaire de Formation et de Recherche de Mayotte (CUFR)DembeniFrance,MARBEC, University of Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Emese Meglécz
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | | | - Hélène Vignes
- CIRAD, University of Montpellier, INRAE, Montpellier SupAgro, AGAPMontpellierFrance
| | - Alexander V. Ereskovsky
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,St. Petersburg State UniversitySt. PetersburgRussia,Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
| | - Rémi Chappaz
- INRAE, Aix Marseille Université, RECOVERAix‐en‐ProvenceFrance
| | - Vincent Dubut
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
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10
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Littleford-Colquhoun BL, Sackett VI, Tulloss CV, Kartzinel TR. Evidence-based strategies to navigate complexity in dietary DNA metabarcoding: A reply. Mol Ecol 2022; 31:5660-5665. [PMID: 36263899 DOI: 10.1111/mec.16712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/06/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023]
Abstract
It is clearly beneficial to eliminate low-abundance sequences that arise in error during dietary DNA metabarcoding studies, but to purge all low-abundance sequences is to risk eliminating real sequences and complicating ecological analyses. Our prior literature review noted that DNA sequence relative read abundance (RRA) thresholds can help ameliorate false-positive taxon occurrences, but that historical emphasis on this utility has fostered uncertainty about the associated risk of inflating the false-negative rate (Littleford-Colquhoun et al., 2022). To address this, we combined a simulation study and an empirical data set to both illustrate the issue and provide blueprints for simulation studies and sensitivity analyses that can help investigators avoid overcorrecting and thereby bolster confidence in ecological inferences. Awareness of both the costs and the benefits of abundance-filtering is needed because accurately characterizing dietary distributions can be critically important for understanding animal diets, nutrition and trophic networks. Highlighting the need to raise awareness, a critique of our paper emphasized the misleading notion that "false positive interactions between species can present fundamentally incorrect network structures in network ecology, whereas false negatives will provide a correct but incomplete version of the network" (Tercel & Cuff, 2022). Asserting that the reliability of results will be eroded by false positives but resilient to the omission of true positives is risky and runs counter to evidence. Unfortunately, abundance-filtering methods can introduce false negatives at higher rates than they eliminate false positives and thereby undermine the analysis of otherwise reliable sequencing data. Overcorrecting can qualitatively alter and ultimately undermine ecological interpretations.
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Affiliation(s)
- Bethan L Littleford-Colquhoun
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Violet I Sackett
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Camille V Tulloss
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Tyler R Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
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11
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Brun L, Schneider J, Carrió EM, Dongre P, Taberlet P, Waal VD, Fumagalli L. Focal vs. fecal: Seasonal variation in the diet of wild vervet monkeys from observational and
DNA
metabarcoding data. Ecol Evol 2022; 12:e9358. [PMID: 36203642 PMCID: PMC9526031 DOI: 10.1002/ece3.9358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Eduard Mas Carrió
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Pooja Dongre
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes, CNRS Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - van de Waal
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva, Lausanne University Hospital and University of Lausanne Lausanne Switzerland
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12
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Littleford‐Colquhoun BL, Freeman PT, Sackett VI, Tulloss CV, McGarvey LM, Geremia C, Kartzinel TR. The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation. Mol Ecol 2022; 31:1615-1626. [PMID: 35043486 PMCID: PMC9303378 DOI: 10.1111/mec.16352] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 01/07/2022] [Indexed: 01/13/2023]
Abstract
Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data-or similar data such as environmental DNA, microbiomes, or pathobiomes-should be aware of drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.
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Affiliation(s)
- Bethan L. Littleford‐Colquhoun
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Patrick T. Freeman
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Violet I. Sackett
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Camille V. Tulloss
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
| | - Lauren M. McGarvey
- Yellowstone Center for Resources, Yellowstone National ParkMammoth Hot SpringsWyomingUSA
| | - Chris Geremia
- Yellowstone Center for Resources, Yellowstone National ParkMammoth Hot SpringsWyomingUSA
| | - Tyler R. Kartzinel
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRhode IslandUSA,Institute at Brown for Environment and SocietyBrown UniversityProvidenceRhode IslandUSA
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